Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 17 of 126
Found at i:5675116 original size:2 final size:2
Alignment explanation
Indices: 5675111--5675158 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5675101 AAAATATTTA
5675111 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5675153 AT AT AT
1 AT AT AT
5675159 TTACAAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5680808 original size:17 final size:17
Alignment explanation
Indices: 5680786--5680819 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5680776 TAACAATACA
*
5680786 TAAAATATTACTAAAAT
1 TAAAATATTAATAAAAT
5680803 TAAAATATTAATAAAAT
1 TAAAATATTAATAAAAT
5680820 ATTAGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAATATTAATAAAAT
Found at i:5684102 original size:16 final size:17
Alignment explanation
Indices: 5684081--5684112 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5684071 CCAAAATCCA
5684081 AAAATTAAG-ATTTTTT
1 AAAATTAAGAATTTTTT
5684097 AAAATTAAGAATTTTT
1 AAAATTAAGAATTTTT
5684113 GCCGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
AAAATTAAGAATTTTTT
Found at i:5684494 original size:20 final size:20
Alignment explanation
Indices: 5684469--5684513 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5684459 TCCATTTTTT
5684469 CTCTTC-TCTTTCTTCTTCTC
1 CTCTTCGTC-TTCTTCTTCTC
*
5684489 CTCTTCGTCTTCTTTTTCTC
1 CTCTTCGTCTTCTTCTTCTC
*
5684509 TTCTT
1 CTCTT
5684514 AAAATCCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (20 bp):
CTCTTCGTCTTCTTCTTCTC
Found at i:5684509 original size:17 final size:17
Alignment explanation
Indices: 5684464--5684512 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 17
5684454 TCAGCTCCAT
5684464 TTTTTCTCTTCTCTTTC
1 TTTTTCTCTTCTCTTTC
5684481 TTCTTCTCCTCTTCGTC-TTC
1 TT-TT-T-CTCTTC-TCTTTC
5684501 TTTTTCTCTTCT
1 TTTTTCTCTTCT
5684513 TAAAATCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 1 0.04
17 8 0.29
18 3 0.11
19 3 0.11
20 11 0.39
21 2 0.07
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTCTCTTCTCTTTC
Found at i:5685784 original size:17 final size:17
Alignment explanation
Indices: 5685762--5685800 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5685752 AGATGATTAC
* * *
5685762 AGTTAGTAGTTAGCAGT
1 AGTTAGCAGCTAGCAGA
5685779 AGTTAGCAGCTAGCAGA
1 AGTTAGCAGCTAGCAGA
5685796 AGTTA
1 AGTTA
5685801 AGTTTGTTAG
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:0.33, C:0.10, G:0.28, T:0.28
Consensus pattern (17 bp):
AGTTAGCAGCTAGCAGA
Found at i:5691422 original size:97 final size:97
Alignment explanation
Indices: 5691256--5691449 Score: 293
Period size: 97 Copynumber: 2.0 Consensus size: 97
5691246 AACCTTGGAA
* * *
5691256 AAGGGTATTTGATAATCCCGATTTGAAAAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATAATCCCGATTTGAAAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTCCA
* *
5691321 AAACCAGAGAT-AAAGAAATATTGTCTCGATTT
66 AAACCAGAAATAAAAG-AATATTGCCTCGATTT
*
5691353 AAGGGTATTCGATTATCCCGATTTGAAGAAAAA-TCGCACCTAGTAAGTTAAGGCACAAATTTCC
1 AAGGGTATTCGATAATCCCGATTTGAA-AAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTCC
*
5691417 AAAACCCGAAATAAAAGAATATTGCCTCGATTT
65 AAAACCAGAAATAAAAGAATATTGCCTCGATTT
5691450 TAAATATTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
97 79 0.90
98 9 0.10
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (97 bp):
AAGGGTATTCGATAATCCCGATTTGAAAAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTCCA
AAACCAGAAATAAAAGAATATTGCCTCGATTT
Found at i:5691804 original size:28 final size:28
Alignment explanation
Indices: 5691756--5691810 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
5691746 AAGTTTTAAG
* *
5691756 GTAAAAATGTCATTTTGGGAATTTTGGA
1 GTAAAAATATCATTTTGGGAAGTTTGGA
*
5691784 GTAAAAATATGATTTAT-GGAAGTTTGG
1 GTAAAAATATCATTT-TGGGAAGTTTGG
5691811 GGGCAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (28 bp):
GTAAAAATATCATTTTGGGAAGTTTGGA
Found at i:5691835 original size:29 final size:29
Alignment explanation
Indices: 5691803--5692011 Score: 174
Period size: 29 Copynumber: 7.2 Consensus size: 29
5691793 TGATTTATGG
*
5691803 AAGTTTGGGGGCAAAAATGAAATTTTTGA
1 AAGTTTGGGGGCAAAAATGTAATTTTTGA
* * * *
5691832 AAGTTCGAGAGCAAAAATGTGATTTTTTGA
1 AAGTTTGGGGGCAAAAATGT-AATTTTTGA
*
5691862 AAGTTTGGGGGTAAAAATGTAATTTTTGA
1 AAGTTTGGGGGCAAAAATGTAATTTTTGA
* ** * *
5691891 AAGTTTAGGGATAAAAATGTAACTTTTGG
1 AAGTTTGGGGGCAAAAATGTAATTTTTGA
* *
5691920 AAGTTTGGGGG--AAAATGTGATTTTTGG
1 AAGTTTGGGGGCAAAAATGTAATTTTTGA
*** *
5691947 AAGTTTAAAGGC-AAAATGGAATTTTTGGA
1 AAGTTTGGGGGCAAAAATGTAATTTTT-GA
* * *
5691976 AAGATCGAGGGTC-AAAATGTAATTTTTGGA
1 AAGTTTG-GGGGCAAAAATGTAATTTTT-GA
5692006 AAGTTT
1 AAGTTT
5692012 TATGGTTAAA
Statistics
Matches: 143, Mismatches: 33, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
27 22 0.15
28 12 0.08
29 63 0.44
30 46 0.32
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
AAGTTTGGGGGCAAAAATGTAATTTTTGA
Found at i:5691971 original size:27 final size:27
Alignment explanation
Indices: 5691904--5691976 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
5691894 TTTAGGGATA
* ** *
5691904 AAAATGTAACTTTTGGAAGTTTGGGGG
1 AAAATGGAACTTTTGGAAGTTTAAGGC
*
5691931 AAAATGTG-ATTTTTGGAAGTTTAAAGGC
1 AAAATG-GAACTTTTGGAAGTTT-AAGGC
*
5691959 AAAATGGAATTTTTGGAA
1 AAAATGGAACTTTTGGAA
5691977 AGATCGAGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 20 0.53
28 18 0.47
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (27 bp):
AAAATGGAACTTTTGGAAGTTTAAGGC
Found at i:5691978 original size:144 final size:144
Alignment explanation
Indices: 5691692--5692011 Score: 339
Period size: 144 Copynumber: 2.2 Consensus size: 144
5691682 GAGAGAAAAA
* * * **
5691692 ATCGAG-GTCGAAAATG-AAGTTTCGAAAAGTTTGGGGTTGAAATGTAATTTTAAAAAGTTTTAA
1 ATCGAGAGTC-AAAATGTAATTTTTGGAAAGTTTGGGGTAAAAATGTAATTTTAAAAAGTTTTAA
* * * ***
5691755 GGTAAAAATGTCATTTTGGGAATTTTGGAGTAAAAATATGATTTATGGAAGTTTGGGGGCAAAAA
65 GGTAAAAATGTAATTTTGGGAAGTTTGGAGGAAAAATATGATTTATGGAAGTTTAAAGGCAAAAA
5691820 TGAAATTTTTGAAAG
130 TGAAATTTTTGAAAG
* * * **
5691835 TTCGAGAG-CAAAAATGTGATTTTTTGAAAGTTTGGGGGTAAAAATGTAATTTTTGAAAG-TTTA
1 ATCGAGAGTC-AAAATGTAATTTTTGGAAAGTTT-GGGGTAAAAATGTAATTTTAAAAAGTTTTA
* * * *
5691898 GGGATAAAAATGTAACTTTT-GGAAGTTTGG-GGGAAAATGTGATTTTTGGAAGTTTAAAGGC-A
64 AGG-TAAAAATGTAA-TTTTGGGAAGTTTGGAGGAAAAATATGATTTATGGAAGTTTAAAGGCAA
*
5691960 AAATGGAATTTTTGGAAAG
127 AAATGAAATTTTT-GAAAG
*
5691979 ATCGAGGGTCAAAATGTAATTTTTGGAAAGTTT
1 ATCGAGAGTCAAAATGTAATTTTTGGAAAGTTT
5692012 TATGGTTAAA
Statistics
Matches: 144, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
143 25 0.17
144 74 0.51
145 41 0.28
146 4 0.03
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.34
Consensus pattern (144 bp):
ATCGAGAGTCAAAATGTAATTTTTGGAAAGTTTGGGGTAAAAATGTAATTTTAAAAAGTTTTAAG
GTAAAAATGTAATTTTGGGAAGTTTGGAGGAAAAATATGATTTATGGAAGTTTAAAGGCAAAAAT
GAAATTTTTGAAAG
Found at i:5693734 original size:23 final size:23
Alignment explanation
Indices: 5693700--5693763 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
5693690 GGACATTATT
5693700 AATTTA-AATAAATTTAAACTTA
1 AATTTATAATAAATTTAAACTTA
*
5693722 AATTTATAATAAATTTAATCTTA
1 AATTTATAATAAATTTAAACTTA
5693745 AATTTATAATAAATTTAAA
1 AATTTATAATAAATTTAAA
5693764 TTCCAAATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 6 0.15
23 33 0.85
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTTATAATAAATTTAAACTTA
Found at i:5693736 original size:11 final size:11
Alignment explanation
Indices: 5693700--5693761 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
5693690 GGACATTATT
5693700 AATTTA-AATA
1 AATTTATAATA
5693710 AATTTA-AACTTA
1 AATTTATAA--TA
5693722 AATTTATAATA
1 AATTTATAATA
**
5693733 AATTTAATCTTA
1 AATTT-ATAATA
5693745 AATTTATAATA
1 AATTTATAATA
5693756 AATTTA
1 AATTTA
5693762 AATTCCAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 8 0.18
11 17 0.39
12 17 0.39
13 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTTATAATA
Found at i:5693739 original size:17 final size:17
Alignment explanation
Indices: 5693714--5693816 Score: 64
Period size: 17 Copynumber: 5.7 Consensus size: 17
5693704 TAAATAAATT
*
5693714 TAAACTTAAATTTATAA
1 TAAATTTAAATTTATAA
5693731 TAAATTTAATCTTAAATTTATAA
1 TAAATTT-A----A-ATTTATAA
*
5693754 TAAATTTAAATTCCA-AA
1 TAAATTTAAATT-TATAA
* * *
5693771 TAGATTTAAACTTATTA
1 TAAATTTAAATTTATAA
* * *
5693788 TAAACTCAAATTTAAAA
1 TAAATTTAAATTTATAA
5693805 TAAATTTAAATT
1 TAAATTTAAATT
5693817 CTGTTGGGCC
Statistics
Matches: 64, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
16 1 0.02
17 43 0.67
18 3 0.05
22 2 0.03
23 15 0.23
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:5693780 original size:34 final size:34
Alignment explanation
Indices: 5693742--5693816 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
5693732 AAATTTAATC
* * * *
5693742 TTAAATTTATAATAAATTTAAATTCCAAATAGAT
1 TTAAATTTATAATAAACTCAAATTCAAAATAAAT
* * *
5693776 TTAAACTTATTATAAACTCAAATTTAAAATAAAT
1 TTAAATTTATAATAAACTCAAATTCAAAATAAAT
5693810 TTAAATT
1 TTAAATT
5693817 CTGTTGGGCC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (34 bp):
TTAAATTTATAATAAACTCAAATTCAAAATAAAT
Found at i:5693814 original size:23 final size:23
Alignment explanation
Indices: 5693700--5693814 Score: 90
Period size: 23 Copynumber: 4.8 Consensus size: 23
5693690 GGACATTATT
*
5693700 AATTT-AAATAAATTTAAACTTA
1 AATTTAAAATAAATTTAAACTCA
* * *
5693722 AATTTATAATAAATTTAATCTTA
1 AATTTAAAATAAATTTAAACTCA
* *
5693745 AATTTATAATAAATTTAAATTCCAAA
1 AATTTAAAATAAATTTAAACT-C--A
* *
5693771 TAGATTTAAACT-TATTATAAACTCA
1 -A-ATTTAAAATAAATT-TAAACTCA
5693796 AATTTAAAATAAATTTAAA
1 AATTTAAAATAAATTTAAA
5693815 TTCTGTTGGG
Statistics
Matches: 74, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
22 5 0.07
23 46 0.62
24 4 0.05
25 1 0.01
26 1 0.01
27 5 0.07
28 12 0.16
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (23 bp):
AATTTAAAATAAATTTAAACTCA
Found at i:5694754 original size:209 final size:209
Alignment explanation
Indices: 5694107--5694974 Score: 1186
Period size: 209 Copynumber: 4.2 Consensus size: 209
5694097 GTTGAGTGTT
* * * * *
5694107 ATTGATTTGGTTTACTTC-CTAGTATCTCATTAGGAAGATGACCTCATCACTTATTTTGATCCAC
1 ATTGATTTGGTCTACTTCTC-AGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCAC
* * * *
5694171 TTATCTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCGGGAAGGTAACC
65 TTCTTTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTAATC
* * * * *
5694236 GCTTTATTGCTTCGACCTGTTTCTCAGTATCTCATTAAGAGGTTGGGGTTCGAAGATTTGCTCAC
130 GCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
5694301 TTTGAGCCTGGTTTC
195 TTTGAGCCTGGTTTC
* * * *
5694316 ATTGATTTGGTTTACTTCTCAATATCTTATCAGGAAGATGACCGCATCACTTGTTTTGATCCACT
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACT
* * * *
5694381 TCTTTGTGTCTCATTAGAAAGATGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAAT--
66 TCTTTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTAATCG
* *
5694444 C------GC--CGACCTTCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGCTCACT
131 CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACT
*
5694501 TTGAGCTTGGTTTC
196 TTGAGCCTGGTTTC
*
5694515 ATTAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACT
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACT
** ** *
5694580 TCTTAATGTCTTTTCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAATCG
66 TCTTTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTAATCG
* *
5694645 CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAATATTTTCTCACT
131 CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACT
5694710 TTGAGCCTGGTTTC
196 TTGAGCCTGGTTTC
*
5694724 ATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGATCGCATCACTTGTTTTGATCCACT
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACT
* *
5694789 TCTTTGTGTCTCATCAAGAAGACGGATTTGGTTCACTTCTCTATATCTCATCAGGAAGGTAA-CT
66 TCTTTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTAATC-
* *
5694853 GCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAG-TTTCACTCA
130 GCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTT-GCTCA
* *** **
5694917 CGTTGAAATTTATTTC
194 CTTTGAGCCTGGTTTC
* ** *
5694933 ATTGAGTTGGAATACTTCTCTGTATCTCATCAGGAAGATGAT
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGAT
5694975 TGCCTCGTTG
Statistics
Matches: 585, Mismatches: 61, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
199 176 0.30
201 3 0.01
207 3 0.01
208 4 0.01
209 398 0.68
210 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.37
Consensus pattern (209 bp):
ATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTTGATCCACT
TCTTTGTGTCTCATCAGGAAGACGGATCTGGTTCACTTCTCTATATCTCATCAGGAAGGTAATCG
CTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACT
TTGAGCCTGGTTTC
Found at i:5706484 original size:97 final size:95
Alignment explanation
Indices: 5706314--5706502 Score: 254
Period size: 97 Copynumber: 2.0 Consensus size: 95
5706304 CTTGAAAATT
* * *
5706314 GGTATTCGATTATCCGATTTGAAGAAAGTCGCGCATAGTAAGTTAAGGCACAAATTTTCAAAACC
1 GGTATTCGATTATCCGATTTGAAAAAAATCGCGCATAGTAAGTTAAGGAACAAATTTTCAAAACC
* *
5706379 AGAGAT-AAAGAAACATTGCCTTGATTTAAG
66 AGAAATAAAAG-AACATTGCCTCGATTTAAG
* * *
5706409 GGTATTCGATTATCCCGGTTTGAAAAAAAATCGTGCCTAGTAAGTTAAGGAACAAATTTTCAAAA
1 GGTATTCGATTAT-CCGATTTG-AAAAAAATCGCGCATAGTAAGTTAAGGAACAAATTTTCAAAA
* *
5706474 CCCGAAATAAAAGAATATTGCCTCGATTT
64 CCAGAAATAAAAGAACATTGCCTCGATTT
5706503 TAAATATTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
95 13 0.16
96 7 0.09
97 57 0.70
98 4 0.05
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (95 bp):
GGTATTCGATTATCCGATTTGAAAAAAATCGCGCATAGTAAGTTAAGGAACAAATTTTCAAAACC
AGAAATAAAAGAACATTGCCTCGATTTAAG
Found at i:5708037 original size:59 final size:57
Alignment explanation
Indices: 5707932--5708154 Score: 193
Period size: 59 Copynumber: 3.8 Consensus size: 57
5707922 GGAAGCTCGT
* * *
5707932 GGGTAAAAATGGAATTTTTGGAA-ATTCG-GGAGCAAAAATGTAAATTTAAGAAGTTTCA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGG-TCAAAAATG-GAATTTAAGAAGTTT-A
* **
5707990 GGGTTAAAAATGGAATTTTTGGAAGTTT-TAGGGTCAAAAATGGAATTTTTGAAAGTTTGA
1 GGG-TAAAAATGGAATTTTTGGAAGTTTCGA-GGTCAAAAATGGAATTTAAG-AAGTTT-A
* * * *
5708050 GGGTAAAAATGTAATTTTTGGAAGTTTCGAGATCAAAAATAGAATTTTTAA-AAGTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAA--TTTAAGAAGTTTA
** * * * *
5708108 GGGGCAAAATGTAATTTTTAGAAGTTTTGAGGTCATAAATGGAATTT
1 GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTT
5708155 TTGGATTGTT
Statistics
Matches: 136, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
56 3 0.02
58 40 0.29
59 67 0.49
60 21 0.15
61 5 0.04
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (57 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTAAGAAGTTTA
Found at i:5708096 original size:30 final size:29
Alignment explanation
Indices: 5707850--5708159 Score: 199
Period size: 30 Copynumber: 10.6 Consensus size: 29
5707840 TGTCGGAGTA
*
5707850 AAAAATGGAATTTTTGGAA-TTTCGGGGT-
1 AAAAATGGAATTTTTGGAAGTTT-GAGGTC
* * *
5707878 AAAAA-GATAATTTTGGGAAGTTTTAGGGTC
1 AAAAATG-GAATTTTTGGAAGTTTGA-GGTC
* *
5707908 AAAACA--AAATTTTTGGAAGCTCGTG-GGT-
1 AAAA-ATGGAATTTTTGGAAG-T-TTGAGGTC
* * *
5707936 AAAAATGGAATTTTTGGAAATTCG-GGAGC
1 AAAAATGGAATTTTTGGAAGTTTGAGG-TC
* * ** * *
5707965 AAAAATGTAAATTTAAGAAGTTTCAGGGTT
1 AAAAATGGAATTTTTGGAAGTTTGA-GGTC
*
5707995 AAAAATGGAATTTTTGGAAGTTTTAGGGTC
1 AAAAATGGAATTTTTGGAAGTTTGA-GGTC
*
5708025 AAAAATGGAATTTTTGAAAGTTTGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTGA-GGTC
* *
5708054 AAAAATGTAATTTTTGGAAGTTTCGAGATC
1 AAAAATGGAATTTTTGGAAGTTT-GAGGTC
* ** * *
5708084 AAAAATAGAATTTTTAAAAGTTTGGGGGC
1 AAAAATGGAATTTTTGGAAGTTTGAGGTC
* *
5708113 -AAAATGTAATTTTTAGAAGTTTTGAGGTC
1 AAAAATGGAATTTTTGGAAG-TTTGAGGTC
*
5708142 ATAAATGGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
5708160 TTGTTTAGGG
Statistics
Matches: 217, Mismatches: 48, Indels: 32
0.73 0.16 0.11
Matches are distributed among these distances:
27 5 0.02
28 36 0.17
29 81 0.37
30 91 0.42
31 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGAGGTC
Found at i:5708153 original size:58 final size:59
Alignment explanation
Indices: 5707976--5708156 Score: 222
Period size: 59 Copynumber: 3.1 Consensus size: 59
5707966 AAAATGTAAA
* * *
5707976 TTTAAGAAGTTTCAGGGTTAAAAATGGAATTTTTGGAAGTTTT-AGGGTCAAAAATGGAATT
1 TTTAA-AAGTTTGAGGG-GAAAAATGTAATTTTTGGAAGTTTTGA-GGTCAAAAATGGAATT
* * * * *
5708037 TTTGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTCGAGATCAAAAATAGAATT
1 TTTAAAAGTTTGAGGGGAAAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATT
* * *
5708096 TTTAAAAGTTTG-GGGGCAAAATGTAATTTTTAGAAGTTTTGAGGTCATAAATGGAATT
1 TTTAAAAGTTTGAGGGGAAAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATT
5708154 TTT
1 TTT
5708157 GGATTGTTTA
Statistics
Matches: 105, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
58 42 0.40
59 48 0.46
60 11 0.10
61 4 0.04
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (59 bp):
TTTAAAAGTTTGAGGGGAAAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATT
Found at i:5709463 original size:3 final size:3
Alignment explanation
Indices: 5709376--5709445 Score: 70
Period size: 3 Copynumber: 22.7 Consensus size: 3
5709366 TTATTAAAAA
* * *
5709376 TAT TAT TAT TAT TAT TAT TAT TAGT TAT TAA TGT TA- TACT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT TAT
*
5709422 TAT TAA TAT TATT TAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TA
5709446 AAACGTTTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 45 0.82
4 8 0.15
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:5710126 original size:17 final size:17
Alignment explanation
Indices: 5710104--5710138 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5710094 TTGATTTAAT
5710104 TTTAATTTAAAAATAAA
1 TTTAATTTAAAAATAAA
* *
5710121 TTTAATTTTAAGATAAA
1 TTTAATTTAAAAATAAA
5710138 T
1 T
5710139 CCAAACTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAATTTAAAAATAAA
Found at i:5710320 original size:30 final size:30
Alignment explanation
Indices: 5710254--5710505 Score: 173
Period size: 30 Copynumber: 8.5 Consensus size: 30
5710244 TCAACATGTC
* **
5710254 ATTTTAGGAAGTTCAAGGGCAAAAATG-GA
1 ATTTTTGGAAGTTCGGGGGCAAAAATGTGA
*
5710283 ATTTTTGGAAGTTCGGGAGCAAAAATGTGA
1 ATTTTTGGAAGTTCGGGGGCAAAAATGTGA
* * ** *
5710313 TTTTTTGGAAGTTTGGGGGTTAAAAT-TTA
1 ATTTTTGGAAGTTCGGGGGCAAAAATGTGA
*
5710342 ATTTTTGGAAGTTTGGGGGCAAAAATG-GA
1 ATTTTTGGAAGTTCGGGGGCAAAAATGTGA
* * *
5710371 ATTTTTGAAAAGTTTGAGGGTC-AAAATGT-A
1 ATTTTTG-GAAGTTCG-GGGGCAAAAATGTGA
*
5710401 CTTTTTGGAAAGTTCGGTGGGTC-AAAATGTG-
1 ATTTTTGG-AAGTTCGG-GGG-CAAAAATGTGA
*** *
5710432 ATTTTTGGAAGTTTAAGGGCAAAAAAG-GA
1 ATTTTTGGAAGTTCGGGGGCAAAAATGTGA
* * *
5710461 ATTTTTAGAAAGTTCAAGGGTC-AAAATGT-A
1 ATTTTT-GGAAGTTC-GGGGGCAAAAATGTGA
5710491 ATTTTTGGAAAGTTC
1 ATTTTTGG-AAGTTC
5710506 ATGGTCAAAA
Statistics
Matches: 177, Mismatches: 31, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
28 2 0.01
29 72 0.41
30 80 0.45
31 23 0.13
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (30 bp):
ATTTTTGGAAGTTCGGGGGCAAAAATGTGA
Found at i:5710345 original size:59 final size:58
Alignment explanation
Indices: 5710249--5710564 Score: 214
Period size: 59 Copynumber: 5.3 Consensus size: 58
5710239 GGGCTTCAAC
* * ** * *
5710249 ATGTCATTTTAGGAAGTTCAAGGG-CAAAAATGGAATTTTTGGAAGTTCGGGAGCAAAA
1 ATGTGATTTTTGGAAGTTTGAGGGTC-AAAATGTAATTTTTGGAAGTTCGGGGGCAAAA
* * * *
5710307 ATGTGATTTTTTGGAAGTTTGGGGGTTAAAATTTAATTTTTGGAAGTTTGGGGGCAAAA
1 ATGTGA-TTTTTGGAAGTTTGAGGGTCAAAATGTAATTTTTGGAAGTTCGGGGGCAAAA
* *
5710366 ATG-GAATTTTTGAAAAGTTTGAGGGTCAAAATGTACTTTTTGGAAAGTTCGGTGGGTC-AAA
1 ATGTG-ATTTTTG-GAAGTTTGAGGGTCAAAATGTAATTTTTGG-AAGTTCGG-GGG-CAAAA
* * * * * *
5710427 ATGTGATTTTTGGAAGTTTAAGGG-CAAAAAAGGAATTTTTAGAAAGTTCAAGGGTC-AAA
1 ATGTGATTTTTGGAAGTTTGAGGGTC-AAAATGTAATTTTT-GGAAGTTC-GGGGGCAAAA
* * * * * * * *
5710486 ATGTAATTTTTGGAAAG-TTCATGGTCAAAATATAGTTTTTGAAATGTTTTGGGGTC-AAA
1 ATGTGATTTTTGG-AAGTTTGAGGGTCAAAATGTAATTTTTGGAA-G-TTCGGGGGCAAAA
*
5710545 ATATGATTTTTGGAGAGTTT
1 ATGTGATTTTTGGA-AGTTT
5710565 AAGGACCTCC
Statistics
Matches: 206, Mismatches: 35, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
58 17 0.08
59 125 0.61
60 44 0.21
61 18 0.09
62 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.36
Consensus pattern (58 bp):
ATGTGATTTTTGGAAGTTTGAGGGTCAAAATGTAATTTTTGGAAGTTCGGGGGCAAAA
Found at i:5710506 original size:30 final size:30
Alignment explanation
Indices: 5710244--5710568 Score: 170
Period size: 30 Copynumber: 11.0 Consensus size: 30
5710234 AAATTGGGCT
* * *
5710244 TCAACATGTCATTTTAGG-AAGTTCAAGGG
1 TCAAAATGTAATTTTTGGAAAGTTCAAGGG
*
5710273 -CAAAAATGGAATTTTTGG-AAGTTC--GGG
1 TC-AAAATGTAATTTTTGGAAAGTTCAAGGG
* * ***
5710300 AGCAAAAATGTGATTTTTTGG-AAGTTTGGGGG
1 -TC-AAAATGT-AATTTTTGGAAAGTTCAAGGG
* * **
5710332 TTAAAATTTAATTTTTGG-AAGTT-TGGGG
1 TCAAAATGTAATTTTTGGAAAGTTCAAGGG
* * * **
5710360 GCAAAAATGGAATTTTTGAAAAGTTTGAGGG
1 TC-AAAATGTAATTTTTGGAAAGTTCAAGGG
* **
5710391 TCAAAATGTACTTTTTGGAAAGTTCGGTGGG
1 TCAAAATGTAATTTTTGGAAAGTTC-AAGGG
* *
5710422 TCAAAATGTGATTTTTGG-AAGTTTAAGGG
1 TCAAAATGTAATTTTTGGAAAGTTCAAGGG
* * *
5710451 -CAAAAAAGGAATTTTTAGAAAGTTCAAGGG
1 TC-AAAATGTAATTTTTGGAAAGTTCAAGGG
*
5710481 TCAAAATGTAATTTTTGGAAAGTTC-ATGG
1 TCAAAATGTAATTTTTGGAAAGTTCAAGGG
* * ***
5710510 TCAAAATATAGTTTTT-GAAATGTTTTGGGG
1 TCAAAATGTAATTTTTGGAAA-GTTCAAGGG
* * * *
5710540 TCAAAATATGATTTTTGGAGAGTTTAAGG
1 TCAAAATGTAATTTTTGGAAAGTTCAAGG
5710569 ACCTCCTAGG
Statistics
Matches: 231, Mismatches: 49, Indels: 31
0.74 0.16 0.10
Matches are distributed among these distances:
27 3 0.01
28 10 0.04
29 87 0.38
30 100 0.43
31 28 0.12
32 3 0.01
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.35
Consensus pattern (30 bp):
TCAAAATGTAATTTTTGGAAAGTTCAAGGG
Found at i:5710545 original size:90 final size:90
Alignment explanation
Indices: 5710270--5710545 Score: 246
Period size: 90 Copynumber: 3.1 Consensus size: 90
5710260 GGAAGTTCAA
* * * * * *
5710270 GGGCAAAAATGGAATTTTTG-GAAGTTC--GGGAGCAAAAATGTGATTTTTTGG-AAGTTTG-GG
1 GGGCAAAAAAGGAATTTTTGAAAAGTTCAAGGG-TC-AAAATGT-AATTTTTGGAAAGTTCGATG
* * * * *
5710330 GGTTAAAATTTAATTTTTGGAAGTTTGG
63 GGTCAAAATATGATTTTTGAAAGTTTTG
* ** * *
5710358 GGGCAAAAATGGAATTTTTGAAAAGTTTGAGGGTCAAAATGTACTTTTTGGAAAGTTCGGTGGGT
1 GGGCAAAAAAGGAATTTTTGAAAAGTTCAAGGGTCAAAATGTAATTTTTGGAAAGTTCGATGGGT
* * **
5710423 CAAAATGTGATTTTTGGAAGTTTAA
66 CAAAATATGATTTTTGAAAGTTTTG
5710448 GGGCAAAAAAGGAATTTTT-AGAAAGTTCAAGGGTCAAAATGTAATTTTTGGAAAGTTC-AT-GG
1 GGGCAAAAAAGGAATTTTTGA-AAAGTTCAAGGGTCAAAATGTAATTTTTGGAAAGTTCGATGGG
5710510 TCAAAATAT-AGTTTTTGAAATGTTTTG
65 TCAAAATATGA-TTTTTGAAA-GTTTTG
5710537 GGGTCAAAA
1 GGG-CAAAA
5710546 TATGATTTTT
Statistics
Matches: 159, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
87 1 0.01
88 46 0.29
89 27 0.17
90 82 0.52
91 3 0.02
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (90 bp):
GGGCAAAAAAGGAATTTTTGAAAAGTTCAAGGGTCAAAATGTAATTTTTGGAAAGTTCGATGGGT
CAAAATATGATTTTTGAAAGTTTTG
Found at i:5711593 original size:3 final size:3
Alignment explanation
Indices: 5711585--5711637 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
5711575 CGAATATCTT
* *
5711585 TTA TTA TTA TTA TTA TTA TTA TTA TAA ATA TTTA TTA TGTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA -TTA TTA
5711633 -TA TTA
1 TTA TTA
5711638 AATATGTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 2 0.05
3 33 0.79
4 6 0.14
5 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5711658 original size:20 final size:20
Alignment explanation
Indices: 5711620--5711662 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5711610 AAATATTTAT
5711620 TATGTATTTATTATATTAAA
1 TATGTATTTATTATATTAAA
*
5711640 TATGTTATTTATT-TGTTAAA
1 TATG-TATTTATTATATTAAA
5711660 TAT
1 TAT
5711663 ATTTTCAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (20 bp):
TATGTATTTATTATATTAAA
Found at i:5712323 original size:11 final size:11
Alignment explanation
Indices: 5712287--5712327 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
5712277 TGATATTATT
5712287 AATTT-AAATA
1 AATTTAAAATA
*
5712297 AATTTAAACTTA
1 AATTTAAA-ATA
5712309 AATTTAAAATA
1 AATTTAAAATA
5712320 AATTTAAA
1 AATTTAAA
5712328 TTCTGTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 5 0.19
11 12 0.44
12 10 0.37
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
AATTTAAAATA
Found at i:5713373 original size:18 final size:18
Alignment explanation
Indices: 5713347--5713384 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
5713337 AAAAAATAAA
*
5713347 TAATTTTTTCTA-ATTTT
1 TAATTTTTTTTATATTTT
5713364 TAATTTTTTTTATATTTT
1 TAATTTTTTTTATATTTT
5713382 TAA
1 TAA
5713385 AAATTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TAATTTTTTTTATATTTT
Found at i:5717651 original size:27 final size:25
Alignment explanation
Indices: 5717614--5717666 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
5717604 TGTTTTTTAA
5717614 TTTTTTAAAATTTAAGTCCAATTAT
1 TTTTTTAAAATTTAAGTCCAATTAT
* *
5717639 TTTTTTAGTAAATTTAGGTCGAATTAT
1 TTTTTTA--AAATTTAAGTCCAATTAT
5717666 T
1 T
5717667 AACATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
27 17 0.71
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (25 bp):
TTTTTTAAAATTTAAGTCCAATTAT
Found at i:5718882 original size:24 final size:24
Alignment explanation
Indices: 5718855--5718907 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5718845 ATTAAACAGA
5718855 GTTTAACTGATGCAATTAAACTCT
1 GTTTAACTGATGCAATTAAACTCT
** * *
5718879 GTTTATTTGTTTCAATTAAACTCT
1 GTTTAACTGATGCAATTAAACTCT
5718903 GTTTA
1 GTTTA
5718908 TTTATTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.47
Consensus pattern (24 bp):
GTTTAACTGATGCAATTAAACTCT
Found at i:5720187 original size:23 final size:23
Alignment explanation
Indices: 5720139--5720187 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
5720129 TGATCTAAGG
* *
5720139 AAAAATAAAAGAAACTGAATTAA
1 AAAAATAAAAGAAAATGAACTAA
5720162 AAAAATAAAAGAAAATAGAACTAA
1 AAAAATAAAAGAAAAT-GAACTAA
5720186 AA
1 AA
5720188 GAAGTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (23 bp):
AAAAATAAAAGAAAATGAACTAA
Found at i:5721027 original size:19 final size:19
Alignment explanation
Indices: 5721003--5721045 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5720993 AAATATAAAT
5721003 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
5721022 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
5721041 TAAAT
1 TAAAT
5721046 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:5721359 original size:4 final size:4
Alignment explanation
Indices: 5721350--5721403 Score: 53
Period size: 4 Copynumber: 13.8 Consensus size: 4
5721340 TCCTGGACAA
5721350 AAAT AAAT AAAT AAAT AAAAT AAGAT AGAA- AAAT AAA- AAA- AAAT AAA-
1 AAAT AAAT AAAT AAAT -AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT AAAT
5721397 AAAT AAA
1 AAAT AAA
5721404 AATAATTGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
3 11 0.25
4 24 0.55
5 8 0.18
6 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:5721363 original size:8 final size:8
Alignment explanation
Indices: 5721350--5721403 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 8
5721340 TCCTGGACAA
5721350 AAATAAAT
1 AAATAAAT
5721358 AAATAAAT
1 AAATAAAT
5721366 AAAATAAGAT
1 -AAATAA-AT
5721376 AGAA-AAAT
1 A-AATAAAT
5721384 AAA-AAA-
1 AAATAAAT
5721390 AAATAAA-
1 AAATAAAT
5721397 AAATAAA
1 AAATAAA
5721404 AATAATTGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.07
7 15 0.36
8 11 0.26
9 9 0.21
10 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.17
Consensus pattern (8 bp):
AAATAAAT
Found at i:5721371 original size:17 final size:16
Alignment explanation
Indices: 5721349--5721404 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 16
5721339 TTCCTGGACA
5721349 AAAATAAATAAATAAAT
1 AAAATAAATAAA-AAAT
5721366 AAAATAAGATAGAAAAAT
1 AAAATAA-ATA-AAAAAT
*
5721384 AAAAAAAAATAAAAAAT
1 -AAAATAAATAAAAAAT
5721401 AAAA
1 AAAA
5721405 ATAATTGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
16 4 0.11
17 13 0.37
18 10 0.29
19 8 0.23
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (16 bp):
AAAATAAATAAAAAAT
Found at i:5721405 original size:18 final size:18
Alignment explanation
Indices: 5721348--5721405 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 18
5721338 TTTCCTGGAC
5721348 AAAAATAAATAAATAAATAA
1 AAAAATAAA-AAATAAA-AA
5721368 AATAAGATAGAAAAAT-AAAA
1 AA-AA-ATA-AAAAATAAAAA
5721388 AAAAATAAAAAATAAAAA
1 AAAAATAAAAAATAAAAA
5721406 TAATTGGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 2 0.06
20 6 0.18
21 4 0.12
22 7 0.21
23 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (18 bp):
AAAAATAAAAAATAAAAA
Found at i:5725469 original size:21 final size:21
Alignment explanation
Indices: 5725443--5725485 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5725433 TTAATAGATG
*
5725443 CCACAGTTTTCTTTTGGAAAT
1 CCACAGTTTGCTTTTGGAAAT
5725464 CCACAGTTTGCTTTTGGAAAT
1 CCACAGTTTGCTTTTGGAAAT
5725485 C
1 C
5725486 TATAGATTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (21 bp):
CCACAGTTTGCTTTTGGAAAT
Found at i:5725495 original size:21 final size:21
Alignment explanation
Indices: 5725443--5725496 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5725433 TTAATAGATG
* *
5725443 CCACAGTTTTCTTTTGGAAAT
1 CCACAGATTGCTTTTGGAAAT
*
5725464 CCACAGTTTGCTTTTGGAAAT
1 CCACAGATTGCTTTTGGAAAT
* *
5725485 CTATAGATTGCT
1 CCACAGATTGCT
5725497 GCTAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (21 bp):
CCACAGATTGCTTTTGGAAAT
Found at i:5727083 original size:23 final size:23
Alignment explanation
Indices: 5727035--5727083 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
5727025 TGATCTAAGG
* *
5727035 AAAAATAAAAGAAACTGAATTAA
1 AAAAATAAAAGAAAATGAACTAA
5727058 AAAAATAAAAGAAAATAGAACTAA
1 AAAAATAAAAGAAAAT-GAACTAA
5727082 AA
1 AA
5727084 GAAGTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.14
Consensus pattern (23 bp):
AAAAATAAAAGAAAATGAACTAA
Found at i:5727923 original size:19 final size:19
Alignment explanation
Indices: 5727899--5727941 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5727889 AAATATAAAT
5727899 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
5727918 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
5727937 TAAAT
1 TAAAT
5727942 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:5729107 original size:24 final size:24
Alignment explanation
Indices: 5729066--5729132 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
5729056 GAAATAATAT
***
5729066 TTCAATTAAACAGAGTTTAACTAA
1 TTCAATTAAACTCTGTTTAACTAA
** **
5729090 TTCAATTAAACTCTGTTTATTTGT
1 TTCAATTAAACTCTGTTTAACTAA
*
5729114 TTCAATTAAACTTTGTTTA
1 TTCAATTAAACTCTGTTTA
5729133 TTTGTTTGAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (24 bp):
TTCAATTAAACTCTGTTTAACTAA
Found at i:5729146 original size:28 final size:24
Alignment explanation
Indices: 5729090--5729139 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
5729080 GTTTAACTAA
5729090 TTCAATTAAACTCTGTTTATTTGT
1 TTCAATTAAACTCTGTTTATTTGT
*
5729114 TTCAATTAAACTTTGTTTATTTGT
1 TTCAATTAAACTCTGTTTATTTGT
5729138 TT
1 TT
5729140 GAGTCAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.58
Consensus pattern (24 bp):
TTCAATTAAACTCTGTTTATTTGT
Found at i:5729148 original size:24 final size:24
Alignment explanation
Indices: 5729090--5729149 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
5729080 GTTTAACTAA
*
5729090 TTCAATTAAACTCTGTTTATTTGT
1 TTCAATCAAACTCTGTTTATTTGT
* *
5729114 TTCAATTAAACTTTGTTTATTTGT
1 TTCAATCAAACTCTGTTTATTTGT
* *
5729138 TTGAGTCAAACT
1 TTCAATCAAACT
5729150 GTTATTAGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.52
Consensus pattern (24 bp):
TTCAATCAAACTCTGTTTATTTGT
Found at i:5769187 original size:18 final size:18
Alignment explanation
Indices: 5769166--5769204 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5769156 TACTCATCAT
*
5769166 TTTAATTTCGATTTTAAA
1 TTTAATTTCAATTTTAAA
*
5769184 TTTAATTTTAATTTTAAA
1 TTTAATTTCAATTTTAAA
5769202 TTT
1 TTT
5769205 GTACTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTAATTTCAATTTTAAA
Found at i:5771145 original size:7 final size:7
Alignment explanation
Indices: 5771135--5771175 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
5771125 TTATGTTTAG
5771135 GGTTTGA
1 GGTTTGA
5771142 GGTTTGA
1 GGTTTGA
5771149 -GTTTG-
1 GGTTTGA
5771154 GAGTTTGA
1 G-GTTTGA
5771162 GGTTTG-
1 GGTTTGA
5771168 GGTTTGA
1 GGTTTGA
5771175 G
1 G
5771176 ATTCAGGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 11 0.37
7 18 0.60
8 1 0.03
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (7 bp):
GGTTTGA
Found at i:5771152 original size:20 final size:20
Alignment explanation
Indices: 5771136--5771173 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5771126 TATGTTTAGG
5771136 GTTTGAGGTTTGAGTTTGGA
1 GTTTGAGGTTTGAGTTTGGA
*
5771156 GTTTGAGGTTTGGGTTTG
1 GTTTGAGGTTTGAGTTTG
5771174 AGATTCAGGA
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:0.11, C:0.00, G:0.42, T:0.47
Consensus pattern (20 bp):
GTTTGAGGTTTGAGTTTGGA
Found at i:5771370 original size:17 final size:17
Alignment explanation
Indices: 5771334--5771367 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
5771324 CTTCCTTCAA
5771334 ATAAGATAAATTTAGCC
1 ATAAGATAAATTTAGCC
5771351 ATAATGATAAATTTAGC
1 ATAA-GATAAATTTAGC
5771368 ATATTTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (17 bp):
ATAAGATAAATTTAGCC
Found at i:5777033 original size:3 final size:3
Alignment explanation
Indices: 5777025--5777055 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5777015 TCACTAGGTG
*
5777025 GAT GAT GAT GGT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
5777056 GTCAGGTCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.39, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:5793731 original size:31 final size:31
Alignment explanation
Indices: 5793694--5793754 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
5793684 CTAAATTTTA
*
5793694 AATTTCAAAATTCGGAA-AGTACAAGGACTAT
1 AATTTCAAAATTC-AAAGAGTACAAGGACTAT
5793725 AATTTCAAAATTCAAAGAGTACAAGGACTA
1 AATTTCAAAATTCAAAGAGTACAAGGACTA
5793755 AAAATGATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.25
Consensus pattern (31 bp):
AATTTCAAAATTCAAAGAGTACAAGGACTAT
Found at i:5799881 original size:23 final size:23
Alignment explanation
Indices: 5799853--5799902 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5799843 AAGGATTGTT
* *
5799853 TTTAAATTTTA-TTTTATTTTAAA
1 TTTAAA-TTTACTTTGAGTTTAAA
5799876 TTTAAATTTACTTTGAGTTTAAA
1 TTTAAATTTACTTTGAGTTTAAA
5799899 TTTA
1 TTTA
5799903 TTTTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTAAATTTACTTTGAGTTTAAA
Found at i:5799885 original size:17 final size:17
Alignment explanation
Indices: 5799852--5799911 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
5799842 CAAGGATTGT
* *
5799852 TTTTAAATTTTATTTTA
1 TTTTAAATTTAAATTTA
5799869 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
* * *
5799886 CTTTGAGTTTAAATTTA
1 TTTTAAATTTAAATTTA
*
5799903 TTTTTAATT
1 TTTTAAATT
5799912 AAAAGTATCC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:5800974 original size:31 final size:31
Alignment explanation
Indices: 5800936--5800998 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5800926 CGGAGGCGCG
5800936 TGGCGTGGGTATGACGTGGGATCCGGGCGGT
1 TGGCGTGGGTATGACGTGGGATCCGGGCGGT
5800967 TGGCGTGGGTATGACGTGGGATCCGGGCGGT
1 TGGCGTGGGTATGACGTGGGATCCGGGCGGT
5800998 T
1 T
5800999 CGTAACGGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.10, C:0.16, G:0.51, T:0.24
Consensus pattern (31 bp):
TGGCGTGGGTATGACGTGGGATCCGGGCGGT
Found at i:5801719 original size:30 final size:30
Alignment explanation
Indices: 5801658--5801791 Score: 100
Period size: 30 Copynumber: 4.5 Consensus size: 30
5801648 CGATTTCTCC
* * *
5801658 AAAAATTACCA-TTTACCCCTAAA-TGTCT
1 AAAAATTACCATTTTAACCTTAAACTTTCT
5801686 AAAAATT-CCATTTTAAACCTTAAACTTTCT
1 AAAAATTACCATTTT-AACCTTAAACTTTCT
* *
5801716 AAAAATTACCATTTTATCCCTAAA-TGTT-T
1 AAAAATTACCATTTTAACCTTAAACT-TTCT
* * * *
5801745 AAAAATT-TCATTTTTTGACCTCAAACTTTCCC
1 AAAAATTACCA--TTTTAACCTTAAACTTT-CT
5801777 AAAAATTACCATTTT
1 AAAAATTACCATTTT
5801792 GCCCTTAAGT
Statistics
Matches: 83, Mismatches: 12, Indels: 19
0.73 0.11 0.17
Matches are distributed among these distances:
27 3 0.04
28 12 0.14
29 16 0.19
30 31 0.37
31 12 0.14
32 7 0.08
33 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAAATTACCATTTTAACCTTAAACTTTCT
Found at i:5801757 original size:59 final size:61
Alignment explanation
Indices: 5801651--5801791 Score: 189
Period size: 59 Copynumber: 2.3 Consensus size: 61
5801641 TTGACCCCGA
*
5801651 TTTCTCCAAAAATTACCA-TTTACCCCTAAATGTCTAAAAATTCCA-TTTTAAACCTTAAAC
1 TTTC-CCAAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTTAAACCTCAAAC
* * * * **
5801711 TTT-CTAAAAATTACCATTTTATCCCTAAATGTTTAAAAATTTCATTTTTTGACCTCAAAC
1 TTTCCCAAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTTAAACCTCAAAC
5801771 TTTCCCAAAAATTACCATTTT
1 TTTCCCAAAAATTACCATTTT
5801792 GCCCTTAAGT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
58 12 0.17
59 24 0.34
60 18 0.26
61 16 0.23
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (61 bp):
TTTCCCAAAAATTACCATTTTACCCCTAAATGTCTAAAAATTCCATTTTTAAACCTCAAAC
Found at i:5812662 original size:49 final size:47
Alignment explanation
Indices: 5812597--5813172 Score: 329
Period size: 49 Copynumber: 11.8 Consensus size: 47
5812587 CTACAGGTCT
* * * * *
5812597 CAGTACCGCGAAACATGGAGGGAAAGGTTTAAGTCGCAACGACAAAC
1 CAGTACCACGAGACATGAAGGGAAAGATTTAAGCCGCAACGACAAAC
* * *
5812644 CTTGTACCTTA-GAGACATGAAAGGAAAGATTTAAGCCGCAACGACGAATC
1 C-AGTACC--ACGAGACATGAAGGGAAAGATTTAAGCCGCAACGAC-AAAC
* * * **
5812694 CAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCGCAACGATGAAC
1 CAGTACCACG-AGACATGAAGGGAAAGATTTAAGCCGCAACGACAAAC
* * * ** *
5812742 CTTA-TACCTCAAAGACATGAAGGGAAAGATTTAAGCCGCAATGGTGAATC
1 C--AGTACCAC-GAGACATGAAGGGAAAGATTTAAGCCGCAA-CGACAAAC
* * *
5812792 CAGTACCACGAAAGCATAAAGGGAAAGATTTAAGCCGCAACGACGAATC
1 CAGTACCACGAGA-CATGAAGGGAAAGATTTAAGCCGCAACGAC-AAAC
* * * *
5812841 CAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCGCAACGACGAAC
1 CAGTACCACG-AGACATGAAGGGAAAGATTTAAGCCGCAACGACAAAC
* * * *
5812889 CTTA-TACCTA-GAGACATGAAAGGAAAGATTTAAGCCGCAATGGCGAATC
1 C--AGTACC-ACGAGACATGAAGGGAAAGATTTAAGCCGCAACGAC-AAAC
** * * * * * *
5812938 CAGTACCATTAAGACACGAAGGGGAAGGTTTAAGTCGCAACGGCGAAC
1 CAGTACCA-CGAGACATGAAGGGAAAGATTTAAGCCGCAACGACAAAC
* *
5812986 CTTGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACTG-CGAATC
1 C-AGTACCACG-AGACATGAAGGGAAAGATTTAAGCCGCAAC-GAC-AAAC
* * * * * * * *
5813036 TAGTACCACGAAGGCA-CAAGGGAAAGGTTTAAGTCGCAATGGCGAAC
1 CAGTACCACG-AGACATGAAGGGAAAGATTTAAGCCGCAACGACAAAC
* * * * * * *
5813083 CTACTACCTCAGAGGCATAAAGGGAAAGATTTAAGCCACAACAACGAATC
1 C-AGTACCAC-GAGACATGAAGGGAAAGATTTAAGCCGCAACGAC-AAAC
* * * *
5813133 CAGCACCACGAAGACA-CAAGGGGAAAGGTTTAAGTCGCAA
1 CAGTACCACG-AGACATGAA-GGGAAAGATTTAAGCCGCAA
5813173 TGGTGAACCT
Statistics
Matches: 402, Mismatches: 95, Indels: 62
0.72 0.17 0.11
Matches are distributed among these distances:
47 7 0.02
48 85 0.21
49 291 0.72
50 19 0.05
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (47 bp):
CAGTACCACGAGACATGAAGGGAAAGATTTAAGCCGCAACGACAAAC
Found at i:5812743 original size:98 final size:97
Alignment explanation
Indices: 5812597--5813135 Score: 435
Period size: 98 Copynumber: 5.5 Consensus size: 97
5812587 CTACAGGTCT
* * * * * *
5812597 CAGTACCGCGAA-ACATGGAGGGAAAGGTTTAAGTCGCAACGAC-AAACCTTGTACCTTAGAGAC
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC-AGTACCTTAGAGAC
* *
5812660 ATGAAAGGAAAGATTTAAGCCGCAACGACGAATC
65 ACGAAGGGAAAGATTTAAGCCGCAACGACGAA-C
* * * * * *
5812694 CAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCGCAACGATGAA-CCTTA-TACCTCAAAGA
1 CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC--AGTACCTTAGAGA
* * **
5812757 CATGAAGGGAAAGATTTAAGCCGCAATGGTGAATC
64 CACGAAGGGAAAGATTTAAGCCGCAACGACGAA-C
*
5812792 CAGTACCACGAA-AGCATAAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACC--ACGAAG
1 CAGTACCACGAAGA-CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCTTA-G-AG
* *
5812854 ACACGAAGGGAAAGGTTTAAGTCGCAACGACGAAC
63 ACACGAAGGGAAAGATTTAAGCCGCAACGACGAAC
* * *
5812889 CTTA-TACCTA-G-AGACATGAAAGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCATTA-A
1 C--AGTACC-ACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACC-TTAGA
* * * *
5812950 GACACGAAGGGGAAGGTTTAAGTCGCAACGGCGAAC
62 GACACGAAGGGAAAGATTTAAGCCGCAACGACGAAC
* *
5812986 CTTGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACTG-CGAATCTAGTACC--ACGAA
1 C-AGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAAC-GACGAATCCAGTACCTTA-G-A
* * * * *
5813048 GGCAC-AAGGGAAAGGTTTAAGTCGCAATGGCGAAC
62 GACACGAAGGGAAAGATTTAAGCCGCAACGACGAAC
* * * * * *
5813083 CTACTACCTC-AGAGGCATAAAGGGAAAGATTTAAGCCACAACAACGAATCCAG
1 C-AGTACCACGA-AGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAG
5813136 CACCACGAAG
Statistics
Matches: 374, Mismatches: 44, Indels: 48
0.80 0.09 0.10
Matches are distributed among these distances:
95 1 0.00
96 4 0.01
97 165 0.44
98 195 0.52
99 8 0.02
100 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (97 bp):
CAGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCTTAGAGACA
CGAAGGGAAAGATTTAAGCCGCAACGACGAAC
Found at i:5812944 original size:97 final size:97
Alignment explanation
Indices: 5812813--5813224 Score: 494
Period size: 97 Copynumber: 4.2 Consensus size: 97
5812803 AAGCATAAAG
* *
5812813 GGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCG
1 GGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGACAC-AAGGGAAAGGTTTAAGTCG
*
5812878 CAACGACGAACCTTATACCT-AGAGACATGAAA
65 CAACGGCGAACCTTATACCTCAGAGACATGAAA
** *
5812910 GGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCATTAAGACACGAAGGGGAAGGTTTAAGTCG
1 GGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGACAC-AAGGGAAAGGTTTAAGTCG
* * *
5812975 CAACGGCGAACCTTGTACCAC-GAAGACATGAAG
65 CAACGGCGAACCTTATACCTCAG-AGACATGAAA
* *
5813008 GGAAAGATTTAAGCCGCAACT-GCGAATCTAGTACCACGAAGGCACAAGGGAAAGGTTTAAGTCG
1 GGAAAGATTTAAGCCGCAA-TGGCGAATCCAGTACCACGAAGACACAAGGGAAAGGTTTAAGTCG
* *
5813072 CAATGGCGAACC-TACTACCTCAGAGGCAT-AAA
65 CAACGGCGAACCTTA-TACCTCAGAGACATGAAA
* *** *
5813104 GGGAAAGATTTAAGCCACAACAACGAATCCAGCACCACGAAGACACAAGGGGAAAGGTTTAAGTC
1 -GGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGACACAA-GGGAAAGGTTTAAGTC
* * * * * *
5813169 GCAATGGTGAACCTTATGCCTCAAAAATATGAAA
64 GCAACGGCGAACCTTATACCTCAGAGACATGAAA
*
5813203 -GAAAAATTTAAGCCGCAATGGC
1 GGAAAGATTTAAGCCGCAATGGC
5813225 AAATTTAGTA
Statistics
Matches: 269, Mismatches: 36, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
96 3 0.01
97 174 0.65
98 86 0.32
99 6 0.02
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.16
Consensus pattern (97 bp):
GGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGACACAAGGGAAAGGTTTAAGTCGC
AACGGCGAACCTTATACCTCAGAGACATGAAA
Found at i:5813026 original size:244 final size:243
Alignment explanation
Indices: 5812597--5813074 Score: 726
Period size: 244 Copynumber: 2.0 Consensus size: 243
5812587 CTACAGGTCT
* * * *
5812597 CAGTACCGCGAAACATGGAGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTACCTTAGAGACAT
1 CAGTACCACGAAACACGAAGGGAAAGGTTTAAGTCGCAACGACAAACCTTATACCTTAGAGACAT
5812662 GAAAGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
66 GAAAGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
* * *
5812727 GTCGCAACGATGAACCTTATACCTCAAAGACATGAAGGGAAAGATTTAAGCCGCAA-TGGTGAAT
131 GTCGCAACGACGAACCTTATACCACAAAGACATGAAGGGAAAGATTTAAGCCGCAACT-GCGAAT
5812791 CCAGTACCACGAAAGCATAAAGGGAAAGATTTAAGCCGCAACGACGAATC
195 CCAGTACCACGAAAGCA-AAAGGGAAAGATTTAAGCCGCAACGACGAATC
*
5812841 CAGTACCACGAAGACACGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTATACC-TAGAGACA
1 CAGTACCACGAA-ACACGAAGGGAAAGGTTTAAGTCGCAACGACAAACCTTATACCTTAGAGACA
* * ** *
5812905 TGAAAGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCATTAAGACACGAAGGGGAAGGTTTA
65 TGAAAGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTA
* * *
5812970 AGTCGCAACGGCGAACCTTGTACCACGAAGACATGAAGGGAAAGATTTAAGCCGCAACTGCGAAT
130 AGTCGCAACGACGAACCTTATACCACAAAGACATGAAGGGAAAGATTTAAGCCGCAACTGCGAAT
* * * * *
5813035 CTAGTACCACGAAGGCACAAGGGAAAGGTTTAAGTCGCAA
195 CCAGTACCACGAAAGCAAAAGGGAAAGATTTAAGCCGCAA
5813075 TGGCGAACCT
Statistics
Matches: 211, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
243 20 0.09
244 151 0.72
245 40 0.19
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (243 bp):
CAGTACCACGAAACACGAAGGGAAAGGTTTAAGTCGCAACGACAAACCTTATACCTTAGAGACAT
GAAAGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
GTCGCAACGACGAACCTTATACCACAAAGACATGAAGGGAAAGATTTAAGCCGCAACTGCGAATC
CAGTACCACGAAAGCAAAAGGGAAAGATTTAAGCCGCAACGACGAATC
Found at i:5813106 original size:146 final size:147
Alignment explanation
Indices: 5812647--5813224 Score: 640
Period size: 146 Copynumber: 4.0 Consensus size: 147
5812637 GACAAACCTT
*
5812647 GTACCTTAGAGACATGAAA-GGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACAC
1 GTACCTCAGAGACAT-AAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACAC
* * *
5812711 GAAGGGAAAGGTTTAAGTCGCAACGATGAACCTTATACCTCAAAGACATGAAGGGAAAGATTTAA
65 GAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTATACCACGAAGACATGAAGGGAAAGATTTAA
*
5812776 GCCGCAATGGTGAATCCA
130 GCCGCAATGGCGAATCCA
* *
5812794 GTACCAC-GAAAGCATAAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACAC
1 GTACCTCAGAGA-CATAAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACAC
*
5812858 GAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTATACCTA-G-AGACATGAAAGGAAAGATTTA
65 GAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTATACC-ACGAAGACATGAAGGGAAAGATTTA
5812921 AGCCGCAATGGCGAATCCA
129 AGCCGCAATGGCGAATCCA
* ** * * * * *
5812940 GTACCATTA-AGACACGAAGGGGAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCACGAAGACA
1 GTACC-TCAGAGACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCC-AGTACCACGAAGACA
* * * * * * *
5813003 TGAAGGGAAAGATTTAAGCCGCAACTG-CGAATC-TAGTACCACGAAGGCA-CAAGGGAAAGGTT
64 CGAAGGGAAAGGTTTAAGTCGCAAC-GACGAACCTTA-TACCACGAAGACATGAAGGGAAAGATT
*
5813065 TAAGTCGCAATGGCGAA-CCTA
127 TAAGCCGCAATGGCGAATCC-A
* * * * *
5813086 CTACCTCAGAGGCATAAAGGGAAAGATTTAAGCCACAACAACGAATCCAGCACCACGAAGACAC-
1 GTACCTCAGAGACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACACG
* ** * * * * * * *
5813150 AAGGGGAAAGGTTTAAGTCGCAATGGTGAACCTTATGCCTCAAAAATATGAA-AGAAAAATTTAA
66 AA-GGGAAAGGTTTAAGTCGCAACGACGAACCTTATACCACGAAGACATGAAGGGAAAGATTTAA
5813214 GCCGCAATGGC
130 GCCGCAATGGC
5813225 AAATTTAGTA
Statistics
Matches: 357, Mismatches: 57, Indels: 35
0.80 0.13 0.08
Matches are distributed among these distances:
145 12 0.03
146 241 0.68
147 104 0.29
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (147 bp):
GTACCTCAGAGACATAAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGACACG
AAGGGAAAGGTTTAAGTCGCAACGACGAACCTTATACCACGAAGACATGAAGGGAAAGATTTAAG
CCGCAATGGCGAATCCA
Found at i:5813652 original size:17 final size:17
Alignment explanation
Indices: 5813639--5813693 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
5813629 TTTATTTTAT
5813639 TTTATTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
* * *
5813656 CTTACTTTAAGTTTAAA
1 TTTATTTTAAATTTAAA
*
5813673 TTTATTTTAAATTAAAA
1 TTTATTTTAAATTTAAA
5813690 TTTA
1 TTTA
5813694 ATTAAAAGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:5814299 original size:3 final size:3
Alignment explanation
Indices: 5814291--5814366 Score: 64
Period size: 3 Copynumber: 25.0 Consensus size: 3
5814281 TAAAGGGTAC
* * * * *
5814291 TAA TAA TAA TTAA TAA TAG TAT TAA TAC TAA TAA -ATA TAA CAT TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
**
5814337 TAA TTT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5814367 AGCCGAAACG
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 1 0.02
3 52 0.91
4 4 0.07
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5815422 original size:29 final size:28
Alignment explanation
Indices: 5815390--5815619 Score: 137
Period size: 29 Copynumber: 7.9 Consensus size: 28
5815380 AAAAATCATA
* *
5815390 TTTTACCCCTGAACTTTCAAAAATTCTAT
1 TTTTA-CCCTAAACTTTCAAAAATTCCAT
** *
5815419 TTTTGACCC-CGATTTCTCTAAAAATTACCA-
1 TTTT-ACCCTAAACTT-TC-AAAAATT-CCAT
* * *
5815449 TTTTACCCTCGAACTTCCAAAAATTCTAT
1 TTTTACCCT-AAACTTTCAAAAATTCCAT
*
5815478 TTTTGACCCT-AATTTTCCAAAAATTACCA-
1 TTTT-ACCCTAAACTTT-CAAAAATT-CCAT
* *
5815507 TTTTACCCTCAAACTTCCAAATATTCCAT
1 TTTTACCCT-AAACTTTCAAAAATTCCAT
***
5815536 TTTTAACCCTATTTTTTCAAAAATTACCA-
1 TTTT-ACCCTAAACTTTCAAAAATT-CCAT
* *
5815565 TTTTACCCCAAAATTTCTAAAAATTCCAT
1 TTTTACCCTAAACTTTC-AAAAATTCCAT
*
5815594 TTTAAACCCTAAACTTTCCAAAAATT
1 TTT-TACCCTAAACTTT-CAAAAATT
5815620 ACCCTCAAAT
Statistics
Matches: 155, Mismatches: 27, Indels: 37
0.71 0.12 0.17
Matches are distributed among these distances:
28 29 0.19
29 71 0.46
30 49 0.32
31 6 0.04
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (28 bp):
TTTTACCCTAAACTTTCAAAAATTCCAT
Found at i:5815523 original size:58 final size:58
Alignment explanation
Indices: 5815367--5815622 Score: 257
Period size: 58 Copynumber: 4.4 Consensus size: 58
5815357 CCCTAAAGGC
* * * ** * * *
5815367 CCCTAAATTGTCCAAAAATCA-TATTTTACCCCTGAACTTTCAAAAATTCTATTTTTGA
1 CCCT-AATTTTCCAAAAATTACCATTTTACCCCAAAACTTCCAAAAATTCCATTTTTAA
** * * * *
5815425 CCCCGATTTCTCTAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATTCTATTTTTGA
1 CCCTAATTT-TCCAAAAATTACCATTTTACCC-CAAAACTTCCAAAAATTCCATTTTTAA
*
5815484 CCCTAATTTTCCAAAAATTACCATTTTACCCTC-AAACTTCCAAATATTCCATTTTTAA
1 CCCTAATTTTCCAAAAATTACCATTTTACCC-CAAAACTTCCAAAAATTCCATTTTTAA
* * * * *
5815542 CCCTATTTTTTCAAAAATTACCATTTTACCCCAAAATTTCTAAAAATTCCATTTTAAA
1 CCCTAATTTTCCAAAAATTACCATTTTACCCCAAAACTTCCAAAAATTCCATTTTTAA
*
5815600 CCCTAAACTTTCCAAAAATTACC
1 CCCT-AATTTTCCAAAAATTACC
5815623 CTCAAATGTC
Statistics
Matches: 170, Mismatches: 23, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
57 4 0.02
58 110 0.65
59 55 0.32
60 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (58 bp):
CCCTAATTTTCCAAAAATTACCATTTTACCCCAAAACTTCCAAAAATTCCATTTTTAA
Found at i:5815619 original size:30 final size:29
Alignment explanation
Indices: 5815438--5815622 Score: 159
Period size: 29 Copynumber: 6.3 Consensus size: 29
5815428 CGATTTCTCT
*
5815438 AAAAATTACCATTTTACCCTCGAAC-TTCC
1 AAAAATTACCATTTTACCCT-AAACTTTCC
* *
5815467 AAAAATT-CTATTTTTGACCCT-AATTTTCC
1 AAAAATTACCA-TTTT-ACCCTAAACTTTCC
5815496 AAAAATTACCATTTTACCCTCAAAC-TTCC
1 AAAAATTACCATTTTACCCT-AAACTTTCC
* ** *
5815525 AAATATT-CCATTTTTAACCCT-ATTTTTTC
1 AAAAATTACCA-TTTT-ACCCTAAACTTTCC
* * *
5815554 AAAAATTACCATTTTACCCCAAAATTTCT
1 AAAAATTACCATTTTACCCTAAACTTTCC
5815583 AAAAATT-CCATTTTAAACCCTAAACTTTCC
1 AAAAATTACCATTTT--ACCCTAAACTTTCC
5815613 AAAAATTACC
1 AAAAATTACC
5815623 CTCAAATGTC
Statistics
Matches: 125, Mismatches: 17, Indels: 26
0.74 0.10 0.15
Matches are distributed among these distances:
28 24 0.19
29 64 0.51
30 35 0.28
31 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTAAACTTTCC
Found at i:5821908 original size:12 final size:12
Alignment explanation
Indices: 5821891--5821915 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5821881 AACTTAATCC
5821891 ATAAACACCTCT
1 ATAAACACCTCT
5821903 ATAAACACCTCT
1 ATAAACACCTCT
5821915 A
1 A
5821916 AGTTGATTGC
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:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAACACCTCT
Found at i:5837354 original size:2 final size:2
Alignment explanation
Indices: 5837349--5837373 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5837339 CGTGTGTGTA
5837349 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
5837374 CAGAACACGT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5837626 original size:17 final size:18
Alignment explanation
Indices: 5837617--5837677 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 18
5837607 TAAATTTTAA
*
5837617 TTTAGTTTAAGTTTAAACT
1 TTTAATTTAAGTTTAAA-T
**
5837636 TTTCTTTTAAGTTTAAAT
1 TTTAATTTAAGTTTAAAT
5837654 TTTAA-TTAAGTTTAAA-
1 TTTAATTTAAGTTTAAAT
5837670 TTTAATTT
1 TTTAATTT
5837678 GAATTCAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 5 0.14
17 13 0.35
18 4 0.11
19 15 0.41
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (18 bp):
TTTAATTTAAGTTTAAAT
Found at i:5837646 original size:19 final size:17
Alignment explanation
Indices: 5837617--5837677 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
5837607 TAAATTTTAA
5837617 TTTAGTTTAAGTTTAAACT
1 TTTA-TTTAAGTTTAAA-T
*
5837636 TTTCTTTTAAGTTTAAAT
1 TTT-ATTTAAGTTTAAAT
*
5837654 TTTAATTAAGTTTAAAT
1 TTTATTTAAGTTTAAAT
*
5837671 TTAATTT
1 TTTATTT
5837678 GAATTCAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 17 0.47
18 4 0.11
19 15 0.42
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (17 bp):
TTTATTTAAGTTTAAAT
Found at i:5837690 original size:23 final size:22
Alignment explanation
Indices: 5837641--5837699 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
5837631 AAACTTTTCT
* * *
5837641 TTTAAGTTTAAATTTTAATTAAG
1 TTTAAATTT-AATTTGAATTAAA
5837664 TTTAAATTTAATTTGAATTCAAA
1 TTTAAATTTAATTTGAATT-AAA
*
5837687 TTTAAAATTAATT
1 TTTAAATTTAATT
5837700 AAAAAGTCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 9 0.29
23 22 0.71
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTAAATTTAATTTGAATTAAA
Found at i:5838831 original size:18 final size:16
Alignment explanation
Indices: 5838783--5838832 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
5838773 TAGTTTTAAA
*
5838783 AAAGAAAATAAAGAGAG
1 AAAGAAAAAAAAG-GAG
*
5838800 AAAGATAAAAAAGGAG
1 AAAGAAAAAAAAGGAG
5838816 TAAAGAAAAGAAAAGGA
1 -AAAGAAAA-AAAAGGA
5838833 AGGGAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.11
17 18 0.64
18 7 0.25
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAAAAGGAG
Found at i:5839560 original size:29 final size:30
Alignment explanation
Indices: 5839528--5839644 Score: 155
Period size: 30 Copynumber: 3.9 Consensus size: 30
5839518 ATAAGTCCGT
* *
5839528 AAACTTTCTAAAAATTATATTTTAA-CCTT
1 AAACTTTCTAAAAATTACATTTTAACCCTA
*
5839557 AAACTTTCTAAAAATTACATTTTAACCCCA
1 AAACTTTCTAAAAATTACATTTTAACCCTA
* *
5839587 AAACTTACTAAAAATTATATTTTAACCCTA
1 AAACTTTCTAAAAATTACATTTTAACCCTA
* * *
5839617 AAACTTTTTGAAAATTACATTTTGACCC
1 AAACTTTCTAAAAATTACATTTTAACCC
5839645 CCCAAAACTT
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
29 24 0.32
30 52 0.68
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (30 bp):
AAACTTTCTAAAAATTACATTTTAACCCTA
Found at i:5839598 original size:30 final size:30
Alignment explanation
Indices: 5839528--5839665 Score: 154
Period size: 30 Copynumber: 4.6 Consensus size: 30
5839518 ATAAGTCCGT
* **
5839528 AAACTTTCTAAAAATTATATTTTAA-CCTT
1 AAACTTTCTAAAAATTACATTTTAACCCCA
5839557 AAACTTTCTAAAAATTACATTTTAACCCCA
1 AAACTTTCTAAAAATTACATTTTAACCCCA
* * *
5839587 AAACTTACTAAAAATTATATTTTAACCCTA
1 AAACTTTCTAAAAATTACATTTTAACCCCA
* * *
5839617 AAACTTTTTGAAAATTACATTTTGACCCCCCA
1 AAACTTTCTAAAAATTACATTTT-A-ACCCCA
5839649 AAACTTT-TCAAAAATTA
1 AAACTTTCT-AAAAATTA
5839666 GAATTTACCT
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
29 24 0.26
30 48 0.52
31 2 0.02
32 18 0.20
ACGTcount: A:0.43, C:0.19, G:0.01, T:0.37
Consensus pattern (30 bp):
AAACTTTCTAAAAATTACATTTTAACCCCA
Found at i:5839608 original size:59 final size:62
Alignment explanation
Indices: 5839528--5839654 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 62
5839518 ATAAGTCCGT
* *
5839528 AAACTTTCTAAAAATTATATTTTAA-CCTTAAACTTTCTAAAAATTACATTTT-A-ACCCCA
1 AAACTTACTAAAAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTGACACCCCA
* * *
5839587 AAACTTACTAAAAATTATATTTTAACCCTAAAACTTTTTGAAAATTACATTTTGACCCCCCA
1 AAACTTACTAAAAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTGACACCCCA
5839649 AAACTT
1 AAACTT
5839655 TTCAAAAATT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
59 24 0.40
60 24 0.40
61 1 0.02
62 11 0.18
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.37
Consensus pattern (62 bp):
AAACTTACTAAAAATTATATTTTAACCCTAAAACTTTCTAAAAATTACATTTTGACACCCCA
Found at i:5839743 original size:60 final size:59
Alignment explanation
Indices: 5839687--5839850 Score: 240
Period size: 60 Copynumber: 2.8 Consensus size: 59
5839677 CGAACTTTCC
* *
5839687 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGCCCCCTTAACTTCTA
1 AAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGCCCCC-GAACTTCTA
* *
5839747 AAAATCCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTCTA
1 AAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGCCCCCGAACTTCTA
* * * *
5839806 AAAATCCCATTTTTAA-CCCAATTCCAACTAAAATTACCATTTTGC
1 AAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGC
5839851 TCTTGGGTAT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
58 23 0.24
59 24 0.26
60 47 0.50
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTGCCCCCGAACTTCTA
Found at i:5839780 original size:30 final size:29
Alignment explanation
Indices: 5839676--5839824 Score: 83
Period size: 30 Copynumber: 5.0 Consensus size: 29
5839666 GAATTTACCT
*
5839676 CCGAACTTTCC-AAAATTCCATTTTTAACC
1 CCGAAC-TTCCAAAAATCCCATTTTTAACC
* * **
5839705 CCG-ATTTCACCAAAAATTACCA-TTTTGCCC
1 CCGAACTT--CCAAAAA-TCCCATTTTTAACC
* *
5839735 CCTTAACTTCTAAAAATCCCATTTTTAACC
1 CC-GAACTTCCAAAAATCCCATTTTTAACC
* * * *
5839765 TCG-ATTTCACCAAAAATTACCA-TTTTACCC
1 CCGAACTT--CCAAAAA-TCCCATTTTTAACC
*
5839795 CCGAACTTCTAAAAATCCCATTTTTAACC
1 CCGAACTTCCAAAAATCCCATTTTTAACC
5839824 C
1 C
5839825 AATTCCAACT
Statistics
Matches: 87, Mismatches: 21, Indels: 24
0.66 0.16 0.18
Matches are distributed among these distances:
27 2 0.02
28 8 0.09
29 23 0.26
30 40 0.46
31 11 0.13
32 3 0.03
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.33
Consensus pattern (29 bp):
CCGAACTTCCAAAAATCCCATTTTTAACC
Found at i:5841650 original size:25 final size:24
Alignment explanation
Indices: 5841603--5841650 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
5841593 AATTTTGGAG
* **
5841603 TTCTATTGCCTTCGGGCTTTACAC
1 TTCTATTGCCTTCGAGCCCTACAC
5841627 TTCTATTAGCCTTCGAGCCCTACA
1 TTCTATT-GCCTTCGAGCCCTACA
5841651 TTCACGTGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.17, C:0.31, G:0.15, T:0.38
Consensus pattern (24 bp):
TTCTATTGCCTTCGAGCCCTACAC
Found at i:5847035 original size:60 final size:59
Alignment explanation
Indices: 5846967--5847083 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 59
5846957 ATTGATTGTT
* *
5846967 ATGTGATAG-TACAAAGTATAAATGTGAAAATATGAATGATTCCAAGGTATGAAAATGCAA
1 ATGTGATAGATACAAAGTAT-AATATGAAAATATGAATGA-TACAAGGTATGAAAATGCAA
* * * * *
5847027 ATGTGATAGATTACAAGGTATGATATGCAAATGTGAATGATACAGGGTATGAAAATG
1 ATGTGATAGA-TACAAAGTATAATATGAAAATATGAATGATACAAGGTATGAAAATG
5847084 TAATATGTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 24 0.50
61 15 0.31
62 9 0.19
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (59 bp):
ATGTGATAGATACAAAGTATAATATGAAAATATGAATGATACAAGGTATGAAAATGCAA
Found at i:5847044 original size:31 final size:31
Alignment explanation
Indices: 5846994--5847083 Score: 114
Period size: 31 Copynumber: 3.0 Consensus size: 31
5846984 ATAAATGTGA
* *
5846994 AAATATGAATGATTCCAAGGTATGAAAATGC
1 AAATGTGAATGATTACAAGGTATGAAAATGC
*
5847025 AAATGTG-ATAGATTACAAGGTATG-ATATGC
1 AAATGTGAAT-GATTACAAGGTATGAAAATGC
*
5847055 AAATGTGAATGA-TACAGGGTATGAAAATG
1 AAATGTGAATGATTACAAGGTATGAAAATG
5847084 TAATATGTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.20
30 20 0.39
31 21 0.41
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (31 bp):
AAATGTGAATGATTACAAGGTATGAAAATGC
Found at i:5847095 original size:29 final size:29
Alignment explanation
Indices: 5847009--5847097 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 29
5846999 TGAATGATTC
5847009 CAAGGTATGAAAATGCAAATGTGATAGATTA
1 CAAGGTATGAAAATGCAAATGTGAT-GA-TA
*
5847040 CAAGGTATG-ATATGCAAATGTGAATGATA
1 CAAGGTATGAAAATGCAAATGTG-ATGATA
* *
5847069 CAGGGTATGAAAATGTAATATGT-ATGATA
1 CAAGGTATGAAAATGCAA-ATGTGATGATA
5847098 TATGTGCATG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
29 16 0.31
30 20 0.39
31 15 0.29
ACGTcount: A:0.43, C:0.06, G:0.24, T:0.28
Consensus pattern (29 bp):
CAAGGTATGAAAATGCAAATGTGATGATA
Found at i:5859990 original size:21 final size:21
Alignment explanation
Indices: 5859939--5860033 Score: 69
Period size: 21 Copynumber: 4.8 Consensus size: 21
5859929 AAAATTTATT
* *
5859939 AAATATTAGAAATATATATAA
1 AAATCTTAAAAATATATATAA
*
5859960 AAGTCTTAAAAATATATATAA
1 AAATCTTAAAAATATATATAA
*
5859981 AAAT-TGT--AAAT-TTTATAA
1 AAATCT-TAAAAATATATATAA
*
5859999 TAATCTTAAAAA-AT-TATAA
1 AAATCTTAAAAATATATATAA
*
5860018 AATAT-ATAAAAATATA
1 AA-ATCTTAAAAATATA
5860034 AAATTTTATA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
18 10 0.17
19 17 0.29
20 9 0.16
21 22 0.38
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (21 bp):
AAATCTTAAAAATATATATAA
Found at i:5860043 original size:10 final size:9
Alignment explanation
Indices: 5859929--5860045 Score: 51
Period size: 9 Copynumber: 12.3 Consensus size: 9
5859919 ATTTTAATAA
5859929 AAAATTTAT
1 AAAATTTAT
* *
5859938 TAAATATTAG
1 AAAAT-TTAT
*
5859948 AAATATATAT
1 AAA-ATTTAT
5859958 AAAAGTCTTA-
1 AAAA-T-TTAT
5859968 AAAATATATAT
1 AAAAT-T-TAT
* *
5859979 AAAAATTGT
1 AAAATTTAT
*
5859988 AAATTTTAT
1 AAAATTTAT
5859997 AATAATCTTA-
1 AA-AAT-TTAT
*
5860007 AAAAATTAT
1 AAAATTTAT
*
5860016 AAAATATAT
1 AAAATTTAT
*
5860025 AAAA-ATAT
1 AAAATTTAT
5860033 AAAATTTTAT
1 AAAA-TTTAT
5860043 AAA
1 AAA
5860046 GGCGAAAAAA
Statistics
Matches: 80, Mismatches: 17, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
8 11 0.14
9 30 0.38
10 28 0.35
11 11 0.14
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (9 bp):
AAAATTTAT
Found at i:5861882 original size:2 final size:2
Alignment explanation
Indices: 5861871--5861909 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
5861861 ATCAAACACC
*
5861871 CT CT -T CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5861910 TGGCTCTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:5865181 original size:3 final size:3
Alignment explanation
Indices: 5865173--5865197 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5865163 ACACAAAAGG
5865173 CAA CAA CAA CAA CAA CAA CAA CAA C
1 CAA CAA CAA CAA CAA CAA CAA CAA C
5865198 TGCTGCTGAT
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:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:5868690 original size:13 final size:13
Alignment explanation
Indices: 5868672--5868697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5868662 GGGCAAGTGG
5868672 GAGATTATTACGA
1 GAGATTATTACGA
5868685 GAGATTATTACGA
1 GAGATTATTACGA
5868698 TCTAGTATAA
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:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
GAGATTATTACGA
Found at i:5869344 original size:13 final size:13
Alignment explanation
Indices: 5869311--5869349 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5869301 TTTAATTGAG
5869311 AAATTAATTAAATT
1 AAATTAATT-AATT
5869325 AAATTAATTAATT
1 AAATTAATTAATT
* *
5869338 GACTTAATTAAT
1 AAATTAATTAAT
5869350 ATTTTGGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:5872950 original size:18 final size:17
Alignment explanation
Indices: 5872914--5872953 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5872904 TAGTAAAAAT
5872914 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
5872931 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
5872946 ATAATTTT
1 ATAATTTT
5872954 TAAAAGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:5873863 original size:2 final size:2
Alignment explanation
Indices: 5873856--5873883 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5873846 AAAGCTATGA
5873856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5873884 TTTAGGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5874807 original size:2 final size:2
Alignment explanation
Indices: 5874800--5874832 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5874790 ACAATAATAT
5874800 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5874833 GCACCCTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5892373 original size:12 final size:12
Alignment explanation
Indices: 5892356--5892380 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5892346 GTTTTTAGTT
5892356 AAAAAAAAAGAA
1 AAAAAAAAAGAA
5892368 AAAAAAAAAGAA
1 AAAAAAAAAGAA
5892380 A
1 A
5892381 GAAAGTGGGC
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:5898116 original size:59 final size:59
Alignment explanation
Indices: 5897745--5898118 Score: 533
Period size: 59 Copynumber: 6.4 Consensus size: 59
5897735 TTGGATACCT
* *
5897745 GGGGGCAAAATGGTAA-TTTTGGTGAAATC-GGGTT-AAAATGGAATTTTGGAAAG-TTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-AAAAGATTC
* * *
5897801 GAGGGTAAAATGGTGATTTTTGGTGAAATCGGGGTGAAAAATGGAATTTTAAAAGATAT-
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGAT-TC
* * * *
5897860 GGGGGTAAAATGGTAATTTTCGATGAAATCGGGGTTTAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTC
* *
5897919 GGGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTC
* * *
5897978 GGGGGTAAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGAATTTTAAAAGATTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTC
* * *
5898037 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTTAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTC
*
5898096 AGGGGTAAAATGGTAATTTTTGG
1 GGGGGTAAAATGGTAATTTTTGG
5898119 AAGTTTCGAG
Statistics
Matches: 285, Mismatches: 27, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
56 13 0.05
57 13 0.05
58 9 0.03
59 249 0.87
60 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTC
Found at i:5898132 original size:177 final size:176
Alignment explanation
Indices: 5897746--5898117 Score: 588
Period size: 177 Copynumber: 2.1 Consensus size: 176
5897736 TGGATACCTG
* * *
5897746 GGGGCAAAATGGTAATTTTGGTGAAATCG-GGTT-AAAATGGAATTTTGGAAAGTTCGAGGGTAA
1 GGGGTAAAATGGTAATTTTTGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTCGAGGGTAA
* * * *
5897809 AATGGTGATTTTTGGTGAAATCGGGGTGAAAAATGGAATTTTAAAAGATATGGGGGTAAAATGGT
66 AATGGTAATTTTTGGTAAAATCAGGGTGAAAAATGGAATTTTAAAAGATATAGGGGTAAAATGGT
*
5897874 AATTTTCGATGAAATCGGGGTTTAAAATGGAATTTTAGAAGATTCG
131 AATTTTCGATGAAATCGGGGTTTAAAATGGAATTTTAGAAGATTCA
*
5897920 GGGGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTT-AAAAGATTCGGGGGT
1 GGGGTAAAATGGTAATTTTTG-TGAAATCGAGGTTAAAAATGGAATTTTGAAAAG-TTCGAGGGT
* *
5897984 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGAATTTTAAAAGATTTAGGGGTAAAATG
64 AAAATGGTAATTTTTGGTAAAATCAGGGTGAAAAATGGAATTTTAAAAGATATAGGGGTAAAATG
* *
5898049 GTAATTTTTGGTGAAATCGGGGTTTAAAATGGAATTTTAGAAGATTCA
129 GTAATTTTCGATGAAATCGGGGTTTAAAATGGAATTTTAGAAGATTCA
5898097 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
5898118 GAAGTTTCGA
Statistics
Matches: 181, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
174 19 0.10
175 8 0.04
176 8 0.04
177 146 0.81
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (176 bp):
GGGGTAAAATGGTAATTTTTGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTCGAGGGTAA
AATGGTAATTTTTGGTAAAATCAGGGTGAAAAATGGAATTTTAAAAGATATAGGGGTAAAATGGT
AATTTTCGATGAAATCGGGGTTTAAAATGGAATTTTAGAAGATTCA
Found at i:5898448 original size:161 final size:162
Alignment explanation
Indices: 5898247--5898584 Score: 491
Period size: 161 Copynumber: 2.1 Consensus size: 162
5898237 AGGCATCCAG
* * * * **
5898247 CAGTCAAAGGATTAAGTTGTAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAAGGACTAAGTTATAAATCATGAAAAACTCTTGGGCCAATTTCATAATTAAATAAAAGT
*
5898312 TGATTTGGGGATTAAATTAAGACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCC-AAA
66 TGATTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAA
***
5898376 GGTGACACGTGGTAG-CTCTTGGTACAGTCAAA
131 AAAGACACGTGGTAGCCTC-TGGTACAGTCAAA
* *
5898408 CAGTCAAAGGACTAATTTATAAATCATGAAAAGCTCTTGGGCCAATTTCATAATTAAATAAAAGT
1 CAGTCAAAGGACTAAGTTATAAATCATGAAAAACTCTTGGGCCAATTTCATAATTAAATAAAAGT
*** * *
5898473 TGATTTGGGGATTAAATTAAAACAAATTAAAAATGCCAGGGACTAAATGCATAAATAATCCAAAA
66 TGATTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAA
5898538 AAAGACACGTGGTAGCCTCTGGTACAGTCAAA
131 AAAGACACGTGGTAGCCTCTGGTACAGTCAAA
*
5898570 CAGTCAAATGACTAA
1 CAGTCAAAGGACTAA
5898585 ATTGAAAAGC
Statistics
Matches: 157, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
161 112 0.71
162 42 0.27
163 3 0.02
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (162 bp):
CAGTCAAAGGACTAAGTTATAAATCATGAAAAACTCTTGGGCCAATTTCATAATTAAATAAAAGT
TGATTTGGGGATTAAATTAAAACAAATTAAAAATAAAAAGGACTAAATGCATAAATAAGCCAAAA
AAAGACACGTGGTAGCCTCTGGTACAGTCAAA
Found at i:5899164 original size:12 final size:14
Alignment explanation
Indices: 5899146--5899176 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5899136 TTTTTTTCTT
5899146 TATTT-TCTTTTAA
1 TATTTCTCTTTTAA
5899159 TATTTCTCTTTTAA
1 TATTTCTCTTTTAA
5899173 TATT
1 TATT
5899177 CCGTTCCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTCTCTTTTAA
Found at i:5899339 original size:15 final size:15
Alignment explanation
Indices: 5899319--5899356 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5899309 TATAAAATAT
* *
5899319 TTATTATTATTACTG
1 TTATTATTATCACTA
5899334 TTATTATTATCACTA
1 TTATTATTATCACTA
5899349 TTATTATT
1 TTATTATT
5899357 GTTATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTATTATCACTA
Found at i:5899359 original size:24 final size:24
Alignment explanation
Indices: 5899323--5899378 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
5899313 AAATATTTAT
*
5899323 TATTATTACTGTTATT-ATTATCAC
1 TATTATTACTGTTATTAATGAT-AC
*
5899347 TATTATTATTGTTATTAATGATAC
1 TATTATTACTGTTATTAATGATAC
5899371 TATTATTA
1 TATTATTA
5899379 ACCATCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.55
Consensus pattern (24 bp):
TATTATTACTGTTATTAATGATAC
Found at i:5900049 original size:6 final size:6
Alignment explanation
Indices: 5900040--5900130 Score: 78
Period size: 6 Copynumber: 15.0 Consensus size: 6
5900030 TTTTTTAATG
* ** * * *
5900040 TTAAAT TTAATAT TTTAAT TTTTAT TCAAAT TTAAAT TCAAA- GTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
5900088 TTAAAT AATTAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAAT
1 TTAAAT --TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
5900131 AAAATTAAAG
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
5 7 0.10
6 50 0.74
7 5 0.07
8 6 0.09
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (6 bp):
TTAAAT
Found at i:5900087 original size:17 final size:16
Alignment explanation
Indices: 5900067--5900139 Score: 87
Period size: 17 Copynumber: 4.6 Consensus size: 16
5900057 ATTTTTATTC
*
5900067 AAATTTAAATTCAAAGT
1 AAATTTAAATTTAAA-T
*
5900084 AAATTTAAA--TAATT
1 AAATTTAAATTTAAAT
5900098 AAATTTAAATTTAAAAT
1 AAATTTAAATTT-AAAT
5900115 AAATTTAAATTTAAAT
1 AAATTTAAATTTAAAT
*
5900131 AAAATTAAA
1 AAATTTAAA
5900140 GATCAATTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 13 0.27
17 24 0.49
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (16 bp):
AAATTTAAATTTAAAT
Found at i:5900157 original size:28 final size:27
Alignment explanation
Indices: 5900103--5900158 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
5900093 TAATTAAATT
* *
5900103 TAAATTTAAAATAAATTTAAATTTAAA
1 TAAAATTAAAATAAATTTAAATCTAAA
* *
5900130 TAAAATTAAAGATCAATTTAACTCTAAA
1 TAAAATTAAA-ATAAATTTAAATCTAAA
5900158 T
1 T
5900159 TAAACGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAAATTAAAATAAATTTAAATCTAAA
Found at i:5900686 original size:76 final size:72
Alignment explanation
Indices: 5900561--5901128 Score: 624
Period size: 69 Copynumber: 7.9 Consensus size: 72
5900551 GATGACGTTG
* * *
5900561 CTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATTGG
5900626 AAACGATGTTA
65 --AC-ATGTTA
* *
5900637 CTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA-T-G
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATTGG
*
5900700 AC--GTTG
65 ACATGTTA
* * * * * * *
5900706 CTCTTACTTCAATTGCAGAGATAAAGACTTGATATCCAGTTATACTTCAATTTCAAGAGGATAAG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGAGGAT-TG
*
5900771 AAACGATGTTA
64 -GAC-ATGTTA
* * *
5900782 CTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATTGG
5900847 AAACGATGTTA
65 --AC-ATGTTA
* * * *
5900858 CTCCTACTTCAATTTCAGAGATAAAGGCGTGTTATCCACTCTACTTCAATTTCAAGCGGATTGG-
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATTGGA
*
5900922 CA--TTG
66 CATGTTA
* * *
5900927 CTCTTACTTCAATTTCAGAGATGAAGGCGTGTTATCCACTCTACTTCAATTTCACGCGGATTGG-
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATTGGA
*
5900991 CA--TTG
66 CATGTTA
* * *
5900996 CTCTTACTTCAATTTTAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCACGCGGATTGG-
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATTGGA
5901060 CACTG---
66 CA-TGTTA
* * *
5901065 CTCTTACTTCAATTTTAGAGATGAAGACGCGTTATCCACTCTACTTCAATTTCAAGCGGATTGG
1 CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATTGG
5901129 CATTGATCTT
Statistics
Matches: 442, Mismatches: 36, Indels: 35
0.86 0.07 0.07
Matches are distributed among these distances:
68 1 0.00
69 250 0.57
71 1 0.00
72 3 0.01
73 2 0.00
74 1 0.00
75 26 0.06
76 157 0.36
77 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (72 bp):
CTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATTGGA
CATGTTA
Found at i:5900763 original size:145 final size:144
Alignment explanation
Indices: 5900435--5901125 Score: 777
Period size: 145 Copynumber: 4.8 Consensus size: 144
5900425 GCTCTTCAGG
* * * * * * * *
5900435 GAGATAAAGACTTTGCTATCCAACTTTACTTCAATTTCTAGAGGATAGGAAATGATCTTGCTTTT
1 GAGATAAAGAC-GTGTTATCC-ACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCTT
* * *
5900500 ATTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTC-A-A-GATGACGTTGC
64 ACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGC
5900562 TCTTACTTCAATTTCA
129 TCTTACTTCAATTTCA
* *
5900578 GAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCCTA
1 GAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCTTA
*
5900643 CTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCT
65 CTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCT
*
5900708 CTTACTTCAATTGCA
130 CTTACTTCAATTTCA
* * * * * *
5900723 GAGATAAAGACTTGATATCCAGTTATACTTCAATTTCAAGAGGATAAGAAACGATGTTACTCCTA
1 GAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCTTA
*
5900788 CTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGGGAAACGA
65 CTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT--G--AC--
* *
5900853 TGTTACTCCTACTTCAATTTCA
124 -GTTGCTCTTACTTCAATTTCA
* * * *
5900875 GAGATAAAGGCGTGTTATCCACTCTACTTCAATTTCAAGCGGATTGG---C-A--TTGCTCTTAC
1 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCTTAC
* * * * *
5900934 TTCAATTTCAGAGATGAAGGCGTGTTATCC-ACTCTACTTCAATTTCACGCGGATTGGCATTGCT
66 TTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGA-TGACGTTGCT
*
5900998 CTTACTTCAATTTTA
130 CTTACTTCAATTTCA
* * * * *
5901013 GAGATGAAGACGTGTTATCCACTCTACTTCAATTTCACGCGGATTGG-CAC--TG---CTCTTAC
1 GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCTTAC
* * *
5901072 TTCAATTTTAGAGATGAAGACGCGTTATCC-ACTCTACTTCAATTTCAAGCGGAT
66 TTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
5901126 TGGCATTGAT
Statistics
Matches: 482, Mismatches: 50, Indels: 38
0.85 0.09 0.07
Matches are distributed among these distances:
137 1 0.00
138 117 0.24
140 1 0.00
141 1 0.00
142 89 0.18
143 12 0.02
144 23 0.05
145 176 0.37
147 2 0.00
148 1 0.00
149 2 0.00
151 21 0.04
152 36 0.07
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (144 bp):
GAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCTTAC
TTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCTC
TTACTTCAATTTCA
Found at i:5900940 original size:32 final size:32
Alignment explanation
Indices: 5900899--5901010 Score: 100
Period size: 32 Copynumber: 3.3 Consensus size: 32
5900889 TTATCCACTC
5900899 TACTTCAATTTCAAGCGGATTGGCATTGCTCT
1 TACTTCAATTTCAAGCGGATTGGCATTGCTCT
** * * * *
5900931 TACTTCAATTTCAGAGATGA-AGGCGTGTTATCCACT
1 TACTTCAATTTCA-AGCGGATTGGC---AT-TGCTCT
*
5900967 CTACTTCAATTTCACGCGGATTGGCATTGCTCT
1 -TACTTCAATTTCAAGCGGATTGGCATTGCTCT
5901000 TACTTCAATTT
1 TACTTCAATTT
5901011 TAGAGATGAA
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
32 27 0.45
33 8 0.13
34 1 0.02
35 1 0.02
36 7 0.12
37 16 0.27
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (32 bp):
TACTTCAATTTCAAGCGGATTGGCATTGCTCT
Found at i:5912833 original size:29 final size:27
Alignment explanation
Indices: 5912803--5913080 Score: 172
Period size: 29 Copynumber: 9.6 Consensus size: 27
5912793 GGATACCCGA
5912803 GGGTAAAATGGTAATTTTGGTAAAATCG
1 GGGTAAAATGG-AATTTTGGTAAAATCG
* *
5912831 AGGTTAAAATGGAATTTTTGGTGAAATCG
1 -GGGTAAAATGGAA-TTTTGGTAAAATCG
* *
5912860 GGGTTAAAATGGAATTTTAG-AAGATTCG
1 GGG-TAAAATGGAATTTTGGTAA-AATCG
* *
5912888 GGGTAAAATGGTAATTTTTAGTGAAATCG
1 GGGTAAAATGG-AA-TTTTGGTAAAATCG
*
5912917 GGGTTAAAATGGAATTTT--AAAAGATTCG
1 GGG-TAAAATGGAATTTTGGTAAA-A-TCG
* *
5912945 GGGTAAAATGGTAATTTTTGATAAAATTAG
1 GGGTAAAATGG-AA-TTTTGGTAAAA-TCG
* *
5912975 GGTTAAAAATGGAATTTT--AAAAGATTCG
1 GGGT-AAAATGGAATTTTGGTAAA-A-TCG
*
5913003 AGGGTAAAATGGTAATTTTCGGTGAAATCG
1 -GGGTAAAATGG-AATTTT-GGTAAAATCG
* *
5913033 GGGTTAAAAATGGAATTTTAG-AAGATTCAG
1 GGG-T-AAAATGGAATTTTGGTAA-AATC-G
5913063 GGGTAAAATGGTAATTTT
1 GGGTAAAATGG-AATTTT
5913081 CGAAAGTTTT
Statistics
Matches: 203, Mismatches: 21, Indels: 50
0.74 0.08 0.18
Matches are distributed among these distances:
26 2 0.01
27 21 0.10
28 49 0.24
29 79 0.39
30 32 0.16
31 18 0.09
32 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (27 bp):
GGGTAAAATGGAATTTTGGTAAAATCG
Found at i:5913082 original size:59 final size:57
Alignment explanation
Indices: 5912835--5913080 Score: 377
Period size: 57 Copynumber: 4.3 Consensus size: 57
5912825 AAATCGAGGT
*
5912835 TAAAATGG-AATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAGAAGATTCGGGG
1 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAAAAGATTCGGGG
*
5912891 TAAAATGGTAATTTTTAGTGAAATCGGGGTTAAAATGGAATTTTAAAAGATTCGGGG
1 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAAAAGATTCGGGG
* * **
5912948 TAAAATGGTAATTTTTGATAAAATTAGGGTTAAAAATGGAATTTTAAAAGATTCGAGGG
1 TAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAAAAGATTCG-GGG
* *
5913007 TAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGGGG
1 TAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTAAAAGATTC-GGGG
5913066 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
5913081 CGAAAGTTTT
Statistics
Matches: 173, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
56 8 0.05
57 72 0.42
58 23 0.13
59 69 0.40
60 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (57 bp):
TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTAAAAGATTCGGGG
Found at i:5913095 original size:59 final size:54
Alignment explanation
Indices: 5912853--5913085 Score: 295
Period size: 59 Copynumber: 4.1 Consensus size: 54
5912843 AATTTTTGGT
* *
5912853 GAAATCGGGGTTAAAATGGAATTTTAGAAGATTCGGGGTAAAATGGTAATTTTTAGT
1 GAAATCGGGGTTAAAATGGAATTTTAAAAGATTCGGGGTAAAATGGTAA-TTTT--C
*
5912910 GAAATCGGGGTTAAAATGGAATTTTAAAAGATTCGGGGTAAAATGGTAATTTTT
1 GAAATCGGGGTTAAAATGGAATTTTAAAAGATTCGGGGTAAAATGGTAATTTTC
**
5912964 GATAAAATTAGGGTTAAAAATGGAATTTTAAAAGATTCGAGGGTAAAATGGTAATTTTC
1 G---AAATCGGGGTT-AAAATGGAATTTTAAAAGATTCG-GGGTAAAATGGTAATTTTC
*
5913023 GGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGGGGTAAAATGGTAATTTTC
1 ---GAAATCGGGGTT-AAAATGGAATTTTAAAAGATTC-GGGGTAAAATGGTAATTTTC
5913082 GAAA
1 GAAA
5913086 GTTTTGGGGT
Statistics
Matches: 160, Mismatches: 7, Indels: 19
0.86 0.04 0.10
Matches are distributed among these distances:
54 2 0.01
56 8 0.05
57 57 0.36
58 23 0.14
59 68 0.43
60 1 0.01
62 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (54 bp):
GAAATCGGGGTTAAAATGGAATTTTAAAAGATTCGGGGTAAAATGGTAATTTTC
Found at i:5913405 original size:161 final size:162
Alignment explanation
Indices: 5913212--5913534 Score: 497
Period size: 161 Copynumber: 2.0 Consensus size: 162
5913202 AGGCATCCAG
* * * *
5913212 CAGTCAAAGGATTAAGTTGTAAATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAAGGACTAAGTTATAAACCATGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGT
*
5913277 TGATTAGGGGATTAAATTAAGACAAATTAAAAATAAAAG-GACTAAATGCATAAATAAGCCAAAA
66 TGATTAGGGGATTAAATTAAAACAAATTAAAAATAAAAGAGACTAAATGCATAAATAAGCCAAAA
***
5913341 GGTGACACGTGGCAG-CTCCTGGTACAGTCAAA
131 AAAGACACGTGGCAGCCT-CTGGTACAGTCAAA
*
5913373 CAGTCAAAGGACTAATTTATAAACCATGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAAGGACTAAGTTATAAACCATGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGT
* *** *
5913438 TGATTTGGGGATTAAATTAAAACAAATTAAAAATGTTAGAGACTAAATGCATAAATAATCCAAAA
66 TGATTAGGGGATTAAATTAAAACAAATTAAAAATAAAAGAGACTAAATGCATAAATAAGCCAAAA
5913503 AAAGACACGTGGCAGCCTCTGGTACAGTCAAA
131 AAAGACACGTGGCAGCCTCTGGTACAGTCAAA
5913535 GGACTAAATT
Statistics
Matches: 146, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
161 94 0.64
162 50 0.34
163 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (162 bp):
CAGTCAAAGGACTAAGTTATAAACCATGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGT
TGATTAGGGGATTAAATTAAAACAAATTAAAAATAAAAGAGACTAAATGCATAAATAAGCCAAAA
AAAGACACGTGGCAGCCTCTGGTACAGTCAAA
Found at i:5914141 original size:14 final size:14
Alignment explanation
Indices: 5914119--5914151 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
5914109 TTTTTTTCTT
5914119 TATTT-TCTTTTAA
1 TATTTCTCTTTTAA
5914132 TATTTCTCTTTTAA
1 TATTTCTCTTTTAA
5914146 TATTTC
1 TATTTC
5914152 GTTCCCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTCTCTTTTAA
Found at i:5914235 original size:19 final size:19
Alignment explanation
Indices: 5914211--5914257 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
5914201 GGAAGAACGA
*
5914211 CGGCGACGGGTTCCGGCTC
1 CGGCGACGGGTTCCGACTC
5914230 CGGCGACGGGTTCCGACTC
1 CGGCGACGGGTTCCGACTC
5914249 CGGCGACGG
1 CGGCGACGG
5914258 TGGCAATGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.09, C:0.36, G:0.43, T:0.13
Consensus pattern (19 bp):
CGGCGACGGGTTCCGACTC
Found at i:5914331 original size:15 final size:15
Alignment explanation
Indices: 5914311--5914348 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5914301 TATAAAATAT
* *
5914311 TTATTATTATTACTG
1 TTATTATTATCACTA
5914326 TTATTATTATCACTA
1 TTATTATTATCACTA
5914341 TTATTATT
1 TTATTATT
5914349 GTTATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTATTATCACTA
Found at i:5914351 original size:24 final size:24
Alignment explanation
Indices: 5914315--5914370 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
5914305 AAATATTTAT
*
5914315 TATTATTACTGTTATT-ATTATCAC
1 TATTATTACTGTTATTAATGAT-AC
*
5914339 TATTATTATTGTTATTAATGATAC
1 TATTATTACTGTTATTAATGATAC
5914363 TATTATTA
1 TATTATTA
5914371 ACCATCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.55
Consensus pattern (24 bp):
TATTATTACTGTTATTAATGATAC
Found at i:5915077 original size:6 final size:6
Alignment explanation
Indices: 5915068--5915131 Score: 69
Period size: 6 Copynumber: 10.7 Consensus size: 6
5915058 ATTTTTATTC
* * *
5915068 AAATTT AAATTC AAA-GT AAATTT AAATAATT AAATTT AAATTT AAA-AT
1 AAATTT AAATTT AAATTT AAATTT AAAT--TT AAATTT AAATTT AAATTT
5915116 AAATTT AAATTT AAAT
1 AAATTT AAATTT AAAT
5915132 AAAATTAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 7 0.15
6 35 0.73
8 6 0.12
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
AAATTT
Found at i:5915088 original size:17 final size:16
Alignment explanation
Indices: 5915068--5915140 Score: 87
Period size: 17 Copynumber: 4.6 Consensus size: 16
5915058 ATTTTTATTC
*
5915068 AAATTTAAATTCAAAGT
1 AAATTTAAATTTAAA-T
*
5915085 AAATTTAAA--TAATT
1 AAATTTAAATTTAAAT
5915099 AAATTTAAATTTAAAAT
1 AAATTTAAATTT-AAAT
5915116 AAATTTAAATTTAAAT
1 AAATTTAAATTTAAAT
*
5915132 AAAATTAAA
1 AAATTTAAA
5915141 GATCAATTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 13 0.27
17 24 0.49
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (16 bp):
AAATTTAAATTTAAAT
Found at i:5915158 original size:28 final size:27
Alignment explanation
Indices: 5915104--5915159 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
5915094 TAATTAAATT
* *
5915104 TAAATTTAAAATAAATTTAAATTTAAA
1 TAAAATTAAAATAAATTTAAATCTAAA
* *
5915131 TAAAATTAAAGATCAATTTAACTCTAAA
1 TAAAATTAAA-ATAAATTTAAATCTAAA
5915159 T
1 T
5915160 TAAACGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAAATTAAAATAAATTTAAATCTAAA
Found at i:5918946 original size:2 final size:2
Alignment explanation
Indices: 5918939--5918964 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5918929 TTAAAACTAA
5918939 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5918965 TTTCACTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5927402 original size:31 final size:30
Alignment explanation
Indices: 5927367--5927487 Score: 88
Period size: 31 Copynumber: 4.0 Consensus size: 30
5927357 TTGATATTCG
5927367 AATTTGACATTTTTTCTTAATTTGGTATCTA
1 AATTTGACATTTTTTCTTAATTTGGTA-CTA
* *
5927398 AATTT---TTTTTTTGAGTTCAATTTGGTACTCA
1 AATTTGACATTTTTT--CTT-AATTTGGTACT-A
* * *
5927429 AACTTGACACTTTTTCTTATTTTGGTACCTA
1 AATTTGACATTTTTTCTTAATTTGGTA-CTA
* * *
5927460 AA-CTAACATTTTTTCTTAAGTTGGTACT
1 AATTTGACATTTTTTCTTAATTTGGTACT
5927488 TAAACTTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
28 6 0.09
29 2 0.03
30 23 0.33
31 30 0.43
32 4 0.06
34 5 0.07
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.51
Consensus pattern (30 bp):
AATTTGACATTTTTTCTTAATTTGGTACTA
Found at i:5939386 original size:79 final size:80
Alignment explanation
Indices: 5939231--5939390 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 80
5939221 AAGACCATGG
5939231 TCATAATGACCATTTATATTAAGAGAGCTAGAGGTGGTTTTTTGTTGTTGTTGTTGAAGCTAGAG
1 TCATAATGACCATTTATATTAAGAGAGCTAGAGGTGGTTTTTTGTTGTTGTTGTTGAAGCTAGAG
5939296 CTGGATCAAAATCCT
66 CTGGATCAAAATCCT
5939311 TCATAATGACCATTTATATTAAGAGAGCTAGAGGT-GTTTTTTGTTGTTGTTGTTGAAGCTAGAG
1 TCATAATGACCATTTATATTAAGAGAGCTAGAGGTGGTTTTTTGTTGTTGTTGTTGAAGCTAGAG
5939375 CTGGATCAAAATCCT
66 CTGGATCAAAATCCT
5939390 T
1 T
5939391 AACATATGAT
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 45 0.56
80 35 0.44
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (80 bp):
TCATAATGACCATTTATATTAAGAGAGCTAGAGGTGGTTTTTTGTTGTTGTTGTTGAAGCTAGAG
CTGGATCAAAATCCT
Found at i:5941245 original size:25 final size:23
Alignment explanation
Indices: 5941197--5941247 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 23
5941187 TAAAAGTTAA
*
5941197 TTTAATTAAATAATTACATTAAG
1 TTTAATTAAATAATTACATAAAG
5941220 TTTAATTAAAAGTAATTACATAAAG
1 TTTAATT-AAA-TAATTACATAAAG
5941245 TTT
1 TTT
5941248 TTCCAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 7 0.28
24 3 0.12
25 15 0.60
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (23 bp):
TTTAATTAAATAATTACATAAAG
Found at i:5946182 original size:13 final size:15
Alignment explanation
Indices: 5946147--5946183 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
5946137 CGTGATTATT
5946147 CTCAATTTTCATAAA
1 CTCAATTTTCATAAA
*
5946162 CTCGATTTTC-T-AA
1 CTCAATTTTCATAAA
5946175 CTCAATTTT
1 CTCAATTTT
5946184 TGAAGTGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 10 0.50
14 1 0.05
15 9 0.45
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.46
Consensus pattern (15 bp):
CTCAATTTTCATAAA
Done.