Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 33
Found at i:2436590 original size:40 final size:40
Alignment explanation
Indices: 2436501--2436673 Score: 231
Period size: 41 Copynumber: 4.3 Consensus size: 40
2436491 CTTTAAAAAT
* * * *
2436501 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGGATA
* *
2436541 TGTCGTTGCGATTTACGTATTCTCGTTGCGATTTACAGATA
1 CG-CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
*
2436582 CGCATTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
*
2436622 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
*
2436663 CTCGTTGCGAT
1 CGCGTTGCGAT
2436674 AGTCAGAATC
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
40 54 0.46
41 64 0.54
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (40 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:2436691 original size:101 final size:101
Alignment explanation
Indices: 2436503--2436694 Score: 316
Period size: 101 Copynumber: 1.9 Consensus size: 101
2436493 TTAAAAATCG
* *
2436503 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGTATTCTCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACTCGTT
*
2436568 GCGATTTACAGATACGCATTGCGATTTACGTATTCT
66 GCGATGTACAGATACGCATTGCGATTTACGTATTCT
2436604 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACTCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACTCGTT
*
2436669 GCGATAGT-CAGA-ATCGCGTTGCGATT
66 GCGAT-GTACAGATA-CGCATTGCGATT
2436695 CTGGAAAATC
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
100 1 0.01
101 83 0.98
102 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (101 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACTCGTT
GCGATGTACAGATACGCATTGCGATTTACGTATTCT
Found at i:2436726 original size:21 final size:21
Alignment explanation
Indices: 2436702--2436749 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
2436692 ATTCTGGAAA
2436702 ATCGCAATGCGAATTTGTACT
1 ATCGCAATGCGAATTTGTACT
2436723 ATCGCAATGCGAATTTGTACT
1 ATCGCAATGCGAATTTGTACT
2436744 ATCGCA
1 ATCGCA
2436750 TTGTGATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (21 bp):
ATCGCAATGCGAATTTGTACT
Found at i:2436814 original size:20 final size:19
Alignment explanation
Indices: 2436765--2436816 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2436755 ATTCTTCATA
2436765 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
2436784 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
2436805 ATCGCGTTGCGA
1 ATCGCGTTGCGA
2436817 ATTTTATTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:2437474 original size:30 final size:29
Alignment explanation
Indices: 2437391--2437479 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
2437381 ATACCATAAA
2437391 ATAA-ATATTTTCAAAAACTATAATATAT
1 ATAATATATTTTCAAAAACTATAATATAT
*
2437419 AATAATAT-TTTTCAAAAATTATAATATAT
1 -ATAATATATTTTCAAAAACTATAATATAT
* *
2437448 ATAGCATCTATTTTC-AAAACTATAATAAAT
1 ATA--ATATATTTTCAAAAACTATAATATAT
2437478 AT
1 AT
2437480 CTTAAAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.06
29 24 0.46
30 20 0.38
31 5 0.10
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (29 bp):
ATAATATATTTTCAAAAACTATAATATAT
Found at i:2440021 original size:24 final size:24
Alignment explanation
Indices: 2439976--2440022 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2439966 TCTTGAACCC
* * *
2439976 CTTTTTTTATTTTTTTTTATTTTT
1 CTTTTTTTATTTCTTCTCATTTTT
*
2440000 CTTTTTTTCTTTCTTCTCATTTT
1 CTTTTTTTATTTCTTCTCATTTT
2440023 AGGTAAAGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (24 bp):
CTTTTTTTATTTCTTCTCATTTTT
Found at i:2447014 original size:31 final size:30
Alignment explanation
Indices: 2446979--2447048 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
2446969 TACCTATTTG
*
2446979 AATAAAAAAATAAAGTTTAGGTA-TTAATT
1 AATAAAAAAATAAAGTTCAGGTATTTAATT
* * *
2447008 AAAATAAAAAAGTCAAGTTCATGTATTTAATT
1 --AATAAAAAAATAAAGTTCAGGTATTTAATT
2447040 AATAAAAAA
1 AATAAAAAA
2447049 TTAGATATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.26
31 19 0.56
32 6 0.18
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (30 bp):
AATAAAAAAATAAAGTTCAGGTATTTAATT
Found at i:2449895 original size:23 final size:23
Alignment explanation
Indices: 2449854--2450019 Score: 122
Period size: 23 Copynumber: 7.2 Consensus size: 23
2449844 CACCATAGCT
2449854 CGTAGAATATG-CACCGAAGTG-CCA
1 CGTAGAA-ATGTC-CCGAAG-GACCA
*
2449878 TGTAGAAATGTCCCGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
* * **
2449901 CATAGATATGTCCCGAAGGACTG
1 CGTAGAAATGTCCCGAAGGACCA
* *
2449924 TGTAGAAATGTCCTGAAGGACCA
1 CGTAGAAATGTCCCGAAGGACCA
* * * * *
2449947 CATAGATATATCTCGAATGA-CA
1 CGTAGAAATGTCCCGAAGGACCA
*
2449969 GCGTAGAAATGTCTCGAAGGACCA
1 -CGTAGAAATGTCCCGAAGGACCA
* * * *
2449993 TGTAGAATTATCCCGAAGGACCG
1 CGTAGAAATGTCCCGAAGGACCA
2450016 CGTA
1 CGTA
2450020 AAACCCTCGA
Statistics
Matches: 109, Mismatches: 29, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
22 3 0.03
23 97 0.89
24 9 0.08
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGTCCCGAAGGACCA
Found at i:2450019 original size:46 final size:45
Alignment explanation
Indices: 2449879--2450019 Score: 167
Period size: 46 Copynumber: 3.1 Consensus size: 45
2449869 GAAGTGCCAT
* * *
2449879 GTAGAAATGTCCCGAAGGACCACATAGATATGTCCCGAAGGACTGT
1 GTAGAAATGT-CCGAAGGACCACATAGATATATCCCGAAGGACAGC
* *
2449925 GTAGAAATGTCCTGAAGGACCACATAGATATATCTCGAATGACAGC
1 GTAGAAATGTCC-GAAGGACCACATAGATATATCCCGAAGGACAGC
** *
2449971 GTAGAAATGTCTCGAAGGACCATGTAGA-ATTATCCCGAAGGACCGC
1 GTAGAAATGTC-CGAAGGACCACATAGATA-TATCCCGAAGGACAGC
2450017 GTA
1 GTA
2450020 AAACCCTCGA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
45 3 0.04
46 78 0.95
47 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (45 bp):
GTAGAAATGTCCGAAGGACCACATAGATATATCCCGAAGGACAGC
Found at i:2450118 original size:14 final size:14
Alignment explanation
Indices: 2450099--2450163 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
2450089 TTATAATATT
2450099 TCACATAACTTATA
1 TCACATAACTTATA
2450113 TCACATATA-TATATAA
1 TCACATA-ACT-TAT-A
* * *
2450129 TCACATAGCTCATTG
1 TCACATAACTTA-TA
2450144 TCACATAACTTATA
1 TCACATAACTTATA
2450158 TCACAT
1 TCACAT
2450164 TTTCATGTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 15 0.38
15 15 0.38
16 10 0.25
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (14 bp):
TCACATAACTTATA
Found at i:2450237 original size:45 final size:45
Alignment explanation
Indices: 2450103--2450240 Score: 179
Period size: 45 Copynumber: 3.1 Consensus size: 45
2450093 AATATTTCAC
* * * * * *
2450103 ATAACTTATATCACATATAT-ATATAATCACATAGCTCATTGTCAC
1 ATAACTTATATCACAT-TTTCATGTAATCACATAGGTCAATATCAT
*
2450148 ATAACTTATATCACATTTTCATGTAATCACATAGGTTAATATCAT
1 ATAACTTATATCACATTTTCATGTAATCACATAGGTCAATATCAT
* *
2450193 ATATCTTATATCACATTTTCATGTAATCAAATAGGTCAATATCAT
1 ATAACTTATATCACATTTTCATGTAATCACATAGGTCAATATCAT
2450238 ATA
1 ATA
2450241 GCATAAAATA
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 2 0.02
45 80 0.98
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (45 bp):
ATAACTTATATCACATTTTCATGTAATCACATAGGTCAATATCAT
Found at i:2460128 original size:14 final size:14
Alignment explanation
Indices: 2460111--2460143 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2460101 TTAAAATTGT
2460111 TATTATTATTATTA
1 TATTATTATTATTA
2460125 TATTATTATTATTA
1 TATTATTATTATTA
2460139 T-TTAT
1 TATTAT
2460144 GTTTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:2460155 original size:3 final size:3
Alignment explanation
Indices: 2460110--2460140 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2460100 ATTAAAATTG
2460110 TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2460141 TATGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2464222 original size:220 final size:220
Alignment explanation
Indices: 2463840--2464283 Score: 843
Period size: 220 Copynumber: 2.0 Consensus size: 220
2463830 GATATGAAAC
2463840 AATGAATGAGATATTAGTGTGTGTTGGTAGGATCGAGAGAATTTAGGAGCAACTTGTAAAGACCC
1 AATGAATGAGATATTAGTGTGTGTTGGTAGGATCGAGAGAATTTAGGAGCAACTTGTAAAGACCC
*
2463905 AACAAGAAATGATTGATGAAGCAAGGAAGTTCCAAGTTGAATCTAGAGAACATATGTCCAAGTTG
66 AACAAGAAATGATTGATGAAGCAAGGAAGTTCCAAGTTGAATCTAGAGAACAGATGTCCAAGTTG
2463970 ATGAACATGATTATTACAGTGGTATGTGGAGAGAAATCATTAGAGAACCCTATTATCCAAGAGAA
131 ATGAACATGATTATTACAGTGGTATGTGGAGAGAAATCATTAGAGAACCCTATTATCCAAGAGAA
2464035 TATGAAGACTTTGAGTGAAAATCAG
196 TATGAAGACTTTGAGTGAAAATCAG
* *
2464060 AATGAATGAGATATTAGTGTGTGTTGGTAGGATCGAGAGAATTTATGAGCAACTTGTAAAGGCCC
1 AATGAATGAGATATTAGTGTGTGTTGGTAGGATCGAGAGAATTTAGGAGCAACTTGTAAAGACCC
2464125 AACAAGAAATGATTGATGAAGCAAGGAAGTTCCAAGTTGAATCTAGAGAACAGATGTCCAAGTTG
66 AACAAGAAATGATTGATGAAGCAAGGAAGTTCCAAGTTGAATCTAGAGAACAGATGTCCAAGTTG
* *
2464190 ATGAATATGATTATTACAGTGGTATGTGGAGAGAAATCGTTAGAGAACCCTATTATCCAAGAGAA
131 ATGAACATGATTATTACAGTGGTATGTGGAGAGAAATCATTAGAGAACCCTATTATCCAAGAGAA
2464255 TATGAAGACTTTGAGTGAAAATCAG
196 TATGAAGACTTTGAGTGAAAATCAG
2464280 AATG
1 AATG
2464284 TTGATTATGC
Statistics
Matches: 219, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
220 219 1.00
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (220 bp):
AATGAATGAGATATTAGTGTGTGTTGGTAGGATCGAGAGAATTTAGGAGCAACTTGTAAAGACCC
AACAAGAAATGATTGATGAAGCAAGGAAGTTCCAAGTTGAATCTAGAGAACAGATGTCCAAGTTG
ATGAACATGATTATTACAGTGGTATGTGGAGAGAAATCATTAGAGAACCCTATTATCCAAGAGAA
TATGAAGACTTTGAGTGAAAATCAG
Found at i:2466853 original size:7 final size:7
Alignment explanation
Indices: 2466825--2466919 Score: 83
Period size: 7 Copynumber: 14.0 Consensus size: 7
2466815 TACTACACTC
2466825 GAAAAAA
1 GAAAAAA
*
2466832 G-AAGAA
1 GAAAAAA
2466838 -AAAAAA
1 GAAAAAA
*
2466844 GAAAATA
1 GAAAAAA
2466851 GAAAAAA
1 GAAAAAA
* *
2466858 TAAAAAG
1 GAAAAAA
2466865 GAAAAAA
1 GAAAAAA
2466872 GAAAAAA
1 GAAAAAA
2466879 G-AAAAA
1 GAAAAAA
2466885 G-AAAAA
1 GAAAAAA
2466891 GAAAAAAA
1 G-AAAAAA
*
2466899 GAATAAA
1 GAAAAAA
*
2466906 TAATAAAA
1 GAA-AAAA
2466914 -AAAAAA
1 GAAAAAA
2466920 TAAGGAAGAT
Statistics
Matches: 72, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
6 24 0.33
7 39 0.54
8 9 0.12
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (7 bp):
GAAAAAA
Found at i:2466876 original size:6 final size:6
Alignment explanation
Indices: 2466827--2466896 Score: 70
Period size: 6 Copynumber: 10.8 Consensus size: 6
2466817 CTACACTCGA
*
2466827 AAAAAG AAGAAA- AAAAAG AAAATAG AAAAAAT AAAAAGG AAAAAAG AAAAAAG
1 AAAAAG AA-AAAG AAAAAG AAAA-AG -AAAAAG AAAAA-G -AAAAAG -AAAAAG
2466880 AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAA
2466897 AAGAATAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
5 3 0.05
6 30 0.54
7 14 0.25
8 9 0.16
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:2466917 original size:27 final size:26
Alignment explanation
Indices: 2466837--2466901 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 26
2466827 AAAAAGAAGA
*
2466837 AAAAAAAGAAAATAGAAAAAATAAAAAG
1 AAAAAAAGAAAA-AG-AAAAAGAAAAAG
*
2466865 GAAAAAAGAAAAAAGAAAAAGAAAAAG
1 AAAAAAAG-AAAAAGAAAAAGAAAAAG
2466892 AAAAAAAGAA
1 AAAAAAAGAA
2466902 TAAATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 2 0.06
27 18 0.55
28 9 0.27
29 4 0.12
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (26 bp):
AAAAAAAGAAAAAGAAAAAGAAAAAG
Found at i:2469686 original size:55 final size:55
Alignment explanation
Indices: 2469617--2470682 Score: 862
Period size: 55 Copynumber: 19.3 Consensus size: 55
2469607 GAAGTAGAAG
* * * * *
2469617 CGTTGGCAGAAGATTGTTTGAGTTCCATACTCCCTGAAGCAATAGGAAGCAAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* *
2469672 CGTTGGTAGAAGATTGTTCGAGTTCCATACTCCCTAAAGCAATAGGGAGCGAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * * * * * **
2469727 CGTTCGCAGAAGATTATTCGAGCTCCATACTCCCTGAAGCAATAAGGAGAAAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * * * * * * *
2469782 CATTGGAAAAAGATTGTTTGAGTTCCATACTCCCTGAAGCAATAGAGAGTGAACT
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * * * *
2469837 TGTTCGTAAAAGATTGTTTC-AGTTCCATACTCCCTAAAGCAATAGGGAG-GAACC
1 CGTTGGTAGAAGATTG-TTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * * * *
2469891 CGTTGGAAAAAGATTATTCGAGTTCTATACTCCCTGAAACAAGAGGGAGCGAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
*** * **
2469946 CGTTTACAGAAGATTGTTCGAGTT-TCATACTCCCTGAAGTAATAGGGAGCGAATT
1 CGTTGGTAGAAGATTGTTCGAGTTCT-ATACTCCCTGAAGCAATAGGGAGCGAACC
* * * * * *
2470001 CGTTGGCAAAAGATTATTCGAGTTCTATACTCCCTGAAGTAAGAAGGAGCGAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * * * *
2470056 AGTTTGCAGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAATAGGGAGCAAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * * * * * *
2470111 CATTTGCAGAAGATTGTCCGAATTCTATACTCCCTGAAAAG-AATAGGAAGCAAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTG--AAGCAATAGGGAGCGAACC
* * * * * * *
2470167 CGTTGGCAGAAGATTATTCGAGTTATATACTCCCTGAAGCAAGAAGGTGTGAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
** * * * * ** * *
2470222 TATTGGCAGAAGATTTTTTGAGTTCTATACTTCCTGAAGTGATATGGAGTGAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* **
2470277 CTTTTTTAGAAGATTGTTCGAGTTCTATACTCCCTGAAAAG-AATAGGGAGCGAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTG--AAGCAATAGGGAGCGAACC
* * * * * * * *
2470333 CATT-TTCTGAAGATTATTCAAGTTTTATACTCCCTGAAACAATATGGAGCGAACC
1 CGTTGGT-AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* ** *
2470388 CATTTTTAGAAGATT-TCTCGAGTTCTATACTCCCTGAAGTAATAGGGAGCGAACC
1 CGTTGGTAGAAGATTGT-TCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
** * * ** * **
2470443 CGTTTTTAGAAG-TTTTCTCGAGTTCCATACTCCCTGAAATAAATAAGGAGAAAACC
1 CGTTGGTAGAAGATTGT-TCGAGTTCTATACTCCCTG-AAGCAATAGGGAGCGAACC
* * *
2470499 CACTT--TCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAAGGAGTGAACC
1 C-GTTGGT-AGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
** * * * * *
2470554 C-TTTTTCAGCAGATT-TCTTGAGTTCCATACTCCCTGAAAAG-AATAGGGAGCAAAAC
1 CGTTGGT-AGAAGATTGT-TCGAGTTCTATACTCCCTG--AAGCAATAGGGAGCGAACC
* * * *
2470610 CATTTGTAGAAGATTGTTCGATTTCTATACTCCCTGAAGCAATAGGGAGTGAACC
1 CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * *
2470665 CGCTGATCGAAGATTGTT
1 CGTTGGTAGAAGATTGTT
2470683 GAAAGAAGAG
Statistics
Matches: 829, Mismatches: 155, Indels: 54
0.80 0.15 0.05
Matches are distributed among these distances:
53 5 0.01
54 54 0.07
55 589 0.71
56 162 0.20
57 19 0.02
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (55 bp):
CGTTGGTAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
Found at i:2470679 original size:166 final size:165
Alignment explanation
Indices: 2469624--2470682 Score: 972
Period size: 166 Copynumber: 6.4 Consensus size: 165
2469614 AAGCGTTGGC
* * *
2469624 AGAAGATTGTTTGAGTTCCATACTCCCTGAAGCAATAGGAAGCAAACCCGTTGGT-AGAAGATTG
1 AGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAATAGGGAGCGAACCCGTT-GTCAGAAGATTG
* * * * *
2469688 TTCGAGTTCCATACTCCCTAAAGCAATAGGGAGCGAACCCGTTCGCAGAAGATTATTCGAGCTCC
65 TTCGAGTTCTATACTCCCTGAAGCAATAAGGAGCGAACCCGTTTGCAGAAGATTATTCGAGTTCC
* * * *
2469753 ATACTCCCTGAAGCAATAAGGAGAAAACCCATTGGA
130 ATACTCCCTGAAGCAATAGGGAGCAAACCCATTTGT
* * * * ** *
2469789 AAAAGATTGTTTGAGTTCCATACTCCCTGAAGCAATAGAGAGTGAACTTGTTCGT-AAAAGATTG
1 AGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAATAGGGAGCGAACCCGTT-GTCAGAAGATTG
* * * * * *
2469853 TTTC-AGTTCCATACTCCCTAAAGCAATAGGGAG-GAACCCGTTGGAAAAAGATTATTCGAGTTC
65 -TTCGAGTTCTATACTCCCTGAAGCAATAAGGAGCGAACCCGTTTGCAGAAGATTATTCGAGTTC
* * * * * **
2469916 TATACTCCCTGAAACAAGAGGGAGCGAACCCGTTTAC
129 CATACTCCCTGAAGCAATAGGGAGCAAACCCATTTGT
* * ** * * *
2469953 AGAAGATTGTTCGAGTTTCATACTCCCTGAAGTAATAGGGAGCGAATTCGTTGGCAAAAGATTAT
1 AGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAATAGGGAGCGAACCCGTTGTCAGAAGATTGT
* * * *
2470018 TCGAGTTCTATACTCCCTGAAGTAAGAAGGAGCGAACCAGTTTGCAGAAGATTGTTCGAGTTCCA
66 TCGAGTTCTATACTCCCTGAAGCAATAAGGAGCGAACCCGTTTGCAGAAGATTATTCGAGTTCCA
*
2470083 TACTCCCTGAAGCAATAGGGAGCAAACCCATTTGC
131 TACTCCCTGAAGCAATAGGGAGCAAACCCATTTGT
* * * * * *
2470118 AGAAGATTGTCCGAATTCTATACTCCCTGAAAAG-AATAGGAAGCAAACCCGTTGGCAGAAGATT
1 AGAAGATTGTTCGAGTTCCATACTCCCTG--AAGCAATAGGGAGCGAACCCGTTGTCAGAAGATT
* * * * * ** * * *
2470182 ATTCGAGTTATATACTCCCTGAAGCAAGAAGGTGTGAACCTATTGGCAGAAGATTTTTTGAGTTC
64 GTTCGAGTTCTATACTCCCTGAAGCAATAAGGAGCGAACCCGTTTGCAGAAGATTATTCGAGTTC
* * ** * ** * *
2470247 TATACTTCCTGAAGTGATATGGAGTGAACCCTTTTTT
129 CATACTCCCTGAAGCAATAGGGAGCAAACCCATTTGT
* * * *
2470284 AGAAGATTGTTCGAGTTCTATACTCCCTGAAAAG-AATAGGGAGCGAACCCATTTTCTGAAGATT
1 AGAAGATTGTTCGAGTTCCATACTCCCTG--AAGCAATAGGGAGCGAACCCGTTGTCAGAAGATT
* * * * * * **
2470348 ATTCAAGTTTTATACTCCCTGAAACAATATGGAGCGAACCCATTTTTAGAAGATT-TCTCGAGTT
64 GTTCGAGTTCTATACTCCCTGAAGCAATAAGGAGCGAACCCGTTTGCAGAAGATTAT-TCGAGTT
* * * * *
2470412 CTATACTCCCTGAAGTAATAGGGAGCGAACCCGTTTTT
128 CCATACTCCCTGAAGCAATAGGGAGCAAACCCATTTGT
* ** * ** *
2470450 AGAAG-TTTTCTCGAGTTCCATACTCCCTGAAATAAATAAGGAGAAAACCCACTT-TCAGAAGAT
1 AGAAGATTGT-TCGAGTTCCATACTCCCTG-AAGCAATAGGGAGCGAACCC-GTTGTCAGAAGAT
* * * * *
2470513 TGTTCGAGTTCTATACTCCCTGAAGCAATAAGGAGTGAACCCTTTTTCAGCAGATT-TCTTGAGT
63 TGTTCGAGTTCTATACTCCCTGAAGCAATAAGGAGCGAACCCGTTTGCAGAAGATTAT-TCGAGT
*
2470577 TCCATACTCCCTGAAAAG-AATAGGGAGCAAAACCATTTGT
127 TCCATACTCCCTG--AAGCAATAGGGAGCAAACCCATTTGT
* * * *
2470617 AGAAGATTGTTCGATTTCTATACTCCCTGAAGCAATAGGGAGTGAACCCGCTGATC-GAAGATTG
1 AGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAATAGGGAGCGAACCCGTTG-TCAGAAGATTG
2470681 TT
65 TT
2470683 GAAAGAAGAG
Statistics
Matches: 744, Mismatches: 135, Indels: 29
0.82 0.15 0.03
Matches are distributed among these distances:
163 4 0.01
164 129 0.17
165 173 0.23
166 385 0.52
167 47 0.06
168 6 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (165 bp):
AGAAGATTGTTCGAGTTCCATACTCCCTGAAGCAATAGGGAGCGAACCCGTTGTCAGAAGATTGT
TCGAGTTCTATACTCCCTGAAGCAATAAGGAGCGAACCCGTTTGCAGAAGATTATTCGAGTTCCA
TACTCCCTGAAGCAATAGGGAGCAAACCCATTTGT
Found at i:2470926 original size:29 final size:29
Alignment explanation
Indices: 2470892--2470955 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
2470882 GGGTTATCAA
*
2470892 TATTATATTAAAATTATTATTATTATTAT
1 TATTATATTAAAATTATTATTATCATTAT
**
2470921 TATTATATTATTATTATTATTATCATTAT
1 TATTATATTAAAATTATTATTATCATTAT
2470950 TATTAT
1 TATTAT
2470956 TTATGTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (29 bp):
TATTATATTAAAATTATTATTATCATTAT
Found at i:2470971 original size:3 final size:3
Alignment explanation
Indices: 2470904--2470956 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
2470894 TTATATTAAA
*
2470904 ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2470951 ATT ATT
1 ATT ATT
2470957 TATGTTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2475057 original size:27 final size:27
Alignment explanation
Indices: 2475019--2475070 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2475009 CTCTTGCTGA
* *
2475019 TCAGGCATCAGTTTAGACTCCTACTGG
1 TCAGGCACCAGTTCAGACTCCTACTGG
2475046 TCAGGCACCAGTTCAGACTCCTACT
1 TCAGGCACCAGTTCAGACTCCTACT
2475071 CATACTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (27 bp):
TCAGGCACCAGTTCAGACTCCTACTGG
Found at i:2483500 original size:10 final size:10
Alignment explanation
Indices: 2483487--2483541 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
2483477 ATAAAAATCC
*
2483487 AAATATAGAA
1 AAATATATAA
*
2483497 AAATA-AAAGA
1 AAATATATA-A
*
2483507 AAAAAT-TAA
1 AAATATATAA
2483516 AAATATATAA
1 AAATATATAA
2483526 AAATATATAA
1 AAATATATAA
2483536 AAATAT
1 AAATAT
2483542 CTAATGAGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 8 0.21
10 30 0.79
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (10 bp):
AAATATATAA
Found at i:2486790 original size:576 final size:576
Alignment explanation
Indices: 2485698--2486846 Score: 1807
Period size: 576 Copynumber: 2.0 Consensus size: 576
2485688 TCATCATCCT
*
2485698 AGTCTGTGTATTTATTGAGTTGTAGAATATCACCACTTGTCCATACGAGGAATCCGTACATGGGA
1 AGTCTGTGTATTTATTGAGTTGTAGAACATCACCACTTGTCCATACGAGGAATCCGTACATGGGA
* **
2485763 CATCTTCGTAAAAGCTCTATGTATCACTCCCAAGCTTCGTACATGGATTCATCATTTGCCTGTTG
66 CATCTTCGTAAAAGCTCCATGTATCACTCCCAAGCTTCGTACATGGATTCATCATTTGCCTGTCA
* *
2485828 GAAATAAGTAATATAATTACGTAATTTATCAATTATAGTTATAGAACCAAATCTAGCAAGGAAAT
131 GAAAGAAGTAATATAATTACGTAATTTATCAATCATAGTTATAGAACCAAATCTAGCAAGGAAAT
* *
2485893 CACAGCATAAATTCATCCAAGACTTAAGAGATCCGAATGGGATACTATTCAAGCACAATTTTGCC
196 CACAGCATAAATTCATCCAAGACTTAAGAGATCCGAATGGGATACTATTCAACCACAATTTCGCC
* * * *
2485958 CTATCCCTTAGTGAATGGGGGAATAATTTCAGTCTTAAGACATCCTCATGGACTCCTTGTTGCTT
261 CTATCCCTCAGTAAATGGAGGAATAATTTCAGTCTTAAGACATCCTCATGGACTCCATGTTGCTT
**
2486023 GAATGAATTGAAAATTTCCAGGAATGATTTGAGATGTTGTATGGTATCTTCTATTGTTGATCCAC
326 GAATGAATTGAAAATTTCCAGGAATGATTTGAGATGTTGTATGACATCTTCTATTGTTGATCCAC
* * * *
2486088 CAAATTGACAAATTATGTTGATCATATTAAACATTATTGACTTTAATTTGAAATAGGTAACTTTT
391 CAAATTGACAAATTATGTTGATCATATTAAACATTACTGACTTTAATTCGAAATAGGCAACTTCT
* * * *
2486153 ATTTCAGGTGTGATAACTCTTGGATTGAGATCTTTGATATGTTCCTCTAAGTAGTCTCGAATGAG
456 ATTTCAGGTGTGACAACTCTTGAATTGAGATCTCTGATATCTTCCTCTAAGTAGTCTCGAATGAG
* *
2486218 TTTGTTTCTTACTTGAGCATGTCTCTCAACTAAAGCTCCTCCTCTAGCTTCGAAAG
521 TTTGTTTCTTACTTGAGCATGTCGCTCAACTAAAGCTCCTCATCTAGCTTCGAAAG
** * *
2486274 AGTCTGTGTATTTATTGAGTTGTAGAACATCGTCACTTGTCCATACGAGGAATTCGTGCATGGGA
1 AGTCTGTGTATTTATTGAGTTGTAGAACATCACCACTTGTCCATACGAGGAATCCGTACATGGGA
***
2486339 CATCTTCGTAAAAGCTCCATGTATCACTTTTAAGCTTCGTACATGGATTCATCATTTGCCTGTCA
66 CATCTTCGTAAAAGCTCCATGTATCACTCCCAAGCTTCGTACATGGATTCATCATTTGCCTGTCA
* * * *
2486404 GAAAGAAGTAATATCATTATGTAATTTATCAGTCATAGTTGTAGAACCAAATCTAGCAAGGAAAT
131 GAAAGAAGTAATATAATTACGTAATTTATCAATCATAGTTATAGAACCAAATCTAGCAAGGAAAT
* *
2486469 CAC-GACATAAATTCATCCAAGACTTAAGAGATTCGAATGGGATACTATTCAACCATAATTTCGC
196 CACAG-CATAAATTCATCCAAGACTTAAGAGATCCGAATGGGATACTATTCAACCACAATTTCGC
* *
2486533 CCTATCCCTCAGTAAATGGAGGAATAATTTCAGTCTTAGGACATCCTGATGGACTCCATGTTGCT
260 CCTATCCCTCAGTAAATGGAGGAATAATTTCAGTCTTAAGACATCCTCATGGACTCCATGTTGCT
* **
2486598 TGAATGAATTGAAAATTTCCAGGAATGATTTGAGATGTTGTCTGACATCTTCTATTGTTGATCTG
325 TGAATGAATTGAAAATTTCCAGGAATGATTTGAGATGTTGTATGACATCTTCTATTGTTGATCCA
* * * * *
2486663 CCAAATTGACCAATTGTGTTGATCATATTGAACATTACTGACTTTAATTCGAAATATGCATCTTC
390 CCAAATTGACAAATTATGTTGATCATATTAAACATTACTGACTTTAATTCGAAATAGGCAACTTC
* * *
2486728 TATTTTAGGTGTGGCAACTCTTGAATTGAGA-CTGCTGATATCTTCCTCTAAGTAGTCTCGAATT
455 TATTTCAGGTGTGACAACTCTTGAATTGAGATCT-CTGATATCTTCCTCTAAGTAGTCTCGAATG
*
2486792 AGTTTGTTTCTTACTTGAGCATGTCGCTCAACTAAAGCTCCTCATCTTGCTTCGA
519 AGTTTGTTTCTTACTTGAGCATGTCGCTCAACTAAAGCTCCTCATCTAGCTTCGA
2486847 TTATCTGGTC
Statistics
Matches: 520, Mismatches: 51, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
575 3 0.01
576 517 0.99
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (576 bp):
AGTCTGTGTATTTATTGAGTTGTAGAACATCACCACTTGTCCATACGAGGAATCCGTACATGGGA
CATCTTCGTAAAAGCTCCATGTATCACTCCCAAGCTTCGTACATGGATTCATCATTTGCCTGTCA
GAAAGAAGTAATATAATTACGTAATTTATCAATCATAGTTATAGAACCAAATCTAGCAAGGAAAT
CACAGCATAAATTCATCCAAGACTTAAGAGATCCGAATGGGATACTATTCAACCACAATTTCGCC
CTATCCCTCAGTAAATGGAGGAATAATTTCAGTCTTAAGACATCCTCATGGACTCCATGTTGCTT
GAATGAATTGAAAATTTCCAGGAATGATTTGAGATGTTGTATGACATCTTCTATTGTTGATCCAC
CAAATTGACAAATTATGTTGATCATATTAAACATTACTGACTTTAATTCGAAATAGGCAACTTCT
ATTTCAGGTGTGACAACTCTTGAATTGAGATCTCTGATATCTTCCTCTAAGTAGTCTCGAATGAG
TTTGTTTCTTACTTGAGCATGTCGCTCAACTAAAGCTCCTCATCTAGCTTCGAAAG
Found at i:2488171 original size:59 final size:59
Alignment explanation
Indices: 2488079--2488207 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
2488069 CGTAGTGCTA
* **
2488079 TCCCGAATATGACACATAAGGTCGTGCCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* * * ** *
2488138 TCCCGAATATGACACATAAGGTCGTTCCCACCATATACACTAGGTATTCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
2488197 TCCCGAATATG
1 TCCCGAATATG
2488208 CAGCCTGCTG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:2494459 original size:3 final size:3
Alignment explanation
Indices: 2494453--2494526 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
2494443 GTATCATTTG
2494453 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2494501 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2494527 TATGAACAGG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2495060 original size:42 final size:42
Alignment explanation
Indices: 2494974--2495080 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 42
2494964 ACCCAAAGGT
* * * *
2494974 CTGACGGATGACCCTAAGGACTT-ATCATCTTGCTCAAAAGA
1 CTGACAGATGACCCTAAGGATTTAAGCATCATGCTCAAAAGA
* *
2495015 CTGATAGATGACCCTAAGGATTTAAGCATCATGCTCGAAAGA
1 CTGACAGATGACCCTAAGGATTTAAGCATCATGCTCAAAAGA
* *
2495057 CTGACAGATGATCCGAAGGATTTA
1 CTGACAGATGACCCTAAGGATTTA
2495081 CAAATTTGTG
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
41 20 0.36
42 36 0.64
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (42 bp):
CTGACAGATGACCCTAAGGATTTAAGCATCATGCTCAAAAGA
Found at i:2495171 original size:249 final size:249
Alignment explanation
Indices: 2494867--2495434 Score: 956
Period size: 249 Copynumber: 2.3 Consensus size: 249
2494857 GGAAATCACT
* * *
2494867 TTCTTACTTTTTAAGAATTTCATTTTCTAGAACATTAAATGTGAAATTTTGAAAATCACTTTCTC
1 TTCTTACTTTTCAAGAATTTCATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTC
* *
2494932 ATTTTCATGTGAAAATCATATATAAACATCCTACCCAAAGGTCTGACGGATGACCCTAAGGACTT
66 ATTTTCATGCGAAAATCATATATAAACATCCTACCCAAAGGTCTGACAGATGACCCTAAGGACTT
* *
2494997 ATCATCTTGCTCAAAAGACTGATAGATGACCCTAAGGATTTAAGCATCATGCTCGAAAGACTGAC
131 ATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTGAC
* * *
2495062 AGATGATCCGAAGGATTTACAAATTTGTGGGAAATAATTTACTGGCTAAGAAAC
196 AGATAACCCGAAGGATTGACAAATTTGTGGGAAATAATTTACTGGCTAAGAAAC
* *
2495116 TTCTTACTTTTCAAAAATTTCATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCGCTTTCTC
1 TTCTTACTTTTCAAGAATTTCATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTC
* * *
2495181 ATTTTCATGCGAAAATCATATGTAAACATCCTACCCAAAGGTCTGGCAGATGGCCCTAAGGACTT
66 ATTTTCATGCGAAAATCATATATAAACATCCTACCCAAAGGTCTGACAGATGACCCTAAGGACTT
*
2495246 ATCATCTTGCTCAAAAGACTGACATATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTGAC
131 ATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTGAC
*
2495311 AGATAACCCGAAGGATTGACAAATTTGTGGGAAATAATTTACTGGGTAAGAAAC
196 AGATAACCCGAAGGATTGACAAATTTGTGGGAAATAATTTACTGGCTAAGAAAC
* * *
2495365 TTCTTATTTTTCAAGAATTTCATTTTCTATAACATTAAATGAGAAACTTTGAAAATCATTTTCTC
1 TTCTTACTTTTCAAGAATTTCATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTC
2495430 ATTTT
66 ATTTT
2495435 TCGAAACAAC
Statistics
Matches: 297, Mismatches: 22, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
249 297 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (249 bp):
TTCTTACTTTTCAAGAATTTCATTTTCTAGAACATTAAATGAGAAACTTTGAAAATCACTTTCTC
ATTTTCATGCGAAAATCATATATAAACATCCTACCCAAAGGTCTGACAGATGACCCTAAGGACTT
ATCATCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTGAC
AGATAACCCGAAGGATTGACAAATTTGTGGGAAATAATTTACTGGCTAAGAAAC
Found at i:2495299 original size:42 final size:42
Alignment explanation
Indices: 2495248--2495327 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
2495238 AAGGACTTAT
* * *
2495248 CATCTTGCTCAAAAGACTGACATATGACCCGAAGGATTTAAG
1 CATCATGCTCAAAAGACTGACAGATAACCCGAAGGATTTAAG
*
2495290 CATCATGCTCGAAAGACTGACAGATAACCCGAAGGATT
1 CATCATGCTCAAAAGACTGACAGATAACCCGAAGGATT
2495328 GACAAATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
CATCATGCTCAAAAGACTGACAGATAACCCGAAGGATTTAAG
Found at i:2501468 original size:23 final size:22
Alignment explanation
Indices: 2501436--2501481 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2501426 GTTTAATATA
* * *
2501436 TATATTATACTTATTACATTTTG
1 TATATCATACATA-TACATATTG
2501459 TATATCATACATATACATATTG
1 TATATCATACATATACATATTG
2501481 T
1 T
2501482 TTCACAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (22 bp):
TATATCATACATATACATATTG
Found at i:2501840 original size:23 final size:23
Alignment explanation
Indices: 2501806--2501874 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2501796 CACCACAACT
* *
2501806 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2501829 CGTAGAATTGCACTGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
2501852 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2501875 TATAAGATTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2502207 original size:6 final size:6
Alignment explanation
Indices: 2502198--2502223 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2502188 CATATCATTC
2502198 ACATAT ACATAT ACATAT ACATAT AC
1 ACATAT ACATAT ACATAT ACATAT AC
2502224 TCATATAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (6 bp):
ACATAT
Found at i:2503525 original size:14 final size:14
Alignment explanation
Indices: 2503496--2503533 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
2503486 ACCACCAAAC
2503496 TTAACTACAACCATT
1 TTAACTA-AACCATT
*
2503511 TTAACTAACCCATT
1 TTAACTAAACCATT
2503525 TTAACTAAA
1 TTAACTAAA
2503534 TTCTATCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (14 bp):
TTAACTAAACCATT
Found at i:2507859 original size:3 final size:3
Alignment explanation
Indices: 2507853--2507916 Score: 85
Period size: 3 Copynumber: 21.7 Consensus size: 3
2507843 ATATTATTTG
* * *
2507853 TAA TAA TAA AAA TAA T-A TAC TAA TAC TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2507900 TAA TAA TAA CAA TAA TA
1 TAA TAA TAA TAA TAA TA
2507917 TATATGAACA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2516413 original size:19 final size:19
Alignment explanation
Indices: 2516389--2516441 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2516379 AGAATGTTTA
*
2516389 AAAGTATCGATACTTGTAG
1 AAAGTATCGATACTTGTAC
* *
2516408 AAAGTATCGAAACTTTTAC
1 AAAGTATCGATACTTGTAC
*
2516427 AGGAGTATCGATACT
1 A-AAGTATCGATACT
2516442 CTTGGGCTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACTTGTAC
Found at i:2520502 original size:23 final size:24
Alignment explanation
Indices: 2520462--2520508 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
2520452 CACCAGATAC
2520462 CATTTTAACATCAAATTTT-TATT
1 CATTTTAACATCAAATTTTATATT
*
2520485 CATTTTATCA-CAATATTTTATATT
1 CATTTTAACATCAA-ATTTTATATT
2520509 GATACTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 14 0.67
24 4 0.19
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (24 bp):
CATTTTAACATCAAATTTTATATT
Found at i:2520692 original size:116 final size:116
Alignment explanation
Indices: 2520488--2520719 Score: 448
Period size: 116 Copynumber: 2.0 Consensus size: 116
2520478 TTTTATTCAT
2520488 TTTATCACAATATTTTATATTGATACTACATTGAATTTTAGTTTCGTCTTCAATTATATCGTTAG
1 TTTATCACAATATTTTATATTGATACTACATTGAATTTTAGTTTCGTCTTCAATTATATCGTTAG
2520553 ACAATTAACTCTAAAACAAAATGGAAATGTGGACGATAGTTCTATCGAGAC
66 ACAATTAACTCTAAAACAAAATGGAAATGTGGACGATAGTTCTATCGAGAC
2520604 TTTATCACAAT-TTTTAATATTGATACTACATTGAATTTTAGTTTCGTCTTCAATTATATCGTTA
1 TTTATCACAATATTTT-ATATTGATACTACATTGAATTTTAGTTTCGTCTTCAATTATATCGTTA
2520668 GACAATTAACTCTAAAACAAAATGGAAATGTGGACGATAGTTCTATCGAGAC
65 GACAATTAACTCTAAAACAAAATGGAAATGTGGACGATAGTTCTATCGAGAC
2520720 GATGACATTA
Statistics
Matches: 115, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
115 4 0.03
116 111 0.97
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (116 bp):
TTTATCACAATATTTTATATTGATACTACATTGAATTTTAGTTTCGTCTTCAATTATATCGTTAG
ACAATTAACTCTAAAACAAAATGGAAATGTGGACGATAGTTCTATCGAGAC
Found at i:2521488 original size:136 final size:136
Alignment explanation
Indices: 2521244--2521515 Score: 544
Period size: 136 Copynumber: 2.0 Consensus size: 136
2521234 ATGATAGTTA
2521244 GGTATGACAAGAAATTGAAGACACGAGTATGTGCCATGGCAATTTCAACCCATTTGGAAGTGGTG
1 GGTATGACAAGAAATTGAAGACACGAGTATGTGCCATGGCAATTTCAACCCATTTGGAAGTGGTG
2521309 GTGGCATTGTGAAATTCCAACAACCGACGACAATAGCTGACACGGCGGTCAATGAAGGAGAACAC
66 GTGGCATTGTGAAATTCCAACAACCGACGACAATAGCTGACACGGCGGTCAATGAAGGAGAACAC
2521374 TGATCG
131 TGATCG
2521380 GGTATGACAAGAAATTGAAGACACGAGTATGTGCCATGGCAATTTCAACCCATTTGGAAGTGGTG
1 GGTATGACAAGAAATTGAAGACACGAGTATGTGCCATGGCAATTTCAACCCATTTGGAAGTGGTG
2521445 GTGGCATTGTGAAATTCCAACAACCGACGACAATAGCTGACACGGCGGTCAATGAAGGAGAACAC
66 GTGGCATTGTGAAATTCCAACAACCGACGACAATAGCTGACACGGCGGTCAATGAAGGAGAACAC
2521510 TGATCG
131 TGATCG
2521516 ATTGATGCAA
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 136 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (136 bp):
GGTATGACAAGAAATTGAAGACACGAGTATGTGCCATGGCAATTTCAACCCATTTGGAAGTGGTG
GTGGCATTGTGAAATTCCAACAACCGACGACAATAGCTGACACGGCGGTCAATGAAGGAGAACAC
TGATCG
Found at i:2533467 original size:20 final size:22
Alignment explanation
Indices: 2533428--2533485 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2533418 TTGGTGCAGA
2533428 GGGAATCGA-TCCCCCCTTG-A-
1 GGGAA-CGATTCCCCCCTTGAAG
* *
2533448 GGGACCGATTCCCCCTTTGAAG
1 GGGAACGATTCCCCCCTTGAAG
2533470 GGGAACGATTCCCCCC
1 GGGAACGATTCCCCCC
2533486 ACAAGGGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 3 0.10
20 13 0.42
21 1 0.03
22 14 0.45
ACGTcount: A:0.19, C:0.36, G:0.26, T:0.19
Consensus pattern (22 bp):
GGGAACGATTCCCCCCTTGAAG
Found at i:2533478 original size:22 final size:20
Alignment explanation
Indices: 2533426--2533485 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
2533416 TTTTGGTGCA
2533426 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAA-CGATTCCCCCCTT
* *
2533446 GAGGGACCGATTCCCCCTTT
1 GAGGGAACGATTCCCCCCTT
2533466 GAAGGGGAACGATTCCCCCC
1 G-A-GGGAACGATTCCCCCC
2533486 ACAAGGGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.09
20 15 0.45
21 1 0.03
22 14 0.42
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACGATTCCCCCCTT
Found at i:2533652 original size:35 final size:35
Alignment explanation
Indices: 2533608--2533677 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
2533598 AAATCTCCAT
2533608 TTTTGCCTCAAATTAACGTTCTTAATCGGAATTCA
1 TTTTGCCTCAAATTAACGTTCTTAATCGGAATTCA
2533643 TTTTGCCTCAAATTAACGTTCTTAATCGGAATTCA
1 TTTTGCCTCAAATTAACGTTCTTAATCGGAATTCA
2533678 CTTCAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (35 bp):
TTTTGCCTCAAATTAACGTTCTTAATCGGAATTCA
Found at i:2534251 original size:21 final size:21
Alignment explanation
Indices: 2534227--2534266 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2534217 ACCGTCAACC
*
2534227 AAATCCACTTCCAAATCCTCA
1 AAATCCAATTCCAAATCCTCA
*
2534248 AAATCCAATTCCTAATCCT
1 AAATCCAATTCCAAATCCT
2534267 AATCCCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCCAATTCCAAATCCTCA
Found at i:2543422 original size:16 final size:15
Alignment explanation
Indices: 2543401--2543431 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2543391 ATAATTCTAA
2543401 AAAAAAAATTTAAAAT
1 AAAAAAAA-TTAAAAT
2543417 AAAAAAAATTAAAAT
1 AAAAAAAATTAAAAT
2543432 TATATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAAAATTAAAAT
Found at i:2548856 original size:2 final size:2
Alignment explanation
Indices: 2548849--2548884 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2548839 ACTAAAGTAA
2548849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2548885 TAGGGTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2549992 original size:16 final size:16
Alignment explanation
Indices: 2549971--2550006 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2549961 ATCTCCTTGC
**
2549971 TGTTGTGTTTTTGTGT
1 TGTTGTGTTACTGTGT
2549987 TGTTGTGTTACTGTGT
1 TGTTGTGTTACTGTGT
2550003 TGTT
1 TGTT
2550007 ATGTGTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.03, C:0.03, G:0.31, T:0.64
Consensus pattern (16 bp):
TGTTGTGTTACTGTGT
Found at i:2550573 original size:3 final size:3
Alignment explanation
Indices: 2550567--2550631 Score: 105
Period size: 3 Copynumber: 22.0 Consensus size: 3
2550557 ATTTATTATT
*
2550567 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2550614 TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
2550632 AGGATGGACA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2551136 original size:42 final size:42
Alignment explanation
Indices: 2551037--2551137 Score: 96
Period size: 42 Copynumber: 2.4 Consensus size: 42
2551027 AGGTCTTATG
* * * * * * *
2551037 AATGGCCCGAAGGACTT-ATCATCTTGTTCGAAAGGCTTATT
1 AATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
* * * *
2551078 GATGAACTGAATGATTTAAGCATCATGCTCGAAAGACTTACT
1 AATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
2551120 AATGACCCGAAGGATTTA
1 AATGACCCGAAGGATTTA
2551138 TAAATCAAGA
Statistics
Matches: 44, Mismatches: 15, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
41 11 0.25
42 33 0.75
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (42 bp):
AATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
Found at i:2551259 original size:35 final size:35
Alignment explanation
Indices: 2551217--2551287 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2551207 TTCCTTTAAC
2551217 AACTCTTTTGAGATAATTAAGAAACCCCTAAAACA
1 AACTCTTTTGAGATAATTAAGAAACCCCTAAAACA
2551252 AACTCTTTTGAGATAATTAAGAAACCCCTAAAACA
1 AACTCTTTTGAGATAATTAAGAAACCCCTAAAACA
2551287 A
1 A
2551288 CTTAGTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.08, T:0.25
Consensus pattern (35 bp):
AACTCTTTTGAGATAATTAAGAAACCCCTAAAACA
Found at i:2551348 original size:21 final size:21
Alignment explanation
Indices: 2551315--2551356 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2551305 CATTTGAAAA
2551315 CATCCTGCCCG-AAGGTCTTAT
1 CATCCTGCCCGAAAGG-CTTAT
* *
2551336 CATCTTGCTCGAAAGGCTTAT
1 CATCCTGCCCGAAAGGCTTAT
2551357 AGATGACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (21 bp):
CATCCTGCCCGAAAGGCTTAT
Found at i:2551404 original size:42 final size:42
Alignment explanation
Indices: 2551336--2551417 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
2551326 AAGGTCTTAT
* *
2551336 CATCTTGCTCGAAAGGCTTATAGATGACCCAAAGAATTTAAG
1 CATCATGCTCGAAAGACTTATAGATGACCCAAAGAATTTAAG
* *
2551378 CATCATGCTCGAAAGACTTACT-GATGACCCGAAGGATTTA
1 CATCATGCTCGAAAGACTTA-TAGATGACCCAAAGAATTTA
2551418 CTTTAATCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTATAGATGACCCAAAGAATTTAAG
Found at i:2551630 original size:42 final size:42
Alignment explanation
Indices: 2551563--2551682 Score: 177
Period size: 42 Copynumber: 2.9 Consensus size: 42
2551553 AAGGTCTTAT
* *
2551563 CATCTTGCTCGAAAGGCTTACAGATGACCCGAAGGATTTAAA
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAA
* * *
2551605 CATCATGCTCGAAAGACTTATAGATGACCTGAATGATTTAAA
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAA
* *
2551647 CATCATGCTCGAAAGACTTACAGATGGCCCAAAGGA
1 CATCATGCTCGAAAGACTTACAGATGACCCGAAGGA
2551683 CTTACAAATC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAA
Found at i:2551821 original size:50 final size:51
Alignment explanation
Indices: 2551725--2551821 Score: 119
Period size: 52 Copynumber: 1.9 Consensus size: 51
2551715 TTCATAGTTG
* * *
2551725 TTAAGGAACCCCTTAAAAGGCTTAGCTTCATTTAAAAATTCTTTTGAGATAA
1 TTAAGAAACCCCTAAAAAGGCTTAGCTT-ATTTAAAAATTCATTTGAGATAA
2551777 TTAAGAAACCCCTAAAACAGGCTTAG-TT-TTT-AAAATCTCATTTGA
1 TTAAGAAACCCCTAAAA-AGGCTTAGCTTATTTAAAAAT-TCATTTGA
2551822 AAACATCCTG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
49 5 0.12
50 10 0.25
52 17 0.43
53 8 0.20
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (51 bp):
TTAAGAAACCCCTAAAAAGGCTTAGCTTATTTAAAAATTCATTTGAGATAA
Found at i:2553384 original size:40 final size:40
Alignment explanation
Indices: 2553348--2553432 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
2553338 TGAAATGCTT
*
2553348 AAACATTTGCTTCCTGATGATATAAGCTTTCAAAATGCCC
1 AAACATTTGCTTCCTGATAATATAAGCTTTCAAAATGCCC
* * * * *
2553388 CAACATTTTCTTCTTGCTAATATGAGCTTTCAAAATGCCCC
1 AAACATTTGCTTCCTGATAATATAAGCTTTCAAAATG-CCC
2553429 AAAC
1 AAAC
2553433 TTTCATACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 31 0.84
41 6 0.16
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.33
Consensus pattern (40 bp):
AAACATTTGCTTCCTGATAATATAAGCTTTCAAAATGCCC
Found at i:2553451 original size:36 final size:39
Alignment explanation
Indices: 2553367--2553463 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 39
2553357 CTTCCTGATG
* * * *
2553367 ATATAAGCTTTCAAAATGCCCCAACATTTTCTTCTTGCTA
1 ATATGAGCTTTCAAAATGCCCCAACA-TCTCTTCATACTA
2553407 ATATGAGCTTTCAAAATGCCCCAA-A-CT-TTCATACTA
1 ATATGAGCTTTCAAAATGCCCCAACATCTCTTCATACTA
* *
2553443 ATGTGAGCTTTCACAATGCCC
1 ATATGAGCTTTCAAAATGCCC
2553464 TACATGGATC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
36 26 0.51
37 1 0.02
39 1 0.02
40 23 0.45
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (39 bp):
ATATGAGCTTTCAAAATGCCCCAACATCTCTTCATACTA
Found at i:2554190 original size:17 final size:17
Alignment explanation
Indices: 2554168--2554204 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2554158 TTATAACCTC
*
2554168 TTTTTTTTATTTTTTTA
1 TTTTTTTTATTTTTCTA
*
2554185 TTTTTTTTCTTTTTCTA
1 TTTTTTTTATTTTTCTA
2554202 TTT
1 TTT
2554205 GAAAATTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTTTTTTATTTTTCTA
Found at i:2560313 original size:8 final size:8
Alignment explanation
Indices: 2560297--2560336 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
2560287 TGTATCTCCT
2560297 TGTTGTTG
1 TGTTGTTG
*
2560305 TGTTTTTG
1 TGTTGTTG
2560313 TGTTGTTG
1 TGTTGTTG
*
2560321 TGTTGTTA
1 TGTTGTTG
2560329 TG-TGTTG
1 TGTTGTTG
2560336 T
1 T
2560337 TTCTTCGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 5 0.18
8 23 0.82
ACGTcount: A:0.03, C:0.00, G:0.33, T:0.65
Consensus pattern (8 bp):
TGTTGTTG
Found at i:2560316 original size:16 final size:18
Alignment explanation
Indices: 2560297--2560337 Score: 68
Period size: 16 Copynumber: 2.4 Consensus size: 18
2560287 TGTATCTCCT
2560297 TGTTGTTGTGTT-TT-TG
1 TGTTGTTGTGTTGTTATG
2560313 TGTTGTTGTGTTGTTATG
1 TGTTGTTGTGTTGTTATG
2560331 TGTTGTT
1 TGTTGTT
2560338 TCTTCGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 12 0.52
17 2 0.09
18 9 0.39
ACGTcount: A:0.02, C:0.00, G:0.32, T:0.66
Consensus pattern (18 bp):
TGTTGTTGTGTTGTTATG
Found at i:2560422 original size:118 final size:118
Alignment explanation
Indices: 2560214--2560451 Score: 476
Period size: 118 Copynumber: 2.0 Consensus size: 118
2560204 TTGATGGTTG
2560214 GTTGTTTCTTCGAATCTATACCTCTGTTTTACTCTTTTGTTGATGTCTATTCCTATTTCTTCCTT
1 GTTGTTTCTTCGAATCTATACCTCTGTTTTACTCTTTTGTTGATGTCTATTCCTATTTCTTCCTT
2560279 GTTCTGTTTGTATCTCCTTGTTGTTGTGTTTTTGTGTTGTTGTGTTGTTATGT
66 GTTCTGTTTGTATCTCCTTGTTGTTGTGTTTTTGTGTTGTTGTGTTGTTATGT
2560332 GTTGTTTCTTCGAATCTATACCTCTGTTTTACTCTTTTGTTGATGTCTATTCCTATTTCTTCCTT
1 GTTGTTTCTTCGAATCTATACCTCTGTTTTACTCTTTTGTTGATGTCTATTCCTATTTCTTCCTT
2560397 GTTCTGTTTGTATCTCCTTGTTGTTGTGTTTTTGTGTTGTTGTGTTGTTATGT
66 GTTCTGTTTGTATCTCCTTGTTGTTGTGTTTTTGTGTTGTTGTGTTGTTATGT
2560450 GT
1 GT
2560452 GTTGCTTAGT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 120 1.00
ACGTcount: A:0.08, C:0.15, G:0.18, T:0.58
Consensus pattern (118 bp):
GTTGTTTCTTCGAATCTATACCTCTGTTTTACTCTTTTGTTGATGTCTATTCCTATTTCTTCCTT
GTTCTGTTTGTATCTCCTTGTTGTTGTGTTTTTGTGTTGTTGTGTTGTTATGT
Found at i:2560431 original size:8 final size:8
Alignment explanation
Indices: 2560415--2560493 Score: 56
Period size: 8 Copynumber: 9.4 Consensus size: 8
2560405 TGTATCTCCT
2560415 TGTTGTTG
1 TGTTGTTG
*
2560423 TGTTTTTG
1 TGTTGTTG
2560431 TGTTGTTG
1 TGTTGTTG
*
2560439 TGTTGTTA
1 TGTTGTTG
2560447 TGTGTGTTG
1 TGT-TGTTG
2560456 CT-TAGTGTTG
1 -TGT--TGTTG
2560466 T-TATG-TG
1 TGT-TGTTG
2560473 TGTTGCTTG
1 TGTTG-TTG
2560482 TTGTTGTTG
1 -TGTTGTTG
2560491 TGT
1 TGT
2560494 CTCTCTTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
7 5 0.08
8 30 0.51
9 12 0.20
10 12 0.20
ACGTcount: A:0.04, C:0.03, G:0.33, T:0.61
Consensus pattern (8 bp):
TGTTGTTG
Found at i:2560434 original size:16 final size:18
Alignment explanation
Indices: 2560415--2560477 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 18
2560405 TGTATCTCCT
2560415 TGTTGTTGTGTT-TT-TG
1 TGTTGTTGTGTTGTTATG
2560431 TGTTGTTGTGTTGTTATGTG
1 TGTTGTTGTGTTGTTA--TG
2560451 TGTTGCTTAGTGTTGTTATG
1 TGTTG-TT-GTGTTGTTATG
2560471 TG-TGTTG
1 TGTTGTTG
2560478 CTTGTTGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
16 12 0.29
17 3 0.07
18 2 0.05
19 2 0.05
20 11 0.27
21 2 0.05
22 9 0.22
ACGTcount: A:0.05, C:0.02, G:0.33, T:0.60
Consensus pattern (18 bp):
TGTTGTTGTGTTGTTATG
Found at i:2560439 original size:22 final size:21
Alignment explanation
Indices: 2560429--2560489 Score: 97
Period size: 22 Copynumber: 2.9 Consensus size: 21
2560419 GTTGTGTTTT
2560429 TGTGTTG-TTGTGTTGTTATG
1 TGTGTTGCTTGTGTTGTTATG
2560449 TGTGTTGCTTAGTGTTGTTATG
1 TGTGTTGCTT-GTGTTGTTATG
2560471 TGTGTTGCTTGTTGTTGTT
1 TGTGTTGCTTG-TGTTGTT
2560490 GTGTCTCTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.18
21 3 0.08
22 28 0.74
ACGTcount: A:0.05, C:0.03, G:0.33, T:0.59
Consensus pattern (21 bp):
TGTGTTGCTTGTGTTGTTATG
Found at i:2560454 original size:12 final size:12
Alignment explanation
Indices: 2560437--2560489 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
2560427 TTTGTGTTGT
2560437 TGTGTTGTTATG
1 TGTGTTGTTATG
2560449 TGTGTTGCTTA--
1 TGTGTTG-TTATG
2560460 -GTGTTGTTATG
1 TGTGTTGTTATG
*
2560471 TGTGTTGCT-TG
1 TGTGTTGTTATG
2560482 T-TGTTGTT
1 TGTGTTGTT
2560490 GTGTCTCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
9 3 0.09
10 12 0.34
11 3 0.09
12 14 0.40
13 3 0.09
ACGTcount: A:0.06, C:0.04, G:0.32, T:0.58
Consensus pattern (12 bp):
TGTGTTGTTATG
Found at i:2560774 original size:16 final size:16
Alignment explanation
Indices: 2560726--2560774 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
2560716 AACGAGATGA
*
2560726 TAACCCTAGGGTTTCA
1 TAACCCTAGGGTTTCC
*
2560742 TAACCCTAGGGTATCC
1 TAACCCTAGGGTTTCC
2560758 TAACCCTAGGGTTTCC
1 TAACCCTAGGGTTTCC
2560774 T
1 T
2560775 CTAAATCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (16 bp):
TAACCCTAGGGTTTCC
Found at i:2560902 original size:30 final size:30
Alignment explanation
Indices: 2560868--2560935 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
2560858 ACTGCATCTA
* * ** *
2560868 GATCGGGTTTGTTGGGTTGGGTCTGGACCG
1 GATCGGGTCTATTGGGCCGGGTCTAGACCG
*
2560898 GATCGGGTCTATTGGGCCGGGTCTAGATCG
1 GATCGGGTCTATTGGGCCGGGTCTAGACCG
2560928 GATCGGGT
1 GATCGGGT
2560936 ATGAATCTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.10, C:0.16, G:0.44, T:0.29
Consensus pattern (30 bp):
GATCGGGTCTATTGGGCCGGGTCTAGACCG
Found at i:2561052 original size:3 final size:3
Alignment explanation
Indices: 2561046--2561081 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
2561036 ATTTATTATT
* *
2561046 TAA TAA TAA TAA TAA TAA TAG TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2561082 AGGATGGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2563196 original size:15 final size:15
Alignment explanation
Indices: 2563176--2563206 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2563166 TTTTCTCTTT
2563176 TGGGTTATCCGAAAG
1 TGGGTTATCCGAAAG
2563191 TGGGTTATCCGAAAG
1 TGGGTTATCCGAAAG
2563206 T
1 T
2563207 AAGCTTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.29
Consensus pattern (15 bp):
TGGGTTATCCGAAAG
Found at i:2564776 original size:42 final size:42
Alignment explanation
Indices: 2564701--2564781 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
2564691 CAAATCTCCG
* * * *
2564701 GAAATTGAACCGAAGATCGAGGAGAAGGGTAATGCAGGCTCA
1 GAAATTGAAACGAAGATCGACGAGAAAGCTAATGCAGGCTCA
* * *
2564743 GAAATTGAAATGAAGATTGACGAGAAAGCTAATGGAGGC
1 GAAATTGAAACGAAGATCGACGAGAAAGCTAATGCAGGC
2564782 AAGAATGAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (42 bp):
GAAATTGAAACGAAGATCGACGAGAAAGCTAATGCAGGCTCA
Found at i:2582228 original size:3 final size:3
Alignment explanation
Indices: 2582220--2582245 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2582210 AAGCATAAAT
2582220 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
2582246 ATCTCTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2588156 original size:26 final size:26
Alignment explanation
Indices: 2588127--2588191 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
2588117 GATCAAACAT
2588127 GTATTTCAAACAGGGTGGTTACGTAG
1 GTATTTCAAACAGGGTGGTTACGTAG
2588153 GTATTTCAAACAGGGTGGTTACGTAG
1 GTATTTCAAACAGGGTGGTTACGTAG
2588179 GTATTTCAAACAG
1 GTATTTCAAACAG
2588192 AAAAATATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (26 bp):
GTATTTCAAACAGGGTGGTTACGTAG
Found at i:2592160 original size:31 final size:30
Alignment explanation
Indices: 2592108--2592213 Score: 196
Period size: 30 Copynumber: 3.5 Consensus size: 30
2592098 TGCAAAATAT
2592108 GAAGGGAAATTAAG-TTTTTTTTTGACTGA
1 GAAGGGAAATTAAGTTTTTTTTTTGACTGA
2592137 GAAGGGAAATTAAGTTTTTTTTTTTGACTGA
1 GAAGGGAAATTAAG-TTTTTTTTTTGACTGA
2592168 GAAGGGAAATTAAGTTTTTTTTTTGACTGA
1 GAAGGGAAATTAAGTTTTTTTTTTGACTGA
2592198 GAAGGGAAATTAAGTT
1 GAAGGGAAATTAAGTT
2592214 AAATGGTCAT
Statistics
Matches: 75, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
29 14 0.19
30 32 0.43
31 29 0.39
ACGTcount: A:0.32, C:0.03, G:0.25, T:0.41
Consensus pattern (30 bp):
GAAGGGAAATTAAGTTTTTTTTTTGACTGA
Found at i:2592878 original size:28 final size:28
Alignment explanation
Indices: 2592838--2592934 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 28
2592828 CTTAAAAGTG
* *
2592838 CAATTTGGCACCTAAACTTTTTTTGGTT
1 CAATTAGGTACCTAAACTTTTTTTGGTT
* *
2592866 CAATTAGGTACCTGAA-TTTGCTTTAAGGTT
1 CAATTAGGTACCTAAACTTT--TTT-TGGTT
* * *
2592896 CAATTTGGTATCTAAACCTTTTTTGG-T
1 CAATTAGGTACCTAAACTTTTTTTGGTT
2592923 CTAATTAGGTAC
1 C-AATTAGGTAC
2592935 TTGAACTTGG
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
27 5 0.09
28 23 0.43
29 6 0.11
30 17 0.32
31 2 0.04
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (28 bp):
CAATTAGGTACCTAAACTTTTTTTGGTT
Found at i:2592911 original size:58 final size:58
Alignment explanation
Indices: 2592808--2592955 Score: 163
Period size: 58 Copynumber: 2.5 Consensus size: 58
2592798 GTGAATATAC
* * * * *
2592808 ATTATGGTACCTGAGTTTAGCTTAAAAGTGCAATTTGGCACCTAAACTTTTTTTGGT-TCA
1 ATTA-GGTACCTGAATTT-GCTTTAAGGTTCAATTTGGCACCTAAACCTTTTTTGGTCT-A
* *
2592868 ATTAGGTACCTGAATTTGCTTTAAGGTTCAATTTGGTATCTAAACCTTTTTTGGTCTA
1 ATTAGGTACCTGAATTTGCTTTAAGGTTCAATTTGGCACCTAAACCTTTTTTGGTCTA
* * *
2592926 ATTAGGTACTTGAACTTGGCTTTTAGGTTC
1 ATTAGGTACCTGAA-TTTGCTTTAAGGTTC
2592956 GAATCTAAAC
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 46 0.61
59 26 0.34
60 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (58 bp):
ATTAGGTACCTGAATTTGCTTTAAGGTTCAATTTGGCACCTAAACCTTTTTTGGTCTA
Found at i:2603278 original size:22 final size:22
Alignment explanation
Indices: 2603253--2603297 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2603243 TAAATTATTT
*
2603253 ATTAACATTATTTTAAAATTAA
1 ATTAACATTAATTTAAAATTAA
**
2603275 ATTAATTTTAATTTAAAATTAA
1 ATTAACATTAATTTAAAATTAA
2603297 A
1 A
2603298 ATTTCCTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTAACATTAATTTAAAATTAA
Found at i:2603282 original size:17 final size:17
Alignment explanation
Indices: 2603253--2603285 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2603243 TAAATTATTT
2603253 ATTAACATTATTTTAAA
1 ATTAACATTATTTTAAA
2603270 ATTAA-ATTAATTTTAA
1 ATTAACATT-ATTTTAA
2603286 TTTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTAACATTATTTTAAA
Found at i:2603390 original size:18 final size:19
Alignment explanation
Indices: 2603367--2603404 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2603357 AAATATCATA
2603367 ATTATAT-ATTTATTTATT
1 ATTATATAATTTATTTATT
*
2603385 ATTATATAATTTTTTTATT
1 ATTATATAATTTATTTATT
2603404 A
1 A
2603405 GAGAGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTATATAATTTATTTATT
Found at i:2603402 original size:16 final size:18
Alignment explanation
Indices: 2603367--2603404 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2603357 AAATATCATA
*
2603367 ATTATATATTTATTTATT
1 ATTATATAATTATTTATT
2603385 ATTATATAATT-TTT-TT
1 ATTATATAATTATTTATT
2603401 ATTA
1 ATTA
2603405 GAGAGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 3 0.16
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTATATAATTATTTATT
Found at i:2605338 original size:146 final size:146
Alignment explanation
Indices: 2605092--2605465 Score: 588
Period size: 146 Copynumber: 2.6 Consensus size: 146
2605082 TCGGGATATC
* *
2605092 CGATCAACATTCCGAGCGGTCAAAAGTTGCGTAAGGCCATCACGAACAACATATTGAAAAATCAG
1 CGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
* * *
2605157 GACGATCAGACGGTGGACGGTGACGGATCGGAGAAAACAAATCCGGGCGGTTTTTAGCCTCTTTC
66 GACGATCAGACGGTGGAAGGTGACGGATCGGAGAAAACAAATCCGGACGGTTTTTAGCCTCTTGC
*
2605222 CGGTGATCGGAATCTT
131 CGGTGATCGGAATCTG
*
2605238 TGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
1 CGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
2605303 GACGATCAGACGGTGGAAGGTGACGGATCGGAGAAAACAAATCCGGACGGTTTTTAGCCTCTTGC
66 GACGATCAGACGGTGGAAGGTGACGGATCGGAGAAAACAAATCCGGACGGTTTTTAGCCTCTTGC
2605368 CGGTGATCGGAATCTG
131 CGGTGATCGGAATCTG
* * * * * *
2605384 CGATCAATATTCCGAACGGTGAAAAGTTGCGCG-ATGCCAACACAAACAACCTATTGAAAAATCA
1 CGATCAACATTCCGAACGGTCAAAAGTTGCG-GAAGGCCATCACGAACAACATATTGAAAAATCA
* * *
2605448 TGACAATCGGACGGTGGA
65 GGACGATCAGACGGTGGA
2605466 TGACGGCAGA
Statistics
Matches: 210, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
146 209 1.00
147 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (146 bp):
CGATCAACATTCCGAACGGTCAAAAGTTGCGGAAGGCCATCACGAACAACATATTGAAAAATCAG
GACGATCAGACGGTGGAAGGTGACGGATCGGAGAAAACAAATCCGGACGGTTTTTAGCCTCTTGC
CGGTGATCGGAATCTG
Found at i:2610401 original size:18 final size:18
Alignment explanation
Indices: 2610361--2610401 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2610351 TGACGACGAC
* *
2610361 AATGATGATGGTGGTTAT
1 AATGATCATGGTGGTGAT
*
2610379 GATGATCATGGTGGTGAT
1 AATGATCATGGTGGTGAT
2610397 AATGA
1 AATGA
2610402 AGGTATGTAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.34, T:0.34
Consensus pattern (18 bp):
AATGATCATGGTGGTGAT
Found at i:2611117 original size:19 final size:20
Alignment explanation
Indices: 2611073--2611117 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2611063 AATTGTTTTT
*
2611073 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
2611093 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
2611112 AATAAA
1 AATAAA
2611118 ATATTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:2611146 original size:14 final size:13
Alignment explanation
Indices: 2611118--2611153 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
2611108 TCAAAATAAA
2611118 ATATTAAAATAGT
1 ATATTAAAATAGT
*
2611131 ATATTAATATTAGT
1 ATATTAA-AATAGT
2611145 ATATTAAAA
1 ATATTAAAA
2611154 GATAACTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (13 bp):
ATATTAAAATAGT
Found at i:2612995 original size:44 final size:44
Alignment explanation
Indices: 2612935--2613021 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
2612925 CTCGATTCCT
*
2612935 TTTCTTCTCTCTATCATCTATGCCAGCCCAATTCTTGAGTCTCC
1 TTTCTTCTCTCTATCATCTATGCCAACCCAATTCTTGAGTCTCC
2612979 TTTCTTCTCTCTATCATCTATGCCAACCCAATTCTTGAGTCTC
1 TTTCTTCTCTCTATCATCTATGCCAACCCAATTCTTGAGTCTC
2613022 GGAGGAGACT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.17, C:0.33, G:0.08, T:0.41
Consensus pattern (44 bp):
TTTCTTCTCTCTATCATCTATGCCAACCCAATTCTTGAGTCTCC
Found at i:2614755 original size:14 final size:14
Alignment explanation
Indices: 2614736--2614816 Score: 72
Period size: 14 Copynumber: 5.4 Consensus size: 14
2614726 CGCTGGGCAT
* *
2614736 CCGAGGCTATTCGA
1 CCGAGGCCATCCGA
2614750 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
2614764 TCGAGGCCATCCGAGAGCA
1 CCGAGGCCATCC----G-A
2614783 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
2614798 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
2614812 ACGAG
1 CCGAG
2614817 CTATGCGAGG
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
14 41 0.73
15 1 0.02
16 1 0.02
18 1 0.02
19 1 0.02
20 11 0.20
ACGTcount: A:0.23, C:0.36, G:0.30, T:0.11
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:2614788 original size:48 final size:47
Alignment explanation
Indices: 2614732--2614836 Score: 147
Period size: 48 Copynumber: 2.2 Consensus size: 47
2614722 AACACGCTGG
* * *
2614732 GCATCCGAGGCTATTCGACCGAGGCCATCCGATCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGA-GCCATCCGAGA
* * *
2614780 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGAGCTATGCGAGG
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGAGCCATCCGAGA
2614827 GCATCCGAGG
1 GCATCCGAGG
2614837 GCAACCGAGC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 18 0.35
48 33 0.65
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.12
Consensus pattern (47 bp):
GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGAGCCATCCGAGA
Found at i:2614791 original size:34 final size:37
Alignment explanation
Indices: 2614750--2614834 Score: 122
Period size: 34 Copynumber: 2.4 Consensus size: 37
2614740 GGCTATTCGA
*
2614750 CCGAGGCCATCCGATCGAGGCCATCCG-A-GAGC-AT
1 CCGAGGCCATCCGACCGAGGCCATCCGAACGAGCTAT
2614784 CCGAGGCCATCCGACCGAGGCCATCCGAACGAGCTAT
1 CCGAGGCCATCCGACCGAGGCCATCCGAACGAGCTAT
* *
2614821 GCGAGGGCATCCGA
1 CCGAGGCCATCCGA
2614835 GGGCAACCGA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.58
35 1 0.02
36 4 0.09
37 14 0.31
ACGTcount: A:0.24, C:0.35, G:0.31, T:0.11
Consensus pattern (37 bp):
CCGAGGCCATCCGACCGAGGCCATCCGAACGAGCTAT
Found at i:2614811 original size:10 final size:10
Alignment explanation
Indices: 2614765--2614797 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
2614755 GCCATCCGAT
2614765 CGAGGCCATC
1 CGAGGCCATC
2614775 CGAGAG-CATC
1 CGAG-GCCATC
2614785 CGAGGCCATC
1 CGAGGCCATC
2614795 CGA
1 CGA
2614798 CCGAGGCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.05
10 19 0.90
11 1 0.05
ACGTcount: A:0.24, C:0.36, G:0.30, T:0.09
Consensus pattern (10 bp):
CGAGGCCATC
Found at i:2614850 original size:33 final size:33
Alignment explanation
Indices: 2614798--2614882 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
2614788 GGCCATCCGA
* * * *
2614798 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
2614831 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
2614864 CCGAGGG-AAGCCGAGCGAG
1 CCGAGGGCAA-CCGAGCGAG
2614883 GGTAGGTCGT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
32 2 0.04
33 45 0.96
ACGTcount: A:0.26, C:0.27, G:0.39, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:2621334 original size:21 final size:21
Alignment explanation
Indices: 2621308--2621347 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2621298 AATTCTTATG
* *
2621308 AACCAGTTACTTTGTAATTTC
1 AACCAGATAATTTGTAATTTC
2621329 AACCAGATAATTTGTAATT
1 AACCAGATAATTTGTAATT
2621348 GAATTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
AACCAGATAATTTGTAATTTC
Found at i:2622890 original size:2 final size:2
Alignment explanation
Indices: 2622883--2622933 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2622873 CACGAATTAG
2622883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2622925 AT AT AT AT A
1 AT AT AT AT A
2622934 AAAAAGAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2627337 original size:29 final size:29
Alignment explanation
Indices: 2627295--2627353 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2627285 ATTTTCACCT
* *
2627295 AACTAAATTGATGTAAGCAATGATATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
2627324 AACTAAATTGATGTAAGAAATGACATCAA
1 AACTAAATTGATGTAAGAAATGACATCAA
2627353 A
1 A
2627354 TTAATGTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (29 bp):
AACTAAATTGATGTAAGAAATGACATCAA
Found at i:2635103 original size:52 final size:52
Alignment explanation
Indices: 2635041--2635144 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
2635031 TAGAAAAGGA
2635041 ACTGAAAACCAAGTTGATGATCACTTATCTAGGCTAGAGAACAATTCTGAAT
1 ACTGAAAACCAAGTTGATGATCACTTATCTAGGCTAGAGAACAATTCTGAAT
2635093 ACTGAAAACCAAGTTGATGATCACTTATCTAGGCTAGAGAACAATTCTGAAT
1 ACTGAAAACCAAGTTGATGATCACTTATCTAGGCTAGAGAACAATTCTGAAT
2635145 GCCATGACAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (52 bp):
ACTGAAAACCAAGTTGATGATCACTTATCTAGGCTAGAGAACAATTCTGAAT
Found at i:2636824 original size:20 final size:20
Alignment explanation
Indices: 2636801--2636845 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2636791 TTAACTTTTT
*
2636801 CTTTTCTCTTTC-TTCCTTAA
1 CTTTTCTATTTCATT-CTTAA
*
2636821 CTTTTCTATTTCATTTTTAA
1 CTTTTCTATTTCATTCTTAA
2636841 CTTTT
1 CTTTT
2636846 ACTTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTCTATTTCATTCTTAA
Found at i:2640144 original size:23 final size:23
Alignment explanation
Indices: 2640114--2640162 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
2640104 TGGTGGTTGG
2640114 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATGTTTA-ACTTTAT
*
2640137 TTTAATGGTATGTTTAAGTTTAT
1 TTTAATGGTATGTTTAACTTTAT
2640160 TTT
1 TTT
2640163 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.24, C:0.02, G:0.16, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATGTTTAACTTTAT
Found at i:2643569 original size:29 final size:29
Alignment explanation
Indices: 2643524--2643582 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2643514 ATTTTCACCT
* *
2643524 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTAATATAAGCAATGACATCAA
2643553 AACTAAATTAATATAAGCAATGACATCAA
1 AACTAAATTAATATAAGCAATGACATCAA
2643582 A
1 A
2643583 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATATAAGCAATGACATCAA
Found at i:2644813 original size:27 final size:25
Alignment explanation
Indices: 2644773--2644850 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 25
2644763 TGTGTTTAGT
* *
2644773 ATATATTTTTTAAAAATAGAAATAAA
1 ATATAATTCTTAAAAATA-AAATAAA
*
2644799 TATATAATTAC-TAAATAATTAAATTAAA
1 -ATATAATT-CTTAAA-AA-TAAAATAAA
*
2644827 ATATAATTCTTAAAAATATAATAA
1 ATATAATTCTTAAAAATAAAATAA
2644851 TAAAAATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
25 6 0.14
26 3 0.07
27 23 0.55
28 8 0.19
29 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (25 bp):
ATATAATTCTTAAAAATAAAATAAA
Found at i:2645487 original size:26 final size:24
Alignment explanation
Indices: 2645425--2645492 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 24
2645415 AAATTTAATC
*
2645425 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAATATATTT
2645449 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAATATATT-T
2645472 AATAATATAATATTATTAATA
1 AA-AATAT-ATATTATTAATA
2645493 AAGATTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
22 2 0.05
23 12 0.32
24 12 0.32
25 3 0.08
26 9 0.24
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAATATATATTATTAATATATTT
Found at i:2645638 original size:19 final size:17
Alignment explanation
Indices: 2645604--2645645 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2645594 ATTAATAAAA
2645604 TTATAA-AAATAATATT
1 TTATAATAAATAATATT
2645620 TTATAATAAATAAAGTATT
1 TTATAATAAAT-AA-TATT
2645639 TT-TAATA
1 TTATAATA
2645646 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.26
17 4 0.17
18 7 0.30
19 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
TTATAATAAATAATATT
Found at i:2645834 original size:14 final size:14
Alignment explanation
Indices: 2645811--2645865 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
2645801 CTGGAAAATG
*
2645811 TAATTAATTTTCCA
1 TAATTCATTTTCCA
2645825 TAATTCATTTTCCA
1 TAATTCATTTTCCA
*
2645839 GTAATCCATTTTCCA
1 -TAATTCATTTTCCA
* *
2645854 GAATTCAATTTC
1 TAATTCATTTTC
2645866 TAGAAAACCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.63
15 13 0.37
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (14 bp):
TAATTCATTTTCCA
Found at i:2645848 original size:15 final size:15
Alignment explanation
Indices: 2645817--2645854 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2645807 AATGTAATTA
*
2645817 ATTTTCCA-TAATTC
1 ATTTTCCAGTAATCC
2645831 ATTTTCCAGTAATCC
1 ATTTTCCAGTAATCC
2645846 ATTTTCCAG
1 ATTTTCCAG
2645855 AATTCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (15 bp):
ATTTTCCAGTAATCC
Found at i:2645864 original size:15 final size:15
Alignment explanation
Indices: 2645812--2645864 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
2645802 TGGAAAATGT
*
2645812 AATT-AATTTTCCAT
1 AATTCAATTTTCCAG
2645826 AATTC-ATTTTCCAG
1 AATTCAATTTTCCAG
*
2645840 TAA-TCCATTTTCCAG
1 -AATTCAATTTTCCAG
2645855 AATTCAATTT
1 AATTCAATTT
2645865 CTAGAAAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 16 0.48
15 17 0.52
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (15 bp):
AATTCAATTTTCCAG
Found at i:2648462 original size:9 final size:10
Alignment explanation
Indices: 2648453--2648522 Score: 62
Period size: 9 Copynumber: 7.5 Consensus size: 10
2648443 TTTACCCATT
2648453 TTATTTA-T-
1 TTATTTATTA
2648461 TTATTTATTA
1 TTATTTATTA
2648471 TTA-TTATTA
1 TTATTTATTA
2648480 TTA-TTATTA
1 TTATTTATTA
*
2648489 -TAATTATTA
1 TTATTTATTA
*
2648498 -TATATATTA
1 TTATTTATTA
*
2648507 TATATATATTA
1 T-TATTTATTA
2648518 TTATT
1 TTATT
2648523 AAAATAATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
8 9 0.17
9 29 0.54
10 6 0.11
11 10 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTTATTA
Found at i:2648473 original size:3 final size:3
Alignment explanation
Indices: 2648465--2648523 Score: 75
Period size: 3 Copynumber: 19.0 Consensus size: 3
2648455 ATTTATTTAT
*
2648465 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA -TA TATA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA
2648511 TATA TTA TTA TTA
1 T-TA TTA TTA TTA
2648524 AAATAATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.76
4 10 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2648531 original size:3 final size:3
Alignment explanation
Indices: 2648525--2648562 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2648515 TTATTATTAA
2648525 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2648563 TACAAACCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2651981 original size:42 final size:43
Alignment explanation
Indices: 2651904--2651985 Score: 130
Period size: 42 Copynumber: 1.9 Consensus size: 43
2651894 GGCTTTAGAG
*
2651904 AAGTCAGGAGGGAAAGTTATCCCTTATATGTAAAGTTTTGCTA
1 AAGTCAGGAGGGAAAGATATCCCTTATATGTAAAGTTTTGCTA
* *
2651947 AAGTTAGGAGTGAAAGATAT-CCTTATATGTAAAGTTTTG
1 AAGTCAGGAGGGAAAGATATCCCTTATATGTAAAGTTTTG
2651986 TTTGATGTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 19 0.53
43 17 0.47
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (43 bp):
AAGTCAGGAGGGAAAGATATCCCTTATATGTAAAGTTTTGCTA
Found at i:2652087 original size:8 final size:7
Alignment explanation
Indices: 2652063--2652104 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
2652053 TTTTCATACA
2652063 TGCA-TT
1 TGCATTT
2652069 TGCATTT
1 TGCATTT
2652076 TGCATCTT
1 TGCAT-TT
2652084 TGCATTT
1 TGCATTT
* *
2652091 TTCATTG
1 TGCATTT
2652098 TGCATTT
1 TGCATTT
2652105 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:2652087 original size:15 final size:14
Alignment explanation
Indices: 2652063--2652104 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2652053 TTTTCATACA
2652063 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
2652076 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
2652091 TTCATTGTGCATTT
1 TGCATTTTGCATTT
2652105 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:2652180 original size:12 final size:12
Alignment explanation
Indices: 2652163--2652216 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
2652153 ACATTCACAT
2652163 ATTTACATTTGC
1 ATTTACATTTGC
2652175 ATTTACATTTGC
1 ATTTACATTTGC
* *
2652187 ATTTTTACGTTTGT
1 A--TTTACATTTGC
*
2652201 ATTTACATTTTC
1 ATTTACATTTGC
2652213 ATTT
1 ATTT
2652217 TTACATAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 25 0.71
14 10 0.29
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.57
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:2652193 original size:26 final size:26
Alignment explanation
Indices: 2652164--2652222 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
2652154 CATTCACATA
2652164 TTTACATTTGCATTTACATTTGCATT
1 TTTACATTTGCATTTACATTTGCATT
* * *
2652190 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGCATTTACATTTGCATT
2652216 TTTACAT
1 TTTACAT
2652223 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.14, G:0.07, T:0.58
Consensus pattern (26 bp):
TTTACATTTGCATTTACATTTGCATT
Found at i:2652219 original size:14 final size:14
Alignment explanation
Indices: 2652140--2652222 Score: 50
Period size: 14 Copynumber: 6.2 Consensus size: 14
2652130 ATACAATTTG
* *
2652140 CATTTTTATTATTA
1 CATTTTCATTTTTA
** *
2652154 CATTCACATATTTA
1 CATTTTCATTTTTA
*
2652168 CATTTGCA--TTTA
1 CATTTTCATTTTTA
*
2652180 CATTTGCATTTTTA
1 CATTTTCATTTTTA
*
2652194 CGTTTGT-A--TTTA
1 CATTT-TCATTTTTA
2652206 CATTTTCATTTTTA
1 CATTTTCATTTTTA
2652220 CAT
1 CAT
2652223 AATTACATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
11 1 0.02
12 21 0.40
14 31 0.58
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.55
Consensus pattern (14 bp):
CATTTTCATTTTTA
Found at i:2657274 original size:114 final size:114
Alignment explanation
Indices: 2656990--2657330 Score: 574
Period size: 114 Copynumber: 3.0 Consensus size: 114
2656980 AAGTGCCATG
2656990 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
2657055 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTTAAAGATGAATT
66 TGGTTTGGTATGAACCCC-AAAACCAATCATTGGATTTAAAAGATGAATT
2657105 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
2657170 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
* *
2657219 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * ** * * *
2657284 TGATTCGGTAGGAACCCCAGTACCGATCATTGGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAA
2657331 CTGCATGATC
Statistics
Matches: 215, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
114 132 0.61
115 83 0.39
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
Found at i:2658568 original size:73 final size:73
Alignment explanation
Indices: 2658481--2658650 Score: 322
Period size: 73 Copynumber: 2.3 Consensus size: 73
2658471 AGATAGATCC
*
2658481 ATGTGGGACATTTTGAAGGCTCATCTCAACAAGAAGTAATGACTAAGCCTACTTTTAGCATCTGT
1 ATGTGGGGCATTTTGAAGGCTCATCTCAACAAGAAGTAATGACTAAGCCTACTTTTAGCATCTGT
2658546 ATCAGCAA
66 ATCAGCAA
2658554 ATGTGGGGCATTTTGAAGGCTCATCTCAACAAGAAGTAATGACTAAGCCTACTTTTAGCATCTGT
1 ATGTGGGGCATTTTGAAGGCTCATCTCAACAAGAAGTAATGACTAAGCCTACTTTTAGCATCTGT
2658619 ATCAGCAA
66 ATCAGCAA
2658627 ATGTTGGGGCATTTTGAAGGCTCA
1 ATG-TGGGGCATTTTGAAGGCTCA
2658651 GATTAACAAG
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
73 75 0.79
74 20 0.21
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (73 bp):
ATGTGGGGCATTTTGAAGGCTCATCTCAACAAGAAGTAATGACTAAGCCTACTTTTAGCATCTGT
ATCAGCAA
Found at i:2660070 original size:22 final size:22
Alignment explanation
Indices: 2660039--2660096 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2660029 TACATCTACA
*
2660039 CTTTTCAAAGATGATAGATTCC
1 CTTTTCAAAGATGACAGATTCC
* *
2660061 CTTTTTAAAGATGACAGATTCT
1 CTTTTCAAAGATGACAGATTCC
2660083 CTTTTCAAAGATGA
1 CTTTTCAAAGATGA
2660097 AAGCTTTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (22 bp):
CTTTTCAAAGATGACAGATTCC
Found at i:2661823 original size:222 final size:219
Alignment explanation
Indices: 2660514--2661807 Score: 2255
Period size: 219 Copynumber: 5.9 Consensus size: 219
2660504 TCCATTATTC
*
2660514 GATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
1 GATGGATCAGCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
2660579 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCC
66 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCC
2660644 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
131 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
2660709 TTATTCAACCTTTTTTCATCATTT
196 TTATTCAACCTTTTTTCATCATTT
* *
2660733 GATGGATCAACATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
1 GATGGATCAGCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
*
2660798 TTCATAATGAGAAGAACTTGTTCAACATTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCC
66 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCC
2660863 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
131 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
*
2660928 TTATTCAACTTTTTTTCATCATTT
196 TTATTCAACCTTTTTTCATCATTT
2660952 GATGGATCAGCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
1 GATGGATCAGCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
2661017 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCC
66 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCC
2661082 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
131 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
2661147 TTATTCAACCTTTTTTCATCATTT
196 TTATTCAACCTTTTTTCATCATTT
*
2661171 GATGGATCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
1 GATGGATCAGCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
2661236 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCC
66 TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCC
2661301 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
131 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
2661366 TTATTCAACCTTTTTTCATCATTT
196 TTATTCAACCTTTTTTCATCATTT
* * * *
2661390 GATGGATCACCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG
1 GATGGATCAGCATTACCAGTTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAAGAAGAAG
* * * * *
2661455 AAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATACATCACTTGATGGATCAGCTTT
63 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTT
2661520 TCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
128 TCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
2661585 AATTTATTCAACCTTTTTTCATCATTT
193 AATTTATTCAACCTTTTTTCATCATTT
* * * *
2661612 GATGGATCAACATTGCCAGGTATAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAG
1 GATGGATCAGCATTACCAGTTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAAGAAGAAG
* * * ** * * *
2661677 AAGTTCATAATAAGAAGAACTTGTTCAACTTTTCGCTCGAATTTATCACTCGATGGATCAACTTT
63 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTT
* * * *
2661742 TCCAGAGAAAGTTCATCATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAG
128 TCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAG
2661807 A
193 A
2661808 GCTTGTTCGA
Statistics
Matches: 1037, Mismatches: 35, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
219 686 0.66
221 1 0.00
222 350 0.34
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (219 bp):
GATGGATCAGCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAG
TTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCC
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
TTATTCAACCTTTTTTCATCATTT
Found at i:2661927 original size:17 final size:17
Alignment explanation
Indices: 2661869--2661927 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
2661859 CAGCATTTCT
*
2661869 AGAAGGAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
2661886 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
2661904 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
2661922 AGAAGA
1 AGAAGA
2661928 GCTTGTGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
18 2 0.06
19 10 0.30
20 3 0.09
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:2662179 original size:3 final size:3
Alignment explanation
Indices: 2662171--2662239 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
2662161 TTTTATTTAT
* *
2662171 TTA TTA TTA TTA TTA TTA TTA TTA TAA TAA TTA TTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
2662216 TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
2662240 AAAAAATAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 4 0.07
3 50 0.83
4 6 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2662250 original size:3 final size:3
Alignment explanation
Indices: 2662244--2662278 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2662234 TTATTAAAAA
2662244 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2662279 TACAAACCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2665234 original size:17 final size:17
Alignment explanation
Indices: 2665212--2665252 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
2665202 TTGTCACAAC
2665212 ATTTCACTCACTTCAAT
1 ATTTCACTCACTTCAAT
2665229 ATTTCACTCACTTCAAT
1 ATTTCACTCACTTCAAT
2665246 ATTTCAC
1 ATTTCAC
2665253 CACAACATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTCACTCACTTCAAT
Found at i:2665877 original size:32 final size:33
Alignment explanation
Indices: 2665840--2665906 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
2665830 AACATAAAAT
*
2665840 AAAAT-AAAAACTACCTTCTTATTTACTAAAGC
1 AAAATAAAAAACTACCTTCTTAATTACTAAAGC
*
2665872 AAAATAAAAAACTACCTTCTTAATTACTGAAGC
1 AAAATAAAAAACTACCTTCTTAATTACTAAAGC
2665905 AA
1 AA
2665907 CATTGGAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 5 0.16
33 27 0.84
ACGTcount: A:0.49, C:0.18, G:0.04, T:0.28
Consensus pattern (33 bp):
AAAATAAAAAACTACCTTCTTAATTACTAAAGC
Found at i:2667091 original size:44 final size:45
Alignment explanation
Indices: 2667025--2667113 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 45
2667015 GCTCATATAA
*
2667025 TTTGCACCTAAGTGCCACATAA-TTGTCCCGAAGGACCACATAGG
1 TTTGCACCAAAGTGCCACATAATTTGTCCCGAAGGACCACATAGG
* *
2667069 TTTGCACCAAAGTGCCATATAATTTTGTCCCGAATGACCACATAG
1 TTTGCACCAAAGTGCCACATAA-TTTGTCCCGAAGGACCACATAG
2667114 AACCCTCGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 20 0.50
46 20 0.50
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (45 bp):
TTTGCACCAAAGTGCCACATAATTTGTCCCGAAGGACCACATAGG
Found at i:2667095 original size:23 final size:23
Alignment explanation
Indices: 2667021--2667095 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 23
2667011 CACAGCTCAT
*
2667021 ATAA-TTTGCACCTAAGTGCCAC
1 ATAATTTTGCACCAAAGTGCCAC
* *
2667043 ATAATTGT-C-CCGAAG-GACCAC
1 ATAATTTTGCACCAAAGTG-CCAC
** *
2667064 ATAGGTTTGCACCAAAGTGCCAT
1 ATAATTTTGCACCAAAGTGCCAC
2667087 ATAATTTTG
1 ATAATTTTG
2667096 TCCCGAATGA
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
20 1 0.03
21 14 0.36
22 6 0.15
23 17 0.44
24 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (23 bp):
ATAATTTTGCACCAAAGTGCCAC
Found at i:2668815 original size:2 final size:2
Alignment explanation
Indices: 2668810--2668860 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2668800 ACAAAAAATG
2668810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2668852 AT AT AT AT A
1 AT AT AT AT A
2668861 GGGAGGAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.