Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007943.1 Hibiscus syriacus cultivar Beakdansim tig00110365_pilon, whole genome shotgun sequence
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: 1187827
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:893070 original size:19 final size:19
Alignment explanation
Indices: 893048--893091 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
893038 TTAGTGAATT
*
893048 GATGCATGAGGAGTGCATC
1 GATGCATGAGGAGCGCATC
893067 GATGCATGAGGAGCGCATC
1 GATGCATGAGGAGCGCATC
893086 GATGCA
1 GATGCA
893092 CCCCCTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.27, C:0.18, G:0.36, T:0.18
Consensus pattern (19 bp):
GATGCATGAGGAGCGCATC
Found at i:893161 original size:12 final size:12
Alignment explanation
Indices: 893144--893169 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
893134 GCATGGGTAG
893144 TGCATCGATACA
1 TGCATCGATACA
893156 TGCATCGATACA
1 TGCATCGATACA
893168 TG
1 TG
893170 GTAGAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (12 bp):
TGCATCGATACA
Found at i:894029 original size:18 final size:18
Alignment explanation
Indices: 893984--894044 Score: 106
Period size: 18 Copynumber: 3.4 Consensus size: 18
893974 AAGAGTCTAC
893984 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
894002 GTGG-CCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
894019 GTGGTCCTTCGGGATATA
1 GTGGTCCTTCGGGACATA
894037 GTGGTCCT
1 GTGGTCCT
894045 ACTGGACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
17 17 0.41
18 24 0.59
ACGTcount: A:0.15, C:0.21, G:0.34, T:0.30
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:896150 original size:21 final size:20
Alignment explanation
Indices: 896112--896150 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
896102 ATGTCATATA
896112 AAGGATAGGATTTTGAGTTT
1 AAGGATAGGATTTTGAGTTT
896132 AAGGA-AGTGATTATTGAGT
1 AAGGATAG-GATT-TTGAGT
896151 AGGAATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (20 bp):
AAGGATAGGATTTTGAGTTT
Found at i:896995 original size:21 final size:21
Alignment explanation
Indices: 896969--897031 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
896959 GTCGAGGGTT
896969 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
* ** *
896990 TCATAGGTTCTTCGAAACATAT
1 TCATAGGTCCTTCGGGACA-AC
* *
897012 TCACAGGTCCTTCAGGACAA
1 TCATAGGTCCTTCGGGACAA
897032 ATCTCATATG
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:898581 original size:17 final size:17
Alignment explanation
Indices: 898559--898594 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
898549 GTATGGAGAT
898559 TTAAAATGAAAAAAA-AA
1 TTAAAAT-AAAAAAATAA
898576 TTAAAATAAAAAAATAA
1 TTAAAATAAAAAAATAA
898593 TT
1 TT
898595 TACAACTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
TTAAAATAAAAAAATAA
Found at i:901541 original size:8 final size:8
Alignment explanation
Indices: 901512--901552 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
901502 GATAGAATAA
901512 AATAAAAT
1 AATAAAAT
* *
901520 AAAAAAAG
1 AATAAAAT
901528 AA-AAAAT
1 AATAAAAT
901535 AATAAAAT
1 AATAAAAT
901543 AAT-AAAT
1 AATAAAAT
901550 AAT
1 AAT
901553 GATTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
7 13 0.45
8 16 0.55
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (8 bp):
AATAAAAT
Found at i:901638 original size:4 final size:4
Alignment explanation
Indices: 901622--901655 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
901612 AGATAAAAAT
*
901622 TAAA TAAA CAAA TAAA TAAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA T-AAA TAAA TAAA TAAA T
901656 TGGGATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:901643 original size:17 final size:17
Alignment explanation
Indices: 901618--901655 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
901608 GATGAGATAA
*
901618 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
901635 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
901652 AAAT
1 AAAT
901656 TGGGATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:904121 original size:5 final size:5
Alignment explanation
Indices: 904111--904173 Score: 58
Period size: 5 Copynumber: 12.6 Consensus size: 5
904101 ATGTTCAGAG
**
904111 AAAAT AAAAT AAAAT AAAAT -AAAT AAAGTAT CTAAT AAAAT AAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA--AT AAAAT AAAAT AAAAT AAAAT
* *
904161 GAAAT GAAAT AAA
1 AAAAT AAAAT AAA
904174 TTTGGCTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
4 8 0.16
5 38 0.78
7 3 0.06
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:907149 original size:8 final size:8
Alignment explanation
Indices: 907121--907160 Score: 50
Period size: 7 Copynumber: 5.4 Consensus size: 8
907111 GATAGAATAA
907121 AATAAAAT
1 AATAAAAT
*
907129 AA-AAAAG
1 AATAAAAT
907136 AA-AAAAT
1 AATAAAAT
907143 AATAAAAT
1 AATAAAAT
907151 AAT-AAAT
1 AATAAAAT
907158 AAT
1 AAT
907161 GATTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 19 0.66
8 10 0.34
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (8 bp):
AATAAAAT
Found at i:907251 original size:17 final size:17
Alignment explanation
Indices: 907226--907259 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
907216 AATGAAATAA
*
907226 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
907243 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
907260 TGGGATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:912367 original size:21 final size:20
Alignment explanation
Indices: 912344--912460 Score: 108
Period size: 21 Copynumber: 5.6 Consensus size: 20
912334 AATTGTCCTG
*
912344 AAGGACCTCATATATGTCCA
1 AAGGACCACATATATGTCCA
912364 GAAGGACCACATATATGTTCCA
1 -AAGGACCACATATATG-TCCA
*
912386 AAGGACCAAATATATGTCCCA
1 AAGGACCACATATATGT-CCA
* *
912407 AAAGACCTCATATATGTTCCA
1 AAGGACCACATATATG-TCCA
** * *
912428 AATTATCACATATATGTCTCG
1 AAGGACCACATATATGTC-CA
*
912449 AATGACCACATA
1 AAGGACCACATA
912461 AAACCTTCAA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
20 3 0.04
21 72 0.90
22 5 0.06
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (20 bp):
AAGGACCACATATATGTCCA
Found at i:912391 original size:42 final size:42
Alignment explanation
Indices: 912344--912460 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 42
912334 AATTGTCCTG
* *
912344 AAGGACCTCATATATGTCCAGAAGGACCACATATATGTTCCA
1 AAGGACCACATATATGTCCAGAAAGACCACATATATGTTCCA
* *
912386 AAGGACCAAATATATGTCCCA-AAAGACCTCATATATGTTCCA
1 AAGGACCACATATATGT-CCAGAAAGACCACATATATGTTCCA
** * *
912428 AATTATCACATATATGTCTC-GAATGACCACATA
1 AAGGACCACATATATGTC-CAGAAAGACCACATA
912461 AAACCTTCAA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.02
42 58 0.94
43 3 0.05
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (42 bp):
AAGGACCACATATATGTCCAGAAAGACCACATATATGTTCCA
Found at i:913737 original size:20 final size:20
Alignment explanation
Indices: 913712--913752 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
913702 TTTGGTTTTA
913712 AGAAATCTTAAGTTTTCCTT
1 AGAAATCTTAAGTTTTCCTT
913732 AGAAATCTTAAGTTTTCCTT
1 AGAAATCTTAAGTTTTCCTT
913752 A
1 A
913753 AGCTTAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
AGAAATCTTAAGTTTTCCTT
Found at i:914156 original size:20 final size:20
Alignment explanation
Indices: 914133--914172 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
914123 TAGAGATAAC
914133 CTAAAATTATATG-GGGCGAA
1 CTAAAATTATA-GAGGGCGAA
914153 CTAAAATTATAGAGGGCGAA
1 CTAAAATTATAGAGGGCGAA
914173 ACATATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (20 bp):
CTAAAATTATAGAGGGCGAA
Found at i:914871 original size:6 final size:6
Alignment explanation
Indices: 914862--914886 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
914852 CACCCTCACC
914862 CTCCCA CTCCCA CTCCCA CTCCCA C
1 CTCCCA CTCCCA CTCCCA CTCCCA C
914887 CGTCAGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.68, G:0.00, T:0.16
Consensus pattern (6 bp):
CTCCCA
Found at i:915965 original size:55 final size:55
Alignment explanation
Indices: 915845--916238 Score: 621
Period size: 55 Copynumber: 7.2 Consensus size: 55
915835 CGTAATAGAG
* * *
915845 ATACGGTAATTCACAAACTCATTATGAATTACGT-GGGTTGCACACATAGTGCCA
1 ATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCA
* * * * *
915899 ATACGGTAATTCACAAACTCATTATGAATTACGTGGGGTTGCACAAATAGTGTCA
1 ATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCA
* * *
915954 ATACAGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACAAAGTGCGA
1 ATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCA
* * *
916009 ATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTACACACATAATGCCA
1 ATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCA
916064 ATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCA
1 ATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCA
*
916119 ACACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACA-ATAGTGCCA
1 ATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCA
* *
916173 ATACAGAAATTCATAAACTCATTATGAATTTTGTGGGGTTGCACACATAGTGCCA
1 ATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCA
916228 ATACGGAAATT
1 ATACGGAAATT
916239 TACAACATAT
Statistics
Matches: 314, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
54 85 0.27
55 229 0.73
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (55 bp):
ATACGGAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCA
Found at i:919722 original size:118 final size:118
Alignment explanation
Indices: 919582--919924 Score: 343
Period size: 123 Copynumber: 2.8 Consensus size: 118
919572 AGATGAATTA
* * * *
919582 AGCTAAGGTTGAACGAGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTAGATGAGTTTTTCTCA
1 AGCTAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTT-GATGAGTTCTTCTCA
* * ** *
919647 TTATGAACTCCTTTGGAAATGTTGATCCCTCGAGTGAGGTATGTAAT-GAATCG
65 TTATGAACTCCTTTGGAAATGTTGATCCATCGAGTCACCTATGCAATAGAATCG
* *
919700 AGCTAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGAATGAGTTCATCTCA
1 AGCTAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTG-ATGAGTTCTTCTCA
** * * * * * *
919765 TTATGAACTCTCCACTGGAAATGTTGATACTGATCTA-TCTCCTTTGCGATAGAGTCG
65 TTATGAA--CTCCTTTGGAAATGTTGAT-C-CATCGAGTCACCTATGCAATAGAATCG
* * *
919822 AGCAAAAGGTTC-AACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTCGGATGAGTTCTTCT
1 AGC-TAAGG-TCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTT-TGATGAGTTCTTCT
*
919886 CATTATGAACT-CTTCACTGGAAATTTTGATCCATCGAGT
63 CATTATGAACTCCTT---TGGAAATGTTGATCCATCGAGT
919925 AATGGATTCG
Statistics
Matches: 183, Mismatches: 29, Indels: 22
0.78 0.12 0.09
Matches are distributed among these distances:
117 1 0.01
118 64 0.35
120 18 0.10
121 13 0.07
122 13 0.07
123 71 0.39
124 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (118 bp):
AGCTAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGATGAGTTCTTCTCAT
TATGAACTCCTTTGGAAATGTTGATCCATCGAGTCACCTATGCAATAGAATCG
Found at i:920136 original size:38 final size:35
Alignment explanation
Indices: 920094--920163 Score: 86
Period size: 38 Copynumber: 1.9 Consensus size: 35
920084 AGATGAACTA
* *
920094 TCTCAAGTAAGATAAATTTCTTGTTTTGAAGAAAATTG
1 TCTCAAGTAAGACAAA-GT-TTGTTTT-AAGAAAATTG
*
920132 TCTCAAGTGAGACAAAGTTTGTTTTAAGAAAA
1 TCTCAAGTAAGACAAAGTTTGTTTTAAGAAAA
920164 ACAATCTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 7 0.24
36 7 0.24
37 1 0.03
38 14 0.48
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (35 bp):
TCTCAAGTAAGACAAAGTTTGTTTTAAGAAAATTG
Found at i:920290 original size:36 final size:36
Alignment explanation
Indices: 920244--920511 Score: 212
Period size: 36 Copynumber: 7.2 Consensus size: 36
920234 TTTCTCTAGC
* **
920244 GAGATGAAATTTGTTTTAAGAAAAACTATCTCGTGT
1 GAGATAAAATTTGTTTTAAGAAAAACTATCTCAAGT
* * * *
920280 GAGATAAAATTTCTTGTTTTAAGTGGAACAATTGTCTCAAGC
1 GAGATAAAA--T-TTGTTTTAA---GAAAAACTATCTCAAGT
* *
920322 GAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGT
1 GAGATAAAATTTGTTTTAAGAAAAACTATCTCAAGT
* * ** * *
920358 GAGATAAATTTCTGTTTTGAGTGAAACTGTCTCAAGC
1 GAGATAAAATT-TGTTTTAAGAAAAACTATCTCAAGT
* * *
920395 GAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGT
1 GAGATAAAATTTGTTTTAAGAAAAACTATCTCAAGT
* ** ** *
920431 GAGATAAATTTCTGTTTCGAGTGAAACTATCTCAAGC
1 GAGATAAAATT-TGTTTTAAGAAAAACTATCTCAAGT
** * *
920468 GAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGT
1 GAGATAAAATTTGTTTTAAGAAAAACTATCTCAAGT
920504 GAGATAAA
1 GAGATAAA
920512 TATCTTTTTC
Statistics
Matches: 176, Mismatches: 48, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
36 82 0.47
37 55 0.31
38 1 0.01
39 18 0.10
40 1 0.01
42 19 0.11
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (36 bp):
GAGATAAAATTTGTTTTAAGAAAAACTATCTCAAGT
Found at i:920424 original size:73 final size:73
Alignment explanation
Indices: 920236--920546 Score: 417
Period size: 73 Copynumber: 4.2 Consensus size: 73
920226 AGGAAGATTT
* * * **
920236 TCTCTAGCGAGATGAAATTTGTTTTAAGAAAAACTATCTCGTGTGAGATAAAATTTCTTGTTTTA
1 TCTCAAGCGAGACGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATTTC-TGTTTTA
*
920301 AGTGGAACAATTG
64 AGT-G-A-AACTG
* *
920314 TCTCAAGCGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTTTTGAG
1 TCTCAAGCGAGACGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTTTTAAG
920379 TGAAACTG
66 TGAAACTG
* * **
920387 TCTCAAGCGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTTTCGAG
1 TCTCAAGCGAGACGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTTTTAAG
*
920452 TGAAACTA
66 TGAAACTG
* *
920460 TCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATATCT-TTTTCAA
1 TCTCAAGCGAGACGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTTTT-AA
*
920524 GTGAAATTG
65 GTGAAACTG
920533 TCTCAAGCGAGACG
1 TCTCAAGCGAGACG
920547 TCGCTGATTC
Statistics
Matches: 213, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
72 3 0.01
73 149 0.70
74 1 0.00
75 1 0.00
76 9 0.04
77 7 0.03
78 43 0.20
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (73 bp):
TCTCAAGCGAGACGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTTTTAAG
TGAAACTG
Found at i:920723 original size:42 final size:41
Alignment explanation
Indices: 920616--920723 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 41
920606 AGGGCTTATG
* * * *
920616 GATGGCCCGTAGGAATTATCATCTTGCTCGAAAGGCTTTCA
1 GATGGCCCGAAGGAATTATCATCATGCTCGAAAGACTTACA
* * * *
920657 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGAATT-ATCATCATGCTCGAAAGACTTACA
* *
920699 GATGGTCCGAAGGACTTACTCATCA
1 GATGGCCCGAAGGAATTA-TCATCA
920724 AGAAACCCTT
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 15 0.28
42 38 0.72
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (41 bp):
GATGGCCCGAAGGAATTATCATCATGCTCGAAAGACTTACA
Found at i:920966 original size:42 final size:42
Alignment explanation
Indices: 920892--920992 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
920882 AGGTCTTATG
* * * * *
920892 GATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGGCTTACA
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACA
**
920933 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACA
920975 GATGACCCGAAGGATTTA
1 GATGACCCGAAGGATTTA
920993 CAAATCAAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
41 15 0.29
42 37 0.71
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (42 bp):
GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACA
Found at i:921217 original size:20 final size:20
Alignment explanation
Indices: 921192--921242 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
921182 TATCATCTGG
921192 CTCGAAAGGATTACAGATGA
1 CTCGAAAGGATTACAGATGA
*
921212 CTCGAAA-GACTTACCGATGA
1 CTCGAAAGGA-TTACAGATGA
*
921232 CCCG-AAGGATT
1 CTCGAAAGGATT
921243 TACAAATTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (20 bp):
CTCGAAAGGATTACAGATGA
Found at i:921622 original size:21 final size:21
Alignment explanation
Indices: 921598--921654 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 21
921588 ATTTTCTATT
921598 ATGCAAATGA-TGTTCTTATGA
1 ATGCAAAT-ATTGTTCTTATGA
921619 ATGCAAAAATATTGTTCTTATGA
1 ATGC--AAATATTGTTCTTATGA
921642 ATGCAAA-ATTGTT
1 ATGCAAATATTGTT
921655 AATGCAATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
20 6 0.18
21 7 0.21
22 1 0.03
23 19 0.58
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (21 bp):
ATGCAAATATTGTTCTTATGA
Found at i:921654 original size:20 final size:22
Alignment explanation
Indices: 921608--921650 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
921598 ATGCAAATGA
921608 TGTTCTTATGAATGCAAAAATAT
1 TGTTCTTATGAATGC-AAAATAT
921631 TGTTCTTATGAATGCAAAAT
1 TGTTCTTATGAATGCAAAAT
921651 TGTTAATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (22 bp):
TGTTCTTATGAATGCAAAATAT
Found at i:924297 original size:9 final size:9
Alignment explanation
Indices: 924285--924318 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
924275 CTTTTCTTCT
924285 TTTTTTTTC
1 TTTTTTTTC
924294 TTTTTTTTC
1 TTTTTTTTC
924303 ATCTTTTTTTC
1 -T-TTTTTTTC
924314 TTTTT
1 TTTTT
924319 CTTATTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 13 0.57
10 2 0.09
11 8 0.35
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:930307 original size:28 final size:26
Alignment explanation
Indices: 930263--930316 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
930253 CCTAAGGGAC
*
930263 TAAATCTGGTATTTTACCTAAATATATA
1 TAAATCTGGTATATTA-CTAAA-ATATA
930291 TAAATACTGGTA-ATTACTAAAATATA
1 TAAAT-CTGGTATATTACTAAAATATA
930317 AATTAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.21
27 5 0.21
28 8 0.33
29 6 0.25
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.39
Consensus pattern (26 bp):
TAAATCTGGTATATTACTAAAATATA
Found at i:933277 original size:6 final size:6
Alignment explanation
Indices: 933266--933290 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
933256 CAAAAGCTAT
933266 ATAATC ATAATC ATAATC ATAATC A
1 ATAATC ATAATC ATAATC ATAATC A
933291 AGAAACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAATC
Found at i:940392 original size:96 final size:95
Alignment explanation
Indices: 940223--940409 Score: 320
Period size: 96 Copynumber: 2.0 Consensus size: 95
940213 GGTATGCGAT
*
940223 TTACCCCTTGTCTTAGGGCTTGTGTTGCTGTTTTCGAAGCTATTTGTTGGCTGCATTTACCTATT
1 TTACCCCTTGTCTCAGGGCTTGTGTTGCTGTTTTCGAAGCTATTTGTTGGCTGCATTTACCTATT
*
940288 TTCTTGTATTATTTAGATTAACTTTTTTTG
66 TTCATGTATTATTTAGATTAACTTTTTTTG
* * *
940318 TTACCCCTTGTCTCAGGGCTTGTGTTGCTGTTTTACGAAGCTATTTGTTGGTTGCATTTATCTGT
1 TTACCCCTTGTCTCAGGGCTTGTGTTGCTGTTTT-CGAAGCTATTTGTTGGCTGCATTTACCTAT
940383 TTTCATGTATTATTTAGATTAACTTTT
65 TTTCATGTATTATTTAGATTAACTTTT
940410 CTTTTTGTTG
Statistics
Matches: 86, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
95 33 0.38
96 53 0.62
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.51
Consensus pattern (95 bp):
TTACCCCTTGTCTCAGGGCTTGTGTTGCTGTTTTCGAAGCTATTTGTTGGCTGCATTTACCTATT
TTCATGTATTATTTAGATTAACTTTTTTTG
Found at i:949039 original size:15 final size:15
Alignment explanation
Indices: 949015--949048 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
949005 ATTTAACTGA
949015 GCGGGCGGATGCGGG
1 GCGGGCGGATGCGGG
*
949030 GCGGGTGGATGCGGG
1 GCGGGCGGATGCGGG
949045 GCGG
1 GCGG
949049 ATGCGGGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.68, T:0.09
Consensus pattern (15 bp):
GCGGGCGGATGCGGG
Found at i:955150 original size:23 final size:23
Alignment explanation
Indices: 955119--955180 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
955109 TTTACCCTAA
*
955119 ATTTAAACATTTTTAATCATTAT
1 ATTTTAACATTTTTAATCATTAT
955142 ATTTTAACATTTTTAATCATTAT
1 ATTTTAACATTTTTAATCATTAT
955165 ATTTTAACATTTTTAA
1 ATTTTAACATTTTTAA
955181 ATTTTTAGTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTTAACATTTTTAATCATTAT
Found at i:955310 original size:2 final size:2
Alignment explanation
Indices: 955305--955332 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
955295 TTTTTTTTAA
955305 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
955333 TATGACTGAC
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:957210 original size:2 final size:2
Alignment explanation
Indices: 957203--957242 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
957193 GCATACATAC
957203 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
957243 TTGAAGCACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:959720 original size:29 final size:30
Alignment explanation
Indices: 959687--959743 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
959677 TTAAAATTTT
959687 AAAATTAT-ATTGAAA-CAAAAAAATATTCC
1 AAAATTATAATT-AAATCAAAAAAATATTCC
*
959716 AAAATTATAATTAAATTAAAAAAATATT
1 AAAATTATAATTAAATCAAAAAAATATT
959744 TCCTCTGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (30 bp):
AAAATTATAATTAAATCAAAAAAATATTCC
Found at i:965876 original size:14 final size:14
Alignment explanation
Indices: 965859--965885 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
965849 TTTTAGTATA
965859 TTTTTTTTTCTCTG
1 TTTTTTTTTCTCTG
965873 TTTTTTTTTCTCT
1 TTTTTTTTTCTCT
965886 CTGTCTCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTCTCTG
Found at i:965878 original size:16 final size:16
Alignment explanation
Indices: 965859--965889 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
965849 TTTTAGTATA
965859 TTTTTTTT-TCTCTGT
1 TTTTTTTTCTCTCTGT
965874 TTTTTTTTCTCTCTGT
1 TTTTTTTTCTCTCTGT
965890 CTCTCTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTTTTTCTCTCTGT
Found at i:966380 original size:9 final size:9
Alignment explanation
Indices: 966354--966386 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
966344 TGGCATGTAA
966354 TTAAT-TAT
1 TTAATATAT
966362 TTATATATAT
1 TTA-ATATAT
966372 TTAATATAT
1 TTAATATAT
966381 TTAATA
1 TTAATA
966387 ATAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 3 0.13
9 14 0.61
10 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTAATATAT
Found at i:966390 original size:3 final size:3
Alignment explanation
Indices: 966382--966460 Score: 140
Period size: 3 Copynumber: 26.3 Consensus size: 3
966372 TTAATATATT
*
966382 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
966430 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
966461 GTGGGTAAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:966963 original size:114 final size:113
Alignment explanation
Indices: 966597--967351 Score: 1072
Period size: 114 Copynumber: 6.6 Consensus size: 113
966587 ATTGAATAAA
* * ** * *
966597 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGATAATCCATC
* * * *
966661 AAATGATGAATTCA-AGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
65 AATTGATGAATTCAGA-AAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * * * *
966710 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCC
* * * *
966774 ATCAAATGATGAATTCA-AGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAATTGATGAATTCAGA-AAAAAGGTTGAACAAATTCTTCTCATTATGAAC
966826 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
966891 ATTTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-TTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
966940 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
*
967005 ATTTGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-TTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
967054 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
*
967119 ATTTGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-TTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
967168 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTGATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
* ** * *
967233 AGTGATAGAATT-AGGCAGAAGGTTGAACAAATTCTTCTCATTATGAAT
66 ATTGAT-GAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * *
967281 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACATTCTCTTGAAATG-TCAATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAT-AATCCATC
*
967345 AAATGAT
65 AATTGAT
967352 AGATTTGAAT
Statistics
Matches: 605, Mismatches: 27, Indels: 20
0.93 0.04 0.03
Matches are distributed among these distances:
112 4 0.01
113 144 0.24
114 349 0.58
115 1 0.00
116 85 0.14
117 20 0.03
118 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
ATTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:968347 original size:167 final size:167
Alignment explanation
Indices: 968068--968710 Score: 956
Period size: 167 Copynumber: 3.8 Consensus size: 167
968058 CCTACTGAAT
* * *
968068 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTCATCTTTCTAAATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCATC-TTCTAAATT
968133 CAATAACTAGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
63 CAATAACTAGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
*
968198 ACATTCATCTTTCAAAATTCAATGATTGGTTCTGTCTAAC
128 AAATTCATCTTTCAAAATTCAATGATTGGTTCTGTCTAAC
* *
968238 CAGATCATATAACTCAAAGAACACTTCCAGAAGATTCTATGAGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
*
968303 TAACTAGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACA
66 TAACTAGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAA
968368 TTCATCTTTCAAAATTCAATGATTGGTTCTGTCTAAC
131 TTCATCTTTCAAAATTCAATGATTGGTTCTGTCTAAC
**
968405 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
* * * * * * * * *
968470 TGATTGGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAA
66 TAACTAGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAA
*
968535 TTCATC-TTCTAAATTCAATGATTGGTTCTG-CTAAAC
131 TTCATCTTTCAAAATTCAATGATTGGTTCTGTCT-AAC
* * * *
968571 CAGATCAGATAACCCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
* *
968636 TGA-TTGTTCTGT-CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GC
66 TAACTAGTT-T-TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGC
968697 AAATTCATCTTTCA
128 AAATTCATCTTTCA
968711 GTTAATGTTT
Statistics
Matches: 435, Mismatches: 33, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
165 57 0.13
166 93 0.21
167 237 0.54
168 8 0.02
169 3 0.01
170 37 0.09
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (167 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
TAACTAGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAA
TTCATCTTTCAAAATTCAATGATTGGTTCTGTCTAAC
Found at i:968351 original size:83 final size:83
Alignment explanation
Indices: 968068--968707 Score: 890
Period size: 83 Copynumber: 7.7 Consensus size: 83
968058 CCTACTGAAT
* * *
968068 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTCATCTTTCTAAATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCATC-TTCTAAATT
* * * * *
968133 CAATAACTAGTTTTACCAAAC
63 CAATGATTGGTTCTGCCAAAC
*
968154 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATC-TTCTAAATTCA
* *
968219 ATGATTGGTTCTGTCTAAC
65 ATGATTGGTTCTGCCAAAC
* *
968238 CAGATCATATAACTCAAAGAACACTTCCAGAAGATTCTATGAGCACATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
* * * * *
968303 TAACTAGTTTTACCAAAC
66 TGATTGGTTCTGCCAAAC
*
968321 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATC-TTCTAAATTCA
* *
968386 ATGATTGGTTCTGTCTAAC
65 ATGATTGGTTCTGCCAAAC
**
968405 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
*
968470 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCCAAAC
* * * *
968488 CAGGTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
*
968553 TGATTGGTTCTGCTAAAC
66 TGATTGGTTCTGCCAAAC
* * * *
968571 CAGATCAGATAACCCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
968636 TGATT-GTTCTGTCC-AAC
66 TGATTGGTTCTG-CCAAAC
*
968653 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTT
968708 TCAGTTAATG
Statistics
Matches: 503, Mismatches: 48, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
82 59 0.12
83 245 0.49
84 157 0.31
85 3 0.01
86 39 0.08
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCTAAATTCAA
TGATTGGTTCTGCCAAAC
Found at i:969838 original size:9 final size:9
Alignment explanation
Indices: 969805--969885 Score: 72
Period size: 9 Copynumber: 8.4 Consensus size: 9
969795 GACCCCCCCT
969805 TTTTTTTTC
1 TTTTTTTTC
*
969814 TTCTTTTTC
1 TTTTTTTTC
969823 TCTTTTTTTC
1 T-TTTTTTTC
*
969833 TTTTTTCTAATT
1 TTTTTT-T--TC
*
969845 TTTTTTTTA
1 TTTTTTTTC
* *
969854 ATTTTTTTA
1 TTTTTTTTC
969863 TTTTTTTTC
1 TTTTTTTTC
969872 TTTTTTTTTC
1 -TTTTTTTTC
969882 TTTT
1 TTTT
969886 CTTCAAGCAT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
9 34 0.57
10 18 0.30
11 1 0.02
12 7 0.12
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:981884 original size:14 final size:14
Alignment explanation
Indices: 981867--981893 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
981857 AGTATATCTT
981867 TTTTTTTTTCTCTG
1 TTTTTTTTTCTCTG
981881 TTTTTTTTTCTCT
1 TTTTTTTTTCTCT
981894 CCGTCTCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTCTCTG
Found at i:982390 original size:3 final size:3
Alignment explanation
Indices: 982376--982466 Score: 157
Period size: 3 Copynumber: 30.3 Consensus size: 3
982366 TATATATATT
982376 TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
982422 -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
982467 GTGGGTAAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
3 79 0.94
4 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:985198 original size:21 final size:21
Alignment explanation
Indices: 985172--985307 Score: 152
Period size: 21 Copynumber: 6.5 Consensus size: 21
985162 GTTTCCAGAT
* *
985172 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
985193 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
985214 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
985235 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
985255 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
*
985276 TCGCAATGCGAACTTGGATTA
1 TCGCAATGCGAACTTGGACTA
*
985297 TCGCATTGCGA
1 TCGCAATGCGA
985308 TTTACATATT
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
20 16 0.16
21 81 0.84
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:985341 original size:62 final size:62
Alignment explanation
Indices: 985213--985343 Score: 160
Period size: 62 Copynumber: 2.1 Consensus size: 62
985203 AACTTGGACT
* **
985213 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACT
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAA
* * *
985275 ATCGCAATGCGAACTTGGATTATCGCATTGCG-AT-T-TACATATTCGCATTGCGATAGTCCAAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCCAAA
985337 ATCGCAA
1 ATCGCAA
985344 CGACTGGTGG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
59 2 0.03
60 2 0.03
61 3 0.05
62 53 0.88
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (62 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAA
Found at i:985436 original size:6 final size:6
Alignment explanation
Indices: 985425--985451 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
985415 GACACATATT
985425 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
985452 CAACCCGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:986086 original size:20 final size:20
Alignment explanation
Indices: 986061--986112 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
986051 ATTTTGGACT
986061 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
986081 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
986101 ATCGCAATGCGA
1 ATCGCAATGCGA
986113 TAGTCCAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:986132 original size:21 final size:21
Alignment explanation
Indices: 986102--986257 Score: 126
Period size: 21 Copynumber: 7.5 Consensus size: 21
986092 AATATGTAAA
*
986102 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
986123 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
986143 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
** *
986164 TCGCATTGCGATAGT-GGACT
1 TCGCATTGCGATAGTCCAAGT
* *
986184 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
986205 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
986226 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
986247 TCGCGTTGCGA
1 TCGCATTGCGA
986258 ATCTGGAAAC
Statistics
Matches: 110, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.01
20 31 0.28
21 76 0.69
22 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:986167 original size:41 final size:41
Alignment explanation
Indices: 986122--986237 Score: 189
Period size: 41 Copynumber: 2.8 Consensus size: 41
986112 ATAGTCCAAG
986122 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
*
986163 TTCGCATTGCGATAGTGGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
* *
986204 TTCGCATTGCGATAGTCCAAGT-TCGCATTGCGAT
1 TTCGCATTGCGATAGT-CGACTATCGCATTGCGAT
986238 AGTCGAAGTT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 68 0.97
42 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
Found at i:986169 original size:20 final size:20
Alignment explanation
Indices: 986144--986216 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
986134 TAGTCGACTA
986144 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
986164 TCGCATTGCGATAGTGGAC-TA-
1 TCGCATTGCGAT--T-TACATAT
986185 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
986205 TCGCATTGCGAT
1 TCGCATTGCGAT
986217 AGTCCAAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
19 3 0.07
20 24 0.52
21 12 0.26
22 3 0.07
23 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:986256 original size:62 final size:62
Alignment explanation
Indices: 986102--986257 Score: 160
Period size: 62 Copynumber: 2.5 Consensus size: 62
986092 AATATGTAAA
* * *
986102 TCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATGTACATAT
* * * *
986164 TCGCATTGCGATAGT-GGACTATCGCATTGCGAT--T-TACATATTCGCATTGCGATAGTCCA-A
1 TCGCATTGCGATAGTCGAAGT-TCGCATTGCGATAGTCGAC-TA-TCGCATTGCGAT-GTACATA
986224 GT
62 -T
*
986226 TCGCATTGCGATAGTCGAAGTTCGCGTTGCGA
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGA
986258 ATCTGGAAAC
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
59 2 0.03
60 3 0.04
61 15 0.19
62 55 0.71
63 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (62 bp):
TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATGTACATAT
Found at i:987815 original size:23 final size:23
Alignment explanation
Indices: 987789--987835 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
987779 GAAAAAAGTT
987789 TCACAAAGACAGAGATAAACGTG
1 TCACAAAGACAGAGATAAACGTG
**
987812 TCACAAAGGTAGAGATAAACGTG
1 TCACAAAGACAGAGATAAACGTG
987835 T
1 T
987836 AACACATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (23 bp):
TCACAAAGACAGAGATAAACGTG
Found at i:995546 original size:44 final size:44
Alignment explanation
Indices: 995483--995589 Score: 151
Period size: 44 Copynumber: 2.4 Consensus size: 44
995473 TTTTGTGCAC
* *
995483 TATGCATCAATACACTATGAAAGTGTACCGATGCATCCCTTGAA
1 TATGCATCGATACACTATGAAAGTGCACCGATGCATCCCTTGAA
* * *
995527 TATGCATCGATACACTATGAAGGTGCACTGATGCATGCCTTGAA
1 TATGCATCGATACACTATGAAAGTGCACCGATGCATCCCTTGAA
* *
995571 TGTGCATCGATACATTATG
1 TATGCATCGATACACTATG
995590 CAGTGTATCA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
TATGCATCGATACACTATGAAAGTGCACCGATGCATCCCTTGAA
Found at i:997606 original size:25 final size:28
Alignment explanation
Indices: 997552--997610 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 28
997542 TTGGCTTTGT
997552 TTGTTTGGATTTTGAATATTTATTTTGGA
1 TTGTTTGGATTTTGAATA-TTATTTTGGA
997581 TTGTTT-G-TTTTGAATA-TATTTTGGA
1 TTGTTTGGATTTTGAATATTATTTTGGA
997606 -TGTTT
1 TTGTTT
997611 TGCTTGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 5 0.17
25 9 0.30
27 9 0.30
28 1 0.03
29 6 0.20
ACGTcount: A:0.19, C:0.00, G:0.20, T:0.61
Consensus pattern (28 bp):
TTGTTTGGATTTTGAATATTATTTTGGA
Found at i:998391 original size:65 final size:64
Alignment explanation
Indices: 998263--998392 Score: 181
Period size: 65 Copynumber: 2.0 Consensus size: 64
998253 ACACCCTAAT
* ** * *
998263 TCGAATGCATTTTGTGTACCGATGCACAGTCATGCATCGATGCACTCCTGATTTTATTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAACCATGCATCGATACACTCCTGATCTTATTGAAACA
*
998327 TCGAATGCATTTTATGTACCGATGCACAAACCATGCATCGATACACTCCTGGCTCTT-TTGAAAC
1 TCGAATGCATTTTATGTACCGATGCAC-AACCATGCATCGATACACTCCT-GATCTTATTGAAAC
998391 A
64 A
998392 T
1 T
998393 TAAATATAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 26 0.45
65 28 0.48
66 4 0.07
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGTACCGATGCACAACCATGCATCGATACACTCCTGATCTTATTGAAACA
Found at i:998410 original size:65 final size:64
Alignment explanation
Indices: 998276--998418 Score: 157
Period size: 65 Copynumber: 2.2 Consensus size: 64
998266 AATGCATTTT
** * * * *
998276 GTGTACCGATGCACAGTCATGCATCGATGCACTCCTGATTTTATTGAAACATCGAATGCATTTTA
1 GTGTACCGATGCACAACCATGCATCGATACACTCCTGATCTTATTGAAACATCAAAT-CATATTA
* *
998341 -TGTACCGATGCACAAACCATGCATCGATACACTCCTGGCTCTT-TTGAAACATTAAAT-ATAAT
1 GTGTACCGATGCAC-AACCATGCATCGATACACTCCT-GATCTTATTGAAACATCAAATCAT-AT
998403 TA
63 TA
998405 GTGTACCGATGCAC
1 GTGTACCGATGCAC
998419 CCCAAGTGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
63 2 0.03
64 16 0.24
65 44 0.67
66 4 0.06
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
GTGTACCGATGCACAACCATGCATCGATACACTCCTGATCTTATTGAAACATCAAATCATATTA
Found at i:1000296 original size:16 final size:17
Alignment explanation
Indices: 1000275--1000308 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1000265 TCAAAAAGAT
1000275 ATAAAA-ATAATTTTGA
1 ATAAAAGATAATTTTGA
*
1000291 ATAAAAGTTAATTTTGA
1 ATAAAAGATAATTTTGA
1000308 A
1 A
1000309 GTCTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
ATAAAAGATAATTTTGA
Found at i:1002455 original size:40 final size:40
Alignment explanation
Indices: 1002372--1002473 Score: 129
Period size: 39 Copynumber: 2.6 Consensus size: 40
1002362 ACATAAAGTT
** *
1002372 TAGTTTTTGTTTC-TTTTAGTACCTTGCCGTTAAAAACTT
1 TAGTTTTTGTTTCATTTTAGTACCTCACCGTTAAAAACTC
* *
1002411 TAGTTTTTGTTTCATTTTGGTACAC-CACCGTTTAAAACTC
1 TAGTTTTTGTTTCATTTTAGTAC-CTCACCGTTAAAAACTC
1002451 TAG-TTTTGTTTCATTTTAGTACC
1 TAGTTTTTGTTTCATTTTAGTACC
1002474 CGTTCAAAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
38 1 0.02
39 31 0.56
40 22 0.40
41 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.50
Consensus pattern (40 bp):
TAGTTTTTGTTTCATTTTAGTACCTCACCGTTAAAAACTC
Found at i:1008031 original size:38 final size:36
Alignment explanation
Indices: 1007949--1008031 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 36
1007939 AATATAATTT
1007949 TAAATACAACAAACTTACAATAAGTATTAAATGATAA
1 TAAATA-AACAAACTTACAATAAGTATTAAATGATAA
* *
1007986 -ATGATAAACAAA-TTACAATAACTGATATTAAATGGTAA
1 TA-AATAAACAAACTTACAATAA--G-TATTAAATGATAA
1008024 TAAATAAA
1 TAAATAAA
1008032 ATTAACCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
35 9 0.24
36 7 0.18
37 4 0.11
38 17 0.45
39 1 0.03
ACGTcount: A:0.57, C:0.08, G:0.07, T:0.28
Consensus pattern (36 bp):
TAAATAAACAAACTTACAATAAGTATTAAATGATAA
Found at i:1009251 original size:2 final size:2
Alignment explanation
Indices: 1009244--1009280 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1009234 AAACTAAAAC
1009244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1009281 CAAAATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1010429 original size:17 final size:17
Alignment explanation
Indices: 1010394--1010447 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
1010384 ATATCTGCAA
* *
1010394 AAAAAATTAATTAAA-T
1 AAAATATTAAATAAATT
1010410 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
1010427 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
1010444 AAAA
1 AAAA
1010448 ACAAAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 18 0.55
17 12 0.36
18 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:1011011 original size:2 final size:2
Alignment explanation
Indices: 1011004--1011029 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1010994 TATAATTTTA
1011004 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
1011030 GTTATAATTA
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:1025941 original size:33 final size:33
Alignment explanation
Indices: 1025899--1025962 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
1025889 AAGTTTGTAA
1025899 ACAAGTAAATGTAAAAATGGTTGATGATGTTTT
1 ACAAGTAAATGTAAAAATGGTTGATGATGTTTT
1025932 ACAAGTAAATGTAAAAATGGTTGATGATGTT
1 ACAAGTAAATGTAAAAATGGTTGATGATGTT
1025963 AATAAAACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (33 bp):
ACAAGTAAATGTAAAAATGGTTGATGATGTTTT
Found at i:1030686 original size:15 final size:16
Alignment explanation
Indices: 1030661--1030696 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1030651 AATTGGAAGA
*
1030661 TTAACTTTATTTTAGT
1 TTAACTTTATTTTAAT
1030677 TTAA-TTTATTTTAAT
1 TTAACTTTATTTTAAT
1030692 TTAAC
1 TTAAC
1030697 AAAGCAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (16 bp):
TTAACTTTATTTTAAT
Found at i:1033478 original size:25 final size:25
Alignment explanation
Indices: 1033450--1033522 Score: 91
Period size: 25 Copynumber: 3.1 Consensus size: 25
1033440 CATTCTCACA
1033450 CCATTTGCAAGCATTATTTACTTAG
1 CCATTTGCAAGCATTATTTACTTAG
** *
1033475 CCATTTGCAAGC--TCGTT-CTCA-
1 CCATTTGCAAGCATTATTTACTTAG
1033496 CCATTTGCAAGCATTATTTACTTAG
1 CCATTTGCAAGCATTATTTACTTAG
1033521 CC
1 CC
1033523 TTCAAGGGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
21 12 0.32
22 3 0.08
23 6 0.16
24 3 0.08
25 14 0.37
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (25 bp):
CCATTTGCAAGCATTATTTACTTAG
Found at i:1033795 original size:12 final size:12
Alignment explanation
Indices: 1033778--1033818 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1033768 GTTCATTCAT
1033778 TCATTTCTTAGC
1 TCATTTCTTAGC
* *
1033790 TCATTT-TCA-T
1 TCATTTCTTAGC
1033800 TCATTTCTTAGC
1 TCATTTCTTAGC
1033812 TCATTTC
1 TCATTTC
1033819 CATTCAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 6 0.26
11 4 0.17
12 13 0.57
ACGTcount: A:0.17, C:0.24, G:0.05, T:0.54
Consensus pattern (12 bp):
TCATTTCTTAGC
Found at i:1033799 original size:26 final size:25
Alignment explanation
Indices: 1033764--1033829 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 25
1033754 TGAATTGGCA
1033764 TCATGTTCATTCATTCATTTCTTAGC
1 TCAT-TTCATTCATTCATTTCTTAGC
1033790 TCA-TT--TTCATTCATTTCTTAGC
1 TCATTTCATTCATTCATTTCTTAGC
1033812 TCATTTCCATTCAATTCA
1 TCATTT-CATTC-ATTCA
1033830 GCTCATAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
22 20 0.57
23 2 0.06
24 2 0.06
26 6 0.17
27 5 0.14
ACGTcount: A:0.21, C:0.24, G:0.05, T:0.50
Consensus pattern (25 bp):
TCATTTCATTCATTCATTTCTTAGC
Found at i:1033800 original size:22 final size:22
Alignment explanation
Indices: 1033773--1033824 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
1033763 ATCATGTTCA
1033773 TTCATTCATTTCTTAGCTCATT
1 TTCATTCATTTCTTAGCTCATT
1033795 TTCATTCATTTCTTAGCTCATT
1 TTCATTCATTTCTTAGCTCATT
*
1033817 TCCATTCA
1 TTCATTCA
1033825 ATTCAGCTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.25, G:0.04, T:0.52
Consensus pattern (22 bp):
TTCATTCATTTCTTAGCTCATT
Found at i:1041081 original size:29 final size:29
Alignment explanation
Indices: 1041056--1041128 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
1041046 ATAACTTTTT
* * *
1041056 AAATTTACATTTTGGTCCCTAAACTTTAC
1 AAATTTACATTTTAGCCCCTAAACTTTAA
* *
1041085 AAATTTATACTTTAGCCCCTAAACTTTCAA
1 AAATTTACATTTTAGCCCCTAAACTTT-AA
1041115 AAA-TTACATTTTAG
1 AAATTTACATTTTAG
1041129 TCATTAGTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 32 0.89
30 4 0.11
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (29 bp):
AAATTTACATTTTAGCCCCTAAACTTTAA
Found at i:1056123 original size:23 final size:24
Alignment explanation
Indices: 1056095--1056147 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1056085 CGTACCATAC
1056095 TAATAAA-AAATATAAAAAAATAGA
1 TAATAAATAAATA-AAAAAAATAGA
*
1056119 -AATAAATTAAATAAAAAAATTAGA
1 TAATAAA-TAAATAAAAAAAATAGA
1056143 TAATA
1 TAATA
1056148 TAAGTCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 6 0.24
24 10 0.40
25 9 0.36
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (24 bp):
TAATAAATAAATAAAAAAAATAGA
Found at i:1060504 original size:23 final size:23
Alignment explanation
Indices: 1060475--1060519 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1060465 AGTGTCATAT
1060475 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
1060498 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
1060520 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:1060525 original size:23 final size:23
Alignment explanation
Indices: 1060476--1060544 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
1060466 GTGTCATATT
* * **
1060476 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
1060499 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
1060522 ATATTATTATAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
1060545 TATTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:1060612 original size:27 final size:30
Alignment explanation
Indices: 1060508--1060607 Score: 102
Period size: 27 Copynumber: 3.4 Consensus size: 30
1060498 TATATTTTAA
* * *
1060508 ATATATTTATTAAA-ATATTATTATATTATT
1 ATAT-TTTATTAAATATATAAATAAATTATT
*
1060538 ATATTAATATTAAATATATAAATAAATTATT
1 ATATT-TTATTAAATATATAAATAAATTATT
*
1060569 -CA--TTATTAAATATATAAA-AAATTATT
1 ATATTTTATTAAATATATAAATAAATTATT
1060595 ATATTTTATTAAA
1 ATATTTTATTAAA
1060608 AATAATAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
26 8 0.14
27 16 0.28
29 9 0.16
30 12 0.21
31 13 0.22
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
ATATTTTATTAAATATATAAATAAATTATT
Found at i:1060623 original size:27 final size:27
Alignment explanation
Indices: 1060509--1060703 Score: 98
Period size: 27 Copynumber: 7.0 Consensus size: 27
1060499 ATATTTTAAA
* *
1060509 TATATT-TATTAAAATATTATTATATTAT
1 TATATTATATTAAAA-ATAATAATA-TAT
* *
1060537 TATATTAATATTAAATAT-ATAAATAAAT
1 TATATT-ATATTAAAAATAAT-AATATAT
* *
1060565 TAT-TCATTATTAAATATATAA-AAAATTAT
1 TATATTA-TATTAAA-A-ATAATAATA-TAT
* *
1060594 TATATTTTATTAAAAATAATAATATCT
1 TATATTATATTAAAAATAATAATATAT
* * * *
1060621 TATATTATAATATAATTAAT--TATTT
1 TATATTATATTAAAAATAATAATATAT
* *
1060646 TATTATAATATTAAAAATATTATATTATAT
1 TA-TATTATATTAAAAATA--ATAATATAT
*
1060676 TATATTAT-TATAAAATTAATAATATAT
1 TATATTATAT-TAAAAATAATAATATAT
1060703 T
1 T
1060704 TTTAATATTT
Statistics
Matches: 127, Mismatches: 24, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
25 6 0.05
26 13 0.10
27 39 0.31
28 23 0.18
29 31 0.24
30 15 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (27 bp):
TATATTATATTAAAAATAATAATATAT
Found at i:1060634 original size:50 final size:52
Alignment explanation
Indices: 1060532--1060690 Score: 132
Period size: 53 Copynumber: 3.0 Consensus size: 52
1060522 ATATTATTAT
*
1060532 ATTATTATATTA-ATATTAAATATATA-AATAAATTATTCATTATTAAATATATAAAAA
1 ATTATTATATTATATATTAAAAATATATAAT--A-TATT-A-TATT--ATATATAAAAA
* **
1060589 ATTATTATATT-T-TATTAAAAATA-ATAATATCTTATATTATAATATAATTA
1 ATTATTATATTATATATTAAAAATATATAATATATTATATTAT-ATATAAAAA
* *
1060639 ATTATTTTATTATAATATTAAAAATATTATATTATATTATATTAT-TATAAAA
1 ATTATTATATTAT-ATATTAAAAATA-TATAATATATTATATTATATATAAAA
1060691 TTAATAATAT
Statistics
Matches: 85, Mismatches: 9, Indels: 20
0.75 0.08 0.18
Matches are distributed among these distances:
49 2 0.02
50 17 0.20
51 5 0.06
52 1 0.01
53 19 0.22
54 1 0.01
55 16 0.19
56 13 0.15
57 11 0.13
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.48
Consensus pattern (52 bp):
ATTATTATATTATATATTAAAAATATATAATATATTATATTATATATAAAAA
Found at i:1060657 original size:8 final size:8
Alignment explanation
Indices: 1060622--1060700 Score: 52
Period size: 8 Copynumber: 9.5 Consensus size: 8
1060612 ATAATATCTT
1060622 ATATTATA
1 ATATTATA
* *
1060630 ATATAATT
1 ATATTATA
*
1060638 A-ATTATT
1 ATATTATA
*
1060645 TTATTATA
1 ATATTATA
*
1060653 ATATTAAAA
1 ATATT-ATA
1060662 ATATTATA
1 ATATTATA
1060670 TTATATTATA
1 --ATATTATA
*
1060680 TTATTATA
1 ATATTATA
*
1060688 AAATTAATA
1 ATATT-ATA
1060697 ATAT
1 ATAT
1060701 ATTTTTAATA
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
7 5 0.09
8 28 0.52
9 13 0.24
10 8 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
ATATTATA
Found at i:1060672 original size:5 final size:5
Alignment explanation
Indices: 1060620--1060683 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
1060610 TAATAATATC
* * * **
1060620 TTATA TTATA ATATAA TTA-A TTATT TTATTA TAATA TTA-A AAATA TTATA
1 TTATA TTATA TTAT-A TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA
1060670 TTATA TTATA TTAT
1 TTATA TTATA TTAT
1060684 TATAAAATTA
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
4 6 0.13
5 33 0.73
6 6 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
TTATA
Found at i:1060685 original size:35 final size:34
Alignment explanation
Indices: 1060635--1060700 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
1060625 TTATAATATA
* *
1060635 ATTAATTATTTTATTATAATATTAAAAATATTAT
1 ATTAATTATATTATTATAAAATTAAAAATATTAT
*
1060669 ATTATATTATATTATTATAAAATTAATAATAT
1 ATTA-ATTATATTATTATAAAATTAAAAATAT
1060701 ATTTTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 4 0.14
35 24 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
ATTAATTATATTATTATAAAATTAAAAATATTAT
Found at i:1060710 original size:55 final size:53
Alignment explanation
Indices: 1060601--1060712 Score: 129
Period size: 55 Copynumber: 2.1 Consensus size: 53
1060591 TATTATATTT
* * *
1060601 TATTAAAAATAATAATATCTTATATTATAATATAATTAATTATTTTATTATAA
1 TATTAAAAATAATAATATATTATATTATAATAAAATTAATTATATTATTATAA
* *
1060654 TATTAAAAATATTATATTATATTATATTATTATAAAATTAATAATATATT-TT-TAA
1 TATTAAAAATA--ATAATATATTATATTATAATAAAATTAAT--TATATTATTATAA
1060709 TATT
1 TATT
1060713 TTAATAATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
53 11 0.22
55 32 0.64
56 2 0.04
57 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (53 bp):
TATTAAAAATAATAATATATTATATTATAATAAAATTAATTATATTATTATAA
Found at i:1060983 original size:41 final size:41
Alignment explanation
Indices: 1060936--1061017 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
1060926 CAAATACTGT
* *
1060936 AAAACATTTTACGGAAAACGAATTACTTGAAACAAACACGG
1 AAAACATTTTACGAAAAACGAATTACATGAAACAAACACGG
*
1060977 AAAACATTTTCCGAAAAACGAATTACATGAAACAAACACGG
1 AAAACATTTTACGAAAAACGAATTACATGAAACAAACACGG
1061018 GATTTCGGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.18
Consensus pattern (41 bp):
AAAACATTTTACGAAAAACGAATTACATGAAACAAACACGG
Found at i:1067011 original size:37 final size:34
Alignment explanation
Indices: 1066930--1067018 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 34
1066920 GTTAATTTTT
*
1066930 TAAATAGTTATTATATTTTATATTAATATATTTATG
1 TAAATA-TTATTAT-TTTTATATTAATATATTTATA
*
1066966 TAAATATTATTATTTTTTTATTAAAATAATATTTATA
1 TAAATATTATTATTTTTATATT--AAT-ATATTTATA
*
1067003 TAATTATTATTTATTT
1 TAAATATTA-TTATTT
1067019 AGAATTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
34 8 0.17
35 7 0.15
36 9 0.20
37 16 0.35
38 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (34 bp):
TAAATATTATTATTTTTATATTAATATATTTATA
Found at i:1067167 original size:17 final size:17
Alignment explanation
Indices: 1067145--1067198 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1067135 AATGTTAATA
1067145 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1067162 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1067179 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1067196 TTT
1 TTT
1067199 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1068774 original size:21 final size:21
Alignment explanation
Indices: 1068731--1068775 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1068721 GCAGGGGTAC
* *
1068731 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1068752 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1068773 ATG
1 ATG
1068776 TCATCTCCGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.38, G:0.13, T:0.24
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1068811 original size:21 final size:21
Alignment explanation
Indices: 1068785--1068854 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
1068775 GTCATCTCCG
*
1068785 CAGGGTTACATTCCGAGCCCA
1 CAGGGTTACATTCCTAGCCCA
* *
1068806 CAGGGTTATATTCCTAGCCCGC
1 CAGGGTTACATTCCTAGCCC-A
* *
1068828 CA-GGTTACATGCCTAGCCCG
1 CAGGGTTACATTCCTAGCCCA
1068848 CAGGGTT
1 CAGGGTT
1068855 TTATACCATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.20, C:0.31, G:0.26, T:0.23
Consensus pattern (21 bp):
CAGGGTTACATTCCTAGCCCA
Found at i:1069406 original size:28 final size:28
Alignment explanation
Indices: 1069374--1069452 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
1069364 AATAAATGTT
* *
1069374 TTTAAAATACAAATTATATTATTCAAAA
1 TTTAAAATAAAAATAATATTATTCAAAA
*
1069402 TTTAAAATAAAAATAATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCAAAA
1069430 TTTAAAATTAAAATATAA-ATTAT
1 TTTAAAA-TAAAA-ATAATATTAT
1069453 AGTATTCGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 32 0.70
29 10 0.22
30 4 0.09
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCAAAA
Found at i:1069441 original size:34 final size:34
Alignment explanation
Indices: 1069398--1069475 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
1069388 TATATTATTC
*
1069398 AAAATTTAAAATAAAAATAATATTATTCGAAATTT
1 AAAA-TTAAAATAAAAATAATAGTATTCGAAATTT
* *
1069433 AAAATTAAAATATAAATTATAGTATTCGAAATTT
1 AAAATTAAAATAAAAATAATAGTATTCGAAATTT
*
1069467 AACATTAAA
1 AAAATTAAA
1069476 TTTCAACTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 35 0.90
35 4 0.10
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (34 bp):
AAAATTAAAATAAAAATAATAGTATTCGAAATTT
Found at i:1069715 original size:23 final size:22
Alignment explanation
Indices: 1069684--1069726 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1069674 AATGTCACAA
*
1069684 TCAACTTATCACTTAACATTTAT
1 TCAACTTATC-CATAACATTTAT
*
1069707 TCAATTTATCCATAACATTT
1 TCAACTTATCCATAACATTT
1069727 TATCTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (22 bp):
TCAACTTATCCATAACATTTAT
Found at i:1070217 original size:128 final size:128
Alignment explanation
Indices: 1069840--1070953 Score: 1934
Period size: 128 Copynumber: 8.7 Consensus size: 128
1069830 ACAATCCATC
1069840 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
1069905 GGAAGGCGC-CCCCCGGGAACGTGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATAT-ATC
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGA-A
* * *
1069967 TAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAACGATAACATATTCTCTG-TAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
1070031 GGAAGGCGCGCCCCTGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
1070094 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
1070159 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* *
1070222 TAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGGTAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
1070287 TGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGT-CCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
1070349 TAGTGTCCCCAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
1070414 GGAAGGCGCGCCCCCAGGAACGCGCCTAT-AAGTCCCCTGAGAAATAATAGGTACTGATAT-ATC
66 GGAAGGCGCGCCCCCGGGAACGCGCCT-TCAAGTCCCCTGAGAAATAATAGGTACTGATATGA-A
1070477 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
1070542 GGAAGGCGCGCCCCCGGGAACGTGCCTTCAAGTCCCCTGAGAAGTAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
1070605 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
1070670 GGAAGGCGCGCCCCCGGGAATGCGCTTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
1070733 TAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * * *
1070798 AGAAGACGCCCCCCCGGGAACGCACCTTCAAGTCCCCTGAGAAATAATAAGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
1070861 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
1070926 GGAAGGCGCCCCCCCGGGAACGCGCCTT
66 GGAAGGCGCGCCCCCGGGAACGCGCCTT
1070954 AATGTGAATA
Statistics
Matches: 936, Mismatches: 43, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
126 17 0.02
127 275 0.29
128 643 0.69
129 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:1071049 original size:8 final size:8
Alignment explanation
Indices: 1071036--1071076 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1071026 TCACAAGCTT
1071036 TCAAATTC
1 TCAAATTC
1071044 TCAAATTC
1 TCAAATTC
* *
1071052 CCAAACTC
1 TCAAATTC
1071060 T-AAATTC
1 TCAAATTC
1071067 TCAAATTC
1 TCAAATTC
1071075 TC
1 TC
1071077 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1078306 original size:18 final size:18
Alignment explanation
Indices: 1078283--1078320 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1078273 GACTTAAAAA
**
1078283 AACCCTAAACTTGACCCG
1 AACCCTAAACCCGACCCG
1078301 AACCCTAAACCCGACCCG
1 AACCCTAAACCCGACCCG
1078319 AA
1 AA
1078321 TATCACACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.42, G:0.11, T:0.11
Consensus pattern (18 bp):
AACCCTAAACCCGACCCG
Found at i:1078852 original size:39 final size:39
Alignment explanation
Indices: 1078797--1078872 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
1078787 CTTATTCTTC
* * **
1078797 TTCTTCTTCTTGGCACAGCTTGTGCACTCTTGATGGACG
1 TTCTTCTTCTTCGCACAACTCATGCACTCTTGATGGACG
*
1078836 TTCTTCTTCTTCGCACAACTCATGCGCTCTTGATGGA
1 TTCTTCTTCTTCGCACAACTCATGCACTCTTGATGGA
1078873 ACCAAGCTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.14, C:0.28, G:0.20, T:0.38
Consensus pattern (39 bp):
TTCTTCTTCTTCGCACAACTCATGCACTCTTGATGGACG
Found at i:1085848 original size:21 final size:21
Alignment explanation
Indices: 1085823--1085880 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
1085813 GGTACACCGC
*
1085823 CAGTTCAGATGGCACTGCAGA
1 CAGTTCAGATGCCACTGCAGA
* * * *
1085844 TAGTTCAGACGCCACTGTAGC
1 CAGTTCAGATGCCACTGCAGA
1085865 CAGTTCAGATGCCACT
1 CAGTTCAGATGCCACT
1085881 ATCTTAGGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (21 bp):
CAGTTCAGATGCCACTGCAGA
Found at i:1102325 original size:57 final size:57
Alignment explanation
Indices: 1102236--1102366 Score: 244
Period size: 57 Copynumber: 2.3 Consensus size: 57
1102226 GCATCCGCCC
*
1102236 TGTTGACAATTTATCCAACCGGTTTTAGATACTATTTAGAATGACAAGAAAGTAAAG
1 TGTTGACAATTTATCCAACCGGTTTTACATACTATTTAGAATGACAAGAAAGTAAAG
*
1102293 TGTTGACAATTTATCCAACCGGTTTTACATACTATTTAGAATGATAAGAAAGTAAAG
1 TGTTGACAATTTATCCAACCGGTTTTACATACTATTTAGAATGACAAGAAAGTAAAG
1102350 TGTTGACAATTTATCCA
1 TGTTGACAATTTATCCA
1102367 CTATCCAGGC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 72 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (57 bp):
TGTTGACAATTTATCCAACCGGTTTTACATACTATTTAGAATGACAAGAAAGTAAAG
Found at i:1104121 original size:17 final size:17
Alignment explanation
Indices: 1104099--1104132 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1104089 TAAACTTCGC
1104099 AAATGGTCACTAATATT
1 AAATGGTCACTAATATT
*
1104116 AAATGGTCCCTAATATT
1 AAATGGTCACTAATATT
1104133 TGGGTAAGTA
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:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (17 bp):
AAATGGTCACTAATATT
Found at i:1104957 original size:171 final size:172
Alignment explanation
Indices: 1104658--1105006 Score: 556
Period size: 171 Copynumber: 2.0 Consensus size: 172
1104648 TCGGATGATA
* *
1104658 ATCAATGTCCAAGTTAGTTATTCGCCAACACCTTGAATGCTTCAAACCTACAATACAACACCTCT
1 ATCAATGTCCAAGGTAGTTATTCACCAACACCTTGAATGCTTCAAACCTACAATACAACACCTCT
* * *
1104723 ATGTGTTTATCTATTTTTCCTCTCCAGATCAAAGCCGGATTAAGATTATCGACAAGGTTGGTCAT
66 ATGTGTTTATCCATTTTTCCTCTCCAGATCAAAGCCAGATCAAGATTATCGACAAGGTTGGTCAT
* *
1104788 GTAAACGATGATTCTTTCGCCATTGCAAGCTGACCCAATCCC
131 GAAAACGATGATTCTTTCGCCATTGCAAGCTAACCCAATCCC
* * *
1104830 GTCAATGTCC-AGGTAGTTATTCACCAACACCTTGAATGCTTCAAACCTACAATACGACATCTCT
1 ATCAATGTCCAAGGTAGTTATTCACCAACACCTTGAATGCTTCAAACCTACAATACAACACCTCT
* * * * *
1104894 ATGTGTTTATCCATTTTTTCTCTCCGGATCAATGCCAGATCAAGCTTCTCGACAAGGTTGGTCAT
66 ATGTGTTTATCCATTTTTCCTCTCCAGATCAAAGCCAGATCAAGATTATCGACAAGGTTGGTCAT
1104959 GAAAACGATGATTCTTTCGCCATTGCAAGCTAACCCAATCCC
131 GAAAACGATGATTCTTTCGCCATTGCAAGCTAACCCAATCCC
1105001 ATCAAT
1 ATCAAT
1105007 AAAGTTCAAC
Statistics
Matches: 161, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
171 152 0.94
172 9 0.06
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (172 bp):
ATCAATGTCCAAGGTAGTTATTCACCAACACCTTGAATGCTTCAAACCTACAATACAACACCTCT
ATGTGTTTATCCATTTTTCCTCTCCAGATCAAAGCCAGATCAAGATTATCGACAAGGTTGGTCAT
GAAAACGATGATTCTTTCGCCATTGCAAGCTAACCCAATCCC
Found at i:1112478 original size:46 final size:48
Alignment explanation
Indices: 1112388--1112488 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 48
1112378 TAAATATTAT
* * *
1112388 TTTA-TTTTCTAAATAAATGCATGTGAACTAGAAATCATGTGGTTAGG
1 TTTATTTTTCTAAACAAATGCATGTGAACTAGAAAACATGAGGTTAGG
1112435 TTTATTTTTCTAAACAAA-GCATG-GAACTAGAAAACATGAGGTTAGG
1 TTTATTTTTCTAAACAAATGCATGTGAACTAGAAAACATGAGGTTAGG
*
1112481 -ATATTTTT
1 TTTATTTTT
1112489 TAATTGGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
45 7 0.14
46 21 0.43
47 9 0.18
48 12 0.24
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (48 bp):
TTTATTTTTCTAAACAAATGCATGTGAACTAGAAAACATGAGGTTAGG
Found at i:1116912 original size:20 final size:20
Alignment explanation
Indices: 1116887--1117012 Score: 164
Period size: 20 Copynumber: 6.3 Consensus size: 20
1116877 TTTCCCACAA
* *
1116887 ATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAACCTTCGGGTC
*
1116907 ATTTGTAAAACCTTCGGGTA
1 ATTTGTAAAACCTTCGGGTC
*
1116927 ATTTGTAAAACCTTCGAGTC
1 ATTTGTAAAACCTTCGGGTC
* *
1116947 ATTTGTAAAACCTTCGGATA
1 ATTTGTAAAACCTTCGGGTC
1116967 ATTTGTAAAACCTTCAGGG-C
1 ATTTGTAAAACCTTC-GGGTC
* *
1116987 ATTTGTAAATCCTTTGGGTC
1 ATTTGTAAAACCTTCGGGTC
1117007 ATTTGT
1 ATTTGT
1117013 CAGTCTTTCG
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.03
20 87 0.95
21 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTTGTAAAACCTTCGGGTC
Found at i:1130578 original size:2 final size:2
Alignment explanation
Indices: 1130571--1130607 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1130561 TTTCATCTAG
1130571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1130608 GGCCTATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1131201 original size:2 final size:2
Alignment explanation
Indices: 1131194--1131218 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1131184 ACTAAAGCCC
1131194 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1131219 CAAAACTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1136712 original size:43 final size:43
Alignment explanation
Indices: 1136660--1136766 Score: 207
Period size: 43 Copynumber: 2.5 Consensus size: 43
1136650 ATAACTAATG
1136660 AATAAAATAATAATAAACTAAACATGTCTTAACTCTAATTCCT
1 AATAAAATAATAATAAACTAAACATGTCTTAACTCTAATTCCT
1136703 AATAAAATAATAATAAACTAAACATGTCTTAACTCTAATTCCT
1 AATAAAATAATAATAAACTAAACATGTCTTAACTCTAATTCCT
1136746 AATAAAATAATAAT-AACTAAA
1 AATAAAATAATAATAAACTAAA
1136767 AATAATATTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 7 0.11
43 57 0.89
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (43 bp):
AATAAAATAATAATAAACTAAACATGTCTTAACTCTAATTCCT
Found at i:1140124 original size:188 final size:189
Alignment explanation
Indices: 1139807--1140181 Score: 725
Period size: 188 Copynumber: 2.0 Consensus size: 189
1139797 TGTGGTTTGT
*
1139807 ATTTAGTTACAGGATTTTGTTTGTATGGCTGCATCTCCCACGTTTTATTTGATGTAACTAACTAC
1 ATTTAGTTACAGGATTTTGTTTGTATGGCTGCATCTCCCACGTCTTATTTGATGTAACTAACTAC
*
1139872 TTGGATGTAGATTTAATATTAATCTCTAGATGCATAGTTGTAAACTTGTAGTATGATTAGTAAGT
66 TTGGATGTAGATTTAATATTAATCTCTAGATGCATAGTTGTAAACCTGTAGTATGATTAGTAAGT
1139937 GTAGACACTCATTTTCGTCCATATTTATTTTATTTTATTTTC-TTTTATACACACACTC
131 GTAGACACTCATTTTCGTCCATATTTATTTTATTTTATTTTCTTTTTATACACACACTC
1139995 ATTTAGTTACAGGATTTTGTTTGTATGGCTGCATCTCCCACGTCTTATTTGATGTAACTAACTAC
1 ATTTAGTTACAGGATTTTGTTTGTATGGCTGCATCTCCCACGTCTTATTTGATGTAACTAACTAC
1140060 TTGGATGTAGATTTAATATTAATCTCTAGATGCATAGTTGTAAACCTGTAGTATGATTAGTAAGT
66 TTGGATGTAGATTTAATATTAATCTCTAGATGCATAGTTGTAAACCTGTAGTATGATTAGTAAGT
1140125 GTAGACACTCATTTTCGTCCATATTTATTTTATTTTATTTTCTTTTTATACACACAC
131 GTAGACACTCATTTTCGTCCATATTTATTTTATTTTATTTTCTTTTTATACACACAC
1140182 GTGTATATAT
Statistics
Matches: 184, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
188 170 0.92
189 14 0.08
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (189 bp):
ATTTAGTTACAGGATTTTGTTTGTATGGCTGCATCTCCCACGTCTTATTTGATGTAACTAACTAC
TTGGATGTAGATTTAATATTAATCTCTAGATGCATAGTTGTAAACCTGTAGTATGATTAGTAAGT
GTAGACACTCATTTTCGTCCATATTTATTTTATTTTATTTTCTTTTTATACACACACTC
Found at i:1140311 original size:38 final size:36
Alignment explanation
Indices: 1140230--1140574 Score: 264
Period size: 38 Copynumber: 9.6 Consensus size: 36
1140220 GAAAAATACG
* * *
1140230 TATATAATATATGATTTTTAAAAAAACATTTTGAAAATA
1 TATATAATATAT-AGTTTTAAAAAAA-TTTTTGAAAA-C
*
1140269 TATATAATATATAGTTTTAAAAAAATACCTTTGAAAAC
1 TATATAATATATAGTTTTAAAAAAAT--TTTTGAAAAC
* **
1140307 TATATAATATATAGTTTTTAAAACGTTTTTAGAAAAC
1 TATATAATATATAGTTTTAAAAAAATTTTT-GAAAAC
**
1140344 ATATATAATATATAGATTTTAAAACCA-TTTTGAAAAC
1 -TATATAATATATAG-TTTTAAAAAAATTTTTGAAAAC
** **
1140381 TTATATAATATATAGTTTTAAAATCA-TTTTGAAATT
1 -TATATAATATATAGTTTTAAAAAAATTTTTGAAAAC
*
1140417 TATATAATATATAGTTTTAAAAAACATTTTTAAAAAC
1 TATATAATATATAGTTTTAAAAAA-ATTTTTGAAAAC
** *
1140454 -ATATAATATA-A-TTTT-AAAACGTTTTTGAAAGC
1 TATATAATATATAGTTTTAAAAAAATTTTTGAAAAC
* * * *
1140486 --TATAACATATAG-TTTGAAAACATTTTT--AAAT
1 TATATAATATATAGTTTTAAAAAAATTTTTGAAAAC
* * * *
1140517 TATATAATATATGGTTTTGAAAATATCTTTGAAATA-
1 TATATAATATATAGTTTTAAAAAAATTTTTGAAA-AC
* *
1140553 TATATTATATAAAGTTTTAAAA
1 TATATAATATATAGTTTTAAAA
1140575 CATTTTTTCT
Statistics
Matches: 254, Mismatches: 36, Indels: 35
0.78 0.11 0.11
Matches are distributed among these distances:
31 10 0.04
32 13 0.05
33 24 0.09
34 17 0.07
35 23 0.09
36 52 0.20
37 34 0.13
38 53 0.21
39 28 0.11
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (36 bp):
TATATAATATATAGTTTTAAAAAAATTTTTGAAAAC
Found at i:1140348 original size:36 final size:35
Alignment explanation
Indices: 1140252--1140581 Score: 241
Period size: 36 Copynumber: 9.3 Consensus size: 35
1140242 GATTTTTAAA
* *
1140252 AAAACA-TTTTGAAAATATATATAATATATAGTTTTA
1 AAAACATTTTTG-AAA-ACATATAATATATAGTTTTT
* *
1140288 AAAAAATACCTTTGAAAACTATATAATATATAGTTTTT
1 AAAACAT--TTTTGAAAAC-ATATAATATATAGTTTTT
* *
1140326 AAAACGTTTTTAGAAAACATATATAATATATAGATTTT
1 AAAACATTTTT-GAAAAC--ATATAATATATAGTTTTT
1140364 AAAACCA-TTTTGAAAACTTATATAATATATAG-TTTT
1 AAAA-CATTTTTGAAAAC--ATATAATATATAGTTTTT
** *
1140400 AAAATCA-TTTTGAAATTTATATAATATATAGTTTTAA
1 AAAA-CATTTTTGAAA-ACATATAATATATAGTTTT-T
*
1140437 AAAACATTTTTAAAAACATATAATATA-A--TTTT
1 AAAACATTTTTGAAAACATATAATATATAGTTTTT
* * * *
1140469 AAAACGTTTTTGAAAGC-TATAACATATAG-TTTG
1 AAAACATTTTTGAAAACATATAATATATAGTTTTT
** * *
1140502 AAAACATTTTT-AAATTATATAATATATGGTTTTG
1 AAAACATTTTTGAAAACATATAATATATAGTTTTT
* * * * *
1140536 AAAATATCTTTGAAATATATATTATATAAAG-TTTT
1 AAAACATTTTTGAAA-ACATATAATATATAGTTTTT
1140571 AAAACATTTTT
1 AAAACATTTTT
1140582 TCTTTATATA
Statistics
Matches: 240, Mismatches: 37, Indels: 35
0.77 0.12 0.11
Matches are distributed among these distances:
31 8 0.03
32 18 0.08
33 26 0.11
34 13 0.05
35 29 0.12
36 52 0.22
37 38 0.16
38 51 0.21
39 5 0.02
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (35 bp):
AAAACATTTTTGAAAACATATAATATATAGTTTTT
Found at i:1140597 original size:102 final size:102
Alignment explanation
Indices: 1140298--1140600 Score: 240
Period size: 102 Copynumber: 2.9 Consensus size: 102
1140288 AAAAAATACC
** * * *
1140298 TTTGAAAACTATATAATATATAGTTTT-TAAAACGTTTTTAGAAAACATATATAATATATAGATT
1 TTTGAAATTTATATAATATATAGTTTTAAAAAAC-ATTTT-GAAAA-ACATAT-A-ATATA-ATT
*
1140362 TTAAAACCA-TTTTGAAAACTTATATAAT-ATATAGTTTTAAAATCAT
60 TTAAAA-CATTTTTG--AA-TTATAT-ATCATATAGTTTGAAAATCAT
*
1140408 TTTGAAATTTATATAATATATAGTTTTAAAAAACATTTTTAAAAACATATAATATAATTTTAAAA
1 TTTGAAATTTATATAATATATAGTTTTAAAAAACATTTTGAAAAACATATAATATAATTTTAAAA
* *** *
1140473 CGTTTTTGAAAGCTATAACATATAGTTTGAAAA-CAT
66 CATTTTTGAATTATATATCATATAGTTTGAAAATCAT
* * * * * * *
1140509 TTTTAAA-TTATATAATATATGGTTTT-GAAAATATCTTTGAAATATATATTATATAAAGTTTTA
1 TTTGAAATTTATATAATATATAGTTTTAAAAAACAT-TTTGAAAAACATATAATAT-AA-TTTTA
***
1140572 AAACATTTTTTCTTTATATATCATATAGT
63 AAACATTTTTGAATTATATATCATATAGT
1140601 ATTTTATTCT
Statistics
Matches: 159, Mismatches: 28, Indels: 20
0.77 0.14 0.10
Matches are distributed among these distances:
99 6 0.04
100 33 0.21
101 12 0.08
102 42 0.26
103 2 0.01
104 1 0.01
105 14 0.09
106 5 0.03
107 1 0.01
108 5 0.03
109 4 0.03
110 29 0.18
111 5 0.03
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (102 bp):
TTTGAAATTTATATAATATATAGTTTTAAAAAACATTTTGAAAAACATATAATATAATTTTAAAA
CATTTTTGAATTATATATCATATAGTTTGAAAATCAT
Found at i:1145672 original size:95 final size:94
Alignment explanation
Indices: 1145500--1145695 Score: 261
Period size: 95 Copynumber: 2.1 Consensus size: 94
1145490 TATAATATTA
*
1145500 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCTCCGGCTTTATGAA
1 TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCTCCAGCTTTATGAA
* * *
1145565 TAATATTTAGCTAGCCTGATAAAGGTAAT
66 TAAGATTCAGCTAACCTGATAAAGGTAAT
* *
1145594 TATACTATGCAATAAAGTTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACGC-CTCAGCTTTAT
1 TATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGTTAAACGCTC-CAGCTTTAT
* * **
1145657 GGATAAGATTCAGCTAACTTGATAAAGGTGTT
63 GAATAAGATTCAGCTAACCTGATAAAGGTAAT
1145689 TATATAT
1 TATATAT
1145696 TAAGTTGTCC
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
94 9 0.10
95 80 0.90
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCTCCAGCTTTATGAA
TAAGATTCAGCTAACCTGATAAAGGTAAT
Found at i:1147201 original size:165 final size:165
Alignment explanation
Indices: 1146873--1147791 Score: 921
Period size: 165 Copynumber: 5.6 Consensus size: 165
1146863 TAAAGAAACT
* * * * *
1146873 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * * * * * * * *
1146934 CTCAGCTCCTAGGGCACATTATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAA
66 CTCAGCTCC-AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-AAA
* * * ** *
1146999 GACCTTTGAGTTCGACTATGCTCAGC-TCCAAGGCATATC
126 GACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCATATC
* *
1147038 ATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCTACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
1147103 TTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
* * * * *
1147168 TCGGGTTTGATTACATTCAGCTTCGAGGGCATATA
131 TCGAGTTCGATTACACTCAGCTTCGAAGGCATATC
* * * * * *
1147203 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TAACCAAGAGACCTTCGAGTTCGACTTC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAA-AGACCTTCGAGTTCGACTAC
* ** *
1147267 GCTCAGCTTCAAGGCACATCATTTGCAATATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * *
1147332 TTCGAGTTCGACTACGCTCAGCTTC-AAGGCATATC
130 CTCGAGTTCGATTACACTCAGCTTCGAAGGCATATC
* *
1147367 ATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAAG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
1147432 CTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAATGGCTATCTGCCAAAGACCC
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
* * *
1147497 TCGAATTCGATTACACTCAGCTTCGAGGGCACATC
131 TCGAGTTCGATTACACTCAGCTTCGAAGGCATATC
* * * * * * * * * *
1147532 ATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTCAGCAAAAGACATTCGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* ** * * * *
1147597 CTCAGCTCCAAGGCATATCATTTGCAGTTTAACTTACGAT-G-GAGGGGTTATCTGCCAACCAAA
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG-TCGAGAAGGGCTATCTG----CCAAA
* * * *
1147660 GACCTTTGAGTTCGATTACACTCAGC-TCAAAGGCACATC
126 GACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCATATC
* * * ** * *
1147699 ATTTGCAGCATAACTTAAGTTGAGAAGGGCTATCTG----CCAAATACCCCCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
1147760 CTCAGCTCCGAGGGCACATCATTTACAGCATA
66 CTCAGCTCC-AAGGCACATCATTTGCAGCATA
1147792 ACTCAAGGCT
Statistics
Matches: 623, Mismatches: 117, Indels: 29
0.81 0.15 0.04
Matches are distributed among these distances:
163 26 0.04
164 191 0.31
165 272 0.44
166 1 0.00
167 40 0.06
168 64 0.10
169 29 0.05
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.26
Consensus pattern (165 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
TCGAGTTCGATTACACTCAGCTTCGAAGGCATATC
Found at i:1147311 original size:249 final size:244
Alignment explanation
Indices: 1146873--1147783 Score: 900
Period size: 249 Copynumber: 3.7 Consensus size: 244
1146863 TAAAGAAACT
1146873 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* * *
1146938 GCTCCTAGGGCACATTATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACC
66 GCTTCTAGGGCACATAATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-ACC-AAAGACC
* * * * *
1147003 TTTGAGTTCGACTAT-GCTCAGCTCCAAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGG
129 TTCGAGTTCGACT-TCGCTCAGCTTCAAGGCACATCATTTGCA-AATAACTTAAGTCGAGAAGGG
*
1147067 TTATCTGCCAACCAAAGACCTTCGAGTTCTACTACGTTCAGCTCCAAGGCATATC
192 TTATCTG-C-ACCAAAGACCTTCGAGTTCTACTACGCTCAGCTCCAAGGCATATC
* * *
1147122 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGGGTTTGATTACATTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* *
1147187 GCTTCGAGGGCATATAATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAGAGACC
66 GCTTCTAGGGCACATAATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-ACCAA-AGACC
*
1147252 TTCGAGTTCGACTTCGCTCAGCTTCAAGGCACATCATTTGCAATATAGCTTAAGTCGAGAAGGGT
129 TTCGAGTTCGACTTCGCTCAGCTTCAAGGCACATCATTTGCAA-ATAACTTAAGTCGAGAAGGGT
* *
1147317 TATCTG--CCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCATATC
193 TATCTGCACCAAAGACCTTCGAGTTCTACTACGCTCAGCTCCAAGGCATATC
* * * * *
1147367 ATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA-A
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACA
* * * * * * * * *
1147431 GCTCAGC-TCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAATGGCTATCTG--CCAAAG
62 -CTCAGCTTCTAGGGCACATAATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTACCAAAG
* * * * * * * *
1147493 ACCCTCGAATTCGA-TTACACTCAGCTTCGAGGGCACATCATTTACAGAATAACTCAAGGCTAGA
126 ACCTTCGAGTTCGACTT-CGCTCAGCTTC-AAGGCACATCATTTGCA-AATAACTTAAGTCGAGA
* *
1147557 AGGGTTATCTGTCAGCAAAAGACATTCGAGTT-TGACTACGCTCAGCTCCAAGGCATATC
188 AGGGTTATCTG-CA-CCAAAGACCTTCGAGTTCT-ACTACGCTCAGCTCCAAGGCATATC
** * * * * * *
1147616 ATTTGCAGTTTAACTTACGAT-G-GAGGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGATTAC
1 ATTTGCAGCATAGCTTAAG-TCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTAC
* * * * * * *
1147679 ACTCAGC-TCAAAGGCACATCATTTGCAGCATAACTTAA-GTTGAGAAGGGCTATCTG--CCAAA
61 ACTCAGCTTCTAGGGCACATAATTTACAGCATAACTCAAGGCT-AGAAGGGTTATCTGTACCAAA
* ** * * *
1147740 TACCCCCGAGTTCGA-TTACACTCAGCTCCGAGGGCACATCATTT
125 GACCTTCGAGTTCGACTT-CGCTCAGCTTC-AAGGCACATCATTT
1147784 ACAGCATAAC
Statistics
Matches: 576, Mismatches: 67, Indels: 39
0.84 0.10 0.06
Matches are distributed among these distances:
243 2 0.00
244 24 0.04
245 116 0.20
246 1 0.00
248 172 0.30
249 260 0.45
250 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.26
Consensus pattern (244 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
GCTTCTAGGGCACATAATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTACCAAAGACCTT
CGAGTTCGACTTCGCTCAGCTTCAAGGCACATCATTTGCAAATAACTTAAGTCGAGAAGGGTTAT
CTGCACCAAAGACCTTCGAGTTCTACTACGCTCAGCTCCAAGGCATATC
Found at i:1147601 original size:329 final size:330
Alignment explanation
Indices: 1146919--1147738 Score: 1128
Period size: 329 Copynumber: 2.5 Consensus size: 330
1146909 CCAAAGACCC
* * * * * * * *
1146919 TCGAGTTCGATTACACTCAGCTCCTAGGGCACATTATTTACAACATAACTCAAGGCT-AGAAGGG
1 TCGAGTTCGACTACGCTCAGCTCC-AAGGCACATCATTTGCAATATAACTTAA-GATGAGAAGGG
* *
1146983 TTATCTGTCACCAAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGTAGCA
64 TTATCTG--ACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGCATATCATTTGTAGCA
* * *
1147048 TAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCTACTACGTTCAGCTCCA
126 TAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAAGCTCAGCTCCA
* ** *
1147113 AGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGGGTTTGA
191 AGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAATTCGA
* * *
1147178 TTACATTCAGCTTCGAGGGCATATAATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAAC
256 TTACACTCAGCTTCGAGGGCACATAATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTAAC
* *
1147243 CAAGAGACCT
321 CAAAAGACAT
* * *
1147253 TCGAGTTCGACTTCGCTCAGCTTCAAGGCACATCATTTGCAATATAGCTTAAG-TCGAGAAGGGT
1 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATAACTTAAGAT-GAGAAGGGT
*
1147317 TATCTG-CCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCATATCATTTGTAGCATAAC
65 TATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGCATATCATTTGTAGCATAAC
*
1147381 TTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAAGCTCAGCTCTAAGGC
130 TTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAAGCTCAGCTCCAAGGC
*
1147446 ACATCATTTGCAGCATAGCTTAAGTCGAGAATGGCTATCTGCCAAAGACCCTCGAATTCGATTAC
195 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAATTCGATTAC
* * *
1147511 ACTCAGCTTCGAGGGCACATCATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTCAGCAAA
260 ACTCAGCTTCGAGGGCACATAATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAA
1147576 AGACAT
325 AGACAT
* * * * * *
1147582 TCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTTTAACTTACGATG-GAGGGGTT
1 TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATAACTTAAGATGAGAAGGGTT
* * * *
1147646 ATCTGCCAACCAAAGACCTTTGAGTTCGATTACACTCAGC-TCAAAGGCACATCATTTGCAGCAT
66 ATCTG---ACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTC-AAGGCATATCATTTGTAGCAT
* *
1147710 AACTTAAGTTGAGAAGGGCTATCTGCCAA
127 AACTTAAGTCGAGAAGGGTTATCTGCCAA
1147739 ATACCCCCGA
Statistics
Matches: 432, Mismatches: 46, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
328 12 0.03
329 283 0.66
330 3 0.01
331 3 0.01
332 75 0.17
333 36 0.08
334 20 0.05
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (330 bp):
TCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAATATAACTTAAGATGAGAAGGGTT
ATCTGACCAAAGACCTTTGAGTTCGACTACGCTCAGCTTCAAGGCATATCATTTGTAGCATAACT
TAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAAGCTCAGCTCCAAGGCA
CATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAATTCGATTACA
CTCAGCTTCGAGGGCACATAATTTACAGAATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAA
GACAT
Found at i:1147920 original size:37 final size:37
Alignment explanation
Indices: 1147837--1147924 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 37
1147827 CTTTGAGATT
* * *
1147837 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAAGTTTGCCTCTCTTAAGACA
1147873 GTTTCCCTTGAAACAAAAGTTTGCCTC-CTCTAAGACA
1 GTTTCCCTTGAAACAAAAGTTTGCCTCTCT-TAAGACA
*
1147910 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
1147925 CAAAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 16 0.35
37 30 0.65
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (37 bp):
GTTTCCCTTGAAACAAAAGTTTGCCTCTCTTAAGACA
Found at i:1147972 original size:34 final size:34
Alignment explanation
Indices: 1147910--1148033 Score: 167
Period size: 34 Copynumber: 3.6 Consensus size: 34
1147900 CTCTAAGACA
1147910 GTTTCTCTTGAAACACAAAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACAC---AAAAAAACCTTTGAAAAT
* *
1147947 GTTTCTATTGAAACACAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
* *
1147981 GTTTATCTTGAAACAAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
* *
1148015 GTTTCTCTTCAAACCCAAA
1 GTTTCTCTTGAAACACAAA
1148034 GACCTTTGAG
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
34 62 0.81
37 15 0.19
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAACCTTTGAAAAT
Found at i:1148766 original size:41 final size:42
Alignment explanation
Indices: 1148715--1148823 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 42
1148705 GCAAAATGGT
1148715 TTTTGAAAAATACGTATATAATATAT-GATTTAAAAAAAAATA-
1 TTTTG-AAAATACGTATATAATATATAG-TTTAAAAAAAAATAC
**
1148757 TTTTGAAAAT--GTATATAATATATAGTTTTTAAAAAAATAC
1 TTTTGAAAATACGTATATAATATATAGTTTAAAAAAAAATAC
*
1148797 CTTTG-AAA-AC-TATATAATATATAGTTT
1 TTTTGAAAATACGTATATAATATATAGTTT
1148824 TTAAAACGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
39 45 0.75
40 5 0.08
41 5 0.08
42 5 0.08
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (42 bp):
TTTTGAAAATACGTATATAATATATAGTTTAAAAAAAAATAC
Found at i:1148842 original size:37 final size:35
Alignment explanation
Indices: 1148757--1149083 Score: 285
Period size: 38 Copynumber: 9.1 Consensus size: 35
1148747 AAAAAAAATA
* *
1148757 TTTTGAAAATGTATATAATATATAGTTTTTAAAAAAAT
1 TTTTGAAAA-CTATATAATATATAG-TTTT-AAAACAT
* *
1148795 ACCTTTGAAAACTATATAATATATAGTTTTTAAAACGT
1 --TTTTGAAAACTATATAATATATAG-TTTTAAAACAT
*
1148833 TTTTAGAAAACATATATAATATGTAGATTTTAAAACCA-
1 TTTT-GAAAAC-TATATAATATATAG-TTTTAAAA-CAT
*
1148871 TTTTGAAAACTTATATAATATACAGTTTTAAAATCA-
1 TTTTGAAAAC-TATATAATATATAGTTTTAAAA-CAT
**
1148907 TTTTGAAATTTATATAATATATAGTTTTAAAAAAACAT
1 TTTTGAAAACTATATAATATATAGTTTT---AAAACAT
*
1148945 TTTTGAAAAC-ATATAATATA-A-TTTTAAAACGT
1 TTTTGAAAACTATATAATATATAGTTTTAAAACAT
* *
1148977 TTTTGAAAAC--TATAACATATAGTTTGAAAACAT
1 TTTTGAAAACTATATAATATATAGTTTTAAAACAT
* * *
1149010 TTTT-AAAATTATATAATATATGGTTTTGAAAATAT
1 TTTTGAAAACTATATAATATATAGTTTT-AAAACAT
* * *
1149045 CTTTGAAATA-TATATTATATAAAGTTTTAAAACAT
1 TTTTGAAA-ACTATATAATATATAGTTTTAAAACAT
1149080 TTTT
1 TTTT
1149084 TTTCTTTATA
Statistics
Matches: 241, Mismatches: 32, Indels: 33
0.79 0.10 0.11
Matches are distributed among these distances:
31 8 0.03
32 21 0.09
33 13 0.05
34 13 0.05
35 39 0.16
36 40 0.17
37 37 0.15
38 42 0.17
39 20 0.08
40 8 0.03
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.43
Consensus pattern (35 bp):
TTTTGAAAACTATATAATATATAGTTTTAAAACAT
Found at i:1148927 original size:35 final size:34
Alignment explanation
Indices: 1148751--1149082 Score: 230
Period size: 36 Copynumber: 9.3 Consensus size: 34
1148741 GATTTAAAAA
* *
1148751 AAAATATTTTGAAAATGTATATAATATATAGTTTTT
1 AAAACATTTTG-AAATATATATAATATATAG-TTTT
*
1148787 AAAAAAATACCTTTGAAA-ACTATATAATATATAGTTTTT
1 -AAAACAT---TTTGAAATA-TATATAATATATAG-TTTT
* * *
1148826 AAAACGTTTTTAGAAAACATATATAATATGTAGATTTT
1 AAAAC-ATTTT-G-AAATATATATAATATATAG-TTTT
*
1148864 AAAACCATTTTGAAA-ACTTATATAATATACAGTTTT
1 AAAA-CATTTTGAAATA--TATATAATATATAGTTTT
*
1148900 AAAATCATTTTGAAATTTATATAATATATAGTTTT
1 AAAA-CATTTTGAAATATATATAATATATAGTTTT
*
1148935 AAAAAAACATTTTTGAAA-ACATATAATATA-A-TTTT
1 ---AAAACA-TTTTGAAATATATATAATATATAGTTTT
* * * *
1148970 AAAACGTTTTTGAAA-A-CTATAACATATAGTTTG
1 AAAAC-ATTTTGAAATATATATAATATATAGTTTT
* *
1149003 AAAACATTTTTAAA-ATTATATAATATATGGTTTT
1 AAAACATTTTGAAATA-TATATAATATATAGTTTT
* * *
1149037 GAAAATATCTTTGAAATATATATTATATAAAGTTTT
1 -AAAACAT-TTTGAAATATATATAATATATAGTTTT
1149073 AAAACATTTT
1 AAAACATTTT
1149083 TTTTCTTTAT
Statistics
Matches: 241, Mismatches: 30, Indels: 51
0.75 0.09 0.16
Matches are distributed among these distances:
31 8 0.03
32 23 0.10
33 8 0.03
34 16 0.07
35 34 0.14
36 46 0.19
37 33 0.14
38 44 0.18
39 25 0.10
40 4 0.02
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (34 bp):
AAAACATTTTGAAATATATATAATATATAGTTTT
Found at i:1149057 original size:34 final size:33
Alignment explanation
Indices: 1148768--1149083 Score: 219
Period size: 35 Copynumber: 8.9 Consensus size: 33
1148758 TTTGAAAATG
* *
1148768 TATATAATATATAGTTTTTAAAAAAATACCTTTGAAAA
1 TATATAATATATAG-TTTT-AAAACAT--TTTTG-AAA
*
1148806 CTATATAATATATAGTTTTTAAAACGTTTTTAGAAAACA
1 -TATATAATATATAG-TTTTAAAACATTTTT-G--AA-A
*
1148845 TATATAATATGTAGATTTTAAAACCA-TTTTGAAAA
1 TATATAATATATAG-TTTTAAAA-CATTTTTG-AAA
*
1148880 CTTATATAATATACAGTTTTAAAATCA-TTTTGAAA
1 --TATATAATATATAGTTTTAAAA-CATTTTTGAAA
1148915 TTTATATAATATATAGTTTTAAAAAAACATTTTTGAAAA
1 --TATATAATATATAGTTTT---AAAACATTTTTG-AAA
* *
1148954 CATATAATATA-A-TTTTAAAACGTTTTTGAAA
1 TATATAATATATAGTTTTAAAACATTTTTGAAA
* * *
1148985 -ACTATAACATATAGTTTGAAAACATTTTTAAAA
1 TA-TATAATATATAGTTTTAAAACATTTTTGAAA
* * *
1149018 TTATATAATATATGGTTTTGAAAATATCTTTGAAA
1 -TATATAATATATAGTTTT-AAAACATTTTTGAAA
*
1149053 TATATATTATATAAAGTTTTAAAACATTTTT
1 TATATA--ATATATAGTTTTAAAACATTTTT
1149084 TTTCTTTATA
Statistics
Matches: 231, Mismatches: 27, Indels: 42
0.77 0.09 0.14
Matches are distributed among these distances:
30 1 0.00
31 11 0.05
32 12 0.05
33 16 0.07
34 19 0.08
35 48 0.21
36 32 0.14
37 26 0.11
38 42 0.18
39 24 0.10
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (33 bp):
TATATAATATATAGTTTTAAAACATTTTTGAAA
Found at i:1149126 original size:19 final size:18
Alignment explanation
Indices: 1149104--1149146 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1149094 TATCATATAG
*
1149104 TATTTTATTCTTTTTTATT
1 TATTTTATT-TTTATTATT
*
1149123 TATTATTGTTTTTATTATT
1 TATT-TTATTTTTATTATT
1149142 TATTT
1 TATTT
1149147 AATCGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 16 0.76
20 4 0.19
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
TATTTTATTTTTATTATT
Found at i:1159862 original size:26 final size:25
Alignment explanation
Indices: 1159827--1159887 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
1159817 CTTTTTTTAA
*
1159827 ATATTATATTTTATTATTA-CATATT
1 ATATTATATTTAATTATTATC-TATT
*
1159852 ATATATATATTTAATTTTTATCTATT
1 ATAT-TATATTTAATTATTATCTATT
1159878 -TATTATATTT
1 ATATTATATTT
1159888 CTCTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 7 0.22
25 7 0.22
26 17 0.53
27 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (25 bp):
ATATTATATTTAATTATTATCTATT
Found at i:1171544 original size:105 final size:105
Alignment explanation
Indices: 1171362--1172012 Score: 1040
Period size: 105 Copynumber: 6.2 Consensus size: 105
1171352 TTTTACCCAT
1171362 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1171427 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
*
1171467 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1171532 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
1171572 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1171637 AAGGGACCGCTGGTTGTCAACAAACGTTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
1171677 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1171742 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* *
1171782 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
1171847 AAGGGACCGCTGGTTGTCACCAAACATTTCTCCAACTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* * * * * * * *
1171887 AGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAGCACAAGCTCGACTTC-CCAGC
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA-C
* * * *
1171951 TAAGGGA-CGAC-CGTCTGTCAGCAAACAATTTCTC-AATTCCAT
65 GAAGGGACCG-CTGGT-TGTCAACAAAC-ATTTCTCAAATT-CAG
*
1171993 AGCCAATTCCAACTTCACAA
1 AGCCAATTTCAACTTCACAA
1172013 ACAGATCAAT
Statistics
Matches: 515, Mismatches: 26, Indels: 9
0.94 0.05 0.02
Matches are distributed among these distances:
104 6 0.01
105 482 0.94
106 27 0.05
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
Done.