Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 132 of 185
Found at i:41003307 original size:16 final size:16
Alignment explanation
Indices: 41003286--41003325 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
41003276 CCTAAGAAAA
41003286 AAATTGGGCT-GGATTT
1 AAATTGGGCTAGG-TTT
41003302 AAATTGGGCTAGGTTT
1 AAATTGGGCTAGGTTT
41003318 AAATTGGG
1 AAATTGGG
41003326 AGGGAGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.35
Consensus pattern (16 bp):
AAATTGGGCTAGGTTT
Found at i:41004247 original size:16 final size:16
Alignment explanation
Indices: 41004223--41004253 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41004213 CTTTATATAT
*
41004223 TAAATTATTATATTAA
1 TAAAATATTATATTAA
41004239 TAAAATATTATATTA
1 TAAAATATTATATTA
41004254 TGTTAATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTATATTAA
Found at i:41008244 original size:26 final size:27
Alignment explanation
Indices: 41008189--41008248 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
41008179 TATTTTCTTG
*
41008189 AAATTTTACCAAATGGAAAAATCATCA
1 AAATTTTACCAAAGGGAAAAATCATCA
* * *
41008216 AAATTTTACC-AAGGGTAAAATCGTTA
1 AAATTTTACCAAAGGGAAAAATCATCA
41008242 AAATTTT
1 AAATTTT
41008249 GATGGGGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.32
Consensus pattern (27 bp):
AAATTTTACCAAAGGGAAAAATCATCA
Found at i:41013353 original size:3 final size:3
Alignment explanation
Indices: 41013341--41013370 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
41013331 AACTCATTTA
41013341 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
41013371 AAAACTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:41017895 original size:3 final size:3
Alignment explanation
Indices: 41017887--41017933 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
41017877 TAGTCACCTT
*
41017887 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41017934 TTGGCATTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41019875 original size:2 final size:2
Alignment explanation
Indices: 41019868--41019892 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41019858 TACTTGTGGT
41019868 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
41019893 GAGTAAAAAC
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:41027547 original size:2 final size:2
Alignment explanation
Indices: 41027540--41027621 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
41027530 ATTTCATTGG
41027540 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41027582 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41027622 TTATTATTCA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:41039968 original size:23 final size:23
Alignment explanation
Indices: 41039942--41040021 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 23
41039932 GCAGGCTACT
41039942 ACATGTATCGGATAGTGATGGTC
1 ACATGTATCGGATAGTGATGGTC
* * *
41039965 ACATGTGTAGTACTATGTGCA-GGCTAC
1 ACATGTATCGGA-TA-GTG-ATGG-T-C
41039992 TACATGTATCGGATAGTGATGGTC
1 -ACATGTATCGGATAGTGATGGTC
41040016 ACATGT
1 ACATGT
41040022 GTAGTACTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
23 15 0.34
24 3 0.07
25 7 0.16
26 7 0.16
27 3 0.07
28 9 0.20
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (23 bp):
ACATGTATCGGATAGTGATGGTC
Found at i:41039977 original size:101 final size:102
Alignment explanation
Indices: 41039854--41040044 Score: 287
Period size: 101 Copynumber: 1.9 Consensus size: 102
41039844 TGAAAGTGAA
* * ***
41039854 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTTGTA
1 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCAGATAGTGAT-GGTCACA
41039917 TGTGTAGTACTATGTGCAGGCTACTACATGTATCGGAT
65 TGTGTAGTACTATGTGCAGGCTACTACATGTATCGGAT
* *
41039955 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTATCGGATAGTGATGGTCACAT
1 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCAGATAGTGATGGTCACAT
*
41040020 GTGTAGTACTATGTGTAGGCTACTA
66 GTGTAGTACTATGTGCAGGCTACTA
41040045 TGTGAACCAG
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 46 0.57
102 30 0.38
103 4 0.05
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (102 bp):
AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTACCAGATAGTGATGGTCACAT
GTGTAGTACTATGTGCAGGCTACTACATGTATCGGAT
Found at i:41039992 original size:51 final size:51
Alignment explanation
Indices: 41039854--41040044 Score: 287
Period size: 51 Copynumber: 3.8 Consensus size: 51
41039844 TGAAAGTGAA
* * * *
41039854 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-
1 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTATCGGAT
***
41039904 A-TGATAGGTTGTATGTGTAGTACTATGTGCAGGCTACTACATGTATCGGAT
1 AGTGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTATCGGAT
41039955 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTATCGGAT
1 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTATCGGAT
*
41040006 AGTGATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
41040045 TGTGAACCAG
Statistics
Matches: 127, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
49 4 0.03
50 38 0.30
51 81 0.64
52 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (51 bp):
AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACATGTATCGGAT
Found at i:41040123 original size:46 final size:44
Alignment explanation
Indices: 41040055--41040142 Score: 115
Period size: 46 Copynumber: 2.0 Consensus size: 44
41040045 TGTGAACCAG
*
41040055 TATCATTAATTATAAAGTGGTTGCTATGTGCTG-ATCTCACCGGA
1 TATCATTAATTACAAAGTGGTTGCTATGTGCTGAATC-CACCGGA
* *
41040099 TATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCCACCG
1 TATCATTAATTACAAA--GTGGTTGCTATGTGCTGAATCCACCG
41040143 TGTATCTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 14 0.37
46 21 0.55
47 3 0.08
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (44 bp):
TATCATTAATTACAAAGTGGTTGCTATGTGCTGAATCCACCGGA
Found at i:41045434 original size:17 final size:16
Alignment explanation
Indices: 41045412--41045443 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41045402 AATTTTTAGG
41045412 ATGTAATTATTATTTTT
1 ATGTAATTATT-TTTTT
41045429 ATGTAATTATTTTTT
1 ATGTAATTATTTTTT
41045444 AATTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
ATGTAATTATTTTTTT
Found at i:41045715 original size:14 final size:14
Alignment explanation
Indices: 41045698--41045731 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41045688 ATATTTTAAA
41045698 ATTTATATATGTAT
1 ATTTATATATGTAT
* *
41045712 ATTTATATATTTTT
1 ATTTATATATGTAT
41045726 ATTTAT
1 ATTTAT
41045732 TTTTATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
ATTTATATATGTAT
Found at i:41045880 original size:14 final size:15
Alignment explanation
Indices: 41045863--41045895 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41045853 GTTTATTGAC
*
41045863 TTATGTTTT-TTCAT
1 TTATATTTTGTTCAT
41045877 TTATATTTTGTTCAT
1 TTATATTTTGTTCAT
41045892 TTAT
1 TTAT
41045896 TTGATATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (15 bp):
TTATATTTTGTTCAT
Found at i:41053531 original size:20 final size:17
Alignment explanation
Indices: 41053491--41053523 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41053481 AGACCAAATA
*
41053491 CAAATAATAAATAAAAC
1 CAAAAAATAAATAAAAC
41053508 CAAAAAATAAATAAAA
1 CAAAAAATAAATAAAA
41053524 AGTCCAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAAAAATAAATAAAAC
Found at i:41054829 original size:18 final size:19
Alignment explanation
Indices: 41054806--41054846 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
41054796 TTAAAATACA
41054806 TTTATTTTA-TTATATCGT
1 TTTATTTTATTTATATCGT
*
41054824 TTTA-TTTATTTATATCTT
1 TTTATTTTATTTATATCGT
41054842 TTTAT
1 TTTAT
41054847 ATATTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTATTTTATTTATATCGT
Found at i:41054851 original size:18 final size:18
Alignment explanation
Indices: 41054815--41054852 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
41054805 ATTTATTTTA
*
41054815 TTATATCGTTTTATTTAT
1 TTATATCGTTTTATATAT
*
41054833 TTATATCTTTTTATATAT
1 TTATATCGTTTTATATAT
41054851 TT
1 TT
41054853 TCAAACTCTA
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:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TTATATCGTTTTATATAT
Found at i:41054885 original size:3 final size:3
Alignment explanation
Indices: 41054864--41054914 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
41054854 CAAACTCTAG
** *
41054864 ATT ATTT ATT ATT CA-T ATT ATT ATT ATT ATT ATT ACC ATT ATC ATT
1 ATT A-TT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41054910 ATT AT
1 ATT AT
41054915 CTTTTTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 1 0.03
3 34 0.87
4 4 0.10
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:41060721 original size:24 final size:20
Alignment explanation
Indices: 41060692--41060756 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 20
41060682 AGATTACAAA
41060692 ATCATATCTTCCAAGATTGCATAT
1 ATCATATCTT--AAGATTGC--AT
41060716 ATCATATC-TAAGATTGCAT
1 ATCATATCTTAAGATTGCAT
*
41060735 ATCATATC-TAAGATTTCAT
1 ATCATATCTTAAGATTGCAT
41060754 ATC
1 ATC
41060757 CTTGAAGATT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 23 0.57
21 8 0.20
23 1 0.03
24 8 0.20
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (20 bp):
ATCATATCTTAAGATTGCAT
Found at i:41060730 original size:21 final size:20
Alignment explanation
Indices: 41060678--41060749 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 20
41060668 AAATTAAATC
* *
41060678 TCTAAGATTACAAAATCATA
1 TCTAAGATTGCAATATCATA
41060698 TCTTCCAAGATTGCATATATCATA
1 TC-T--AAGATTGCA-ATATCATA
41060722 TCTAAGATTGC-ATATCATA
1 TCTAAGATTGCAATATCATA
41060741 TCTAAGATT
1 TCTAAGATT
41060750 TCATATCCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
19 17 0.37
20 2 0.04
21 9 0.20
23 9 0.20
24 9 0.20
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:41060736 original size:19 final size:19
Alignment explanation
Indices: 41060704--41060756 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
41060694 CATATCTTCC
41060704 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCATATCT
41060725 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCT
*
41060744 AAGATTTCATATC
1 AAGATTGCATATC
41060757 CTTGAAGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 23 0.74
21 8 0.26
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (19 bp):
AAGATTGCATATCATATCT
Found at i:41061179 original size:44 final size:43
Alignment explanation
Indices: 41061125--41061269 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 43
41061115 TGCTGCAACT
*
41061125 CAGGGAGGCAAGACTGGTGTCTTCGATCTGCTTCGCTATCGGTG
1 CAGGAAGGCAAGACTGGTGTCTTCGATCTGCTTCGCT-TCGGTG
* * ** * * ****
41061169 CAGGAAGGCAAGATCTGCTAT-TTTTATCCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGA-CTGGTGTCTTCGAT-CTGCTTCGCTTCGGTG
* *
41061213 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGACTGGTGTCTTCGATCTGCTTCGCT-TCGGTG
*
41061257 CAGGAAGACAAGA
1 CAGGAAGGCAAGA
41061270 TCTACTATTT
Statistics
Matches: 71, Mismatches: 26, Indels: 8
0.68 0.25 0.08
Matches are distributed among these distances:
43 14 0.20
44 43 0.61
45 14 0.20
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.25
Consensus pattern (43 bp):
CAGGAAGGCAAGACTGGTGTCTTCGATCTGCTTCGCTTCGGTG
Found at i:41061269 original size:88 final size:88
Alignment explanation
Indices: 41061116--41062150 Score: 1180
Period size: 88 Copynumber: 11.8 Consensus size: 88
41061106 AACTTGATCT
* * * * * * *
41061116 GCTGCAACTCAGGGAGGCAAGACTGGTGTCTTCGATCTGCTTCGCTATCGGTGCAGGAAGGCAAG
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
*
41061181 ATCTGCTATTTTTATCCTGCTCC
66 ATCTGCTATTTTTAACCTGCTCC
* * * * *
41061204 GCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGACAAG
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
*
41061269 ATCTACTATTTTTAACCTGCTCC
66 ATCTGCTATTTTTAACCTGCTCC
* * *
41061292 GCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCACTACAGGAAGGCAAG
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
41061357 ATCTGCTATTTTTAACCTGCTCC
66 ATCTGCTATTTTTAACCTGCTCC
*
41061380 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCAATCTGCTTCACTGTCAGTACAGGAAGGCAAG
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
*
41061445 ATCTGCTATCTTTAACCTGCTCC
66 ATCTGCTATTTTTAACCTGCTCC
* * * * * * *
41061468 GTTGCCACCAAGGGAGGCAACGCTAGTGTCTTCAATCTGCTTCACTGTTA-TACAGGAGGGCAAG
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
*
41061532 ATCTGCTATCTTTAACCTGCTCC
66 ATCTGCTATTTTTAACCTGCTCC
* * * ** * * *
41061555 ACTACCACTGAGGGAGGCAAGGCTGGTGTCTTCAATCTGCTTCACTGTCAGTACAGAAAGGCAAG
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
* *
41061620 ATCTGCTATCTTTAACCTGCTTC
66 ATCTGCTATTTTTAACCTGCTCC
* * ** * * *
41061643 GCTGCCACCGAAAGAGGCAAGGCTAGT-TCTTCAATCTGTTTCACTGTCAGTACAGGAAGGCAAT
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
*
41061707 ATCTGCTATCTTTAACCTGCTCC
66 ATCTGCTATTTTTAACCTGCTCC
* * * * * * * * **
41061730 GCTGCCACCGAGGGAGGCAAGGCTAGTGTCTTCGATCTACTCCACTACTC-CT-TAGGGAGATAA
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACT-GTCAGTACAGGAAGGCAA
* * * *
41061793 GATCTGCAATTTTCAACATGCTCT
65 GATCTGCTATTTTTAACCTGCTCC
* * * * * * * * *
41061817 GCTGTAACCTAAGGAGGCAAGGCTGGAGTCTTTGATCTGCTTCATTGCCGGTACAGGAAGGCAAG
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
* *
41061882 ATCTGCTATTTTTAACCTACTCT
66 ATCTGCTATTTTTAACCTGCTCC
* * * * *
41061905 GCTGCAACCTAGGGAGTCTAGGCTAGTGTCTTCGATCTGCTTC-GTAGTTAGTACAGGAAGGCAA
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACT-GTCAGTACAGGAAGGCAA
* *
41061969 GATATGCTATTTTCAACCTGCTCC
65 GATCTGCTATTTTTAACCTGCTCC
* * * ** * * * *
41061993 GCTGTAACCCAGTGAGGCAAGGTTAGTGTCTTCGATCTGCTTTGCTATCGGTGCAGGAAGACAAG
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
*
41062058 ATCTGCTATTTTTAATCTGCTCC
66 ATCTGCTATTTTTAACCTGCTCC
* * * * * *
41062081 GCTACAACCCAGGGAGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAG
1 GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
41062146 ATCTG
66 ATCTG
41062151 TTATCTTCAC
Statistics
Matches: 820, Mismatches: 120, Indels: 14
0.86 0.13 0.01
Matches are distributed among these distances:
86 1 0.00
87 222 0.27
88 594 0.72
89 3 0.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (88 bp):
GCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAG
ATCTGCTATTTTTAACCTGCTCC
Found at i:41061398 original size:44 final size:44
Alignment explanation
Indices: 41061169--41061750 Score: 209
Period size: 44 Copynumber: 13.3 Consensus size: 44
41061159 GCTATCGGTG
* *
41061169 CAGGAAGGCAAGATCTGCTATTTTTATCCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACC
* * * * ** * * ****
41061213 CAGGGAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTG-CAACC
* * *
41061257 CAGGAAGACAAGATCTACTATTTTTAACCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACC
* * * * ** * * *
41061301 CAGGGAGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTC-ACTA
1 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTG-CAAC-C
*
41061345 CAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACC
1 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACC
* * * * * * * ***
41061389 CAGGGAGGCAAG-GCTAG-TGTCTTCAATCTGCTTCACTGTCAGTA
1 CAGGAAGGCAAGATCT-GCTATCTTTAACCTGCTCCGCTG-CAACC
* *
41061433 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGTTGCCACC
1 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACC
* * * * * * * ** **
41061477 AAGGGAGGCAACG--CTAG-TGTCTTCAATCTGCTTCACTGTTATA
1 CAGGAAGGCAA-GATCT-GCTATCTTTAACCTGCTCCGCTGCAACC
* * * * *
41061520 CAGGAGGGCAAGATCTGCTATCTTTAACCTGCTCCACTACCACT
1 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACC
* * * * * * * * * ***
41061564 GAGGGAGGCAAG-GCTGGTGTCTTCAATCTGCTTCACTGTCAGTA
1 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTG-CAACC
* * *
41061608 CAGAAAGGCAAGATCTGCTATCTTTAACCTGCTTCGCTGCCACC
1 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACC
* * * * * * * * ***
41061652 GA-AAGAGGCAAG-GCTAG-T-TCTTCAATCTGTTTCACTGTCAGTA
1 CAGGA-AGGCAAGATCT-GCTATCTTTAACCTGCTCCGCTG-CAACC
* *
41061695 CAGGAAGGCAATATCTGCTATCTTTAACCTGCTCCGCTGCCACC
1 CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACC
* *
41061739 GAGGGAGGCAAG
1 CAGGAAGGCAAG
41061751 GCTAGTGTCT
Statistics
Matches: 363, Mismatches: 151, Indels: 48
0.65 0.27 0.09
Matches are distributed among these distances:
42 16 0.04
43 113 0.31
44 145 0.40
45 89 0.25
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACC
Found at i:41062145 original size:44 final size:43
Alignment explanation
Indices: 41062007--41062145 Score: 107
Period size: 44 Copynumber: 3.2 Consensus size: 43
41061997 TAACCCAGTG
* *
41062007 AGGCAAGGTTAGTGTCTTCGATCTGCTTTGCTATCGGTGCAGGA
1 AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCT-TCGGTGCAGGA
* * * * * ** * * **** *
41062051 AGACAAGATCTGCTATTTTTAATCTGCTCCGCTACAACCCAGGG
1 AGGCAAGGT-TGGTGTCTTCGATCTGCTTCGCTTCGGTGCAGGA
41062095 AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCT-TCGGTGCAGGA
41062139 AGGCAAG
1 AGGCAAG
41062146 ATCTGTTATC
Statistics
Matches: 63, Mismatches: 30, Indels: 4
0.65 0.31 0.04
Matches are distributed among these distances:
43 17 0.27
44 31 0.49
45 15 0.24
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (43 bp):
AGGCAAGGTTGGTGTCTTCGATCTGCTTCGCTTCGGTGCAGGA
Found at i:41071282 original size:4 final size:4
Alignment explanation
Indices: 41071275--41071300 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41071265 TTTATTTGTG
41071275 ATCT ATCT ATCT ATCT ATCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT AT
41071301 ATATATATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:41075162 original size:22 final size:24
Alignment explanation
Indices: 41075131--41075180 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
41075121 TTTTGTGTTG
*
41075131 TTATTATTGT-TTTATC-TTATAT
1 TTATTATTGTGTTCATCATTATAT
* *
41075153 TTATTTTTGTGTTCATCATTATTT
1 TTATTATTGTGTTCATCATTATAT
41075177 TTAT
1 TTAT
41075181 GAAATGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 9 0.39
23 5 0.22
24 9 0.39
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.68
Consensus pattern (24 bp):
TTATTATTGTGTTCATCATTATAT
Found at i:41075920 original size:110 final size:110
Alignment explanation
Indices: 41075660--41076062 Score: 645
Period size: 110 Copynumber: 3.7 Consensus size: 110
41075650 ATATTTGGCA
41075660 TTTGGAAATAT-GAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATA
1 TTTGGAAAT-TCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATA
*
41075724 GCTAAATATCCTTTTTTAAAAATTTCAAAATAAGGCAATGTTTTGCG
65 GCTAAATATCC-TTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCG
41075771 TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
1 TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
41075836 CTAAATATCCTTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCG
66 CTAAATATCCTTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCG
* *
41075881 TTTGGGAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
1 TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
** *
41075946 CTAAATATCC-TTCCAAAAATTTCAAAATAAGGTAATGTTTTGCG
66 CTAAATATCCTTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCG
* * * * *
41075990 TTTAGAAATTTGAG-GAACGTGCCCTAATGTGCTGGGTTTCGA--TTTCTCGTTGAACCAAATTG
1 TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
*
41076052 CCAAATATCCT
66 CTAAATATCCT
41076063 CTTGAATTTT
Statistics
Matches: 276, Mismatches: 14, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
106 27 0.10
108 26 0.09
109 42 0.15
110 108 0.39
111 73 0.26
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (110 bp):
TTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAACCAAATAG
CTAAATATCCTTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCG
Found at i:41081012 original size:24 final size:24
Alignment explanation
Indices: 41080977--41081023 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
41080967 AATGTTTCAA
*
41080977 AAAAAC-ATAAAAATAAAAGAAAAC
1 AAAAACAAAAAAAATAAAA-AAAAC
41081001 AAAAACAAAAAAAATAAAAAAAA
1 AAAAACAAAAAAAATAAAAAAAA
41081024 TAGAAGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.85, C:0.06, G:0.02, T:0.06
Consensus pattern (24 bp):
AAAAACAAAAAAAATAAAAAAAAC
Found at i:41081234 original size:44 final size:43
Alignment explanation
Indices: 41081140--41081262 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
41081130 AAAAAGGGCG
* * * *
41081140 GCTCAAATTTTGGAACAAATTGGGGCACGA-AGTGATCAGAGC
1 GCTCAAATTTTGGATCAAATTGGGGCATGATGGTGATCAGAAC
41081182 GACTCAAATTTTGGATCAAATTGGGGCATGATGGTGATCAGAAC
1 G-CTCAAATTTTGGATCAAATTGGGGCATGATGGTGATCAGAAC
* * *
41081226 AGCTCAAATTTT-GATCAGATCGGGGCAT-ATGATGATC
1 -GCTCAAATTTTGGATCAAATTGGGGCATGATGGTGATC
41081263 TTGCCATACC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
42 9 0.13
43 41 0.58
44 20 0.28
45 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (43 bp):
GCTCAAATTTTGGATCAAATTGGGGCATGATGGTGATCAGAAC
Found at i:41082511 original size:50 final size:50
Alignment explanation
Indices: 41082437--41082818 Score: 243
Period size: 50 Copynumber: 7.6 Consensus size: 50
41082427 GCAGCGGAAC
* * ** * *
41082437 AGATTGAAGTCACAACAGCAAATCTTGCTTCCCCGATATTGCAATTCAAA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCCGACATTGCAATTCAAA
* * ***** *
41082487 AGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGA-TGCAGCGGGAC
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCCGAC-ATTGCAATTCAAA
* * * * * * *
41082537 AGATTGAAGCTACGACGGTGAATCTCACTTCCCGGACATCGTAATTTAAA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCCGACATTGCAATTCAAA
* * * ** **** *
41082587 ATATTGAAGCCACAACAGTGAATCTTACTTCCCAGGTGA-TGCAGCGGAAC
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCC-CGACATTGCAATTCAAA
* * * * *
41082637 AGATTGAAGCTACGATGGCGAATCTCACTTCCCCGACATTGCAATTCAAA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCCGACATTGCAATTCAAA
* * *
41082687 AGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGA-TGC-A-GCAGAA
1 AGATTGAAGCCACAACGGTGAATCTTACTTCCCCGAC-ATTGCAATTCA-AA
* ** ** * *
41082736 CAGATTGAAGCTATGACGACGAATCTCACTTCCCCGACATTGCAATTTAAA
1 -AGATTGAAGCCACAACGGTGAATCTTACTTCCCCGACATTGCAATTCAAA
***
41082787 AGATTGAAGCCACAACAACGAATCTTACTTCC
1 AGATTGAAGCCACAACGGTGAATCTTACTTCC
41082819 TCGGCGAACA
Statistics
Matches: 243, Mismatches: 79, Indels: 20
0.71 0.23 0.06
Matches are distributed among these distances:
48 2 0.01
49 7 0.03
50 225 0.93
51 8 0.03
52 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGTGAATCTTACTTCCCCGACATTGCAATTCAAA
Found at i:41082561 original size:100 final size:100
Alignment explanation
Indices: 41082375--41082818 Score: 611
Period size: 100 Copynumber: 4.4 Consensus size: 100
41082365 AAACCATAGT
* * * * * *
41082375 TTGCAATTTAAAATATTGAAGCCACAACGGCGATTCTTATTTCCTAGGCAATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * * ** *
41082440 TTGAAG-TCACAACAGCAAATCTTGCTTCCCCGATA
66 TTGAAGCT-ACGACGGCGAATCTCACTTCCCCGACA
* *
41082475 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGGACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* *
41082540 TTGAAGCTACGACGGTGAATCTCACTTCCCGGACA
66 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
* * * * *
41082575 TCGTAATTTAAAATATTGAAGCCACAACAGTGAATCTTACTTCCCAGGTGATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
*
41082640 TTGAAGCTACGATGGCGAATCTCACTTCCCCGACA
66 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
* *
41082675 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCAGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* *
41082740 TTGAAGCTATGACGACGAATCTCACTTCCCCGACA
66 TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
***
41082775 TTGCAATTTAAAAGATTGAAGCCACAACAACGAATCTTACTTCC
1 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCC
41082819 TCGGCGAACA
Statistics
Matches: 303, Mismatches: 40, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
100 302 1.00
101 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
TTGAAGCTACGACGGCGAATCTCACTTCCCCGACA
Found at i:41085772 original size:111 final size:110
Alignment explanation
Indices: 41085577--41085986 Score: 659
Period size: 110 Copynumber: 3.8 Consensus size: 110
41085567 AGAGGGAATA
*
41085577 TTTTGCATTTGGAAATAT-GAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAA
1 TTTTGCGTTTGGAAAT-TCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAA
41085641 CCAAATAGCTAAATATCCTTTTTAAAAAATTTCAAAATAAGGCAATG
65 CCAAATAGCTAAATATCC-TTTTAAAAAATTTCAAAATAAGGCAATG
* *
41085688 TTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTTCAATTTTTCTCGTTCAAC
1 TTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAAC
*
41085753 CAAATAGCTAAATACCCTTTTAAAAAATTTCAAAATAAGGCAATG
66 CAAATAGCTAAATATCCTTTTAAAAAATTTCAAAATAAGGCAATG
*
41085798 TTTTGCGTTTGGGAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAAC
1 TTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAAC
**
41085863 CAAATAGCTAAATATCC-TTCCAAAAATTTCAAAATAAGGCAATG
66 CAAATAGCTAAATATCCTTTTAAAAAATTTCAAAATAAGGCAATG
* * *
41085907 CTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAATGTGCTGGGTTTCGA--TTTCTCGTTGAAC
1 TTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAAC
* *
41085969 CAAATTGCCAAATATCCT
66 CAAATAGCTAAATATCCT
41085987 CTTGAATTTT
Statistics
Matches: 281, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
106 27 0.10
108 27 0.10
109 44 0.16
110 107 0.38
111 76 0.27
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (110 bp):
TTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCAAC
CAAATAGCTAAATATCCTTTTAAAAAATTTCAAAATAAGGCAATG
Found at i:41090819 original size:29 final size:29
Alignment explanation
Indices: 41090785--41090856 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
41090775 ACCAAAATTT
*
41090785 TATTTTAAAAATA-AAAAAAATTTAAAAAG
1 TATTTTAAAAATACAAAAAAA-TAAAAAAG
* **
41090814 TATTTTAAAAACACTTTAAAAATAAAAAAG
1 TATTTTAAAAATAC-AAAAAAATAAAAAAG
41090844 TATTTTAAAAATA
1 TATTTTAAAAATA
41090857 TTTTAAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 12 0.33
30 19 0.53
31 5 0.14
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (29 bp):
TATTTTAAAAATACAAAAAAATAAAAAAG
Found at i:41090853 original size:11 final size:11
Alignment explanation
Indices: 41090805--41090906 Score: 67
Period size: 11 Copynumber: 9.6 Consensus size: 11
41090795 ATAAAAAAAA
41090805 TTTAAAAAGTAT
1 TTTAAAAA-TAT
* *
41090817 TTTAAAAACAC
1 TTTAAAAATAT
41090828 TTTAAAAATA-
1 TTTAAAAATAT
41090838 ---AAAAAGTAT
1 TTTAAAAA-TAT
41090847 TTTAAAAATAT
1 TTTAAAAATAT
41090858 TTT--AAA-A-
1 TTTAAAAATAT
*
41090865 TTTAAAAATAAA
1 TTTAAAAAT-AT
**
41090877 AATAAAAAGTAT
1 TTTAAAAA-TAT
41090889 TTTAAAAATAT
1 TTTAAAAATAT
41090900 TTTAAAA
1 TTTAAAA
41090907 TTAAAAAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 23
0.70 0.08 0.23
Matches are distributed among these distances:
7 8 0.11
8 3 0.04
9 6 0.08
11 27 0.38
12 26 0.37
13 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (11 bp):
TTTAAAAATAT
Found at i:41090869 original size:37 final size:37
Alignment explanation
Indices: 41090788--41090958 Score: 193
Period size: 42 Copynumber: 4.4 Consensus size: 37
41090778 AAAATTTTAT
*
41090788 TTTAAAAATAAAAAA--AATTTAAAAAGTATTTTAAAAACA
1 TTTAAAAATAAAAAAGTATTTTAAAAA-TATTTT--AAA-A
41090827 CTTTAAAAATAAAAAAGTATTTTAAAAATATTTTAAAA
1 -TTTAAAAATAAAAAAGTATTTTAAAAATATTTTAAAA
41090865 TTTAAAAATAAAAATAAAAAGTATTTTAAAAATATTTTAAAA
1 TTTAAAAAT----A-AAAAAGTATTTTAAAAATATTTTAAAA
* *
41090907 TTAAAAAATAAAAAAGTATTTTTAAAATATTTTAAAA
1 TTTAAAAATAAAAAAGTATTTTAAAAATATTTTAAAA
*
41090944 TTAAAAAAATAAAAA
1 TT-TAAAAATAAAAA
41090959 TATTTTTTAT
Statistics
Matches: 120, Mismatches: 3, Indels: 18
0.85 0.02 0.13
Matches are distributed among these distances:
37 37 0.31
38 14 0.12
39 3 0.03
40 15 0.12
41 7 0.06
42 44 0.37
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (37 bp):
TTTAAAAATAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:41090872 original size:30 final size:30
Alignment explanation
Indices: 41090801--41090872 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
41090791 AAAAATAAAA
41090801 AAAATTTAAAAAGTATTTTAAAAACACTTT
1 AAAATTTAAAAAGTATTTTAAAAACACTTT
* * * *
41090831 AAAAATAAAAAAGTATTTTAAAAATATTTT
1 AAAATTTAAAAAGTATTTTAAAAACACTTT
41090861 AAAATTTAAAAA
1 AAAATTTAAAAA
41090873 TAAAAATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTTAAAAAGTATTTTAAAAACACTTT
Found at i:41090950 original size:36 final size:36
Alignment explanation
Indices: 41090865--41090965 Score: 143
Period size: 37 Copynumber: 2.8 Consensus size: 36
41090855 TATTTTAAAA
* *
41090865 TTTAAAAATAAAAAT-AAAAAGTATTTTAAAAATAT
1 TTTAAAATTAAAAATAAAAAAGTATTTTTAAAATAT
41090900 TTTAAAATTAAAAAATAAAAAAGTATTTTTAAAATAT
1 TTTAAAATT-AAAAATAAAAAAGTATTTTTAAAATAT
*
41090937 TTTAAAATTAAAAA-AATAAAAATATTTTT
1 TTTAAAATTAAAAATAA-AAAAGTATTTTT
41090966 TATATTCGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
35 10 0.17
36 22 0.37
37 28 0.47
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (36 bp):
TTTAAAATTAAAAATAAAAAAGTATTTTTAAAATAT
Found at i:41097199 original size:56 final size:57
Alignment explanation
Indices: 41097081--41097211 Score: 165
Period size: 56 Copynumber: 2.3 Consensus size: 57
41097071 TAATTCATAT
* * * * * *
41097081 AATAATTATATTAAGGATGTTATTAAATTATATATTATTTTATTAAATTGTATTTAAT
1 AATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAAATATATTTAAC
* *
41097139 AATAATTATGTTAAAATATGATTAAATTATTTATTA-TTTATTAAAATATATTTAAC
1 AATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAAATATATTTAAC
*
41097195 AATAATTTTATTAAAAT
1 AATAATTATATTAAAAT
41097212 TTAATAACAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
56 32 0.51
57 18 0.29
58 13 0.21
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.50
Consensus pattern (57 bp):
AATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAAATATATTTAAC
Found at i:41097219 original size:25 final size:26
Alignment explanation
Indices: 41097175--41097224 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
41097165 TTATTTATTA
*
41097175 TTTATTAAAATATATTTAACAATAAT
1 TTTATTAAAATATATATAACAATAAT
*
41097201 TTTATTAAAATTTA-ATAACAATAA
1 TTTATTAAAATATATATAACAATAA
41097225 CAATAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
TTTATTAAAATATATATAACAATAAT
Found at i:41097405 original size:16 final size:16
Alignment explanation
Indices: 41097384--41097435 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
41097374 GAAATTACTG
41097384 ATTACAGCTCTATTTC
1 ATTACAGCTCTATTTC
*
41097400 ATTACAACTCTA-TTC
1 ATTACAGCTCTATTTC
*
41097415 AATTACAGCTCTATTCC
1 -ATTACAGCTCTATTTC
41097432 ATTA
1 ATTA
41097436 GATTGAACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 3 0.10
16 26 0.84
17 2 0.06
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTTC
Found at i:41102599 original size:228 final size:228
Alignment explanation
Indices: 41102202--41103322 Score: 1724
Period size: 228 Copynumber: 4.9 Consensus size: 228
41102192 CTCTCCAAAG
* * * *
41102202 ATGCAGATCTTCGTCAAAACCCTT-ACCGGCAAGACCATCACCCTCGAGGTTGAGAGTTCTGACA
1 ATGCAGATCTTCGTCAAAA-CCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACA
* *
41102266 CCATCGACAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
65 CCATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTT
41102331 ATCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
130 ATCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
*
41102396 TACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
195 CACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
41102430 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
41102495 CATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTTA
66 CATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTTA
*
41102560 TCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCT
131 TCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
41102625 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
196 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
41102658 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
41102723 CATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTTA
66 CATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTTA
41102788 TCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
131 TCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
* *
41102853 ACCCTCCACCTTGTCTTACGTCTTCGTGGGGGT
196 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
* *
41102886 ATGCAGATCTTCGTCAAAACTTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
* *
41102951 CATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 CATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTTA
* * * * * *
41103016 TCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCCTGGCCGATTATAATATCCAGAAGGAATCC
131 TCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
* * *
41103081 ACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGA
196 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
* * * * * * * *
41103114 ATGCAGATCTTCGTGAAAACCTTGACCGGCAAGACCATCACCTTGGAGGTGGAGAGTTCGGACAC
1 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
* * * * * * * * * *
41103179 CATCGACAATGTAAAGGCGAAGATTCAGGACAAGGAAGGGATCCCGCCAGACCAACAACGT-TTG
66 CATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTT-
* * * * * * ** * * *
41103243 ATCTTTGCAGGGAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATC
130 ATCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
* *
41103308 GACCCTTCACCTTGT
195 CACCCTCCACCTTGT
41103323 TTTGAGGCTT
Statistics
Matches: 833, Mismatches: 58, Indels: 4
0.93 0.06 0.00
Matches are distributed among these distances:
227 5 0.01
228 828 0.99
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.20
Consensus pattern (228 bp):
ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
CATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTTA
TCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCC
ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
Found at i:41103417 original size:228 final size:227
Alignment explanation
Indices: 41102202--41103565 Score: 1379
Period size: 228 Copynumber: 6.0 Consensus size: 227
41102192 CTCTCCAAAG
* * * * *
41102202 ATGCAGATCTTCGTCAAAACCCTT-ACCGGCAAGACCATCACCCTCGAGGTTGAGAGTTCTGACA
1 ATGCAGATCTTCGTCAAAA-CATTGACCGGCAAGACCATCACCTTGGAGGTGGAGAGTTCGGACA
* * *
41102266 CCATCGACAATGTGAAGTCTAAA-ATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCT
65 CCATCGACAATGTAAAGGC-AAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCT
* * * * *
41102330 CATCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAAT
129 CATCTTCGCCGGCAAACAGCTCGAGGATGGCAGGACCTTGGCCGATTATAACATCCAGAAGGAAT
* ** *
41102395 CTACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
194 CCACCCTCCACCTTGT-CTTAGTCTTCGTGGGGGA
* * * * * * * *
41102430 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTCAAAACATTGACCGGCAAGACCATCACCTTGGAGGTGGAGAGTTCGGACAC
* * * * *
41102495 CATCGATAATGTGAAGTCTAAA-ATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTT
66 CATCGACAATGTAAAGGC-AAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC
* * * * *
41102559 ATCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
130 ATCTTCGCCGGCAAACAGCTCGAGGATGGCAGGACCTTGGCCGATTATAACATCCAGAAGGAATC
* ** *
41102624 TACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGT
195 CACCCTCCACCTTGT-CTTAGTCTTCGTGGGGGA
* * * * * * * *
41102658 ATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACAC
1 ATGCAGATCTTCGTCAAAACATTGACCGGCAAGACCATCACCTTGGAGGTGGAGAGTTCGGACAC
* * * * *
41102723 CATCGATAATGTGAAGTCTAAA-ATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTT
66 CATCGACAATGTAAAGGC-AAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC
* * * * *
41102787 ATCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
130 ATCTTCGCCGGCAAACAGCTCGAGGATGGCAGGACCTTGGCCGATTATAACATCCAGAAGGAATC
*
41102852 CACCCTCCACCTTGTCTTACGTCTTCGTGGGGGT
195 CACCCTCCACCTTGTCTTA-GTCTTCGTGGGGGA
* * * * * * * *
41102886 ATGCAGATCTTCGTCAAAACTTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACAC
1 ATGCAGATCTTCGTCAAAACATTGACCGGCAAGACCATCACCTTGGAGGTGGAGAGTTCGGACAC
* * *
41102951 CATCGATAATGTAAAGTCTAAA-ATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
66 CATCGACAATGTAAAGGC-AAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTC
* * * * *
41103015 ATCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCCTGGCCGATTATAATATCCAGAAGGAATC
130 ATCTTCGCCGGCAAACAGCTCGAGGATGGCAGGACCTTGGCCGATTATAACATCCAGAAGGAATC
* ** *
41103080 CACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGA
195 CACCCTCCACCTTGT-CTTAGTCTTCGTGGGGGA
* *
41103114 ATGCAGATCTTCGTGAAAACCTTGACCGGCAAGACCATCACCTTGGAGGTGGAGAGTTCGGACAC
1 ATGCAGATCTTCGTCAAAACATTGACCGGCAAGACCATCACCTTGGAGGTGGAGAGTTCGGACAC
* * * * * * *
41103179 CATCGACAATGTAAAGGCGAAGATTCAGGACAAGGAAGGGATCCCGCCAGACCAACAACGTTTGA
66 CATCGACAATGTAAAGGCAAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* * * * * * * *
41103244 TCTTTGCAGGGAAGCAGCTTGAGGATGGGAGGACCTTGGCTGATTATAACATCCAGAAGGAATCG
131 TCTTCGCCGGCAAACAGCTCGAGGATGGCAGGACCTTGGCCGATTATAACATCCAGAAGGAATCC
* * * * *
41103309 ACCCTTCACCTTGTTTTGAGGCTTCGTGGAGGC
196 ACCCTCCACCTTGTCTT-AGTCTTCGTGGGGGA
* * * * * * * * * *
41103342 ATGCAGATTTTCGTTAAGACATTGACTGGGAAAACAATCACATTGGAGGTGGAAAGTTCGGATAC
1 ATGCAGATCTTCGTCAAAACATTGACCGGCAAGACCATCACCTTGGAGGTGGAGAGTTCGGACAC
* * * * * * * * *
41103407 AATTGACAATGTGAAGGCAAAGATTCAGGACAAGGAAGGTATCCCCCCAGATCAGCAAAGGCTCA
66 CATCGACAATGTAAAGGCAAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
* * * ** * * * * * * * *
41103472 TCTTTGCTGGCAAGCAATTGGAGGATGGGAGGACTTTAGCTGATTATAACATTCAGAAAGAGTCC
131 TCTTCGCCGGCAAACAGCTCGAGGATGGCAGGACCTTGGCCGATTATAACATCCAGAAGGAATCC
* * *
41103537 ACCCTTCACCTTGTTCTTCGTCTCCGTGG
196 ACCCTCCACCTTG-TCTTAGTCTTCGTGG
41103566 TGGGCAGTGA
Statistics
Matches: 1027, Mismatches: 103, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
227 9 0.01
228 1013 0.99
229 5 0.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (227 bp):
ATGCAGATCTTCGTCAAAACATTGACCGGCAAGACCATCACCTTGGAGGTGGAGAGTTCGGACAC
CATCGACAATGTAAAGGCAAAGATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAACGTCTCA
TCTTCGCCGGCAAACAGCTCGAGGATGGCAGGACCTTGGCCGATTATAACATCCAGAAGGAATCC
ACCCTCCACCTTGTCTTAGTCTTCGTGGGGGA
Found at i:41103540 original size:684 final size:684
Alignment explanation
Indices: 41102202--41103565 Score: 1728
Period size: 684 Copynumber: 2.0 Consensus size: 684
41102192 CTCTCCAAAG
* * *
41102202 ATGCAGATCTTCGTCAAAACCCTTACCGGCAAGACCATCACCCTCGAGGTTGAGAGTTCTGACAC
1 ATGCAGATCTTCGTCAAAACCCTTACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACAC
*
41102267 CATCGACAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
66 CATCGACAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
* * *
41102332 TCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATCT
131 TCTTCGCCGGAAAACAGCTCGAAGACGGCCGTACCCTGGCCGATTACAACATCCAGAAGGAATCC
* * *
41102397 ACCCTCCACCTTGTCCTCCGTCTTCGTGGGGGTATGCAGATCTTCGTCAAAACCTTAACCGGCAA
196 ACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGAATGCAGATCTTCGTCAAAACCTTAACCGGCAA
* * * *
41102462 GACCATCACCCTCGAAGTCGAGAGCTCCGACACCATCGATAATGTGAAGTCTAAAATTCAAGACA
261 GACCATCACCCTCGAAGTCGAGAGCTCCGACACCATCGACAATGTAAAGGCGAAAATTCAAGACA
* * * * *
41102527 AGGAAGGCATCCCACCAGACCAGCAGCGTCTTATCTTCGCCGGAAAACAGCTCGAGGACGGCCGT
326 AGGAAGGCATCCCACCAGACCAACAACGTCTTATCTTCGCAGGAAAACAGCTCGAGGACGGCAGG
* * * *
41102592 ACCTTGGCCGATTACAACATCCAGAAGGAATCTACCCTCCACCTTGTCCTCCGTCTTCGTGGGGG
391 ACCTTGGCCGATTACAACATCCAGAAGGAATCGACCCTCCACCTTGTCCTCAGGCTTCGTGGAGG
* * * * * *
41102657 TATGCAGATCTTCGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCCGACA
456 CATGCAGATCTTCGTCAAAACATTAACCGGCAAAACAATCACACTCGAAGTCGAAAGCTCCGACA
* * * ** * *
41102722 CCATCGATAATGTGAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTT
521 CAATCGACAATGTGAAGGCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAAAGGCTC
* * * * *
41102787 ATCTTCGCCGGAAAACAGCTCGAGGACGGCCGTACCTTGGCCGATTACAACATCCAGAAGGAATC
586 ATCTTCGCCGGAAAACAACTCGAGGACGGCAGGACCTTAGCCGATTACAACATCCAGAAAGAATC
*
41102852 CACCCTCCACCTTG-TCTTACGTCTTCGTGGGGGT
651 CACCCTCCACCTTGTTCTT-CGTCTCCGTGGGGGT
*
41102886 ATGCAGATCTTCGTCAAAA-CTTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACA
1 ATGCAGATCTTCGTCAAAACCCTT-ACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACA
*
41102950 CCATCGATAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
65 CCATCGACAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTC
* * * *
41103015 ATCTTCGCCGGCAAACAGCTCGAAGATGGCCGTACCCTGGCCGATTATAATATCCAGAAGGAATC
130 ATCTTCGCCGGAAAACAGCTCGAAGACGGCCGTACCCTGGCCGATTACAACATCCAGAAGGAATC
* *
41103080 CACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGAATGCAGATCTTCGTGAAAACCTTGACCGGCA
195 CACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGAATGCAGATCTTCGTCAAAACCTTAACCGGCA
* * * * * * * *
41103145 AGACCATCACCTTGGAGGTGGAGAGTTCGGACACCATCGACAATGTAAAGGCGAAGATTCAGGAC
260 AGACCATCACCCTCGAAGTCGAGAGCTCCGACACCATCGACAATGTAAAGGCGAAAATTCAAGAC
* * * * * * * *
41103210 AAGGAAGGGATCCCGCCAGACCAACAACGT-TTGATCTTTGCAGGGAAGCAGCTTGAGGATGGGA
325 AAGGAAGGCATCCCACCAGACCAACAACGTCTT-ATCTTCGCAGGAAAACAGCTCGAGGACGGCA
* * * ** *
41103274 GGACCTTGGCTGATTATAACATCCAGAAGGAATCGACCCTTCACCTTGTTTTGAGGCTTCGTGGA
389 GGACCTTGGCCGATTACAACATCCAGAAGGAATCGACCCTCCACCTTGTCCTCAGGCTTCGTGGA
* * * * * * * * * * * *
41103339 GGCATGCAGATTTTCGTTAAGACATTGACTGGGAAAACAATCACATTGGAGGTGGAAAGTTCGGA
454 GGCATGCAGATCTTCGTCAAAACATTAACCGGCAAAACAATCACACTCGAAGTCGAAAGCTCCGA
* * * * * *
41103404 TACAATTGACAATGTGAAGGC-AAAGATTCAGGACAAGGAAGGTATCCCCCCAGATCAGCAAAGG
519 CACAATCGACAATGTGAAGGCTAAA-ATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAAAGG
* * * * * * * * * * * *
41103468 CTCATCTTTGCTGGCAAGCAATTGGAGGATGGGAGGACTTTAGCTGATTATAACATTCAGAAAGA
583 CTCATCTTCGCCGGAAAACAACTCGAGGACGGCAGGACCTTAGCCGATTACAACATCCAGAAAGA
* *
41103533 GTCCACCCTTCACCTTGTTCTTCGTCTCCGTGG
648 ATCCACCCTCCACCTTGTTCTTCGTCTCCGTGG
41103566 TGGGCAGTGA
Statistics
Matches: 572, Mismatches: 104, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
683 8 0.01
684 560 0.98
685 4 0.01
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (684 bp):
ATGCAGATCTTCGTCAAAACCCTTACCGGCAAGACCATCACCCTCGAAGTCGAGAGCTCTGACAC
CATCGACAATGTAAAGTCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAGCGTCTCA
TCTTCGCCGGAAAACAGCTCGAAGACGGCCGTACCCTGGCCGATTACAACATCCAGAAGGAATCC
ACCCTCCACCTCGTCCTCCGTCTTCGCGGGGGAATGCAGATCTTCGTCAAAACCTTAACCGGCAA
GACCATCACCCTCGAAGTCGAGAGCTCCGACACCATCGACAATGTAAAGGCGAAAATTCAAGACA
AGGAAGGCATCCCACCAGACCAACAACGTCTTATCTTCGCAGGAAAACAGCTCGAGGACGGCAGG
ACCTTGGCCGATTACAACATCCAGAAGGAATCGACCCTCCACCTTGTCCTCAGGCTTCGTGGAGG
CATGCAGATCTTCGTCAAAACATTAACCGGCAAAACAATCACACTCGAAGTCGAAAGCTCCGACA
CAATCGACAATGTGAAGGCTAAAATTCAAGACAAGGAAGGCATCCCACCAGACCAGCAAAGGCTC
ATCTTCGCCGGAAAACAACTCGAGGACGGCAGGACCTTAGCCGATTACAACATCCAGAAAGAATC
CACCCTCCACCTTGTTCTTCGTCTCCGTGGGGGT
Found at i:41105844 original size:3 final size:3
Alignment explanation
Indices: 41105836--41105862 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
41105826 TGGTAAACAG
41105836 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
41105863 AAGAATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:41118169 original size:29 final size:29
Alignment explanation
Indices: 41118122--41118183 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
41118112 TGTAATGTTG
* *
41118122 TACATGAACTTTGATTTTG-TTCAATTTT
1 TACATGAAATTTGAATTTGATTCAATTTT
*
41118150 ATACATGAAATTTTAATTTGATTCAATTTT
1 -TACATGAAATTTGAATTTGATTCAATTTT
41118180 TACA
1 TACA
41118184 AACAACTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (29 bp):
TACATGAAATTTGAATTTGATTCAATTTT
Found at i:41119416 original size:20 final size:20
Alignment explanation
Indices: 41119391--41119435 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
41119381 AAAATAACGT
41119391 ATATGTATATAAATGTAT-AG
1 ATATGTATATAAAT-TATAAG
41119411 ATATGTATATAAATTATAAG
1 ATATGTATATAAATTATAAG
41119431 ATATG
1 ATATG
41119436 AAAAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (20 bp):
ATATGTATATAAATTATAAG
Found at i:41119547 original size:3 final size:3
Alignment explanation
Indices: 41119539--41119591 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
41119529 CAAAAGTGTA
* * * * *
41119539 AAT AAT AAT AAG CAT AAT AAT AGT AAT AAC AAT AAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
41119587 GAT AA
1 AAT AA
41119592 CATTATTGAA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:41122374 original size:16 final size:16
Alignment explanation
Indices: 41122350--41122403 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
41122340 TTTGGTTCGC
* *
41122350 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
41122366 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
41122382 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
41122398 TGTAAT
1 TGTAAT
41122404 AGCAAATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:41122448 original size:45 final size:44
Alignment explanation
Indices: 41122382--41122476 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
41122372 GGAATAGAGG
*
41122382 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
41122427 TGTAATGGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
41122471 TGTAAT
1 TGTAAT
41122477 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:41122657 original size:18 final size:17
Alignment explanation
Indices: 41122636--41122670 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41122626 TTATTATTAA
*
41122636 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41122654 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41122671 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41123317 original size:6 final size:6
Alignment explanation
Indices: 41123306--41123341 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
41123296 ATTTTCAGGA
41123306 CTGCAT CTGCAT CTGCAT CTGCAT CTGCAT CTGCAT
1 CTGCAT CTGCAT CTGCAT CTGCAT CTGCAT CTGCAT
41123342 TAATTTAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (6 bp):
CTGCAT
Found at i:41128871 original size:17 final size:18
Alignment explanation
Indices: 41128845--41128887 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
41128835 ATTTGATTAG
41128845 TTTT-AATTTCAA-TACT
1 TTTTAAATTTCAACTACT
41128861 TTTTAAATTTCAAGCTACT
1 TTTTAAATTTCAA-CTACT
*
41128880 TGTTAAAT
1 TTTTAAAT
41128888 CTAGTAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 8 0.35
19 11 0.48
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.51
Consensus pattern (18 bp):
TTTTAAATTTCAACTACT
Found at i:41130299 original size:14 final size:14
Alignment explanation
Indices: 41130280--41130316 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
41130270 GGCCCACTTG
41130280 TATTAATTTTTTTA
1 TATTAATTTTTTTA
*
41130294 TATTAA-CTTTTTA
1 TATTAATTTTTTTA
41130307 TA-TAATTTTT
1 TATTAATTTTT
41130317 AAAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 3 0.15
13 11 0.55
14 6 0.30
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTAATTTTTTTA
Found at i:41131757 original size:43 final size:43
Alignment explanation
Indices: 41131702--41131850 Score: 264
Period size: 43 Copynumber: 3.5 Consensus size: 43
41131692 TTTTTATAAT
*
41131702 AAACGCCGCTATAGACCATGGTCTTTATCGGCGCTTACCAAAC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCAAAC
41131745 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCTAAA-
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACC-AAAC
*
41131788 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAAC
1 AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCAAAC
41131831 AAACGCCGCTATAGACCATG
1 AAACGCCGCTATAGACCATG
41131851 CTTACCCAAC
Statistics
Matches: 102, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
42 2 0.02
43 97 0.95
44 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCAAAC
Found at i:41131808 original size:86 final size:87
Alignment explanation
Indices: 41131680--41131850 Score: 283
Period size: 86 Copynumber: 2.0 Consensus size: 87
41131670 GCGTCGGTAA
** *
41131680 CTTTAGCGGCGCTTTTTATAATAAACGCCGCTATAGACCATGGTCTTTATCGGCGCTTACCAAAC
1 CTTTAGCGGCGCTTCCTATAATAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCAAAC
41131745 AAACGCCGCTATAGACCATGGT
66 AAACGCCGCTATAGACCATGGT
*
41131767 CTTTAGCGGCGCTTACCTA-AA-AAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAA
1 CTTTAGCGGCGCTT-CCTATAATAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCAAA
41131830 CAAACGCCGCTATAGACCATG
65 CAAACGCCGCTATAGACCATG
41131851 CTTACCCAAC
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
86 61 0.77
87 16 0.20
88 2 0.03
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (87 bp):
CTTTAGCGGCGCTTCCTATAATAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCAAAC
AAACGCCGCTATAGACCATGGT
Found at i:41131856 original size:30 final size:30
Alignment explanation
Indices: 41131820--41131880 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
41131810 CTTTAGCGGC
41131820 GCTTACCCAACAAACGCCGCTATAGACCAT
1 GCTTACCCAACAAACGCCGCTATAGACCAT
41131850 GCTTACCCAACAAACGCCGCTATAGACCAT
1 GCTTACCCAACAAACGCCGCTATAGACCAT
41131880 G
1 G
41131881 GTCTTTAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.36, G:0.15, T:0.16
Consensus pattern (30 bp):
GCTTACCCAACAAACGCCGCTATAGACCAT
Found at i:41131896 original size:73 final size:73
Alignment explanation
Indices: 41131777--41131912 Score: 236
Period size: 73 Copynumber: 1.9 Consensus size: 73
41131767 CTTTAGCGGC
*
41131777 GCTTACCTAAAAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACAAACGCCGCTA
1 GCTTACCCAAAAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACAAACGCCGCTA
41131842 TAGACCAT
66 TAGACCAT
* * *
41131850 GCTTACCCAACAAACGCCGCTATAGACCATGGTCTTTAGTGGCGCTTACCCAATAAACGCCGC
1 GCTTACCCAAAAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACAAACGCCGC
41131913 GAAAGCCAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 59 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (73 bp):
GCTTACCCAAAAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAACAAACGCCGCTA
TAGACCAT
Found at i:41131911 original size:43 final size:42
Alignment explanation
Indices: 41131850--41132026 Score: 180
Period size: 43 Copynumber: 4.1 Consensus size: 42
41131840 TATAGACCAT
* *
41131850 GCTTACCCAACAAACGCCGCTATAGACCATGGTCTTTAGTGGC
1 GCTTACCCAACAAACGCCGCTAAAG-CCATGGTCTTTAGCGGC
* * **
41131893 GCTTACCCAATAAACGCCGCGAAAGCCAATGACCTTTAGCGGC
1 GCTTACCCAACAAACGCCGCTAAAGCC-ATGGTCTTTAGCGGC
* *
41131936 GCTTACCGTGAA-AAACGCCGCTATAGACCATGGTCTTTAGCGGC
1 GCTTACC--CAACAAACGCCGCTAAAG-CCATGGTCTTTAGCGGC
*
41131980 GCCTT-CACC-ACAAACGCCGCTAAAGCTCATGGTTTTTAGCGGC
1 G-CTTAC-CCAACAAACGCCGCTAAAGC-CATGGTCTTTAGCGGC
41132023 GCTT
1 GCTT
41132027 TTAGAAAAAC
Statistics
Matches: 112, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
42 7 0.06
43 70 0.62
44 27 0.24
45 8 0.07
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (42 bp):
GCTTACCCAACAAACGCCGCTAAAGCCATGGTCTTTAGCGGC
Found at i:41131938 original size:116 final size:116
Alignment explanation
Indices: 41131734--41131967 Score: 346
Period size: 116 Copynumber: 2.0 Consensus size: 116
41131724 CTTTATCGGC
* *
41131734 GCTTACCAAACAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCTAAAAAACGCCGCTA
1 GCTTACCAAACAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAAAAAACGCCGCGA
* **
41131799 TAGACCATGGTCTTTAGCGGCGCTTACC-CAACAAACGCCGCTATAGACCAT
66 AAGACCATGACCTTTAGCGGCGCTTACCGCAA-AAACGCCGCTATAGACCAT
* * *
41131850 GCTTACCCAACAAACGCCGCTATAGACCATGGTCTTTAGTGGCGCTTACCCAATAAACGCCGCGA
1 GCTTACCAAACAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAAAAAACGCCGCGA
*
41131915 AAG-CCAATGACCTTTAGCGGCGCTTACCGTGAAAAACGCCGCTATAGACCAT
66 AAGACC-ATGACCTTTAGCGGCGCTTACCG-CAAAAACGCCGCTATAGACCAT
41131967 G
1 G
41131968 GTCTTTAGCG
Statistics
Matches: 106, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
115 2 0.02
116 82 0.77
117 20 0.19
118 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (116 bp):
GCTTACCAAACAAACGCCGCTATAGACCATGGTCTTTAGCGGCGCTTACCCAAAAAACGCCGCGA
AAGACCATGACCTTTAGCGGCGCTTACCGCAAAAACGCCGCTATAGACCAT
Found at i:41132418 original size:21 final size:21
Alignment explanation
Indices: 41132345--41132411 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
41132335 AGCTGTTCTG
*
41132345 CTTCCCTCGCTGCAGCCTCTA
1 CTTCCTTCGCTGCAGCCTCTA
41132366 CTTCCTTCGCTGCAGCCTCTA
1 CTTCCTTCGCTGCAGCCTCTA
*
41132387 CTTCCTTCGCTGCAGCCTCTG
1 CTTCCTTCGCTGCAGCCTCTA
41132408 CTTC
1 CTTC
41132412 TCTCGCTACC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.07, C:0.45, G:0.15, T:0.33
Consensus pattern (21 bp):
CTTCCTTCGCTGCAGCCTCTA
Found at i:41132491 original size:21 final size:21
Alignment explanation
Indices: 41132467--41132528 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
41132457 CTTTCGTTGA
41132467 ACCTCAGCTTCTCTCGCTGCT
1 ACCTCAGCTTCTCTCGCTGCT
* *
41132488 ACCTCTGCTTCTCTCGCTACT
1 ACCTCAGCTTCTCTCGCTGCT
41132509 ACCTCTA-CTTCTCTCGCTGC
1 ACCTC-AGCTTCTCTCGCTGC
41132529 CGCATCTGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.10, C:0.44, G:0.11, T:0.35
Consensus pattern (21 bp):
ACCTCAGCTTCTCTCGCTGCT
Found at i:41138111 original size:16 final size:16
Alignment explanation
Indices: 41138090--41138270 Score: 107
Period size: 16 Copynumber: 12.2 Consensus size: 16
41138080 TTATTATGTC
*
41138090 GTATTATGTAAGTTAT
1 GTATTATATAAGTTAT
*
41138106 GTATTA-AAAATGTTAT
1 GTATTATATAA-GTTAT
41138122 GTATTA-ATAAGTTAT
1 GTATTATATAAGTTAT
41138137 G-------TAAGTTAT
1 GTATTATATAAGTTAT
41138146 GTATTATATAAGTTAT
1 GTATTATATAAGTTAT
41138162 GTATTA-ATAAGTTAT
1 GTATTATATAAGTTAT
*
41138177 GTAAGTTATGT-A-TTAT
1 GT-A-TTATATAAGTTAT
41138193 -T-TTA-A-AA--TAT
1 GTATTATATAAGTTAT
*
41138203 ATATTA-ATAAGTTATGT
1 GTATTATATAAGTTA--T
41138220 CGTATTATATAAGTTAT
1 -GTATTATATAAGTTAT
*
41138237 GTATTA-AAAATGTTAT
1 GTATTATATAA-GTTAT
41138253 GTATTA-ATAAGTTAT
1 GTATTATATAAGTTAT
41138268 GTA
1 GTA
41138271 AGTTATGTAT
Statistics
Matches: 135, Mismatches: 8, Indels: 45
0.72 0.04 0.24
Matches are distributed among these distances:
9 9 0.07
10 3 0.02
11 2 0.01
12 7 0.05
13 2 0.01
15 33 0.24
16 59 0.44
17 6 0.04
18 6 0.04
19 8 0.06
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.47
Consensus pattern (16 bp):
GTATTATATAAGTTAT
Found at i:41138134 original size:31 final size:30
Alignment explanation
Indices: 41138090--41138270 Score: 120
Period size: 31 Copynumber: 6.1 Consensus size: 30
41138080 TTATTATGTC
*
41138090 GTATTATGTAAGTTATGTATTAAAAATGTTAT
1 GTATTATATAAGTTATGTATT-AAAA-GTTAT
41138122 GTATTA-ATAAGTTATG---T--AAGTTAT
1 GTATTATATAAGTTATGTATTAAAAGTTAT
41138146 GTATTATATAAGTTATGTATTAATAAGTTAT
1 GTATTATATAAGTTATGTATTAA-AAGTTAT
*
41138177 GTAAGTTATGT-A-TTAT-T-TTAAAA--TAT
1 GT-A-TTATATAAGTTATGTATTAAAAGTTAT
*
41138203 ATATTA-ATAAGTTATGTCGTATTATATAAGTTAT
1 GTATTATATAAGTTA--T-GTATTA-A-AAGTTAT
*
41138237 GTATTA-AAAATGTTATGTATTAATAAGTTAT
1 GTATTATATAA-GTTATGTATTAA-AAGTTAT
41138268 GTA
1 GTA
41138271 AGTTATGTAT
Statistics
Matches: 122, Mismatches: 6, Indels: 43
0.71 0.04 0.25
Matches are distributed among these distances:
23 1 0.01
24 15 0.12
25 16 0.13
26 4 0.03
27 1 0.01
28 4 0.03
29 5 0.04
30 4 0.03
31 35 0.29
32 16 0.13
33 6 0.05
34 11 0.09
35 4 0.03
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.47
Consensus pattern (30 bp):
GTATTATATAAGTTATGTATTAAAAGTTAT
Found at i:41138139 original size:40 final size:40
Alignment explanation
Indices: 41138093--41138255 Score: 182
Period size: 40 Copynumber: 4.2 Consensus size: 40
41138083 TTATGTCGTA
41138093 TTATGTAAGTTATGTATTA-AAAATGTTATGTATTAATAAG
1 TTATGTAAGTTATGTATTATAAAA-GTTATGTATTAATAAG
*
41138133 TTATGTAAGTTATGTATTATATAAGTTATGTATTAATAAG
1 TTATGTAAGTTATGTATTATAAAAGTTATGTATTAATAAG
*
41138173 TTATGTAAGTTATGTATTATTTTAAAA--TATATATTAATAAG
1 TTATGTAAGTTATGTATTA---TAAAAGTTATGTATTAATAAG
* *
41138214 TTATGT-CG-TAT-TA-TAT--AAGTTATGTATTAAAAATG
1 TTATGTAAGTTATGTATTATAAAAGTTATGTATTAATAA-G
41138249 TTATGTA
1 TTATGTA
41138256 TTAATAAGTT
Statistics
Matches: 109, Mismatches: 6, Indels: 20
0.81 0.04 0.15
Matches are distributed among these distances:
32 2 0.02
34 12 0.11
35 7 0.06
37 2 0.02
38 2 0.02
39 3 0.03
40 55 0.50
41 22 0.20
43 4 0.04
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (40 bp):
TTATGTAAGTTATGTATTATAAAAGTTATGTATTAATAAG
Found at i:41138143 original size:9 final size:9
Alignment explanation
Indices: 41138129--41138188 Score: 67
Period size: 9 Copynumber: 7.2 Consensus size: 9
41138119 TATGTATTAA
41138129 TAAGTTATG
1 TAAGTTATG
41138138 TAAGTTATG
1 TAAGTTATG
*
41138147 T-A-TTATA
1 TAAGTTATG
41138154 TAAGTTATG
1 TAAGTTATG
*
41138163 T-A-TTA-A
1 TAAGTTATG
41138169 TAAGTTATG
1 TAAGTTATG
41138178 TAAGTTATG
1 TAAGTTATG
41138187 TA
1 TA
41138189 TTATTTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 1 0.02
7 9 0.21
8 6 0.14
9 26 0.62
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:41138242 original size:91 final size:93
Alignment explanation
Indices: 41138133--41138312 Score: 303
Period size: 91 Copynumber: 2.0 Consensus size: 93
41138123 TATTAATAAG
* * *
41138133 TTATGTAAGTTATGTATTATATAA-GTTATGTATTAATAAGTTATGTAAGTTATGTATTATTTT-
1 TTATATAAGTTATGTATTA-AAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTTTA
41138196 AAA-ATATATATTAATAAGTTATGTCGTA
65 AAATATATATATTAATAAGTTATGTCGTA
41138224 TTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTTTAA
1 TTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTTTAA
41138289 AATATATATATTAATAAGTTATGT
66 AATATATATATTAATAAGTTATGT
41138313 AATGTATGTA
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
90 3 0.04
91 56 0.67
92 3 0.04
93 21 0.25
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (93 bp):
TTATATAAGTTATGTATTAAAAATGTTATGTATTAATAAGTTATGTAAGTTATGTATCATTTTAA
AATATATATATTAATAAGTTATGTCGTA
Found at i:41139649 original size:12 final size:12
Alignment explanation
Indices: 41139632--41139675 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
41139622 CTTCTACCCT
41139632 TTCCCCTTTCCC
1 TTCCCCTTTCCC
*
41139644 TTCCCCTTCCCC
1 TTCCCCTTTCCC
*
41139656 TTCCCTTTTCCC
1 TTCCCCTTTCCC
41139668 TTCCCCTT
1 TTCCCCTT
41139676 GGATTGCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (12 bp):
TTCCCCTTTCCC
Found at i:41139650 original size:6 final size:6
Alignment explanation
Indices: 41139632--41139675 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
41139622 CTTCTACCCT
* * *
41139632 TTCCCC TTTCCC TTCCCC TTCCCC TTCCCT TTTCCC TTCCCC TT
1 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TT
41139676 GGATTGCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (6 bp):
TTCCCC
Found at i:41139769 original size:25 final size:25
Alignment explanation
Indices: 41139735--41139784 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
41139725 CAGGTAAGGC
*
41139735 TCCTTCTTCTTCTTCCGTTTTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
* *
41139760 TCCTTTTTCTTCTTCTGTTCTTCAT
1 TCCTTCTTCTTCTTCCGTTCTTCAT
41139785 CTTCTCTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.04, C:0.30, G:0.04, T:0.62
Consensus pattern (25 bp):
TCCTTCTTCTTCTTCCGTTCTTCAT
Found at i:41143152 original size:15 final size:15
Alignment explanation
Indices: 41143113--41143165 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
41143103 GAACATTTGG
41143113 AATTTAATTAGATAAAA
1 AATTT-ATTA-ATAAAA
41143130 AACTTTTATTAATAAAA
1 AA--TTTATTAATAAAA
*
41143147 AATTTATTTATAAATA
1 AATTTATTAATAAA-A
41143163 AAT
1 AAT
41143166 CATTGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.34
16 4 0.12
17 10 0.31
18 4 0.12
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTTATTAATAAAA
Found at i:41143239 original size:22 final size:20
Alignment explanation
Indices: 41143196--41143234 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41143186 TAATTTAAAA
41143196 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
41143216 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
41143235 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:41143358 original size:20 final size:20
Alignment explanation
Indices: 41143333--41143372 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41143323 AATATTTTCC
*
41143333 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
41143353 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
41143373 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:41143378 original size:34 final size:35
Alignment explanation
Indices: 41143321--41143387 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
41143311 CAAACACTAG
*
41143321 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
41143356 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
41143388 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:41143379 original size:14 final size:14
Alignment explanation
Indices: 41143356--41143395 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
41143346 ACAGAAAAGT
*
41143356 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
41143370 AAATCATTTTACGG
1 AAAACATTTTACAG
41143384 AAAACATTTTAC
1 AAAACATTTTAC
41143396 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:41145936 original size:74 final size:74
Alignment explanation
Indices: 41145815--41146063 Score: 394
Period size: 74 Copynumber: 3.4 Consensus size: 74
41145805 ATAACTATCA
*
41145815 TTTGCGGCGTTTGTACCAA-AAACGCCGCTAATACCAATAAACAGTATAAAAAATGAAGTCGTTT
1 TTTGCGGCGTTTGTA-CAATAAACGCCGCTAATACCAATAAACAGTATAAAAAACGAAGTCGTTT
41145879 TGGTTAAACT
65 TGGTTAAACT
* * *
41145889 TTTGCGGCGTTTGTACCAGAAACGCCGCTAATACCAATAAACAGTATACAAAACGAAGTCGTTTT
1 TTTGCGGCGTTTGTACAATAAACGCCGCTAATACCAATAAACAGTATAAAAAACGAAGTCGTTTT
41145954 GGTTAAACT
66 GGTTAAACT
* * *
41145963 TTTGTGGCGTTTTTACAATAAACGCCACTAATACCAATAAACAGTAT-AAAAACGAAGTCGTTTT
1 TTTGCGGCGTTTGTACAATAAACGCCGCTAATACCAATAAACAGTATAAAAAACGAAGTCGTTTT
41146027 GGTTAAACT
66 GGTTAAACT
* *
41146036 TTTGTGGCGTTTTTACAATAAACGCCGC
1 TTTGCGGCGTTTGTACAATAAACGCCGC
41146064 AAATTCGTGC
Statistics
Matches: 164, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
73 54 0.33
74 110 0.67
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (74 bp):
TTTGCGGCGTTTGTACAATAAACGCCGCTAATACCAATAAACAGTATAAAAAACGAAGTCGTTTT
GGTTAAACT
Found at i:41147227 original size:41 final size:41
Alignment explanation
Indices: 41147141--41147231 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
41147131 AGCTACAAAA
* **
41147141 CGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTCTAATATG
1 CGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTCTAAGAAC
*
41147182 CGCCGCTAATGCTGC-GGTTTTTAGCGGCGCTTTT-TAAGAAC
1 CGCCGCTAATGCT-CTGGTCTTTAGCGGCG-TTTTCTAAGAAC
41147223 CGCCGCTAA
1 CGCCGCTAA
41147232 AGACCTGAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 39 0.89
42 5 0.11
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.32
Consensus pattern (41 bp):
CGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTCTAAGAAC
Found at i:41147247 original size:41 final size:41
Alignment explanation
Indices: 41147202--41147410 Score: 260
Period size: 41 Copynumber: 5.1 Consensus size: 41
41147192 GCTGCGGTTT
** * *
41147202 TTAGCGGCGCTTTTTAAGAACCGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTCGTAAAAAACGCCGCTAAAGACCTGAGCA
*
41147243 TTAGCGGCACTTCGTAAAAAACGCCGCTAAAGACCTGAGCA
1 TTAGCGGCGCTTCGTAAAAAACGCCGCTAAAGACCTGAGCA
*
41147284 TTAGCGGCGCTTCGTAAAAAACGCCGCTAAAGACC-GTAGTA
1 TTAGCGGCGCTTCGTAAAAAACGCCGCTAAAGACCTG-AGCA
* ***
41147325 TTAGCGGCGCTTTGTAAAAAACGAATCTAAAGACCTGAGCA
1 TTAGCGGCGCTTCGTAAAAAACGCCGCTAAAGACCTGAGCA
* ** *
41147366 TTAGCGGCGCATATTAGAAAACGCCGCTAAAGACC-GCAGCA
1 TTAGCGGCGCTTCGTAAAAAACGCCGCTAAAGACCTG-AGCA
41147407 TTAG
1 TTAG
41147411 TGGCAATTAT
Statistics
Matches: 146, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
40 2 0.01
41 143 0.98
42 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (41 bp):
TTAGCGGCGCTTCGTAAAAAACGCCGCTAAAGACCTGAGCA
Found at i:41147614 original size:41 final size:40
Alignment explanation
Indices: 41147540--41147630 Score: 96
Period size: 41 Copynumber: 2.2 Consensus size: 40
41147530 TTACATATAT
*
41147540 CGCCGCTAATGCTCGTATCTTTTGCGGCGTTTTTCGT-AAA
1 CGCCGCTAATGCTAGTATCTTTTGCGGCGTTTTT-GTCAAA
* * *
41147580 GCGCCGCTAATGCTAG-ATTTTTTGTGTCGTTTTTTGTCCAAA
1 -CGCCGCTAATGCTAGTATCTTTTGCGGCG-TTTTTGT-CAAA
41147622 CGCCGCTAA
1 CGCCGCTAA
41147631 AAGTCTGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
40 12 0.28
41 28 0.65
42 3 0.07
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.37
Consensus pattern (40 bp):
CGCCGCTAATGCTAGTATCTTTTGCGGCGTTTTTGTCAAA
Found at i:41150553 original size:22 final size:22
Alignment explanation
Indices: 41150525--41150571 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
41150515 ATGAAAACAA
* *
41150525 AAAAAATAATACTGATAATAAT
1 AAAAAATAATAATAATAATAAT
*
41150547 AAAAAATAGTAATAATAATAAT
1 AAAAAATAATAATAATAATAAT
41150569 AAA
1 AAA
41150572 GAAGTTCACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAAAATAATAATAATAATAAT
Found at i:41151459 original size:16 final size:17
Alignment explanation
Indices: 41151432--41151477 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
41151422 AAAAGGTATT
*
41151432 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
41151449 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
41151465 ATAAATATATTTA
1 TTAAAAATATTTA
41151478 TTATATCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:41152692 original size:85 final size:85
Alignment explanation
Indices: 41152580--41152740 Score: 188
Period size: 85 Copynumber: 1.9 Consensus size: 85
41152570 TGTTACTTCA
* * *
41152580 ATCTGCTCCATTGCATTCTCGGGGAGATACGA-T-T-GG-TTTATTCAGTCTGCTCCGCTGCAAC
1 ATCTGCTCCATTGCACTCTCGGAGAGATACGATTATCGGCTTTA---A-TCTGCTCCACTGCAAC
41152641 TTCAAGGAGATAAGACCTGATGAG
62 TTCAAGGAGATAAGACCTGATGAG
* *
41152665 ATCTGCTCTATTGCAACT-TCGGAGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTC
1 ATCTGCTCCATTGC-ACTCTCGGAGAGATACGATTATCGGCTTTAATCTGCTCCACTGCAACTTC
*
41152729 AGGGAGATAAGA
65 AAGGAGATAAGA
41152741 TTCTCTATCT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
85 54 0.83
86 4 0.06
87 1 0.02
88 2 0.03
89 4 0.06
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (85 bp):
ATCTGCTCCATTGCACTCTCGGAGAGATACGATTATCGGCTTTAATCTGCTCCACTGCAACTTCA
AGGAGATAAGACCTGATGAG
Found at i:41152893 original size:51 final size:50
Alignment explanation
Indices: 41152804--41153090 Score: 216
Period size: 51 Copynumber: 5.8 Consensus size: 50
41152794 CTTCAACTTT
* * * * * *
41152804 AACGCCAGGGAGATAAGATCCGCTGCCTACAACATTAATCTACTCCGCTGC
1 AACGCCAAGGAAAT-AGATTCGCTGCCTTCAACTTTAATCTACTCCACTGC
**
41152855 AACGCCAAGGAAATACGATTAACTGCCTTCAACTTTAATCTACT--AC-G-
1 AACGCCAAGGAAATA-GATTCGCTGCCTTCAACTTTAATCTACTCCACTGC
* * * * **
41152902 -ATGCCAAGGAAATAAGATTTGCTGCCTTGAGCTTTAATCTGTTCCACTGC
1 AACGCCAAGGAAAT-AGATTCGCTGCCTTCAACTTTAATCTACTCCACTGC
* * * *
41152952 AACGCCAAAGAAATGATATTCGCTGTCTTCAGCTTTAATCTA-T----TGC
1 AACGCCAAGGAAAT-AGATTCGCTGCCTTCAACTTTAATCTACTCCACTGC
* * * * * **
41152998 AATGCCAGGGAAACAAGATTCGCCGCCTTCAGCTTTAATCTGTTCCACTGC
1 AACGCCAAGGAAA-TAGATTCGCTGCCTTCAACTTTAATCTACTCCACTGC
*
41153049 AACGCCAAGGAAATGAGTTTCGCTGCCTTCAACTTTAATCTA
1 AACGCCAAGGAAAT-AGATTCGCTGCCTTCAACTTTAATCTA
41153091 TTTCAATGCC
Statistics
Matches: 184, Mismatches: 38, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
46 70 0.38
47 2 0.01
48 3 0.02
49 2 0.01
50 2 0.01
51 105 0.57
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (50 bp):
AACGCCAAGGAAATAGATTCGCTGCCTTCAACTTTAATCTACTCCACTGC
Found at i:41152927 original size:46 final size:46
Alignment explanation
Indices: 41152851--41153135 Score: 230
Period size: 46 Copynumber: 6.0 Consensus size: 46
41152841 ATCTACTCCG
* * ** *
41152851 CTGCAACGCCAAGGAAATACGATTAACTGCCTTCAACTTTAATCTA
1 CTGCAATGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTA
* * * *
41152897 CTACGATGCCAAGGAAATAAGATTTGCTGCCTTGAGCTTTAATCTGTTCCA
1 CTGCAATGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T--A
* * * * *
41152948 CTGCAACGCCAAAGAAATGATATTCGCTGTCTTCAGCTTTAATCTA
1 CTGCAATGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTA
* * * *
41152994 TTGCAATGCCAGGGAAACAAGATTCGCCGCCTTCAGCTTTAATCTGTTCCA
1 CTGCAATGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T--A
* * * *
41153045 CTGCAACGCCAAGGAAATGAGTTTCGCTGCCTTCAACTTTAATCTA
1 CTGCAATGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTA
* * * *
41153091 TTTCAATGCCAGGGAAACAAGATTCG-TCGCCTTCAGCTTTAATCT
1 CTGCAATGCCAAGGAAATAAGATTCGCT-GCCTTCAGCTTTAATCT
41153136 GTTCCATTGT
Statistics
Matches: 186, Mismatches: 42, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
45 1 0.01
46 108 0.58
48 2 0.01
49 2 0.01
51 73 0.39
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (46 bp):
CTGCAATGCCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTA
Found at i:41152982 original size:97 final size:97
Alignment explanation
Indices: 41152807--41153141 Score: 397
Period size: 97 Copynumber: 3.5 Consensus size: 97
41152797 CAACTTTAAC
* * * * * * ** * *
41152807 GCCAGGGAGATAAGATCCGCTGCCTACAACATTAATCTACTCCGCTGCAACGCCAAGGAAAT-AC
1 GCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATGA-
* ** * *
41152871 GATTAACTGCCTTCAACTTTAATCTACTACGAT
65 GTTTCGCTGCCTTCAACTTTAATCTATTACAAT
* * * *
41152904 GCCAAGGAAATAAGATTTGCTGCCTTGAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATGA-
1 GCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATGAG
* * *
41152968 TATTCGCTGTCTTCAGCTTTAATCTATTGCAAT
66 T-TTCGCTGCCTTCAACTTTAATCTATTACAAT
* *
41153001 GCCAGGGAAACAAGATTCGCCGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATGAG
1 GCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATGAG
*
41153066 TTTCGCTGCCTTCAACTTTAATCTATTTCAAT
66 TTTCGCTGCCTTCAACTTTAATCTATTACAAT
41153098 GCCAGGGAAACAAGATTCG-TCGCCTTCAGCTTTAATCTGTTCCA
1 GCCAGGGAAACAAGATTCGCT-GCCTTCAGCTTTAATCTGTTCCA
41153142 TTGTAACTTT
Statistics
Matches: 204, Mismatches: 30, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
97 202 0.99
98 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (97 bp):
GCCAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAAGAAATGAG
TTTCGCTGCCTTCAACTTTAATCTATTACAAT
Found at i:41153468 original size:24 final size:24
Alignment explanation
Indices: 41153441--41153496 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
41153431 CAGATTGCCC
*
41153441 CCACTGTAATCTTCAAGGTTTAAT
1 CCACTGTAATCTTCAAGGTTCAAT
*
41153465 CCACTATAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTCAAT
41153489 CCACTGTA
1 CCACTGTA
41153497 CTTTTGGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGGTTCAAT
Found at i:41154009 original size:13 final size:13
Alignment explanation
Indices: 41153991--41154017 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41153981 AGGAGAATAT
41153991 ATAAAAAAATAAA
1 ATAAAAAAATAAA
41154004 ATAAAAAAATAAA
1 ATAAAAAAATAAA
41154017 A
1 A
41154018 AGGAATTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAAAATAAA
Found at i:41161574 original size:22 final size:22
Alignment explanation
Indices: 41161549--41161615 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
41161539 AACTTCTAAA
41161549 CATCTATGTCTAGTCTCAAATT
1 CATCTATGTCTAGTCTCAAATT
*
41161571 CATC--T-TCTA-ACTTCTAAA--
1 CATCTATGTCTAGTC-TC-AAATT
41161589 CATCTATGTCTAGTCTCAAATT
1 CATCTATGTCTAGTCTCAAATT
41161611 CATCT
1 CATCT
41161616 TCTTTACTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 16
0.66 0.04 0.30
Matches are distributed among these distances:
18 5 0.14
19 6 0.17
20 8 0.23
21 6 0.17
22 10 0.29
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.40
Consensus pattern (22 bp):
CATCTATGTCTAGTCTCAAATT
Found at i:41161579 original size:40 final size:40
Alignment explanation
Indices: 41161535--41161618 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
41161525 ATTTATCAGT
41161535 TTCTAACTTCTAAACATCTATGTCTAGTCTCAAATTCATC
1 TTCTAACTTCTAAACATCTATGTCTAGTCTCAAATTCATC
41161575 TTCTAACTTCTAAACATCTATGTCTAGTCTCAAATTCATC
1 TTCTAACTTCTAAACATCTATGTCTAGTCTCAAATTCATC
41161615 TTCT
1 TTCT
41161619 TTACTTCCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.42
Consensus pattern (40 bp):
TTCTAACTTCTAAACATCTATGTCTAGTCTCAAATTCATC
Found at i:41164676 original size:3 final size:3
Alignment explanation
Indices: 41164663--41164717 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
41164653 TAATGAAAAC
* * * *
41164663 AAT AA- AAT AAT AAT ACT GAT AAT AAT AAA AAT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41164710 AAT AAT AA
1 AAT AAT AA
41164718 GTTCACGAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:41166072 original size:11 final size:12
Alignment explanation
Indices: 41166052--41166084 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
41166042 GGACATTTAA
41166052 TTTTATTTTGGT
1 TTTTATTTTGGT
41166064 TTTTA-TTTGGT
1 TTTTATTTTGGT
*
41166075 TTTTTTTTTG
1 TTTTATTTTG
41166085 TCTTTGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.06, C:0.00, G:0.15, T:0.79
Consensus pattern (12 bp):
TTTTATTTTGGT
Found at i:41172949 original size:48 final size:48
Alignment explanation
Indices: 41172870--41172963 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
41172860 AGGGAATTCT
* *
41172870 GTTGAATCCTTTATTGTTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
1 GTTGAATCCTTTATCGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
41172918 GTTGAATCCTTTATCGGTG-GAAGTT-AGGCTGACTTAGGCGTTTTTA
1 GTTGAATCCTTTATCGGTGCG-AGTTGA-GCTGACTTAGGCGTTTTTA
41172964 AGCCAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 2 0.05
48 40 0.95
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.40
Consensus pattern (48 bp):
GTTGAATCCTTTATCGGTGCGAGTTGAGCTGACTTAGGCGTTTTTACG
Found at i:41185471 original size:26 final size:29
Alignment explanation
Indices: 41185442--41185500 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
41185432 AAGCATAGAA
*
41185442 GTATATAT-AAAT-AAAT-TTTAAAATAT
1 GTATATATAAAATAAAATCATTAAAATAT
41185468 GTAT-TATAAAATAAAATCATTAAAATAT
1 GTATATATAAAATAAAATCATTAAAATAT
*
41185496 ATATA
1 GTATA
41185501 AATCATATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 3 0.11
26 8 0.30
27 4 0.15
28 12 0.44
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (29 bp):
GTATATATAAAATAAAATCATTAAAATAT
Found at i:41185659 original size:3 final size:3
Alignment explanation
Indices: 41185651--41185733 Score: 71
Period size: 3 Copynumber: 27.7 Consensus size: 3
41185641 ATATATAAAA
* * * *
41185651 AAT AAT AAT AAT AAT AAT GAT AGT AAT AAT AAT AAT AAT AAT TAT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
41185699 AAT -AT CAAA AATT ATT AAT ATT AAT AAT AA- AAT AA
1 AAT AAT -AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA
41185734 CCAAAATAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
2 4 0.06
3 58 0.91
4 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:41189275 original size:21 final size:21
Alignment explanation
Indices: 41189230--41189277 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
41189220 TTTTTCTTGG
* **
41189230 GTCCAAGCTGATGTACTGTTG
1 GTCCAAGCTGATGTACTATCA
41189251 GTCCAAGCTGATGTACTATCA
1 GTCCAAGCTGATGTACTATCA
41189272 GTCCAA
1 GTCCAA
41189278 TCAATCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (21 bp):
GTCCAAGCTGATGTACTATCA
Found at i:41190771 original size:83 final size:83
Alignment explanation
Indices: 41190673--41190841 Score: 266
Period size: 83 Copynumber: 2.0 Consensus size: 83
41190663 GGGGTGGGGT
* *
41190673 GGGGTGGGGTGAGAATGAATGCACCAACATCCCATGGAAGTGATAATGATATTCAAAATTATACA
1 GGGGTGGGGTGAGAATGAATGCACAAACATCCCATGGAAGTGATAATGATATTCAAAATCATACA
* *
41190738 TCCATAGTGAAGTGGAGC
66 TCCATAATGAAGTAGAGC
* * *
41190756 GGGGTGGGGTGAGAATGGATGCACAAACATCCCATGGAGGTGATAATGATTTTCAAAATCATACA
1 GGGGTGGGGTGAGAATGAATGCACAAACATCCCATGGAAGTGATAATGATATTCAAAATCATACA
*
41190821 TCTATAATGAAGTAGAGC
66 TCCATAATGAAGTAGAGC
41190839 GGG
1 GGG
41190842 TTGAGGTGGA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (83 bp):
GGGGTGGGGTGAGAATGAATGCACAAACATCCCATGGAAGTGATAATGATATTCAAAATCATACA
TCCATAATGAAGTAGAGC
Found at i:41199451 original size:42 final size:42
Alignment explanation
Indices: 41199392--41199497 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 42
41199382 GAGACATTAA
* *
41199392 ATTGGTGGATGGTGTTGTGGTGGGATCCATAGAAGTGGGAAG
1 ATTGGTGGGTGGTGTTGTGGTGGGATCCATAGAAGTAGGAAG
* * *
41199434 ATTGGTGGGTGGTGTTGTGATGGGGTCCATAGGAGTAGGAAG
1 ATTGGTGGGTGGTGTTGTGGTGGGATCCATAGAAGTAGGAAG
*
41199476 ATTGGTAGGTGGTGTTGTGGTG
1 ATTGGTGGGTGGTGTTGTGGTG
41199498 TGACTCATAG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.18, C:0.04, G:0.47, T:0.31
Consensus pattern (42 bp):
ATTGGTGGGTGGTGTTGTGGTGGGATCCATAGAAGTAGGAAG
Found at i:41199515 original size:42 final size:41
Alignment explanation
Indices: 41199392--41199515 Score: 130
Period size: 42 Copynumber: 3.0 Consensus size: 41
41199382 GAGACATTAA
*
41199392 ATTGGTGGATGGTGTTGTGGTGGGATCCATAGA-AGTGGGAAG
1 ATTGGTGG-TGGTGTTGTGGT-GGATCCATAGAGAGTAGGAAG
* *
41199434 ATTGGTGGGTGGTGTTGTGATGGGGTCCATAG-GAGTAGGAAG
1 ATTGGT-GGTGGTGTTGTGGT-GGATCCATAGAGAGTAGGAAG
41199476 ATTGGTAGGTGGTGTTGTGGTGTGA-CTCATAGAGA-TAGGA
1 ATTGGT-GGTGGTGTTGTGGTG-GATC-CATAGAGAGTAGGA
41199516 GAATGTATGT
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
41 2 0.03
42 65 0.92
43 4 0.06
ACGTcount: A:0.21, C:0.05, G:0.44, T:0.30
Consensus pattern (41 bp):
ATTGGTGGTGGTGTTGTGGTGGATCCATAGAGAGTAGGAAG
Found at i:41205481 original size:22 final size:21
Alignment explanation
Indices: 41205456--41205496 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
41205446 TCTTCTTCTT
41205456 CTTTGAATCCTCTGCTTTCTAG
1 CTTTGAATCCTCTG-TTTCTAG
**
41205478 CTTTGTTTCCTCTGTTTCT
1 CTTTGAATCCTCTGTTTCT
41205497 TCTTCGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.07, C:0.27, G:0.12, T:0.54
Consensus pattern (21 bp):
CTTTGAATCCTCTGTTTCTAG
Found at i:41218810 original size:47 final size:47
Alignment explanation
Indices: 41218712--41218810 Score: 130
Period size: 47 Copynumber: 2.1 Consensus size: 47
41218702 AAAATTTAAA
* * *
41218712 AAAATGGAAAAATATTTTTTAAAAATAAAATAAAATAAACATTACTTT
1 AAAATGGAAAAAAACTTTTAAAAAATAAAATAAAATAAACATTA-TTT
41218760 AAAAT-GAAAAAAACTTTTAAAATAATAAAATAAAATTAAACATT-TTT
1 AAAATGGAAAAAAACTTTTAAAA-AATAAAATAAAA-TAAACATTATTT
41218807 AAAA
1 AAAA
41218811 AGTACATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
47 21 0.46
48 17 0.37
49 8 0.17
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (47 bp):
AAAATGGAAAAAAACTTTTAAAAAATAAAATAAAATAAACATTATTT
Found at i:41223548 original size:26 final size:26
Alignment explanation
Indices: 41223518--41223567 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
41223508 CCACTTAATC
*
41223518 GGGGAATCAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACATAGCAACCCCTT
41223544 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
41223568 CTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.32, G:0.24, T:0.14
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTT
Found at i:41223649 original size:26 final size:26
Alignment explanation
Indices: 41223619--41223670 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
41223609 ACCAATGAAC
*
41223619 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
41223645 CGGGGAATCAGCACATAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
41223671 TTTCACATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:41223742 original size:103 final size:102
Alignment explanation
Indices: 41223485--41223747 Score: 402
Period size: 102 Copynumber: 2.6 Consensus size: 102
41223475 AACCGTTATT
* * * *
41223485 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGAA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
* *
41223550 TCAGCACATAGCAACCCCCTTTTTATTTCAGAGATAC
66 TCAGCACATAGCAACCCCCTTTTCATTTCAAAGATAC
*
41223587 GGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
41223652 TCAGCACATAGCAA-CCCCTTTTCACATTTCAAAGATAC
66 TCAGCACATAGCAACCCCCTTTT--CATTTCAAAGATAC
* * **
41223690 GGTGGATATCGCACATAGCACCACCAATGAATCGGGAAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
41223748 TTATGTACAA
Statistics
Matches: 147, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
101 8 0.05
102 74 0.50
103 65 0.44
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (102 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
TCAGCACATAGCAACCCCCTTTTCATTTCAAAGATAC
Found at i:41224109 original size:30 final size:30
Alignment explanation
Indices: 41224082--41224139 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
41224072 CCACCCAACT
41224082 TTTTGAAAAATTACAATTTTGCCCCCAATC
1 TTTTGAAAAATTACAATTTTGCCCCCAATC
* * * *
41224112 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
41224140 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAATC
Found at i:41224115 original size:31 final size:29
Alignment explanation
Indices: 41224075--41224139 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
41224065 TAATCCACCA
41224075 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
41224105 CCCAATCTTTTGCATAATTACACTTTTGTC
1 CCCAA-CTTTTGAAAAATTACAATTTTGCC
41224135 CCCAA
1 CCCAA
41224140 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.29, C:0.28, G:0.06, T:0.37
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:41227326 original size:49 final size:49
Alignment explanation
Indices: 41227266--41227769 Score: 775
Period size: 47 Copynumber: 10.6 Consensus size: 49
41227256 GATAATTGTG
41227266 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41227313 ATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41227360 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41227409 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41227458 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41227507 ATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41227554 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41227603 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41227650 ATGTGAAAGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
41227697 ATGTGAAAGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41227744 ATGTGAAAATGTATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
41227770 TCCCGAAGGG
Statistics
Matches: 427, Mismatches: 22, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
47 233 0.55
48 3 0.01
49 191 0.45
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (49 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:41227373 original size:96 final size:96
Alignment explanation
Indices: 41227266--41227769 Score: 831
Period size: 96 Copynumber: 5.3 Consensus size: 96
41227256 GATAATTGTG
41227266 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
41227329 ATGTGATAAGGCCGAATGGCCAATGTGATGA
66 ATGTGATAAGGCCGAATGGCCAATGTGATGA
41227360 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TAT
* *
41227425 ATATGTGATAAGGCCTAATGGCCGATGTGATGA
64 ATATGTGATAAGGCCGAATGGCCAATGTGATGA
41227458 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
41227523 ATGTGATAAGGCCGAATGGCCAATGTGATGA
66 ATGTGATAAGGCCGAATGGCCAATGTGATGA
*
41227554 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * *
41227619 ATGTGATAAGGCCTAATAGCCGATGTGATGA
66 ATGTGATAAGGCCGAATGGCCAATGTGATGA
*
41227650 ATGTGAAAGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * * * *
41227713 ATGTGACAGGGCCGAGTGGCCAACGTGATGG
66 ATGTGATAAGGCCGAATGGCCAATGTGATGA
*
41227744 ATGTGAAAATGTATA-A-ATGTGATAAG
1 ATGTGAAAGTGTATATATATGTGATAAG
41227770 TCCCGAAGGG
Statistics
Matches: 384, Mismatches: 20, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
94 97 0.25
95 3 0.01
96 190 0.49
98 94 0.24
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (96 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCGAATGGCCAATGTGATGA
Found at i:41230236 original size:14 final size:14
Alignment explanation
Indices: 41230219--41230245 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41230209 AAAATAAACC
41230219 GTACAAAAGAACAT
1 GTACAAAAGAACAT
41230233 GTACAAAAGAACA
1 GTACAAAAGAACA
41230246 GTGACTTGAA
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:0.59, C:0.15, G:0.15, T:0.11
Consensus pattern (14 bp):
GTACAAAAGAACAT
Found at i:41244916 original size:46 final size:46
Alignment explanation
Indices: 41244855--41245053 Score: 290
Period size: 46 Copynumber: 4.3 Consensus size: 46
41244845 TGATTTGTAC
* * *
41244855 AAAAATAGACAGCATTTAAACAACATTCAGACAGCATAATATGCTA
1 AAAAATGGACAGCATTTAAACAACATTCGGACAACATAATATGCTA
* * * *
41244901 AAAAATGGACAGCATTTAAACATCATTCGGGCAACATAATATCCTC
1 AAAAATGGACAGCATTTAAACAACATTCGGACAACATAATATGCTA
* *
41244947 AAAAATGGACAGCATTTAAACAACATTCGGACAGCATAATATCCTA
1 AAAAATGGACAGCATTTAAACAACATTCGGACAACATAATATGCTA
* * *
41244993 AAAAATGGACATCATTTAAACATCATTCGGATAACATAATATGCTA
1 AAAAATGGACAGCATTTAAACAACATTCGGACAACATAATATGCTA
41245039 AAAAATGGACAGCAT
1 AAAAATGGACAGCAT
41245054 AATATCCTAA
Statistics
Matches: 136, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 136 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (46 bp):
AAAAATGGACAGCATTTAAACAACATTCGGACAACATAATATGCTA
Found at i:41244960 original size:92 final size:92
Alignment explanation
Indices: 41244854--41245053 Score: 328
Period size: 92 Copynumber: 2.2 Consensus size: 92
41244844 TTGATTTGTA
* *
41244854 CAAAAATAGACAGCATTTAAACAACATTCAGACAGCATAATATGCTAAAAAATGGACAGCATTTA
1 CAAAAATGGACAGCATTTAAACAACATTCAGACAGCATAATATCCTAAAAAATGGACAGCATTTA
*
41244919 AACATCATTCGGGCAACATAATATCCT
66 AACATCATTCGGACAACATAATATCCT
* *
41244946 CAAAAATGGACAGCATTTAAACAACATTCGGACAGCATAATATCCTAAAAAATGGACATCATTTA
1 CAAAAATGGACAGCATTTAAACAACATTCAGACAGCATAATATCCTAAAAAATGGACAGCATTTA
* *
41245011 AACATCATTCGGATAACATAATATGCT
66 AACATCATTCGGACAACATAATATCCT
*
41245038 AAAAAATGGACAGCAT
1 CAAAAATGGACAGCAT
41245054 AATATCCTAA
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 100 1.00
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.23
Consensus pattern (92 bp):
CAAAAATGGACAGCATTTAAACAACATTCAGACAGCATAATATCCTAAAAAATGGACAGCATTTA
AACATCATTCGGACAACATAATATCCT
Found at i:41245063 original size:24 final size:24
Alignment explanation
Indices: 41245027--41245075 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
41245017 ATTCGGATAA
*
41245027 CATAATATGCTAAAAAATGGACAG
1 CATAATATCCTAAAAAATGGACAG
41245051 CATAATATCCTAAAAAATGGACAG
1 CATAATATCCTAAAAAATGGACAG
41245075 C
1 C
41245076 TTAAACAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.20
Consensus pattern (24 bp):
CATAATATCCTAAAAAATGGACAG
Found at i:41245113 original size:68 final size:69
Alignment explanation
Indices: 41244975--41245117 Score: 216
Period size: 68 Copynumber: 2.1 Consensus size: 69
41244965 AACAACATTC
* * * * *
41244975 GGACAGCATAATATCCTAAAAAATGGACATCATTTAAACATCATTCGGATAACATAATATGCTAA
1 GGACAGCATAATATCCTAAAAAATGGACAGCA-TTAAACAACATTCAGACAACATAATATCCTAA
41245040 AAAAT
65 AAAAT
*
41245045 GGACAGCATAATATCCTAAAAAATGGACAGC-TTAAACAACATTCAGACAACATAATATCCTCAA
1 GGACAGCATAATATCCTAAAAAATGGACAGCATTAAACAACATTCAGACAACATAATATCCTAAA
41245109 AAAT
66 AAAT
41245113 GGACA
1 GGACA
41245118 TCATTTAAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 37 0.55
70 30 0.45
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (69 bp):
GGACAGCATAATATCCTAAAAAATGGACAGCATTAAACAACATTCAGACAACATAATATCCTAAA
AAAT
Found at i:41245137 original size:114 final size:115
Alignment explanation
Indices: 41244935--41245167 Score: 396
Period size: 114 Copynumber: 2.0 Consensus size: 115
41244925 ATTCGGGCAA
* * *
41244935 CATAATATCCTCAAAAATGGACAGCATTTAAACAACATTCGGACAGCATAATATCCTAAAAAATG
1 CATAATATCCTAAAAAATGGACAGCA-TTAAACAACATTCAGACAACATAATATCCTAAAAAATG
* *
41245000 GACATCATTTAAACATCATTCGGATAACATAATATGCTAAAAAATGGACAG
65 GACATCATTTAAACATCATTCGGACAACATAATATGCCAAAAAATGGACAG
*
41245051 CATAATATCCTAAAAAATGGACAGC-TTAAACAACATTCAGACAACATAATATCCTCAAAAATGG
1 CATAATATCCTAAAAAATGGACAGCATTAAACAACATTCAGACAACATAATATCCTAAAAAATGG
41245115 ACATCATTTAAACATCATTCGGACAACATAATATGCCAAAAAATGGACAG
66 ACATCATTTAAACATCATTCGGACAACATAATATGCCAAAAAATGGACAG
41245165 CAT
1 CAT
41245168 TTTGTTATCA
Statistics
Matches: 111, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
114 87 0.78
116 24 0.22
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.23
Consensus pattern (115 bp):
CATAATATCCTAAAAAATGGACAGCATTAAACAACATTCAGACAACATAATATCCTAAAAAATGG
ACATCATTTAAACATCATTCGGACAACATAATATGCCAAAAAATGGACAG
Found at i:41245143 original size:46 final size:46
Alignment explanation
Indices: 41245045--41245169 Score: 175
Period size: 46 Copynumber: 2.8 Consensus size: 46
41245035 GCTAAAAAAT
*
41245045 GGACAGCATAATATCCTAAAAAATGGACAGC--TTAAACAACATTC
1 GGACAACATAATATCCTAAAAAATGGACAGCATTTAAACAACATTC
* * * *
41245089 AGACAACATAATATCCTCAAAAATGGACATCATTTAAACATCATTC
1 GGACAACATAATATCCTAAAAAATGGACAGCATTTAAACAACATTC
41245135 GGACAACATAATATGCC-AAAAAATGGACAGCATTT
1 GGACAACATAATAT-CCTAAAAAATGGACAGCATTT
41245170 TGTTATCACG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
44 27 0.39
46 41 0.59
47 2 0.03
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (46 bp):
GGACAACATAATATCCTAAAAAATGGACAGCATTTAAACAACATTC
Found at i:41245845 original size:44 final size:42
Alignment explanation
Indices: 41245774--41245930 Score: 181
Period size: 44 Copynumber: 3.6 Consensus size: 42
41245764 GAAAAGCTTG
* *
41245774 TACAATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAA
1 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAA
* * ** *
41245816 TATCATATGCCATTGTCCCAGACAGGGTCTTACACAAAATCATA
1 TA-CA-ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAA
41245860 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAA
1 TACAATGCCAATGTCCCAGACATGGTCTTACACGT-AA--TCAAA
* *
41245905 T-CGATGCCAATGTCCCAGACGTGGTC
1 TACAATGCCAATGTCCCAGACATGGTC
41245931 ATGACATATG
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
42 29 0.30
43 6 0.06
44 56 0.58
45 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (42 bp):
TACAATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAA
Found at i:41247483 original size:20 final size:19
Alignment explanation
Indices: 41247440--41247483 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
41247430 CTTGAAAATA
*
41247440 AGCATTATTATTAGGTTTT
1 AGCATTATTATTAGGCTTT
41247459 A--ATTATTATTAGGACTTT
1 AGCATTATTATTAGG-CTTT
41247477 AGCATTA
1 AGCATTA
41247484 ACTTGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 12 0.57
18 4 0.19
19 1 0.05
20 4 0.19
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.48
Consensus pattern (19 bp):
AGCATTATTATTAGGCTTT
Found at i:41261640 original size:14 final size:14
Alignment explanation
Indices: 41261612--41261662 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
41261602 GCTCAAAATC
*
41261612 TTTTCTTT-CTTTA
1 TTTTCTTTATTTTA
41261625 TTTTCTTTATTTTA
1 TTTTCTTTATTTTA
* *
41261639 TTTACTTTAATTTCA
1 TTTTCTTT-ATTTTA
41261654 TTTT-TTTAT
1 TTTTCTTTAT
41261663 AGTTTCTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 10 0.31
14 14 0.44
15 8 0.25
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTCTTTATTTTA
Found at i:41276421 original size:56 final size:56
Alignment explanation
Indices: 41276335--41276448 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
41276325 CAAAACTTTA
41276335 AATACAATTTTCATTTATATTATTGTACATTCAACTAACCATGTAGTTTAGATTCT
1 AATACAATTTTCATTTATATTATTGTACATTCAACTAACCATGTAGTTTAGATTCT
*
41276391 AATACAATTTTCATTTATATTATTGTACATTCAGCTAACCATGTAGTTTAGATTCT
1 AATACAATTTTCATTTATATTATTGTACATTCAACTAACCATGTAGTTTAGATTCT
41276447 AA
1 AA
41276449 CTTATATTAG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (56 bp):
AATACAATTTTCATTTATATTATTGTACATTCAACTAACCATGTAGTTTAGATTCT
Found at i:41276832 original size:18 final size:19
Alignment explanation
Indices: 41276809--41276856 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
41276799 AACTCTTAAT
41276809 TTATAACCCTA-AAACATA
1 TTATAACCCTATAAACATA
41276827 TTATAACCCTATTGAAACATA
1 TTATAACCCTA-T-AAACATA
*
41276848 TTTTAACCC
1 TTATAACCC
41276857 CTTAAATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.42
21 15 0.58
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.33
Consensus pattern (19 bp):
TTATAACCCTATAAACATA
Found at i:41276892 original size:19 final size:17
Alignment explanation
Indices: 41276866--41276909 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
41276856 CCTTAAATAT
41276866 CTAAAACCTTTCAAACC
1 CTAAAACCTTTCAAACC
*
41276883 TCTCAAAACCTTTTAAACC
1 -CT-AAAACCTTTCAAACC
41276902 CTAAAACC
1 CTAAAACC
41276910 CTATTCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 6 0.25
18 4 0.17
19 14 0.58
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (17 bp):
CTAAAACCTTTCAAACC
Done.