Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003583.1 Hibiscus syriacus cultivar Beakdansim tig00007559_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: 143932
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3259 original size:31 final size:31
Alignment explanation
Indices: 3222--3284 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
3212 GTTGACGTCG
3222 GGCACCTAAAAATG-TAACGAAGAAAACGTTA
1 GGCACCT-AAAATGATAACGAAGAAAACGTTA
* *
3253 GGCACCTAAAATGATAATGGAGAAAACGTTA
1 GGCACCTAAAATGATAACGAAGAAAACGTTA
3284 G
1 G
3285 ACATCTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.17
Consensus pattern (31 bp):
GGCACCTAAAATGATAACGAAGAAAACGTTA
Found at i:5844 original size:48 final size:48
Alignment explanation
Indices: 5773--5869 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
5763 AAGAGTAAGA
5773 AATCGTACTCAGGGCCTTATACCAAAAGGTTTTAGTTCAAGCACTCTG
1 AATCGTACTCAGGGCCTTATACCAAAAGGTTTTAGTTCAAGCACTCTG
5821 AATCGTACTCAGGGCCTTATACCAAAAGGTTTTAGTTCAAGCACTCTG
1 AATCGTACTCAGGGCCTTATACCAAAAGGTTTTAGTTCAAGCACTCTG
5869 A
1 A
5870 CACCCGACTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (48 bp):
AATCGTACTCAGGGCCTTATACCAAAAGGTTTTAGTTCAAGCACTCTG
Found at i:6930 original size:48 final size:48
Alignment explanation
Indices: 6854--6948 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
6844 TTAATAAGTC
6854 TGATGGCTGTTGCAAACTCCGCGCGAAGAATAGTTTCACGAGGTTTCT
1 TGATGGCTGTTGCAAACTCCGCGCGAAGAATAGTTTCACGAGGTTTCT
* *
6902 TGATGGCTGTTGCAAACTCCGCGTGAAGAATAGTTTCGCGAGGTTTC
1 TGATGGCTGTTGCAAACTCCGCGCGAAGAATAGTTTCACGAGGTTTC
6949 ATCTCACTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (48 bp):
TGATGGCTGTTGCAAACTCCGCGCGAAGAATAGTTTCACGAGGTTTCT
Found at i:11225 original size:3 final size:3
Alignment explanation
Indices: 11207--11271 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
11197 AAAGAAAGTT
* * * *
11207 GAA GAA G-A GAA TAA GAA GAT GAT GAA -AA TAGA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA
11251 GAA GAA GAA GAA GAAA GAA GA
1 GAA GAA GAA GAA G-AA GAA GA
11272 CTTACCAATC
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.08
3 44 0.83
4 5 0.09
ACGTcount: A:0.63, C:0.00, G:0.31, T:0.06
Consensus pattern (3 bp):
GAA
Found at i:14471 original size:113 final size:114
Alignment explanation
Indices: 14273--14971 Score: 689
Period size: 114 Copynumber: 6.2 Consensus size: 114
14263 AATATTTTAA
* * * * * * * *
14273 AAATGACATAGAATCTTAACTATTCACGTCATATTATTTTTAGTGAAATATCCCCTAAAATTAGA
1 AAATGACAGAGAATCTTAACTATTCAAGTCCTATTATTTTCAGTGAAATATCACCTTAAATCAAA
* * * *
14338 ACTTCTTTCATATTGAATGAAAAATCTTATCTGATACAATAATTA-TTC
66 ACTTATTTCATAGTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * *
14386 AAATGACAAAGAATGTTAACTATTCAAGTCCTGTTATTTTCAGTGAAATATCACCTTAAATCAAA
1 AAATGACAGAGAATCTTAACTATTCAAGTCCTATTATTTTCAGTGAAATATCACCTTAAATC-AA
** *** * * *
14451 AAC-TATTTCATAGTGAATGAAAAATCAGATCCAATACAATTATGATTTT
65 AACTTATTTCATAGTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * * * *
14500 AAATGAAAGAGAATCTTAGA-TATTCATGTCC-ATTTCTTTTCAGAGAAATATCACCTCAAATCA
1 AAATGACAGAGAATCTTA-ACTATTCAAGTCCTA-TTATTTTCAGTGAAATATCACCTTAAATCA
* * * * *
14563 GAATTTCTTTCATATTGAATGAAAAATCTTATCTGGTGCAATAATAATTTC
64 AAACTTATTTCATAGTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * * * * * *
14614 AAATGAGAGAGAATCTTAACTATTCATGTCATATTTTTTTACAGTGAGATGTCACCTTAAATGAA
1 AAATGACAGAGAATCTTAACTATTCAAGTCCTATTATTTT-CAGTGAAATATCACCTTAAATCAA
** * * *
14679 AACTTATTTCATAGTGAATGAAAAATCAAATATGGTATAATAAAAATTTC
65 AACTTATTTCATAGTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * * ** *
14729 AAATGACAGAGAATCTTAATTGTT-AACGT--TATT-TTTTAAGCAAAATATCACCTCAAATCAA
1 AAATGACAGAGAATCTTAACTATTCAA-GTCCTATTATTTTCAGTGAAATATCACCTTAAATCAA
* * * *
14790 AACTTCTTTCATATTGAATGAAAATTTTTATCTGGTACAATAATAATTTC
65 AACTTATTTCATAGTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * * *
14840 AAATGATAGAGAATCTTAACTATTCACA-TCCTTTTATTTTCAATTAAATATCACCTTAAATCAA
1 AAATGACAGAGAATCTTAACTATTCA-AGTCCTATTATTTTCAGTGAAATATCACCTTAAATCAA
** * * *
14904 AACTTATTT-ATAGTGAATGAAAAATCAGATTTGGCATAATAATAATTTC
65 AACTTATTTCATAGTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
*
14953 AAATGATAGAGAATCTTAA
1 AAATGACAGAGAATCTTAA
14972 TTTCTTATGT
Statistics
Matches: 476, Mismatches: 96, Indels: 28
0.79 0.16 0.05
Matches are distributed among these distances:
111 80 0.17
112 5 0.01
113 150 0.32
114 157 0.33
115 84 0.18
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (114 bp):
AAATGACAGAGAATCTTAACTATTCAAGTCCTATTATTTTCAGTGAAATATCACCTTAAATCAAA
ACTTATTTCATAGTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
Found at i:15006 original size:113 final size:114
Alignment explanation
Indices: 14273--15013 Score: 511
Period size: 113 Copynumber: 6.5 Consensus size: 114
14263 AATATTTTAA
* * * * * * * * * * * * *
14273 AAATGACATAGAATCTTAACTATTCACGTCATATTATTTTTAGTGAAATATCCCCTAAAATTAGA
1 AAATGATAGAGAATCTTAACTATTCACATCCTTTTATTTTCAATTAAAAATCACCTTAAATCAAA
* * ** ** *
14338 ACTTCTTTCATATTGAATGAAAAATCTTATCTGATACAATAATTA-TTC
66 ACTTATTTCATAGTGAATGAAAAATCAGATCTGGCACAATAATAATTTC
* * * * * * *
14386 AAATGACAAAGAATGTTAACTATTCA-AGTCCTGTTATTTTCAGTGAAATATCACCTTAAATCAA
1 AAATGATAGAGAATCTTAACTATTCACA-TCCTTTTATTTTCAATTAAAAATCACCTTAAATC-A
**** * * *
14450 AAAC-TATTTCATAGTGAATGAAAAATCAGATCCAATACAATTATGATTTT
64 AAACTTATTTCATAGTGAATGAAAAATCAGATCTGGCACAATAATAATTTC
* ** * * * * *
14500 AAATGAAAGAGAATCTTAGA-TATTCATGTCCATTTCTTTTCAGA-GAAATATCACCTCAAATCA
1 AAATGATAGAGAATCTTA-ACTATTCACATCCTTTTATTTTCA-ATTAAAAATCACCTTAAATCA
* * * * ** **
14563 GAATTTCTTTCATATTGAATGAAAAATCTTATCTGGTGCAATAATAATTTC
64 AAACTTATTTCATAGTGAATGAAAAATCAGATCTGGCACAATAATAATTTC
* ** * * * * ** *
14614 AAATGAGAGAGAATCTTAACTATTCATGTCATATTT-TTTTACAGTGAGATGTCACCTTAAATGA
1 AAATGATAGAGAATCTTAACTATTCACATCCT-TTTATTTT-CAATTAAAAATCACCTTAAATCA
* * * * *
14678 AAACTTATTTCATAGTGAATGAAAAATCAAATATGGTATAATAAAAATTTC
64 AAACTTATTTCATAGTGAATGAAAAATCAGATCTGGCACAATAATAATTTC
* * * * ** *
14729 AAATGACAGAGAATCTTAATTGTT-A-A-CGTTATT-TTTT-AAGCAAAATATCACCTCAAATCA
1 AAATGATAGAGAATCTTAACTATTCACATCCTT-TTATTTTCAATTAAAA-ATCACCTTAAATCA
* * * *** *
14789 AAACTTCTTTCATATTGAATGAAAATTTTTATCTGGTACAATAATAATTTC
64 AAACTTATTTCATAGTGAATGAAAAATCAGATCTGGCACAATAATAATTTC
*
14840 AAATGATAGAGAATCTTAACTATTCACATCCTTTTATTTTCAATTAAATATCACCTTAAATCAAA
1 AAATGATAGAGAATCTTAACTATTCACATCCTTTTATTTTCAATTAAAAATCACCTTAAATCAAA
* *
14905 ACTTATTT-ATAGTGAATGAAAAATCAGATTTGGCATAATAATAATTTC
66 ACTTATTTCATAGTGAATGAAAAATCAGATCTGGCACAATAATAATTTC
** * * *
14953 AAATGATAGAGAATCTTAA-T-TTCTTATGTTCTTTTATTTTTAGTTAAAAATCACCTTAAAT
1 AAATGATAGAGAATCTTAACTATTC--ACATCCTTTTATTTTCAATTAAAAATCACCTTAAAT
15014 AGAACTTTTC
Statistics
Matches: 504, Mismatches: 104, Indels: 40
0.78 0.16 0.06
Matches are distributed among these distances:
110 3 0.01
111 78 0.15
112 10 0.02
113 174 0.35
114 151 0.30
115 88 0.17
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (114 bp):
AAATGATAGAGAATCTTAACTATTCACATCCTTTTATTTTCAATTAAAAATCACCTTAAATCAAA
ACTTATTTCATAGTGAATGAAAAATCAGATCTGGCACAATAATAATTTC
Found at i:16606 original size:29 final size:29
Alignment explanation
Indices: 16564--16623 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
16554 CCAAATTTTG
* * * *
16564 TTTAGTGACTAAAATGTAAGTTTTGAAAA
1 TTTAATGACTAAAATGAAACTTTGGAAAA
16593 TTTAATGACTAAAATGAAACTTTGGAAAA
1 TTTAATGACTAAAATGAAACTTTGGAAAA
16622 TT
1 TT
16624 GAAGGGTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.37
Consensus pattern (29 bp):
TTTAATGACTAAAATGAAACTTTGGAAAA
Found at i:18486 original size:36 final size:36
Alignment explanation
Indices: 18445--18655 Score: 395
Period size: 36 Copynumber: 5.9 Consensus size: 36
18435 ATTTATCCAT
18445 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
18481 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
18517 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
18553 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
18589 TATCAGCTTTGATACATTAGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
18625 TATCAACTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
18656 CCAGCACCGT
Statistics
Matches: 170, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 170 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:20764 original size:23 final size:23
Alignment explanation
Indices: 20738--20796 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
20728 TTAGCATTTT
*
20738 AAAAATAAAGAAAGCTTGTAAAG
1 AAAAATAAAGAAAGCTTATAAAG
*
20761 AAAAATAAAGAAAGTTTATAAAG
1 AAAAATAAAGAAAGCTTATAAAG
20784 AAAAATAAAGAAA
1 AAAAATAAAGAAA
20797 AGTGAAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.68, C:0.02, G:0.14, T:0.17
Consensus pattern (23 bp):
AAAAATAAAGAAAGCTTATAAAG
Found at i:20817 original size:46 final size:45
Alignment explanation
Indices: 20738--20828 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 45
20728 TTAGCATTTT
*
20738 AAAAATAAAGAAAGCTTGTAAAGAAAAATAAAGAAAGTTTATAAAG
1 AAAAATAAAGAAAGC-TGTAAAGAAAAAAAAAGAAAGTTTATAAAG
*
20784 AAAAATAAAGAAAAG-TG-AAAGTAAAAAGAAAAGAAATTTTATAAA
1 AAAAATAAAG-AAAGCTGTAAAG-AAAAA-AAAAGAAAGTTTATAAA
20829 AACTAAAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
44 4 0.10
45 7 0.17
46 25 0.62
47 4 0.10
ACGTcount: A:0.66, C:0.01, G:0.14, T:0.19
Consensus pattern (45 bp):
AAAAATAAAGAAAGCTGTAAAGAAAAAAAAAGAAAGTTTATAAAG
Found at i:31417 original size:25 final size:25
Alignment explanation
Indices: 31389--31439 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
31379 TATTGAATAT
*
31389 GTTTTATTATTTATTATTTTTTAAA
1 GTTTTATAATTTATTATTTTTTAAA
31414 GTTTTATAATTTATTATTTTTTAAA
1 GTTTTATAATTTATTATTTTTTAAA
31439 G
1 G
31440 GTTCATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (25 bp):
GTTTTATAATTTATTATTTTTTAAA
Found at i:33919 original size:13 final size:13
Alignment explanation
Indices: 33887--33934 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
33877 CTAATAATTC
*
33887 AATAATGATTACT
1 AATAATGATTAGT
33900 AAT-ATGATTAGT
1 AATAATGATTAGT
33912 AATAATGATTAGT
1 AATAATGATTAGT
33925 AATAATGATT
1 AATAATGATT
33935 TACTAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
12 11 0.33
13 22 0.67
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (13 bp):
AATAATGATTAGT
Found at i:33949 original size:27 final size:25
Alignment explanation
Indices: 33887--33941 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 25
33877 CTAATAATTC
*
33887 AATAATGATTACTAATATGATTAGT
1 AATAATGATTACTAATATGATTACT
*
33912 AATAATGATTAGTAATAATGATTTACT
1 AATAATGATTACTAAT-ATGA-TTACT
33939 AAT
1 AAT
33942 TATTATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 15 0.58
26 4 0.15
27 7 0.27
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (25 bp):
AATAATGATTACTAATATGATTACT
Found at i:33956 original size:26 final size:26
Alignment explanation
Indices: 33927--34009 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
33917 TGATTAGTAA
33927 TAATGATTTACTAATTATTATTAATT
1 TAATGATTTACTAATTATTATTAATT
* * ** * *
33953 TAATAATTTGA-TATTTAATGGTTTA-G
1 TAATGATTT-ACTAATT-ATTATTAATT
*
33979 TAATGATTTACTAATTATTATCAATT
1 TAATGATTTACTAATTATTATTAATT
34005 ATAAT
1 -TAAT
34010 AATTATTATC
Statistics
Matches: 39, Mismatches: 13, Indels: 9
0.64 0.21 0.15
Matches are distributed among these distances:
25 5 0.13
26 24 0.62
27 10 0.26
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.51
Consensus pattern (26 bp):
TAATGATTTACTAATTATTATTAATT
Found at i:35449 original size:13 final size:13
Alignment explanation
Indices: 35431--35487 Score: 71
Period size: 13 Copynumber: 4.4 Consensus size: 13
35421 AGAACGTCAA
35431 TATTAGTAATCAT
1 TATTAGTAATCAT
*
35444 TATTAGTAAATCAC
1 TATTAGT-AATCAT
*
35458 TATTAGTAATTAT
1 TATTAGTAATCAT
*
35471 TATTACTAATCA-
1 TATTAGTAATCAT
35483 TATTA
1 TATTA
35488 TGCATTAGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
12 5 0.13
13 21 0.55
14 12 0.32
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (13 bp):
TATTAGTAATCAT
Found at i:35461 original size:14 final size:14
Alignment explanation
Indices: 35431--35466 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
35421 AGAACGTCAA
*
35431 TATTAGT-AATCAT
1 TATTAGTAAATCAC
35444 TATTAGTAAATCAC
1 TATTAGTAAATCAC
35458 TATTAGTAA
1 TATTAGTAA
35467 TTATTATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (14 bp):
TATTAGTAAATCAC
Found at i:35472 original size:27 final size:25
Alignment explanation
Indices: 35430--35487 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 25
35420 AAGAACGTCA
*
35430 ATATTAGTAATCATTATTAGTAAATC
1 ATATTAGTAATCATTATTACT-AATC
*
35456 ACTATTAGTAATTATTATTACTAATC
1 A-TATTAGTAATCATTATTACTAATC
35482 ATATTA
1 ATATTA
35488 TGCATTAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 6 0.21
27 18 0.62
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (25 bp):
ATATTAGTAATCATTATTACTAATC
Found at i:35664 original size:21 final size:21
Alignment explanation
Indices: 35640--35695 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 21
35630 ATTTAATATT
35640 ATTAAATCATTATTAGTAATA
1 ATTAAATCATTATTAGTAATA
*
35661 ATTATAAAATCATTATTAGTAATT
1 A-T-T-AAATCATTATTAGTAATA
35685 ATTAAAT-ATTA
1 ATTAAATCATTA
35696 ATAATAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 5 0.16
22 2 0.06
23 2 0.06
24 18 0.58
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (21 bp):
ATTAAATCATTATTAGTAATA
Found at i:35664 original size:24 final size:23
Alignment explanation
Indices: 35633--35688 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 23
35623 TTATTTTATT
*
35633 TAATATTATTAAATCATTATTAG
1 TAATATTATAAAATCATTATTAG
35656 TAATAATTATAAAATCATTATTAG
1 TAAT-ATTATAAAATCATTATTAG
35680 TAATTATTA
1 TAA-TATTA
35689 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 4 0.13
24 25 0.83
25 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (23 bp):
TAATATTATAAAATCATTATTAG
Found at i:35688 original size:34 final size:33
Alignment explanation
Indices: 35634--35722 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 33
35624 TATTTTATTT
* * * *
35634 AATATTATTAAATCATTATTAGTAATAATTATAA
1 AATATTATT-AGTAATTATTAATAATAATAATAA
*
35668 AATCATTATTAGTAATTATTAAATATTAATAATAA
1 AAT-ATTATTAGTAATTATT-AATAATAATAATAA
35703 AATATTATTAGTAATTATTA
1 AATATTATTAGTAATTATTA
35723 CTAAATCATA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.02
34 27 0.56
35 20 0.42
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45
Consensus pattern (33 bp):
AATATTATTAGTAATTATTAATAATAATAATAA
Found at i:35761 original size:15 final size:15
Alignment explanation
Indices: 35725--35767 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
35715 AATTATTACT
* *
35725 AAATCATATAATTATT
1 AAATCAT-TAAATATC
35741 AAATCATTAAATATC
1 AAATCATTAAATATC
35756 AAATCATTAAAT
1 AAATCATTAAAT
35768 TAATAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:35801 original size:13 final size:13
Alignment explanation
Indices: 35776--35831 Score: 87
Period size: 13 Copynumber: 4.3 Consensus size: 13
35766 ATTAATAATA
35776 ATTAGTAAATCATT
1 ATTAGT-AATCATT
35790 ATTAGTAATCATT
1 ATTAGTAATCATT
*
35803 ATTACTAATCA-T
1 ATTAGTAATCATT
35815 ATTAGTAATCATT
1 ATTAGTAATCATT
35828 ATTA
1 ATTA
35832 AATTATTAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
12 11 0.28
13 22 0.56
14 6 0.15
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (13 bp):
ATTAGTAATCATT
Found at i:35821 original size:25 final size:26
Alignment explanation
Indices: 35783--35831 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
35773 ATAATTAGTA
35783 AATCATTATTAGTAATCATTATTACT
1 AATCATTATTAGTAATCATTATTACT
35809 AATCA-TATTAGTAATCATTATTA
1 AATCATTATTAGTAATCATTATTA
35832 AATTATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (26 bp):
AATCATTATTAGTAATCATTATTACT
Found at i:35851 original size:20 final size:21
Alignment explanation
Indices: 35787--35852 Score: 53
Period size: 25 Copynumber: 3.0 Consensus size: 21
35777 TTAGTAAATC
**
35787 ATTATTAGTAATCATTATTACTA
1 ATTATTAGTAATCAAAATTA--A
**
35810 ATCATATTAGTAATCATTATTAA
1 AT--TATTAGTAATCAAAATTAA
35833 ATTATTAGT-ATCAAAATTAA
1 ATTATTAGTAATCAAAATTAA
35853 GTAATTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 9 0.23
21 7 0.18
23 5 0.13
25 18 0.46
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (21 bp):
ATTATTAGTAATCAAAATTAA
Found at i:36878 original size:20 final size:20
Alignment explanation
Indices: 36853--36986 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
36843 AATTGGGAAA
36853 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
36873 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
36893 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
36914 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
36934 -TCGCAACGCGATGCTGACT
1 ATCGCAATGCGATACTGACT
* * *
36953 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
36973 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
36987 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
19 21 0.22
20 48 0.51
21 24 0.25
22 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:36939 original size:19 final size:20
Alignment explanation
Indices: 36915--36966 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
36905 TAATACAAAA
*
36915 TCGCAACGAGATACTGAC-T
1 TCGCAACGCGATACTGACTT
*
36934 TCGCAACGCGATGCTGACTT
1 TCGCAACGCGATACTGACTT
36954 TCGCAACGCGATA
1 TCGCAACGCGATA
36967 ATACATAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:36965 original size:60 final size:61
Alignment explanation
Indices: 36850--36980 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 61
36840 GCGAATTGGG
* * * * *
36850 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
36911 AAAATCGCAACGAGATACTGACT-TCGCAACGCGATGCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
36971 ATAATCGCAA
1 AAAATCGCAA
36981 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
60 41 0.66
61 21 0.34
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:37500 original size:20 final size:20
Alignment explanation
Indices: 37441--37504 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
37431 GCGATTTTAG
*
37441 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
37461 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
37481 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
37501 TTTC
1 TTTC
37505 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:38868 original size:18 final size:18
Alignment explanation
Indices: 38824--38868 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
38814 TCCACTTCGG
*
38824 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
38842 GAACTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
38860 GAGCCATCA
1 GAGCCATCA
38869 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:39398 original size:19 final size:20
Alignment explanation
Indices: 39344--39410 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
39334 TAGTTTACTT
* *
39344 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
39364 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
39384 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
39403 TCGCAACG
1 TCGCAACG
39411 ATAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:39418 original size:14 final size:14
Alignment explanation
Indices: 39399--39490 Score: 85
Period size: 14 Copynumber: 5.9 Consensus size: 14
39389 ATGCGAAATG
39399 AAAATCGCAACGAT
1 AAAATCGCAACGAT
39413 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
39431 GAAAATCGCAACGAT
1 -AAAATCGCAACGAT
39446 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
*
39464 GAAAATCGCAACGAC
1 -AAAATCGCAACGAT
39479 AAAATCGCAACG
1 AAAATCGCAACG
39491 CGAAATGAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
14 32 0.48
15 3 0.04
16 4 0.06
17 4 0.06
18 4 0.06
19 20 0.30
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:39425 original size:33 final size:33
Alignment explanation
Indices: 39383--39507 Score: 232
Period size: 33 Copynumber: 3.8 Consensus size: 33
39373 GGAAATGGCT
39383 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
39416 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
*
39449 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
*
39482 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
39508 TGCGATTTGT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGATAAA
Found at i:39437 original size:19 final size:19
Alignment explanation
Indices: 39383--39512 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
39373 GGAAATGGCT
39383 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
39402 ATCGCAA--CG--AT-AAA
1 ATCGCAATGCGAAATGAAA
39416 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
39435 ATCGCAA--CG--AT-AAA
1 ATCGCAATGCGAAATGAAA
39449 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
39468 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
39482 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
39501 ATCGCAATGCGA
1 ATCGCAATGCGA
39513 TTTGTGTTTC
Statistics
Matches: 93, Mismatches: 3, Indels: 30
0.74 0.02 0.24
Matches are distributed among these distances:
14 30 0.32
15 5 0.05
16 6 0.06
17 6 0.06
18 5 0.05
19 41 0.44
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40355 original size:42 final size:41
Alignment explanation
Indices: 40288--40397 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 41
40278 ATGAATCGGG
* * *
40288 CTCTTGAATGGTGGGAGGGACCTCTTCAACG-ATGACAGTGGC
1 CTCTTGAACGGTAGGAGGGA-CTCTT-AACGAATGACAGGGGC
* * *
40330 CTCTTGAACGGTAGGAGAGGACTCTTGAGGAATGATAGGGGC
1 CTCTTGAACGGTAGGAG-GGACTCTTAACGAATGACAGGGGC
* *
40372 CTCTTCAACGATAGGAGTGGACTCTT
1 CTCTTGAACGGTAGGAG-GGACTCTT
40398 GAGGGATGAC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.91
43 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.25
Consensus pattern (41 bp):
CTCTTGAACGGTAGGAGGGACTCTTAACGAATGACAGGGGC
Found at i:40398 original size:42 final size:42
Alignment explanation
Indices: 40327--40406 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
40317 CGATGACAGT
* *
40327 GGCCTCTTGAACGGTAGGAGAGGACTCTTGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGAGGACTCTTGAGGAATGATAGG
* *
40369 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGAGGACTCTTGAGGAATGA
40407 CAGGCGAGTC
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:0.25, C:0.16, G:0.36, T:0.23
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGAGGACTCTTGAGGAATGATAGG
Found at i:40802 original size:91 final size:90
Alignment explanation
Indices: 40628--40812 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
40618 ATTTCAAACT
* *
40628 TTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
40693 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
40721 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
40785 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
40812 T
1 T
40813 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:42532 original size:20 final size:19
Alignment explanation
Indices: 42509--42622 Score: 61
Period size: 14 Copynumber: 6.4 Consensus size: 19
42499 ATGAAAATTT
*
42509 CAACGAGATAATGAGAATCG
1 CAACGAGA-AATGACAATCG
* *
42529 CAACGCGGAAATGACTATCG
1 CAACG-AGAAATGACAATCG
42549 CAACGAG--A-G--AATCG
1 CAACGAGAAATGACAATCG
42563 CAACGAG--A-G--AATCG
1 CAACGAGAAATGACAATCG
* *
42577 CAACGCGAAATGA-AAACTG
1 CAACGAGAAATGACAATC-G
* *
42596 CAACGCGAAATGAAAATCG
1 CAACGAGAAATGACAATCG
42615 CAACGAGA
1 CAACGAGA
42623 GAATCGCAAC
Statistics
Matches: 78, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
14 24 0.31
16 2 0.03
17 2 0.03
18 3 0.04
19 23 0.29
20 22 0.28
21 2 0.03
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (19 bp):
CAACGAGAAATGACAATCG
Found at i:42564 original size:14 final size:14
Alignment explanation
Indices: 42545--42581 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
42535 GGAAATGACT
42545 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
42559 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
42573 ATCGCAACG
1 ATCGCAACG
42582 CGAAATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.27, T:0.08
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:42617 original size:19 final size:19
Alignment explanation
Indices: 42572--42648 Score: 94
Period size: 19 Copynumber: 4.3 Consensus size: 19
42562 GCAACGAGAG
42572 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
42591 AA-CTGCAACGCGAAATGAA
1 AATC-GCAACGCGAAATGAA
*
42610 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
42624 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
42643 AATCGC
1 AATCGC
42649 GTTACGATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 31 0.63
20 1 0.02
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:43275 original size:20 final size:20
Alignment explanation
Indices: 43252--43468 Score: 97
Period size: 20 Copynumber: 10.7 Consensus size: 20
43242 CGATAGTAAG
43252 ATTCGCATTGCGATTTACTA
1 ATTCGCATTGCGATTTACTA
*
43272 ATTCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTAC-TA
*
43292 ATTCGCATTGCGAATTA-TGAA
1 ATTCGCATTGCGATTTACT--A
* ** *
43313 AATCGCAACGCGA-ATACGTA
1 ATTCGCATTGCGATTTAC-TA
* * * **
43333 AATCGCAATGCGAATTAGGAA
1 ATTCGCATTGCGATTTA-CTA
* *
43354 AATCGCATTGCGA--TAGTCA
1 ATTCGCATTGCGATTTACT-A
* * * *
43373 GTATCCCATTGCGATTTTCCAA
1 AT-TCGCATTGCGA-TTTACTA
*
43395 ATTCGCATTGCGATAGTTAGT-
1 ATTCGCATTGCGAT--TTACTA
* *
43416 A-TCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACTA
*
43436 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACTA
43456 ATTCGCATTGCGA
1 ATTCGCATTGCGA
43469 ATTGGGAAAA
Statistics
Matches: 149, Mismatches: 30, Indels: 36
0.69 0.14 0.17
Matches are distributed among these distances:
18 2 0.01
19 5 0.03
20 87 0.58
21 49 0.33
22 5 0.03
23 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTA
Found at i:43365 original size:21 final size:21
Alignment explanation
Indices: 43294--43366 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
43284 ATTTACGTAT
* *
43294 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
43315 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
43335 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
*
43356 TCGCATTGCGA
1 TCGCAATGCGA
43367 TAGTCAGTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:43386 original size:41 final size:40
Alignment explanation
Indices: 43231--43483 Score: 165
Period size: 41 Copynumber: 6.2 Consensus size: 40
43221 GGCGCTATGT
* *
43231 AAATCGCATTGCGATAGTAAG-ATTCGCATTGCGATTTAC-T
1 AAATCGCATTGCGATAGT-AGTA-TCGCATTGCGAATTACGA
* * * *
43271 AATTCGCGTTGCGAT-TTACGTATTCGCATTGCGAATTATGA
1 AAATCGCATTGCGATAGTA-GTA-TCGCATTGCGAATTACGA
** * * *
43312 AAATCGCAACGCGAATACGTA-AATCGCAATGCGAATTAGGA
1 AAATCGCATTGCG-ATA-GTAGTATCGCATTGCGAATTACGA
* * * *
43353 AAATCGCATTGCGATAGTCAGTATCCCATTGCGATTTTCCA
1 AAATCGCATTGCGATAGT-AGTATCGCATTGCGAATTACGA
* * * *
43394 AATTCGCATTGCGATAGTTAGTATCGCATTGCGATTTTCCA
1 AAATCGCATTGCGATAG-TAGTATCGCATTGCGAATTACGA
* * * **
43435 AATTCGCATTGCGAT-TTACTTATTCGCATTGCGAATTGGGA
1 AAATCGCATTGCGATAGTA-GTA-TCGCATTGCGAATTACGA
43476 AAATCGCA
1 AAATCGCA
43484 ACGCGAAATT
Statistics
Matches: 170, Mismatches: 32, Indels: 21
0.76 0.14 0.09
Matches are distributed among these distances:
38 1 0.01
39 6 0.04
40 35 0.21
41 122 0.72
42 4 0.02
44 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (40 bp):
AAATCGCATTGCGATAGTAGTATCGCATTGCGAATTACGA
Found at i:43483 original size:82 final size:80
Alignment explanation
Indices: 43231--43483 Score: 215
Period size: 82 Copynumber: 3.1 Consensus size: 80
43221 GGCGCTATGT
* * * *
43231 AAATCGCATTGCGATAGTAAGATTCGCATTGCGATTTACTAATTCGCGTTGCGATTTACGTATTC
1 AAATCGCATTGCGATAGTTAGA-TCGCATTGCGATTTACAAATTCGCATTGCGATTTACTTATTC
*
43296 GCATTGCGAATTATGA
65 GCATTGCGAATTACGA
** * * * * * * *
43312 AAATCGCAACGCGAATACG-TAAATCGCAATGCGAATTAGGAAAATCGCATTGCGA--TAGTCAG
1 AAATCGCATTGCG-ATA-GTTAGATCGCATTGCGATTTA-CAAATTCGCATTGCGATTTACTTA-
* * * *
43374 TATCCCATTGCGATTTTCCA
62 T-TCGCATTGCGAATTACGA
* *
43394 AATTCGCATTGCGATAGTTAGTATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACTTATT
1 AAATCGCATTGCGATAGTTAG-ATCGCATTGCGA-TTTACAAATTCGCATTGCGATTTACTTATT
**
43459 CGCATTGCGAATTGGGA
64 CGCATTGCGAATTACGA
43476 AAATCGCA
1 AAATCGCA
43484 ACGCGAAATT
Statistics
Matches: 127, Mismatches: 35, Indels: 19
0.70 0.19 0.10
Matches are distributed among these distances:
80 4 0.03
81 30 0.24
82 85 0.67
83 4 0.03
84 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (80 bp):
AAATCGCATTGCGATAGTTAGATCGCATTGCGATTTACAAATTCGCATTGCGATTTACTTATTCG
CATTGCGAATTACGA
Found at i:43510 original size:21 final size:22
Alignment explanation
Indices: 43458--43510 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
43448 ATTTACTTAT
43458 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
43479 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
43500 TCGCATTGCGA
1 TCGCATTGCGA
43511 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:45650 original size:18 final size:17
Alignment explanation
Indices: 45596--45644 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
45586 TTGGACTCCT
* *
45596 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
45614 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
45632 AGTGCATTCGATG
1 AGTGCA-TCGATG
45645 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:45665 original size:64 final size:63
Alignment explanation
Indices: 45596--45775 Score: 204
Period size: 64 Copynumber: 2.8 Consensus size: 63
45586 TTGGACTCCT
* *
45596 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-TGAAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAATCAG
* *** * *
45657 CCTGGTGCATCGATGCATGACTTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATGAAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-TAAATC
45722 AG
62 AG
* *
45724 AGTGCATCAATGCATGAAGAGTGCATCGGTGCATGAAATGCATTCGATGTTT
1 AGTGCATCGATGCATGAAGAGTGCATCGATGCATGAAATGCATTCGATGTTT
45776 CAATTTATTC
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
63 1 0.01
64 90 0.93
66 4 0.04
67 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (63 bp):
AGTGCATCGATGCATGAAGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAATCAG
Found at i:45746 original size:19 final size:19
Alignment explanation
Indices: 45722--45760 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
45712 TAATTAAATC
45722 AGAGTGCATCAATGCATGA
1 AGAGTGCATCAATGCATGA
**
45741 AGAGTGCATCGGTGCATGA
1 AGAGTGCATCAATGCATGA
45760 A
1 A
45761 ATGCATTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCAATGCATGA
Found at i:48667 original size:29 final size:30
Alignment explanation
Indices: 48597--48656 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
48587 AAATTTAAGG
48597 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
48628 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
48657 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:48762 original size:21 final size:21
Alignment explanation
Indices: 48736--48793 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
48726 AGGGTGTCAA
48736 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
48757 AGTGCATCCATACATCCCTGC
1 AGTGCATCCATGCACCCCTGC
48778 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
48794 TGCACTAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.40, G:0.17, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:49014 original size:21 final size:21
Alignment explanation
Indices: 48985--49024 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
48975 TTTTAGTAGA
48985 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAA-GGCTCC
49007 AAAA-CATCCCCAAAGGCT
1 AAAATCATCCCCAAAGGCT
49025 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.40, C:0.38, G:0.10, T:0.12
Consensus pattern (21 bp):
AAAATCATCCCCAAAGGCTCC
Found at i:49279 original size:34 final size:32
Alignment explanation
Indices: 49240--49309 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
49230 TTTTGTAAAG
* *
49240 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
49274 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
49306 GGGA
1 GGGA
49310 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:50194 original size:19 final size:20
Alignment explanation
Indices: 50170--50217 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
50160 AACGATTTTC
*
50170 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
50189 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
50209 TTTTGAAAA
1 TTTTGAAAA
50218 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:51523 original size:29 final size:30
Alignment explanation
Indices: 51454--51512 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
51444 AATTTAAGGT
51454 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
51485 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
51513 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:51638 original size:22 final size:21
Alignment explanation
Indices: 51592--51666 Score: 123
Period size: 21 Copynumber: 3.5 Consensus size: 21
51582 AGGGTGTCAA
* *
51592 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATACATCCCTGC
51613 AGTGCATCCATACATCCCTTGC
1 AGTGCATCCATACATCCC-TGC
51635 AGTGCATCCATACATCCCTGC
1 AGTGCATCCATACATCCCTGC
51656 AGTGCATCCAT
1 AGTGCATCCAT
51667 GCACCTGCAC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 30 0.59
22 21 0.41
ACGTcount: A:0.23, C:0.37, G:0.16, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATACATCCCTGC
Found at i:53719 original size:21 final size:20
Alignment explanation
Indices: 53671--53719 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
53661 AATGATTTTC
* * *
53671 TTTT-AAAAGCAAAATTAGA
1 TTTTGAAAAACAAAATGAAA
53690 TTTTGAAAAACAAAATGAAA
1 TTTTGAAAAACAAAATGAAA
53710 TTTTGAAAAA
1 TTTTGAAAAA
53720 TGATTTTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (20 bp):
TTTTGAAAAACAAAATGAAA
Found at i:56178 original size:21 final size:22
Alignment explanation
Indices: 56138--56178 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
56128 TTAAATATTA
*
56138 TAAAGGAAGTACCGATACTCAT
1 TAAAGGAAGTACCAATACTCAT
*
56160 TAAAGG-AGTTCCAATACTC
1 TAAAGGAAGTACCAATACTC
56179 CATGTCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCAATACTCAT
Found at i:62540 original size:35 final size:35
Alignment explanation
Indices: 62496--62695 Score: 278
Period size: 35 Copynumber: 5.8 Consensus size: 35
62486 AAGTAGATTT
*
62496 GAAGAAAGCATCGCACTTTCGATTCAAGTAGAACG
1 GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
* *
62531 GAAAGAAGCATCGTACTTTCGATTCAAGTAGAACG
1 GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
* * * *
62566 GAAGGCAGCATCTCACTTTCCATTCAAGTCGAACG
1 GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
*
62601 GAAGGAAGCATCACACTTTCGATTCAAGTAGAACG
1 GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
* *
62636 GAAGGAAGCA--GCACTTTCGATTCAAATCGAACG
1 GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
* *
62669 GAAAGAAGCATCGCACTTTCAATTCAA
1 GAAGGAAGCATCGCACTTTCGATTCAA
62696 TTGTTCATCT
Statistics
Matches: 145, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
33 29 0.20
35 116 0.80
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (35 bp):
GAAGGAAGCATCGCACTTTCGATTCAAGTAGAACG
Found at i:71826 original size:18 final size:18
Alignment explanation
Indices: 71790--71833 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
71780 ATGAAATTGA
71790 ATTCTAA-TTCATGACAG
1 ATTCTAATTTCATGACAG
* *
71807 ATTCTAATTTCTTTACAG
1 ATTCTAATTTCATGACAG
71825 ATTCTAATT
1 ATTCTAATT
71834 ATCTCATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (18 bp):
ATTCTAATTTCATGACAG
Found at i:77015 original size:17 final size:17
Alignment explanation
Indices: 76993--77025 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
76983 GTTCGAATTG
76993 TTTTTATTATTTAGTTC
1 TTTTTATTATTTAGTTC
*
77010 TTTTTATTTTTTAGTT
1 TTTTTATTATTTAGTT
77026 GTATCATTTT
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:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTTATTATTTAGTTC
Found at i:79440 original size:60 final size:60
Alignment explanation
Indices: 79344--79462 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
79334 CTCCATGATG
* * * * *
79344 TCGACATTTAGGTCGAACAAGCTAGTAGTTGCATGTCTTCCCCTT-GAACTTGAAGGTATC
1 TCGACATTGAGGTCAAAAAAGCTAGTAGTTGAATGTC-TCCCATTGGAACTTGAAGGTATC
*
79404 TCGACATTGAGGTCAAAAAAGCTCGTAGTTGAATGTCTCCCATTGGAACTTGAAGGTAT
1 TCGACATTGAGGTCAAAAAAGCTAGTAGTTGAATGTCTCCCATTGGAACTTGAAGGTAT
79463 TGTGTCAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 6 0.12
60 46 0.88
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (60 bp):
TCGACATTGAGGTCAAAAAAGCTAGTAGTTGAATGTCTCCCATTGGAACTTGAAGGTATC
Found at i:81052 original size:18 final size:18
Alignment explanation
Indices: 81029--81070 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
81019 GGTTTCCGAA
*
81029 ATTTTAAAA-TTATTATAT
1 ATTTTAAAATTTA-AATAT
81047 ATTTTAAAATTTAAATAT
1 ATTTTAAAATTTAAATAT
81065 ATTTTA
1 ATTTTA
81071 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAAAATTTAAATAT
Found at i:81067 original size:25 final size:23
Alignment explanation
Indices: 81035--81083 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
81025 CGAAATTTTA
*
81035 AAATTATTATATATTTTAAAATTT
1 AAATTATTATATA-TTAAAAATTT
*
81059 AAATATATTTTATATTAAAAATTT
1 AAAT-TATTATATATTAAAAATTT
81083 A
1 A
81084 TTTCGTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTATTATATATTAAAAATTT
Found at i:81757 original size:20 final size:20
Alignment explanation
Indices: 81732--81924 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
81722 GATTTTCTAG
* ** *
81732 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
81752 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
81772 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
81792 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
81812 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
81832 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
81852 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
81872 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
81893 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
81913 AATCGCAACGCG
1 AATCGCAACGCG
81925 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:82340 original size:33 final size:33
Alignment explanation
Indices: 82301--82371 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
82291 TTCACTTAGA
82301 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
82334 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
82367 TTTCA
1 TTTCA
82372 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:82529 original size:19 final size:20
Alignment explanation
Indices: 82451--82543 Score: 116
Period size: 21 Copynumber: 4.5 Consensus size: 20
82441 TGCAGAAGAG
82451 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
82472 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
82492 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
*
82514 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
82533 TCGCAACGAGA
1 TCGCAACGAGA
82544 GAATCGCAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 18 0.30
20 9 0.15
21 24 0.39
22 10 0.16
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:82546 original size:42 final size:41
Alignment explanation
Indices: 82451--82543 Score: 134
Period size: 42 Copynumber: 2.3 Consensus size: 41
82441 TGCAGAAGAG
* * **
82451 TCGCAACGAGATAAATGAAAATCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAAATGAAAATCGCAACGCGAAAATGAAAA
82492 TCTGCAACGAGAAAAATGAAAATCGCAACGCG-AAATGAAAA
1 TC-GCAACGAGAAAAATGAAAATCGCAACGCGAAAATGAAAA
82533 TCGCAACGAGA
1 TCGCAACGAGA
82544 GAATCGCAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
40 9 0.19
41 11 0.23
42 27 0.57
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (41 bp):
TCGCAACGAGAAAAATGAAAATCGCAACGCGAAAATGAAAA
Found at i:82588 original size:19 final size:19
Alignment explanation
Indices: 82566--82693 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
82556 GAAACCAAAA
*
82566 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
82585 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
82599 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
82618 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
82632 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
82652 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
82672 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
82692 TC
1 TC
82694 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:82607 original size:14 final size:14
Alignment explanation
Indices: 82588--82644 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
82578 TTTCATTTCG
82588 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
82602 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
82621 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
82635 CGTTGCGATT
1 CGTTGCGATT
82645 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:82613 original size:33 final size:33
Alignment explanation
Indices: 82571--82693 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
82561 CAAAATCGCA
82571 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
82604 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
82637 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
82678 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
82694 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:82655 original size:21 final size:21
Alignment explanation
Indices: 82629--82693 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
82619 CGCGTTGCGA
82629 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
82650 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
82670 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
82691 TTC
1 TTC
82694 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:84536 original size:93 final size:93
Alignment explanation
Indices: 84377--84692 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
84367 TAGATTGCTT
*
84377 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84442 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
84470 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTAAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84535 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84563 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84628 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84656 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
84693 AATACCCTGA
Statistics
Matches: 220, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 220 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:84857 original size:33 final size:33
Alignment explanation
Indices: 84790--84883 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
84780 TAGTTTACTT
* * * *
84790 TCGCAACACGAAACTTAAAAGCGCAACGAGAGAA
1 TCGCAACGCGAAA-TCAAAATCGCAACGACAGAA
*
84824 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
*
84857 TCGCAACGCGAAACCAAAATCGCAACG
1 TCGCAACGCGAAATCAAAATCGCAACG
84884 CGAAACCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 42 0.78
34 12 0.22
ACGTcount: A:0.45, C:0.27, G:0.20, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAATCAAAATCGCAACGACAGAA
Found at i:84905 original size:19 final size:19
Alignment explanation
Indices: 84822--84899 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
84812 GCAACGAGAG
**
84822 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
*
84841 AATCGCAA--CG--A-CAG
1 AATCGCAACGCGAAACCAA
84855 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
84874 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
84893 AATCGCA
1 AATCGCA
84900 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 36 0.71
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:84917 original size:19 final size:19
Alignment explanation
Indices: 84895--85067 Score: 141
Period size: 19 Copynumber: 9.6 Consensus size: 19
84885 GAAACCAAAA
*
84895 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
84914 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
84928 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
84947 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
84963 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
84980 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* **
84999 TCGCGTTGTGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* * *
85018 TCTCGTTGCAATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
85037 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
85057 TCGTGTTGCGA
1 TCGCGTTGCGA
85068 AAGTAAACTA
Statistics
Matches: 122, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
14 17 0.14
16 8 0.07
17 8 0.07
19 77 0.63
20 12 0.10
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:84936 original size:14 final size:14
Alignment explanation
Indices: 84917--84973 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
84907 TTTCATTTCG
84917 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
84931 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
84948 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
84964 CGTTGCGATT
1 CGTTGCGATT
84974 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:84942 original size:33 final size:33
Alignment explanation
Indices: 84900--84992 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
84890 CAAAATCGCA
84900 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
84933 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
84966 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
84993 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:85025 original size:38 final size:38
Alignment explanation
Indices: 84895--85065 Score: 128
Period size: 33 Copynumber: 4.7 Consensus size: 38
84885 GAAACCAAAA
* *
84895 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCAATTCTCATT
* * *
84930 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCAATTCTCATT
* * **
84963 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCAATTCTCATT
* ** *
84999 TCGCGTTGTGATTTTGGTTTCTCGTTGCAATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCAATTCTCATT
* *
85037 TCGCGTTGCGATTTTAAGTTTCGTGTTGC
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGC
85066 GAAAGTAAAC
Statistics
Matches: 110, Mismatches: 18, Indels: 12
0.79 0.13 0.09
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.47
34 1 0.01
35 2 0.02
36 2 0.02
38 41 0.37
39 9 0.08
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCAATTCTCATT
Found at i:87012 original size:14 final size:14
Alignment explanation
Indices: 86993--87028 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
86983 GATTGTTAAT
86993 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
87007 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
87021 TGATTTGT
1 TGATTTGT
87029 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:87196 original size:20 final size:20
Alignment explanation
Indices: 87167--87214 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
87157 GCAACGAGAG
87167 AATCGCAATGCGGAAATGAA
1 AATCGCAATGCGGAAATGAA
*
87187 AATCGTAATGCGGAAATGAA
1 AATCGCAATGCGGAAATGAA
87207 AATCGCAA
1 AATCGCAA
87215 CGAGAGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.17
Consensus pattern (20 bp):
AATCGCAATGCGGAAATGAA
Found at i:87372 original size:72 final size:70
Alignment explanation
Indices: 87245--87484 Score: 269
Period size: 72 Copynumber: 3.4 Consensus size: 70
87235 TTTCATTTCG
* * *
87245 CATTGCGATTTTCATTTCCGCGTTGCGA--TTC-TCTCG--TTGCGATTTTCATTT-CGCATTGC
1 CATTGCGATTTGCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGC
87304 GATTTT
65 GATTTT
* * *
87310 CATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATT
1 CATTGCG-ATTTGC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATT
87374 GCGATTCTCT
63 GCGATT-T-T
* *
87384 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCG
1 CATTGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCG
87449 ATTTT
66 ATTTT
* *
87454 CATGTTGGGATTTTCATTTCGCATTGCGATT
1 CA--TTGCGATTTGCATTTCGCATTGCGATT
87485 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 11, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
65 9 0.06
66 13 0.09
67 1 0.01
68 3 0.02
69 4 0.03
70 2 0.01
71 16 0.11
72 88 0.59
73 5 0.03
74 9 0.06
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (70 bp):
CATTGCGATTTGCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCG
ATTTT
Found at i:87391 original size:105 final size:109
Alignment explanation
Indices: 87229--87498 Score: 425
Period size: 105 Copynumber: 2.6 Consensus size: 109
87219 AGAATCGCAA
*
87229 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCGTTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
87294 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
87334 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
87399 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-AT
*
87445 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
87499 GTAATTTCCG
Statistics
Matches: 156, Mismatches: 3, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 121 0.78
106 14 0.09
107 3 0.02
108 3 0.02
109 3 0.02
111 12 0.08
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (109 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
Found at i:87513 original size:53 final size:52
Alignment explanation
Indices: 87229--87498 Score: 406
Period size: 53 Copynumber: 5.1 Consensus size: 52
87219 AGAATCGCAA
*
87229 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
87282 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
87334 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
87387 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
87445 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
87492 TGCGATT
1 TGCGATT
87499 GTAATTTCCG
Statistics
Matches: 206, Mismatches: 4, Indels: 20
0.90 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 61 0.30
53 109 0.53
54 3 0.01
55 3 0.01
56 3 0.01
58 12 0.06
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:89793 original size:12 final size:12
Alignment explanation
Indices: 89776--89800 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89766 TCTTCGGGGA
89776 CTTTTTCTTCTT
1 CTTTTTCTTCTT
89788 CTTTTTCTTCTT
1 CTTTTTCTTCTT
89800 C
1 C
89801 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:90009 original size:24 final size:24
Alignment explanation
Indices: 89975--90021 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
89965 CTGAAACATC
89975 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
89999 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
90022 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:90741 original size:20 final size:20
Alignment explanation
Indices: 90713--90903 Score: 215
Period size: 20 Copynumber: 9.6 Consensus size: 20
90703 AAATTTCAGT
* * * *
90713 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
90733 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
90753 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
90773 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
90793 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
90813 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
90833 ATTGCAATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
90853 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
90873 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
90893 GTTGCGATTTA
1 GTTGCGATTTA
90904 TGTGTTCGCG
Statistics
Matches: 148, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 3 0.02
20 143 0.97
21 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:90913 original size:20 final size:20
Alignment explanation
Indices: 90890--90941 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
90880 TTTACGGATA
* *
90890 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
*
90910 CGCGTTGTGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
90930 CGCGTTGCGATT
1 CGCGTTGCGATT
90942 CTTGAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.12, C:0.17, G:0.27, T:0.44
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:107251 original size:80 final size:80
Alignment explanation
Indices: 107113--107408 Score: 400
Period size: 80 Copynumber: 3.7 Consensus size: 80
107103 TGTAAGTCCT
*
107113 TACGGACCTAAGGATATCTTGGGTA-ATCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTGCTGT
1 TACGGACCTAAGGATATCTTGGGTAGAT-CCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGT
107177 GTGCATAAGGTAACCC
65 GTGCATAAGGTAACCC
* * *
107193 TACAGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTGTG
1 TACGGACCTAAGGATATCTTGGGTAGATCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
* *
107258 TGTATAAGATAACCC
66 TGCATAAGGTAACCC
* * * * *
107273 TACGGACCTAAGGATATCTTGGGTAG-GCCTCAAAGTATATCCTTAGATTGGTTCCCTTAGTTGT
1 TACGGACCTAAGGATATCTTGGGTAGATCC-CAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGT
*
107337 GTGCTTAAGGTAACCC
65 GTGCATAAGGTAACCC
*** *
107353 TACGGGTATAAGGATATCCTTGGGTAGAT-CCAAGGTATATCCTTAGGTTGGCTCCC
1 TACGGACCTAAGGATAT-CTTGGGTAGATCCCAAGGTATATCCTTAGGTTGGTTCCC
107409 ATTTTTTCTG
Statistics
Matches: 189, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
79 2 0.01
80 176 0.93
81 11 0.06
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (80 bp):
TACGGACCTAAGGATATCTTGGGTAGATCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTG
TGCATAAGGTAACCC
Found at i:112543 original size:71 final size:72
Alignment explanation
Indices: 112427--112649 Score: 286
Period size: 71 Copynumber: 3.0 Consensus size: 72
112417 AGTCCTTACG
* *
112427 GACCTAAGGATATCTTAGGTAGGCCCCAAGGCATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCA
1 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCA
112492 TAAGGT-
66 TAAGGTA
* * * *
112498 GACCTAAGGATATCTTGGGTAGGTCCCAACGTATATCCTTAGGTTGGTTTCCTTTGCTGTGTGTA
1 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCA
112563 TAAGGTAACACTA
66 TAAGG------TA
* *
112576 CGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGATTGGTTCCCTTAGCTGTGTG
1 --GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTG
*
112641 CTTAAGGTA
64 CATAAGGTA
112650 ACCCTACGGA
Statistics
Matches: 130, Mismatches: 13, Indels: 15
0.82 0.08 0.09
Matches are distributed among these distances:
71 64 0.49
74 2 0.02
77 1 0.01
80 63 0.48
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (72 bp):
GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCA
TAAGGTA
Found at i:112637 original size:80 final size:80
Alignment explanation
Indices: 112498--112709 Score: 302
Period size: 80 Copynumber: 2.6 Consensus size: 80
112488 TGCATAAGGT
* * * *
112498 GACCTAAGGATATCTTGGGTAGGTCCCAACGTATATCCTTAGGTTGGTTTCCTTTGCTGTGTG-T
1 GACCTAAGGATATCTTGGGTAGGACCCAAGGTATATCCTTAGGTTGGTTCCCTTAGCTGTGTGCT
112562 ATAAGGTAACACTACG
66 -TAAGGTAACACTACG
* *
112578 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGATTGGTTCCCTTAGCTGTGTGCT
1 GACCTAAGGATATCTTGGGTAGGACCCAAGGTATATCCTTAGGTTGGTTCCCTTAGCTGTGTGCT
*
112643 TAAGGTAACCCTACG
66 TAAGGTAACACTACG
* * *
112658 GATCTAAGGATATCCTTGGGTA-GATCCAAGGTATATCCTTAGGTTGGCTCCC
1 GACCTAAGGATAT-CTTGGGTAGGACCCAAGGTATATCCTTAGGTTGGTTCCC
112710 CTTTTTACTG
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
80 110 0.92
81 9 0.08
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (80 bp):
GACCTAAGGATATCTTGGGTAGGACCCAAGGTATATCCTTAGGTTGGTTCCCTTAGCTGTGTGCT
TAAGGTAACACTACG
Found at i:114889 original size:12 final size:12
Alignment explanation
Indices: 114872--114898 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
114862 TTAAATATAA
114872 AAATAATTTTTT
1 AAATAATTTTTT
114884 AAATAATTTTTT
1 AAATAATTTTTT
114896 AAA
1 AAA
114899 AGTGTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATAATTTTTT
Found at i:117223 original size:3 final size:3
Alignment explanation
Indices: 117217--117254 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
117207 TCTCTTCTTC
117217 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
117255 TTGGTTTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:121619 original size:29 final size:29
Alignment explanation
Indices: 121577--121639 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
121567 TGTACTCATG
121577 GTCGCTGGCAACTCGGACAACACTAGATA
1 GTCGCTGGCAACTCGGACAACACTAGATA
121606 GTCGCTGGCAACTCGGACAACACTAGATA
1 GTCGCTGGCAACTCGGACAACACTAGATA
121635 GTCGC
1 GTCGC
121640 ATACGTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (29 bp):
GTCGCTGGCAACTCGGACAACACTAGATA
Found at i:127053 original size:2 final size:2
Alignment explanation
Indices: 127046--127079 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
127036 AAAAGAATGC
127046 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
127080 TTTATGTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128517 original size:16 final size:16
Alignment explanation
Indices: 128498--128568 Score: 63
Period size: 16 Copynumber: 4.2 Consensus size: 16
128488 TTTCACTTTA
128498 TATTTTTTTTATTTTT
1 TATTTTTTTTATTTTT
128514 TATTTTTTTCCGT-TTGTTT
1 TATTTTTTT---TATT-TTT
* *
128533 TATTTTATTTATTTCT
1 TATTTTTTTTATTTTT
* *
128549 TATTGTCTTTATTTTT
1 TATTTTTTTTATTTTT
128565 TATT
1 TATT
128569 CACTTTCATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 29 0.64
17 2 0.04
18 2 0.04
19 12 0.27
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (16 bp):
TATTTTTTTTATTTTT
Found at i:128538 original size:25 final size:25
Alignment explanation
Indices: 128504--128564 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
128494 TTTATATTTT
*
128504 TTTTATTTTTTATTTTTTTCCGT-TTG
1 TTTTA-TTTTTATTTATTT-CGTATTG
*
128530 TTTTA-TTTTATTTATTTCTTATTG
1 TTTTATTTTTATTTATTTCGTATTG
128554 TCTTTATTTTT
1 T-TTTATTTTT
128565 TATTCACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 2 0.07
24 15 0.50
25 4 0.13
26 9 0.30
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (25 bp):
TTTTATTTTTATTTATTTCGTATTG
Found at i:128574 original size:16 final size:16
Alignment explanation
Indices: 128540--128582 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
128530 TTTTATTTTA
* **
128540 TTTATTTCTTATTGTC
1 TTTATTTTTTATTCAC
128556 TTTATTTTTTATTCAC
1 TTTATTTTTTATTCAC
128572 TTTCATTTTTT
1 TTT-ATTTTTT
128583 CCCCTTAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTATTTTTTATTCAC
Found at i:132620 original size:95 final size:96
Alignment explanation
Indices: 132367--132724 Score: 499
Period size: 94 Copynumber: 3.7 Consensus size: 96
132357 AGATTATAAT
** *
132367 ATTATATATATACAATAAAGCTTGAGCAGTCCCTCTAAAGTAATTGGTTAAATGCCCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGGCTTTA
*
132432 TAGATAAGATTCAGCTAGCCTGATAAAGGTG
66 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
** * * *
132463 A-T-TATATATACAATAAAGCTTGACATGTCCCTCTAAAGTAATTAGTTAAATGCCCTGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGGCTTTA
*
132526 TGGATAAGATTCAGCTAGCCTAATAAAGGTG
66 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
* * *
132557 ATTATA-ATGTACAATAAAGCTTGAGTTGTCTCTCTAGAGCAATTGGTTAAATGCCCCGGCTTTA
1 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGGCTTTA
*
132621 TGGATAATATTCAGCTAGCCTGATAAAGGTG
66 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
* * *
132652 ATTATAATATCTATACAAT-AATCTTGAGTTATCCCTCTAAAGCAATTGGTTAAAAAGCCCCGGC
1 ATTAT-ATA--TATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTT-AAATGCCCCGGC
132716 TTTATGGAT
62 TTTATGGAT
132725 CCAGATAGCC
Statistics
Matches: 232, Mismatches: 23, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
94 86 0.37
95 86 0.37
96 4 0.02
97 1 0.00
98 28 0.12
99 27 0.12
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (96 bp):
ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAATGCCCCGGCTTTA
TGGATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:133654 original size:17 final size:17
Alignment explanation
Indices: 133632--133673 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
133622 TAACATGTTT
133632 CGTATATACATTTTAGG
1 CGTATATACATTTTAGG
133649 CGTATATACATTTTAGG
1 CGTATATACATTTTAGG
*
133666 CATATATA
1 CGTATATA
133674 AGAGCATCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (17 bp):
CGTATATACATTTTAGG
Found at i:134104 original size:36 final size:36
Alignment explanation
Indices: 134052--134168 Score: 182
Period size: 36 Copynumber: 3.2 Consensus size: 36
134042 TAATTTACTC
134052 AAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
*
134089 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
134125 AAAACAAATTTTGTCTCTCTTGAGAC-GATTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTT
*
134161 GAAACAAA
1 AAAACAAA
134169 AACTTTGAAT
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
36 67 0.89
37 8 0.11
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:134241 original size:36 final size:36
Alignment explanation
Indices: 134183--134305 Score: 176
Period size: 36 Copynumber: 3.4 Consensus size: 36
134173 TTGAATTTGT
*
134183 TTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGACAA
1 TTTCTCTTAAAACAAA-TTTTGTCTCTCTTGAGACAA
* *
134219 TTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAT
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAA
**
134255 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAA
*
134291 TTTCCCTTAAAACAA
1 TTTCTCTTAAAACAA
134306 CAAATTTGAA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 70 0.89
37 9 0.11
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (36 bp):
TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAA
Found at i:134304 original size:138 final size:137
Alignment explanation
Indices: 134053--134445 Score: 671
Period size: 138 Copynumber: 2.8 Consensus size: 137
134043 AATTTACTCA
*
134053 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
*
134118 TTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGATTTCCCTTGAAACAAAAACTTTGAATTTGT
66 TTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGATTTCCCTTAAAACAAAAA-TTTGAATTTGT
134183 TTTCCTTG
130 TTTCCTTG
*
134191 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
*
134256 TTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTAAAACAACAAATTTGAATTTGT
66 TTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGATTTCCCTTAAAACAA-AAATTTGAATTTGT
134321 TTTCCTTG
130 TTTCCTTG
*
134329 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACAT
1 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAAAAC-AAATTTTGTCTCTCTTGAGACAT
* * *
134394 TTTCTCGTAAAACAAATTTTGTCTCTCTTGAGAC-ATTTTCTCGTAAAACAAA
65 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGA-TTTCCCTTAAAACAAA
134446 TTTTGTCTCT
Statistics
Matches: 242, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
138 170 0.70
139 72 0.30
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.41
Consensus pattern (137 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
TTCTCTTAAAACAAATTTTGTCTCTCTTGAGACGATTTCCCTTAAAACAAAAATTTGAATTTGTT
TTCCTTG
Found at i:134418 original size:36 final size:36
Alignment explanation
Indices: 134329--134482 Score: 227
Period size: 36 Copynumber: 4.2 Consensus size: 36
134319 GTTTTCCTTG
**
134329 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTTTA
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCGTA
* *
134366 GAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTA
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCGTA
*
134403 AAACAAATTTTGTCTCTCTTGAGACATTTTCTCGTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGTA
* *
134439 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGTA
134475 AAACAAAT
1 AAACAAAT
134483 CTCTGAATTT
Statistics
Matches: 108, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
36 73 0.68
37 32 0.30
38 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCGTA
Found at i:134427 original size:175 final size:173
Alignment explanation
Indices: 134192--134582 Score: 586
Period size: 175 Copynumber: 2.2 Consensus size: 173
134182 TTTTCCTTGA
* *
134192 AACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTT
1 AACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATTT
* * *
134257 TCTCTTAAAACAAATTTTGTCTCTCTTGAGACGGTTTCCCTTAAAACAACAAATTTGAATTTGTT
66 TCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAA-AAATCTGAATTTGTT
**
134322 TTCCTTGAAACAAAGTTTTGTCT-CTCTTGAGACAGTTTCTTTTAG
130 TTCCTTGAAACAAA-TTGCGTCTCCT-TTGAGACAGTTTCTTTTAG
* * *
134367 AACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACATTT
1 AACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATTT
* * **
134432 TCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATCTCTGAATTTGTTT
66 TCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAAATCTGAATTTGTTT
*
134497 TCCTTGAAACAAATTGCGTCTCCTTTGAGACAGTTTCTTTTGG
131 TCCTTGAAACAAATTGCGTCTCCTTTGAGACAGTTTCTTTTAG
* * *
134540 AACAAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 AACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAA
134583 ATATTTGAAT
Statistics
Matches: 195, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
173 62 0.32
174 28 0.14
175 105 0.54
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (173 bp):
AACAAAATTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATTT
TCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAAAATCTGAATTTGTTT
TCCTTGAAACAAATTGCGTCTCCTTTGAGACAGTTTCTTTTAG
Found at i:134486 original size:138 final size:131
Alignment explanation
Indices: 134068--134582 Score: 390
Period size: 138 Copynumber: 3.8 Consensus size: 131
134058 AAGTTTTGTC
*
134068 TCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAA
1 TCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAA
* * *
134133 TTTTGTCTCTCTTGAGACGATTTCCCTTGAAACAAAAACTTTGAATTT--G-TTTTC-CTTGAAA
66 TTTTGTCTCTCTTGAGAC-ATTTCCCTT-AAA-ACAAA-TTTGACTTTGAGAGTTTCTCTTGAAA
134194 CAAAGTTTTGT
127 CAAA------T
*
134205 CTCTCTTGAGACAATTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAA
1 -TCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAA
* * *
134270 ATTTTGTCTCTCTTGAGACGGTTTCCCTTAAAACAACAAATTTGAATTT--G-TTTTC-CTTGAA
65 ATTTTGTCTCTCTTGAGAC-ATTTCCCTT--AA-AACAAATTTGACTTTGAGAGTTTCTCTTGAA
134331 ACAAAGTTTTGT
126 ACAAA------T
* *
134343 CTCTCTTGAGACAGTTTCTTTTAGAACTAAATTTTGTCTCTCTTGAGACATTTTCTCGTAAAACA
1 -TCTCTTGAGACAGTTTCTTTTAAAAC-AAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACA
* * *
134408 AATTTTGTCTCTCTTGAGACATTTTCTCGTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCT
64 AATTTTGTCTCTCTTGAGACA-TTTCCCTTAAAACAAA-TTTG--ACT-TTGAG--AGTTTCTCT
134473 TGAAACAAA-
122 TGAAACAAAT
** * * ** * * **
134482 TCTC-TGA-ATTTGTTT-TCCTTGAAACAAATTGCGTCTC-CTTTGAGACAGTTTCTTTTGGAAC
1 TCTCTTGAGA-CAGTTTCT-TTTAAAACAAATTTTGTCTCTC-TTGAGACATTTTCTCTTAAAAC
* * *
134543 AAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAACAAA
63 -AAATTTTGTCTCTCTTGAGACA-TTTCCCTTAAAACAAA
134583 ATATTTGAAT
Statistics
Matches: 329, Mismatches: 30, Indels: 37
0.83 0.08 0.09
Matches are distributed among these distances:
135 1 0.00
136 35 0.11
137 53 0.16
138 152 0.46
139 69 0.21
140 3 0.01
142 1 0.00
145 4 0.01
146 11 0.03
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (131 bp):
TCTCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAA
TTTTGTCTCTCTTGAGACATTTCCCTTAAAACAAATTTGACTTTGAGAGTTTCTCTTGAAACAAA
T
Found at i:134567 original size:101 final size:102
Alignment explanation
Indices: 134423--134645 Score: 292
Period size: 102 Copynumber: 2.2 Consensus size: 102
134413 TGTCTCTCTT
* * * * *
134423 GAGACATTTTCTCGTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAATCTC
1 GAGACAGTTTCTCTTGAAACAAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAACAAAATATC
* * *
134486 TGAATTTGTTTTCC-TTGAAACAAATTGCGTC-TCCTTT
66 TGAATCTGTTTTCCATT-AAACAAATTGCGTCTTAC-TC
* * *
134523 GAGACAGTTTCTTTTGGAACAAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAACAAAATATT
1 GAGACAGTTTCTCTTGAAACAAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAACAAAATATC
*
134588 TGAATCTGTTTTCCATTAAACAAATTTCGTCTTACTC
66 TGAATCTGTTTTCCATTAAACAAATTGCGTCTTACTC
134625 GAGACAGTTTCTCTTGAAACA
1 GAGACAGTTTCTCTTGAAACA
134646 CAAAAAAAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
100 15 0.14
101 35 0.33
102 51 0.49
103 4 0.04
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (102 bp):
GAGACAGTTTCTCTTGAAACAAAATTTTATCTCTCTTGAGACAGTTTCTCTTGAAACAAAATATC
TGAATCTGTTTTCCATTAAACAAATTGCGTCTTACTC
Found at i:135247 original size:2 final size:2
Alignment explanation
Indices: 135240--135305 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
135230 AAAAGAATGC
135240 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
135282 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
135306 TTTATGTATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:136613 original size:45 final size:43
Alignment explanation
Indices: 136518--136615 Score: 105
Period size: 45 Copynumber: 2.3 Consensus size: 43
136508 TTTTTTATTT
*
136518 TATATATGTATATTTTTAGTTATTTATTATTTATTATTATTAA
1 TATATATATATATTTTTAGTTATTTATTATTTATTATTATTAA
* *
136561 TGCATATATATATATTTTTAG-T-TTT-CTCTTTATTATTATT-A
1 T--ATATATATATATTTTTAGTTATTTATTATTTATTATTATTAA
* *
136602 TCTTTATATATATT
1 TATATATATATATT
136616 CTTTTGTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
39 11 0.23
41 2 0.04
42 13 0.27
43 4 0.08
44 1 0.02
45 17 0.35
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (43 bp):
TATATATATATATTTTTAGTTATTTATTATTTATTATTATTAA
Found at i:136763 original size:16 final size:15
Alignment explanation
Indices: 136692--136769 Score: 52
Period size: 16 Copynumber: 5.1 Consensus size: 15
136682 TTTACATACA
136692 TTTTTCACTTTATTT
1 TTTTTCACTTTATTT
** *
136707 TTTTTCTGTTTGTTT
1 TTTTTCACTTTATTT
136722 TATTTT-A-TTTATTT
1 T-TTTTCACTTTATTT
* **
136736 CTTATTGTCTTTATTT
1 -TTTTTCACTTTATTT
136752 TTTATTCACTTTCATTT
1 TTT-TTCACTTT-ATTT
136769 T
1 T
136770 CCCCCTTAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
14 9 0.19
15 16 0.34
16 17 0.36
17 5 0.11
ACGTcount: A:0.13, C:0.10, G:0.04, T:0.73
Consensus pattern (15 bp):
TTTTTCACTTTATTT
Found at i:143184 original size:12 final size:12
Alignment explanation
Indices: 143167--143247 Score: 78
Period size: 12 Copynumber: 6.7 Consensus size: 12
143157 ATATTTGATT
143167 TTAATTTTAATA
1 TTAATTTTAATA
143179 TTAATTTTTTAA-A
1 TTAA--TTTTAATA
*
143192 TTAA-TTAAATA
1 TTAATTTTAATA
*
143203 TTATTTTATAATA
1 TTAATTT-TAATA
*
143216 TT-ATTATAGATA
1 TTAATTTTA-ATA
143228 TTAATTTTAATA
1 TTAATTTTAATA
143240 TTAATTTT
1 TTAATTTT
143248 TTAAATAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
10 4 0.07
11 6 0.11
12 24 0.43
13 16 0.29
14 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:143194 original size:13 final size:14
Alignment explanation
Indices: 143171--143251 Score: 56
Period size: 13 Copynumber: 6.4 Consensus size: 14
143161 TTGATTTTAA
143171 TTTTAATATTAATT
1 TTTTAATATTAATT
143185 TTTTAA-ATTAA--
1 TTTTAATATTAATT
*
143196 -TTAAATATT-ATT
1 TTTTAATATTAATT
*
143208 TTATAATATT-A--
1 TTTTAATATTAATT
*
143219 TTATAGATATTAA--
1 TTTTA-ATATTAATT
143232 TTTTAATATTAATT
1 TTTTAATATTAATT
143246 TTTTAA
1 TTTTAA
143252 ATAAATAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
10 5 0.09
11 8 0.15
12 12 0.22
13 18 0.33
14 12 0.22
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:143202 original size:24 final size:25
Alignment explanation
Indices: 143174--143236 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 25
143164 ATTTTAATTT
*
143174 TAATATTAATTTTTTAA-ATTAATTA
1 TAATATTAATTTTATAATATT-ATTA
143199 -AATATT-ATTTTATAATATTATTA
1 TAATATTAATTTTATAATATTATTA
143222 TAGATATTAATTTTA
1 TA-ATATTAATTTTA
143237 ATATTAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 12 0.36
24 10 0.30
25 5 0.15
26 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TAATATTAATTTTATAATATTATTA
Found at i:143209 original size:21 final size:24
Alignment explanation
Indices: 143167--143245 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
143157 ATATTTGATT
*
143167 TTAATTTTA-ATATTAATTTTTTAAA
1 TTAATTATAGATATTAA--TTTTAAA
143192 TTAATTA-A-ATATT-ATTTTATAA
1 TTAATTATAGATATTAATTTTA-AA
*
143214 TATTATTATAGATATTAATTTTAATA
1 T-TAATTATAGATATTAATTTTAA-A
143240 TTAATT
1 TTAATT
143246 TTTTAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 5 0.11
22 3 0.07
23 6 0.13
24 7 0.16
25 16 0.36
26 8 0.18
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (24 bp):
TTAATTATAGATATTAATTTTAAA
Found at i:143234 original size:61 final size:60
Alignment explanation
Indices: 143150--143297 Score: 205
Period size: 61 Copynumber: 2.5 Consensus size: 60
143140 TAATTTTATA
* *
143150 TTATATTA-TATTTGAT-TTTAATTTTAATATTAATTTTTTAAATTAATTAAATATT-ATTT
1 TTATATTATTA-TAGATATTTAATTTTAATATTAATTTTTTAAA-TAAATAAATATTAATTT
143209 TATAATATTATTATAGATA-TTAATTTTAATATTAATTTTTTAAATAAATAAATATTAAATTT
1 T-T-ATATTATTATAGATATTTAATTTTAATATTAATTTTTTAAATAAATAAATATT-AATTT
143271 TTATATTATTATAGATATTTAATTTTA
1 TTATATTATTATAGATATTTAATTTTA
143298 TATCATATAA
Statistics
Matches: 80, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
59 1 0.01
60 27 0.34
61 45 0.56
62 7 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (60 bp):
TTATATTATTATAGATATTTAATTTTAATATTAATTTTTTAAATAAATAAATATTAATTT
Found at i:143313 original size:24 final size:25
Alignment explanation
Indices: 143256--143314 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
143246 TTTTAAATAA
* *
143256 ATAAATATTAAATTTTTATATTATT
1 ATAAATATTTAATTTTTATATCATT
*
143281 ATAGATATTTAA-TTTTATATCA-T
1 ATAAATATTTAATTTTTATATCATT
143304 ATAAATTATTT
1 ATAAA-TATTT
143315 TATATATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 5 0.17
24 14 0.48
25 10 0.34
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
ATAAATATTTAATTTTTATATCATT
Found at i:143577 original size:29 final size:29
Alignment explanation
Indices: 143528--143601 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 29
143518 TAATCACAAT
* *
143528 TAAA-TAAAAAATAATCATAAATAATTTGA
1 TAAATTAAAAAATAATCATAAA-AATATCA
**
143557 TAAATTAAAAAATTTTC-TAAAAATATCA
1 TAAATTAAAAAATAATCATAAAAATATCA
143585 TATAATTATAAAAATAA
1 TA-AATTA-AAAAATAA
143602 ATATGAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
28 7 0.19
29 13 0.36
30 16 0.44
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (29 bp):
TAAATTAAAAAATAATCATAAAAATATCA
Found at i:143851 original size:31 final size:31
Alignment explanation
Indices: 143792--143852 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
143782 GTATTGTAGG
* *
143792 AATTATTTAAATTTTCAGTATTGTAAACTCA
1 AATTATTTAAATTCTCAGTATTGAAAACTCA
143823 AATTATTTAAA-TCTCAGTATTGCAAAACTC
1 AATTATTTAAATTCTCAGTATTG-AAAACTC
143853 TTTAAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (31 bp):
AATTATTTAAATTCTCAGTATTGAAAACTCA
Done.