Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167845.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_116, 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: 80777
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 1000 characters in sequence are not A, C, G, or T
Found at i:4026 original size:13 final size:12
Alignment explanation
Indices: 4010--4057 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
4000 AATAATAACT
*
4010 ATAAAAACTAAAA
1 ATAAAAAAT-AAA
4023 ATAATAAAATAAA
1 ATAA-AAAATAAA
*
4036 ATAAAAAATTAA
1 ATAAAAAATAAA
4048 ATAAGAAAAT
1 ATAA-AAAAT
4058 TTTTTACCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 11 0.35
13 16 0.52
14 4 0.13
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:5698 original size:43 final size:43
Alignment explanation
Indices: 5637--5722 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
5627 TACATGTAAG
5637 CTAATGTCATCTTCATCGAAGAATTGAATAATTGAGCTCACTT
1 CTAATGTCATCTTCATCGAAGAATTGAATAATTGAGCTCACTT
5680 CTAATGTCATCTTCATCGAAGAATTGAATAATTGAGCTCACTT
1 CTAATGTCATCTTCATCGAAGAATTGAATAATTGAGCTCACTT
5723 TTGAAGTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (43 bp):
CTAATGTCATCTTCATCGAAGAATTGAATAATTGAGCTCACTT
Found at i:7131 original size:21 final size:20
Alignment explanation
Indices: 7107--7166 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
7097 ATATATGAAT
7107 GAGGATTGATCCTTATTCATA
1 GAGGATTGATCCTTATTCA-A
** *
7128 GAGGACCGATCCTTCACTCAA
1 GAGGATTGATCCTT-ATTCAA
*
7149 AAGGATTGATCCTT-TTCA
1 GAGGATTGATCCTTATTCA
7167 CTTTTTAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 3 0.10
21 24 0.77
22 4 0.13
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (20 bp):
GAGGATTGATCCTTATTCAA
Found at i:9888 original size:15 final size:16
Alignment explanation
Indices: 9870--9902 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
9860 GGAATAGAGA
9870 AAAGAAAGGGAA-AAG
1 AAAGAAAGGGAAGAAG
*
9885 AAAGAAAGTGAAGAAG
1 AAAGAAAGGGAAGAAG
9901 AA
1 AA
9903 TTCTGAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (16 bp):
AAAGAAAGGGAAGAAG
Found at i:10527 original size:104 final size:103
Alignment explanation
Indices: 10419--10610 Score: 255
Period size: 103 Copynumber: 1.8 Consensus size: 103
10409 TTCCCTACCA
* * * *
10419 AAATGATCGGAGGATTTTAATTTTAAAATTATAAATTCTACCAAACT-ATTGGATAATTTCATAA
1 AAATGATCGAAGGATTTAAATCTT-AAATTATAAATTCTACCAAA-TGATTGGAGAATTTCAT-A
10483 TGAA-TTTTTATGAAAAA-TAAAATTGTTTTTTAATTCTATC
63 TGAATTTTTTA-GAAAAACTAAAATTGTTTTTTAATTCTATC
* * *
10523 AAATGATTGAAGGATTTAAATCTTGAATTATGAATTCTACCAAATGATTGGAGAATTTCATATGA
1 AAATGATCGAAGGATTTAAATCTTAAATTATAAATTCTACCAAATGATTGGAGAATTTCATATGA
10588 ATTTTTTGAGAAAAACTAAAATT
66 ATTTTTT-AGAAAAACTAAAATT
10611 TCAATTCTAC
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
102 6 0.08
103 43 0.56
104 28 0.36
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (103 bp):
AAATGATCGAAGGATTTAAATCTTAAATTATAAATTCTACCAAATGATTGGAGAATTTCATATGA
ATTTTTTAGAAAAACTAAAATTGTTTTTTAATTCTATC
Found at i:24207 original size:23 final size:25
Alignment explanation
Indices: 24179--24235 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
24169 TATTTGATAT
24179 TATATTATA-G-TATAGTATATTAA
1 TATATTATATGATATAGTATATTAA
* *
24202 TATATTATATGATATAGTATGTTAT
1 TATATTATATGATATAGTATATTAA
24227 TATTATTAT
1 TA-TATTAT
24236 TATTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 9 0.31
24 1 0.03
25 13 0.45
26 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.53
Consensus pattern (25 bp):
TATATTATATGATATAGTATATTAA
Found at i:24210 original size:13 final size:15
Alignment explanation
Indices: 24175--24232 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
24165 ATATTATTTG
24175 ATATTATATTATAGT
1 ATATTATATTATAGT
*
24190 ATAGTATATTA-A-T
1 ATATTATATTATAGT
24203 ATATTATATGATATAGT
1 ATATTATAT--TATAGT
*
24220 ATGTTATTATTAT
1 ATATTA-TATTAT
24233 TATTATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
13 9 0.26
14 1 0.03
15 12 0.34
16 4 0.11
17 6 0.17
18 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.52
Consensus pattern (15 bp):
ATATTATATTATAGT
Found at i:24231 original size:3 final size:3
Alignment explanation
Indices: 24223--24254 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
24213 ATATAGTATG
24223 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
24255 CCTTTTCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:24851 original size:20 final size:19
Alignment explanation
Indices: 24822--24867 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
24812 TTTCGGCCAA
* *
24822 TTTTTCAAAAACTAGTGGG
1 TTTTTCAAAAACCAGTAGG
24841 TTTTTCAAAAACCAGTAGG
1 TTTTTCAAAAACCAGTAGG
24860 TTTTTCAA
1 TTTTTCAA
24868 TTTTCGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (19 bp):
TTTTTCAAAAACCAGTAGG
Found at i:25159 original size:5 final size:5
Alignment explanation
Indices: 25151--25223 Score: 57
Period size: 5 Copynumber: 15.0 Consensus size: 5
25141 TTCTTTTTCC
*
25151 ATTTT ATTTT -TTTT A-TTT -TTTT ATTTT ATTTT ATTTT -TTAGCTC
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATT---TT
* *
25195 ATTTT ATTTT ATTTT -TTTG GTTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
25224 TGAGAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
4 15 0.27
5 37 0.67
7 1 0.02
8 2 0.04
ACGTcount: A:0.15, C:0.03, G:0.04, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:25164 original size:22 final size:21
Alignment explanation
Indices: 25139--25212 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
25129 GATCGCAAGA
*
25139 TTTTCTTTTTCCATTTTATTT
1 TTTTTTTTTTCCATTTTATTT
**
25160 TTTTTATTTTTTTATTTTATTT
1 TTTTT-TTTTTCCATTTTATTT
* **
25182 TATTTTTTAGCTCATTTTATTT
1 TTTTTTTTTTC-CATTTTATTT
*
25204 TATTTTTTT
1 TTTTTTTTT
25213 GGTTTTATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
21 7 0.17
22 35 0.83
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.78
Consensus pattern (21 bp):
TTTTTTTTTTCCATTTTATTT
Found at i:25181 original size:27 final size:27
Alignment explanation
Indices: 25151--25224 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
25141 TTCTTTTTCC
25151 ATTTTATTTTTTTTATTTTTTTATTTT
1 ATTTTATTTTTTTTATTTTTTTATTTT
*** **
25178 ATTTTATTTTTTAGCTCATTTTATTTT
1 ATTTTATTTTTTTTATTTTTTTATTTT
*
25205 ATTTT-TTTGGTTTTATTTTT
1 ATTTTATTT-TTTTTATTTTT
25225 GAGAAATTTT
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.15, C:0.03, G:0.04, T:0.78
Consensus pattern (27 bp):
ATTTTATTTTTTTTATTTTTTTATTTT
Found at i:25234 original size:35 final size:35
Alignment explanation
Indices: 25161--25242 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 35
25151 ATTTTATTTT
* **
25161 TTTTATTTTTTTATTTTATTTTATTTTTTAGCTCA
1 TTTTATTTTTTTATTTTATTTTATTTTTGAGCAAA
*
25196 TTTTATTTTATTT-TTTTGGTTTTATTTTTGAG-AAA
1 TTTTATTTT-TTTATTTT-ATTTTATTTTTGAGCAAA
*
25231 TTTTATTATTTT
1 TTTTATTTTTTT
25243 GTAAAAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 3 0.08
35 22 0.55
36 15 0.38
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.73
Consensus pattern (35 bp):
TTTTATTTTTTTATTTTATTTTATTTTTGAGCAAA
Found at i:25324 original size:41 final size:43
Alignment explanation
Indices: 25279--25361 Score: 127
Period size: 41 Copynumber: 2.0 Consensus size: 43
25269 ATAGTTATAT
25279 AGAAAA-AGATCTTTTCAAATAAG-TT-AAAAAAAAAAAGAAAA
1 AGAAAACA-ATCTTTTCAAATAAGTTTCAAAAAAAAAAAGAAAA
25320 AGAAAACAATCTTTTCAAATAAGTTTTCAAAAAAAAAAAGAA
1 AGAAAACAATCTTTTCAAATAAG-TTTCAAAAAAAAAAAGAA
25362 GTAGAAAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
41 21 0.55
42 1 0.03
43 2 0.05
44 14 0.37
ACGTcount: A:0.63, C:0.07, G:0.08, T:0.22
Consensus pattern (43 bp):
AGAAAACAATCTTTTCAAATAAGTTTCAAAAAAAAAAAGAAAA
Found at i:25352 original size:42 final size:39
Alignment explanation
Indices: 25279--25383 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 39
25269 ATAGTTATAT
25279 AGAAAAAGATCTTTTCAAATAAGTTAAAAAAAAAAAGAAAA
1 AGAAAAA-ATCTTTTCAAATAAGTTAAAAAAAAAAA-AAAA
** *
25320 AGAAAACAATCTTTTCAAATAAGTTTTCAAAAAAAAAAAGA
1 AGAAAA-AATCTTTTCAAATAAG-TTAAAAAAAAAAAAAAA
*
25361 AGTAGAAAATCTTTTTCAAATAA
1 AG-AAAAAATC-TTTTCAAATAA
25384 AAAATCCCTA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
41 30 0.54
42 26 0.46
ACGTcount: A:0.59, C:0.08, G:0.09, T:0.25
Consensus pattern (39 bp):
AGAAAAAATCTTTTCAAATAAGTTAAAAAAAAAAAAAAA
Found at i:25368 original size:44 final size:41
Alignment explanation
Indices: 25277--25369 Score: 125
Period size: 41 Copynumber: 2.2 Consensus size: 41
25267 AAATAGTTAT
25277 ATAGAAAAAGATCTTTTCAAATAAGTTAAAAAAAAAAAGAA
1 ATAGAAAAAGATCTTTTCAAATAAGTTAAAAAAAAAAAGAA
*
25318 AAAGAAAACA-ATCTTTTCAAATAAGTTTTCAAAAAAAAAAAGAA
1 ATAGAAAA-AGATCTTTTCAAATAAG--TT-AAAAAAAAAAAGAA
*
25362 GTAGAAAA
1 ATAGAAAA
25370 TCTTTTTCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
41 22 0.49
42 1 0.02
43 2 0.04
44 20 0.44
ACGTcount: A:0.62, C:0.06, G:0.10, T:0.22
Consensus pattern (41 bp):
ATAGAAAAAGATCTTTTCAAATAAGTTAAAAAAAAAAAGAA
Found at i:26017 original size:11 final size:10
Alignment explanation
Indices: 25996--26073 Score: 52
Period size: 11 Copynumber: 7.4 Consensus size: 10
25986 AAGAAAATAG
25996 AATAATAAAAA
1 AATAA-AAAAA
*
26007 AAT-AAAGAA
1 AATAAAAAAA
*
26016 AAT-TAAAAA
1 AATAAAAAAA
*
26025 AATAAAGAAA
1 AATAAAAAAA
*
26035 AGTAAAACAAA
1 AATAAAA-AAA
26046 AATAAAAATAA
1 AATAAAAA-AA
26057 AATTAAGATAAAA
1 AA-TAA-A-AAAA
26070 AATA
1 AATA
26074 TTAAATAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
9 14 0.26
10 11 0.21
11 16 0.30
12 5 0.09
13 5 0.09
14 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:26022 original size:18 final size:18
Alignment explanation
Indices: 26001--26041 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
25991 AATAGAATAA
*
26001 TAAAAAAATAAAGAAAAT
1 TAAAAAAATAAAGAAAAG
26019 TAAAAAAATAAAGAAAAG
1 TAAAAAAATAAAGAAAAG
26037 TAAAA
1 TAAAA
26042 CAAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (18 bp):
TAAAAAAATAAAGAAAAG
Found at i:26026 original size:9 final size:8
Alignment explanation
Indices: 25984--26058 Score: 62
Period size: 8 Copynumber: 8.6 Consensus size: 8
25974 GATTTTTATT
25984 TAAAGAAAA
1 TAAA-AAAA
* *
25993 TAGAATAA
1 TAAAAAAA
26001 TAAAAAAA
1 TAAAAAAA
26009 TAAAGAAAA
1 TAAA-AAAA
26018 TTAAAAAAA
1 -TAAAAAAA
26027 TAAAGAAAA
1 TAAA-AAAA
26036 GTAAAACAAA
1 -TAAAA-AAA
26046 -AATAAAAA
1 TAA-AAAAA
26054 TAAAA
1 TAAAA
26059 TTAAGATAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
8 24 0.44
9 20 0.36
10 11 0.20
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.15
Consensus pattern (8 bp):
TAAAAAAA
Found at i:26119 original size:18 final size:18
Alignment explanation
Indices: 25999--26122 Score: 64
Period size: 18 Copynumber: 6.8 Consensus size: 18
25989 AAAATAGAAT
*
25999 AATAAAA-AAATAAAGAA
1 AATAAAATAAATAAATAA
*
26016 AATTAAAA-AAATAAAGAA
1 AA-TAAAATAAATAAATAA
*
26034 AAGTAAAA-CAA-AAATAAA
1 AA-TAAAATAAATAAAT-AA
26052 AATAAAATTAAGATAAA-AA
1 AATAAAA-TAA-ATAAATAA
* * **
26071 ATATTAAATAAATCTAATCT
1 A-ATAAAATAAAT-AAATAA
26091 AAT-AAATAAATAAAT-A
1 AATAAAATAAATAAATAA
26107 AATAAAATAAAATAAA
1 AATAAAAT-AAATAAA
26123 AAACCTGGAG
Statistics
Matches: 86, Mismatches: 10, Indels: 21
0.74 0.09 0.18
Matches are distributed among these distances:
16 3 0.03
17 17 0.20
18 45 0.52
19 11 0.13
20 7 0.08
21 3 0.03
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.21
Consensus pattern (18 bp):
AATAAAATAAATAAATAA
Found at i:27024 original size:4 final size:4
Alignment explanation
Indices: 27015--27127 Score: 53
Period size: 4 Copynumber: 29.2 Consensus size: 4
27005 ATATTATAGG
* * * * *
27015 ATAA ATAA ATAA AT-A AT-A ACAG ATAT ATAA TTAG ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
*
27061 A-AT ATAA A-ATA AT-A AT-A AT-A ATAA ATAA ATTATA ATATA AT-A
1 ATAA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA A-TA-A ATA-A ATAA
* * *
27103 ATAA ATAT ATAA CTAT ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
27128 ATACATATAA
Statistics
Matches: 84, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
3 20 0.24
4 54 0.64
5 8 0.10
6 2 0.02
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (4 bp):
ATAA
Found at i:27052 original size:34 final size:30
Alignment explanation
Indices: 26950--27130 Score: 118
Period size: 34 Copynumber: 5.7 Consensus size: 30
26940 TCCAAAATAA
*
26950 AAATCAAATAAAT-ATAAAAAAATAATAGAT
1 AAAT-AAATAAATAATAAAATAATAATAGAT
* * *
26980 AATTAGCACAGATAAATAAAAAAATATATTATAGGAT
1 AA--A-TA-A-ATAAATAATAAAATA-ATAATA-GAT
27017 AAATAAATAAATAATAACAGATATATAATTAGAT
1 AAATAAATAAATAATAA-A-ATA-ATAA-TAGAT
27051 AAATAAATAAA-ATATAAAATAATAATA-AT
1 AAATAAATAAATA-ATAAAATAATAATAGAT
* * *
27080 -AATAAATAAATTATAATATAATAATAAAT
1 AAATAAATAAATAATAAAATAATAATAGAT
* * *
27109 ATATAACTATATAAATAAAATA
1 AAATAAATAAAT-AATAAAATA
27131 CATATAAATA
Statistics
Matches: 121, Mismatches: 14, Indels: 31
0.73 0.08 0.19
Matches are distributed among these distances:
28 23 0.19
29 4 0.03
30 12 0.10
31 11 0.09
32 15 0.12
33 5 0.04
34 32 0.26
35 9 0.07
36 5 0.04
37 5 0.04
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.29
Consensus pattern (30 bp):
AAATAAATAAATAATAAAATAATAATAGAT
Found at i:27083 original size:28 final size:28
Alignment explanation
Indices: 27052--27106 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
27042 TAATTAGATA
27052 AATAAATAAAATATAAAATAATAATAAT
1 AATAAATAAAATATAAAATAATAATAAT
* *
27080 AATAAATAAATTATAATATAATAATAA
1 AATAAATAAAATATAAAATAATAATAA
27107 ATATATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAAATAAAATATAAAATAATAATAAT
Found at i:27119 original size:25 final size:24
Alignment explanation
Indices: 27019--27141 Score: 84
Period size: 23 Copynumber: 5.3 Consensus size: 24
27009 TATAGGATAA
* *
27019 ATAA-ATAA-ATAATAACAGATAT
1 ATAATATAATATAATAATAAATAT
27041 ATAAT-TAGATA-AATAAATAAA-AT
1 ATAATATA-ATATAAT-AATAAATAT
*
27064 ATAAAATAATAATAATAATAAATA-
1 ATAATATAAT-ATAATAATAAATAT
*
27088 A-ATTATAATATAATAATAAATAT
1 ATAATATAATATAATAATAAATAT
* *
27111 ATAACTATATAAATAA-AATACATAT
1 ATAA-TATA-ATATAATAATAAATAT
27136 A-AATAT
1 ATAATAT
27142 TAACAGAAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
22 19 0.23
23 22 0.27
24 18 0.22
25 17 0.21
26 5 0.06
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
ATAATATAATATAATAATAAATAT
Found at i:27120 original size:22 final size:22
Alignment explanation
Indices: 27015--27122 Score: 68
Period size: 22 Copynumber: 5.0 Consensus size: 22
27005 ATATTATAGG
* *
27015 ATAAATAAATAAATAATAACA-G
1 ATAA-TAAATAAATAATAATATA
* *
27037 ATATATAATTAGATAAATAA-ATA
1 ATA-ATAAATAAAT-AATAATATA
*
27060 A-AATATA-AAATAATAATA--
1 ATAATAAATAAATAATAATATA
*
27078 ATAATAAATAAATTATAATATA
1 ATAATAAATAAATAATAATATA
*
27100 ATAATAAATATATAACT-ATATA
1 ATAATAAATAAATAA-TAATATA
27122 A
1 A
27123 ATAAAATACA
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
18 1 0.01
19 10 0.15
20 14 0.21
21 3 0.04
22 31 0.46
23 8 0.12
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAATAAATAAATAATAATATA
Found at i:27125 original size:28 final size:26
Alignment explanation
Indices: 27022--27130 Score: 73
Period size: 28 Copynumber: 4.0 Consensus size: 26
27012 AGGATAAATA
* *
27022 AATAAATAATAACAGAT--ATATAATT
1 AATAAATAATAATATATAAATATAA-T
*
27047 AGATAAATAAATAAAATATAAA-ATAAT
1 A-ATAAAT-AATAATATATAAATATAAT
*
27074 AAT-AATAATAAATAAATTATAATATAAT
1 AATAAATAAT-AATATA-TA-AATATAAT
*
27102 AATAAATATATAACTATATAAATAAAAT
1 AATAAATA-ATAA-TATATAAATATAAT
27130 A
1 A
27131 CATATAAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
24 3 0.04
25 8 0.12
26 10 0.15
27 12 0.18
28 20 0.30
29 9 0.13
30 5 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (26 bp):
AATAAATAATAATATATAAATATAAT
Found at i:27435 original size:6 final size:6
Alignment explanation
Indices: 27426--27468 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
27416 TTTTTTATAT
* *
27426 TTTTTG TTTTTT TTGTTTG CTTTTG TTTTTG TTTTTTG TTTTT
1 TTTTTG TTTTTG TT-TTTG TTTTTG TTTTTG -TTTTTG TTTTT
27469 TTTAACCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 21 0.68
7 10 0.32
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:27449 original size:19 final size:18
Alignment explanation
Indices: 27427--27471 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
27417 TTTTTATATT
27427 TTTTGTTTTT-TTTGTTTG
1 TTTTGTTTTTGTTT-TTTG
27445 CTTTTGTTTTTGTTTTTTG
1 -TTTTGTTTTTGTTTTTTG
27464 TTTT-TTTT
1 TTTTGTTTT
27472 AACCAAAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.16
18 4 0.16
19 14 0.56
20 3 0.12
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.84
Consensus pattern (18 bp):
TTTTGTTTTTGTTTTTTG
Found at i:27573 original size:41 final size:42
Alignment explanation
Indices: 27479--27756 Score: 375
Period size: 41 Copynumber: 6.9 Consensus size: 42
27469 TTTAACCAAA
* * *
27479 GCTCCTCTAAACAGAGGCTCAACAACTTTGAGAAACA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-AGTAAATT
27522 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* * *
27563 GCTCCTCTAAACAGAGGTACCATGACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
27604 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA-TAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
27645 GCTCCTCT------A---ACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
* *
27678 GCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
27720 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGT
27757 GACTTTGGAA
Statistics
Matches: 211, Mismatches: 11, Indels: 27
0.85 0.04 0.11
Matches are distributed among these distances:
32 17 0.08
33 14 0.07
35 1 0.00
39 1 0.00
40 1 0.00
41 89 0.42
42 62 0.29
43 26 0.12
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
Found at i:27658 original size:32 final size:33
Alignment explanation
Indices: 27622--27687 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
27612 AAACAGAGGC
27622 ACCACGACTTTGGAAAA-TAAATTGCTCCTCTA
1 ACCACGACTTTGGAAAAGTAAATTGCTCCTCTA
27654 ACCACGACTTTGGAAAAGTAAATTGCTCCTCTA
1 ACCACGACTTTGGAAAAGTAAATTGCTCCTCTA
27687 A
1 A
27688 ACAGAGGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (33 bp):
ACCACGACTTTGGAAAAGTAAATTGCTCCTCTA
Found at i:27718 original size:42 final size:42
Alignment explanation
Indices: 27654--27754 Score: 184
Period size: 42 Copynumber: 2.4 Consensus size: 42
27644 TGCTCCTCTA
* *
27654 ACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGT
1 ACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGC
27696 ACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGC
1 ACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGC
27738 ACCACGACTTTGGAAAA
1 ACCACGACTTTGGAAAA
27755 GTGACTTTGG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
ACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGC
Found at i:27753 original size:116 final size:114
Alignment explanation
Indices: 27540--27754 Score: 385
Period size: 116 Copynumber: 1.9 Consensus size: 114
27530 AAACAGAGGC
* * *
27540 ACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCATGACTTTTGAAAGTAAATTG
1 ACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAATAAATTG
27605 CTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATTGCTCCTCTA
66 CTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATTGCTCCTCTA
27654 ACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAAATAAAT
1 ACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGG-AAAATAAAT
27719 TGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA
64 TGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAA
27755 GTGACTTTGG
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
114 11 0.11
115 41 0.43
116 44 0.46
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (114 bp):
ACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGAAAATAAATTG
CTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATTGCTCCTCTA
Found at i:29071 original size:11 final size:11
Alignment explanation
Indices: 29034--29073 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
29024 TCCTTTTTCA
*
29034 TTTTTTCTTAT
1 TTTTTTCTTTT
*
29045 TTCTTTCTTTT
1 TTTTTTCTTTT
29056 TTTTTTCTTTT
1 TTTTTTCTTTT
29067 TTTTTTC
1 TTTTTTC
29074 ATCATCTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:29088 original size:19 final size:19
Alignment explanation
Indices: 29064--29101 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
29054 TTTTTTTTCT
29064 TTTTTTTTTCATCA-TCTTC
1 TTTTTTTTTC-TCATTCTTC
29083 TTTTTTTTTCTCATTCTTC
1 TTTTTTTTTCTCATTCTTC
29102 ACCTATTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTTTTTCTCATTCTTC
Found at i:33243 original size:21 final size:20
Alignment explanation
Indices: 33217--33255 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
33207 AATCTAATCT
*
33217 AACAAATAAATAAATAAACAA
1 AACAAATAAA-AAAAAAACAA
33238 AACAAATAAAAAAAAAAC
1 AACAAATAAAAAAAAAAC
33256 CTGGAGCGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (20 bp):
AACAAATAAAAAAAAAACAA
Found at i:34220 original size:28 final size:28
Alignment explanation
Indices: 34189--34243 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
34179 TAATTAGATA
34189 AATAAATAAAATATAAAATAATAATAAT
1 AATAAATAAAATATAAAATAATAATAAT
* *
34217 AATAAATAAATTATAATATAATAATAA
1 AATAAATAAAATATAAAATAATAATAA
34244 ATATATAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAAATAAAATATAAAATAATAATAAT
Found at i:34256 original size:25 final size:25
Alignment explanation
Indices: 34164--34278 Score: 77
Period size: 23 Copynumber: 4.8 Consensus size: 25
34154 AAATAAAAAA
* *
34164 ATAATAACAGATATATAAT-TAGAT
1 ATAATAATAAATATATAATATAGAT
*
34188 A-AATAAATAAA-ATATAAAATA-AT
1 ATAAT-AATAAATATATAATATAGAT
*
34211 AATAATAATAAATA-A-ATTATA-AT
1 -ATAATAATAAATATATAATATAGAT
* *
34234 ATAATAATAAATATATAACTATATAA
1 ATAATAATAAATATATAA-TATAGAT
*
34260 ATAA-AATACATATA-AATAT
1 ATAATAATAAATATATAATAT
34279 TAACAGAAAG
Statistics
Matches: 74, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
22 13 0.18
23 21 0.28
24 18 0.24
25 17 0.23
26 5 0.07
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAATAATAAATATATAATATAGAT
Found at i:34257 original size:22 final size:22
Alignment explanation
Indices: 34215--34259 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
34205 AATAATAATA
*
34215 ATAATAAATAAATTATAATATA
1 ATAATAAATAAATAATAATATA
*
34237 ATAATAAATATATAACT-ATATA
1 ATAATAAATAAATAA-TAATATA
34259 A
1 A
34260 ATAAAATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAATAAATAAATAATAATATA
Found at i:34262 original size:28 final size:26
Alignment explanation
Indices: 34189--34267 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 26
34179 TAATTAGATA
34189 AATAAATAA-AATATA-AAATAATAAT
1 AATAAATAATAATATATAAAT-ATAAT
34214 AAT-AATAAATAA-AT-TATAATATAAT
1 AATAAAT-AATAATATATA-AATATAAT
*
34239 AATAAATATATAACTATATAAATAAAAT
1 AATAAATA-ATAA-TATATAAATATAAT
34267 A
1 A
34268 CATATAAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
24 3 0.07
25 17 0.39
26 12 0.27
28 10 0.23
29 2 0.05
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (26 bp):
AATAAATAATAATATATAAATATAAT
Found at i:38938 original size:14 final size:13
Alignment explanation
Indices: 38907--38939 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
38897 AAAATGCATT
38907 TTTTAAAATTTTA
1 TTTTAAAATTTTA
38920 TTTTAGAAATTTTA
1 TTTTA-AAATTTTA
38934 TTTTAA
1 TTTTAA
38940 GGAAAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (13 bp):
TTTTAAAATTTTA
Found at i:39002 original size:17 final size:19
Alignment explanation
Indices: 38982--39017 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
38972 TATTTTTTTT
38982 GAAAATTG-TA-TTTTAAA
1 GAAAATTGATACTTTTAAA
38999 GAAAATTGATACTTTTAAA
1 GAAAATTGATACTTTTAAA
39018 CTTTTCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (19 bp):
GAAAATTGATACTTTTAAA
Found at i:39387 original size:20 final size:20
Alignment explanation
Indices: 39362--39399 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39352 AGAAAATCAT
39362 TTAAAA-AAATAAAATAAACA
1 TTAAAATAAA-AAAATAAACA
39382 TTAAAATAAAAAAATAAA
1 TTAAAATAAAAAAATAAA
39400 AAAAATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAATAAAAAAATAAACA
Found at i:39397 original size:25 final size:23
Alignment explanation
Indices: 39363--39408 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
39353 GAAAATCATT
39363 TAAAAAAATAAAATAAACATTAAAA
1 TAAAAAAATAAAA-AAA-ATTAAAA
39388 TAAAAAAATAAAAAAAATTAA
1 TAAAAAAATAAAAAAAATTAA
39409 GAATTCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 13 0.62
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (23 bp):
TAAAAAAATAAAAAAAATTAAAA
Found at i:39479 original size:4 final size:4
Alignment explanation
Indices: 39470--39494 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39460 TAATAATAAT
39470 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
39495 CCTTAACGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:41722 original size:60 final size:60
Alignment explanation
Indices: 41652--41773 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
41642 GCTTTTGTAC
** * * *
41652 AAGGAAAATTGATACTTTTAACTCTTCCTTAAAATGT-TTTTCTTGATAATTTTTCTTTTT
1 AAGGAAAATTGATACTTCCAACTCTTCCTAAAAATATATTTT-TTGATAATTTTTATTTTT
* * *
41712 AAGGAAAATTGGTACTTCCAACTTTTCCTAAAAATATATTTTTTTATAATTTTTATTTTT
1 AAGGAAAATTGATACTTCCAACTCTTCCTAAAAATATATTTTTTGATAATTTTTATTTTT
41772 AA
1 AA
41774 AAATTTTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 49 0.92
61 4 0.08
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (60 bp):
AAGGAAAATTGATACTTCCAACTCTTCCTAAAAATATATTTTTTGATAATTTTTATTTTT
Found at i:41772 original size:15 final size:15
Alignment explanation
Indices: 41752--41785 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41742 AAAATATATT
* *
41752 TTTTTATAATTTTTA
1 TTTTTAAAAATTTTA
41767 TTTTTAAAAATTTTA
1 TTTTTAAAAATTTTA
41782 TTTT
1 TTTT
41786 CAAGAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTAAAAATTTTA
Found at i:41809 original size:75 final size:71
Alignment explanation
Indices: 41708--41915 Score: 258
Period size: 75 Copynumber: 2.9 Consensus size: 71
41698 TAATTTTTCT
* * **
41708 TTTTAAGGAAAATTGGTACTTCCAACTTTTCCTAAAAATATATTTTTTTA-TAATTTTTATTTTT
1 TTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAATAT-TTTTTGGACT--TTTTTA-TTTT
41772 AAAAATTTTA
62 AAAAATTTTA
*
41782 TTTTCAAGAAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTCTGGACTTTTTTATTTTA
1 TTTT-AAGGAAAATTGATACTTTCAAC-TTTTCCTAAAAATATTTTT-TGGACTTTTTTATTTTA
*
41847 GAAATTTTA
63 AAAATTTTA
* * *
41856 TTTTAAGGAAATTTGATACTTTCAACTTTTCCTCAAAATATTTTTTGAAC-TTTTTATTTT
1 TTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTGGACTTTTTTATTTT
41916 CAGGGAAATT
Statistics
Matches: 120, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
70 10 0.08
71 4 0.03
72 18 0.15
73 20 0.17
74 21 0.17
75 29 0.24
76 17 0.14
77 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.51
Consensus pattern (71 bp):
TTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTGGACTTTTTTATTTTAAAA
ATTTTA
Found at i:41912 original size:56 final size:56
Alignment explanation
Indices: 41851--41956 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
41841 ATTTTAGAAA
*
41851 TTTTATTTT-AAGGAAATTTGATACTTTCAACTTT-TCCTCAAAATATTTTTTGAACT
1 TTTTATTTTCAAGGAAA-TTGACACTTTCAACTTTCTCC-CAAAATATTTTTTGAACT
* *
41907 TTTTATTTTCAGGGAAATTGACACTTTCAACTTTCTCCCAAAATGTTTTT
1 TTTTATTTTCAAGGAAATTGACACTTTCAACTTTCTCCCAAAATATTTTT
41957 GAAAATATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
56 36 0.80
57 9 0.20
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.48
Consensus pattern (56 bp):
TTTTATTTTCAAGGAAATTGACACTTTCAACTTTCTCCCAAAATATTTTTTGAACT
Found at i:41925 original size:73 final size:70
Alignment explanation
Indices: 41708--41915 Score: 263
Period size: 74 Copynumber: 2.9 Consensus size: 70
41698 TAATTTTTCT
* * * *
41708 TTTTAAGGAAAATTGGTACTTCCAACTTTTCCTAAAAATATATTTTTTTATAATTTTTATTTTTA
1 TTTTAAGGAAAATTGATACTTTCAACTTTTCCT-AAAA-ATATTTTTTGA-ACTTTTTA-TTTTA
*
41773 AAAATTTTA
62 GAAATTTTA
* *
41782 TTTTCAAGAAAAATTGATACTTTCAACTTTTTCCTAAAAATATTTTTCTGGACTTTTTTATTTTA
1 TTTT-AAGGAAAATTGATACTTTCAAC-TTTTCCTAAAAATATTTTT-TGAAC-TTTTTATTTTA
41847 GAAATTTTA
62 GAAATTTTA
* *
41856 TTTTAAGGAAATTTGATACTTTCAACTTTTCCTCAAAATATTTTTTGAACTTTTTATTTT
1 TTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTGAACTTTTTATTTT
41916 CAGGGAAATT
Statistics
Matches: 119, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
70 10 0.08
71 4 0.03
72 18 0.15
73 20 0.17
74 30 0.25
75 30 0.25
76 7 0.06
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.51
Consensus pattern (70 bp):
TTTTAAGGAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTGAACTTTTTATTTTAGAAA
TTTTA
Found at i:41968 original size:56 final size:55
Alignment explanation
Indices: 41842--41972 Score: 151
Period size: 56 Copynumber: 2.3 Consensus size: 55
41832 GACTTTTTTA
* * *
41842 TTTTAGAAATTTTATTTTAAGGAAATTTGATACTTTCAACTTTTCCTCAAAATAT
1 TTTTTGAAATTTTATTTTAAGGAAATTTGACACTTTCAACTTTTCCTCAAAATAG
* *
41897 TTTTTGAACTTTTTATTTTCAGGGAAA-TTGACACTTTCAACTTTCTCC-CAAAAT-G
1 TTTTTGAA-ATTTTATTTT-AAGGAAATTTGACACTTTCAACTTT-TCCTCAAAATAG
41952 TTTTTGAAAATATTTATTTTA
1 TTTTTG-AAAT-TTTATTTTA
41973 GAAACTTTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
55 15 0.23
56 41 0.63
57 9 0.14
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.48
Consensus pattern (55 bp):
TTTTTGAAATTTTATTTTAAGGAAATTTGACACTTTCAACTTTTCCTCAAAATAG
Found at i:42042 original size:57 final size:58
Alignment explanation
Indices: 41958--42112 Score: 190
Period size: 57 Copynumber: 2.6 Consensus size: 58
41948 AATGTTTTTG
* * *
41958 AAAATATTTATTTTAGAAACTTTATTTTTAATGAAAATTGATACTTTCAAC-TTTTTTCTA
1 AAAATA-TTATTTTAG-AATTTTATTTTTAA-GAAAATTAATACTTTCAACTTTTTTTCAA
42018 AAAATATT-TTTTAGAATTTTATTTTTAAGGAAAATTAATACTTTCAACTTTTTTTCAA
1 AAAATATTATTTTAGAATTTTATTTTTAA-GAAAATTAATACTTTCAACTTTTTTTCAA
*
42076 AAATATATATATTTTGGAATTTT-TATTTTAAGAAAAT
1 AAA-ATAT-TATTTTAGAATTTTAT-TTTTAAGAAAAT
42113 CATTTAAAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
57 31 0.36
58 17 0.20
59 6 0.07
60 14 0.16
61 17 0.20
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (58 bp):
AAAATATTATTTTAGAATTTTATTTTTAAGAAAATTAATACTTTCAACTTTTTTTCAA
Found at i:42567 original size:20 final size:19
Alignment explanation
Indices: 42544--42588 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
42534 GTTTTTAGTT
*
42544 GAAAAATTAATCAAAAACTG
1 GAAAAA-TAACCAAAAACTG
* *
42564 GAAAAATAGCCAGAAACTG
1 GAAAAATAACCAAAAACTG
42583 GAAAAA
1 GAAAAA
42589 CTGACTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.60, C:0.11, G:0.16, T:0.13
Consensus pattern (19 bp):
GAAAAATAACCAAAAACTG
Found at i:42790 original size:14 final size:15
Alignment explanation
Indices: 42771--42799 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42761 GTTTCACCTC
42771 TTTTTTCCT-TTTTT
1 TTTTTTCCTATTTTT
42785 TTTTTTCCTATTTTT
1 TTTTTTCCTATTTTT
42800 GGGTTCTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTCCTATTTTT
Found at i:43022 original size:11 final size:11
Alignment explanation
Indices: 43002--43103 Score: 50
Period size: 11 Copynumber: 9.1 Consensus size: 11
42992 AAGAAAAGAT
43002 AAAATCAATAAA
1 AAAAT-AATAAA
*
43014 AAAATAATAAT
1 AAAATAATAAA
* *
43025 ATAATAGT-AA
1 AAAATAATAAA
*
43035 ATAATAA-AAA
1 AAAATAATAAA
*
43045 TAAATAATAAACAA
1 AAAATAAT--A-AA
*
43059 AAAATAGTAAA
1 AAAATAATAAA
*
43070 AAAATAGTAAA
1 AAAATAATAAA
43081 AATAA-AATAGAA
1 AA-AATAATA-AA
*
43093 ACAA-AATAAA
1 AAAATAATAAA
43103 A
1 A
43104 TTATATTATA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
10 17 0.24
11 35 0.49
12 11 0.15
13 1 0.01
14 8 0.11
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.20
Consensus pattern (11 bp):
AAAATAATAAA
Found at i:43046 original size:21 final size:20
Alignment explanation
Indices: 43016--43123 Score: 53
Period size: 21 Copynumber: 5.3 Consensus size: 20
43006 TCAATAAAAA
*
43016 AATAATAATATAATAGTAAAT
1 AATAAAAATATAATA-TAAAT
43037 AATAAAAATA-AATAATAAA-
1 AATAAAAATATAAT-ATAAAT
* *
43056 CA-AAAAATAGTAA-AAAAAT
1 AATAAAAATA-TAATATAAAT
* * * *
43075 AGTAAAAATAAAATAGAAACAA
1 AATAAAAATATAATA-TAA-AT
* *
43097 AATAAAATTATATTATAAAT
1 AATAAAAATATAATATAAAT
43117 AAATAAA
1 -AATAAA
43124 TAAATAAATG
Statistics
Matches: 65, Mismatches: 13, Indels: 18
0.68 0.14 0.19
Matches are distributed among these distances:
18 11 0.17
19 3 0.05
20 18 0.28
21 21 0.32
22 12 0.18
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
AATAAAAATATAATATAAAT
Found at i:43063 original size:27 final size:27
Alignment explanation
Indices: 43008--43075 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
42998 AGATAAAATC
* **
43008 AATAA-AAAAATAATAATATAATAGTA
1 AATAATAAAAATAATAATATAACAAAA
43034 AATAATAAAAATAAATAATA-AACAAAA
1 AATAATAAAAAT-AATAATATAACAAAA
*
43061 AATAGTAAAAA-AATA
1 AATAATAAAAATAATA
43076 GTAAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 4 0.11
26 5 0.14
27 20 0.56
28 7 0.19
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (27 bp):
AATAATAAAAATAATAATATAACAAAA
Found at i:43074 original size:25 final size:24
Alignment explanation
Indices: 43037--43101 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 24
43027 AATAGTAAAT
43037 AATA-AAAATAAATAATAAACAA-AA
1 AATAGAAAA-AAATAATAAA-AATAA
*
43061 AATAGTAAAAAAATAGTAAAAATAA
1 AATAG-AAAAAAATAATAAAAATAA
43086 AATAGAAACAAAATAA
1 AATAGAAA-AAAATAA
43102 AATTATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
24 9 0.26
25 22 0.63
26 4 0.11
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (24 bp):
AATAGAAAAAAATAATAAAAATAA
Found at i:46602 original size:21 final size:21
Alignment explanation
Indices: 46578--46622 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
46568 GATGGGCCCA
46578 TTTA-TTTATTTATAATTTTAT
1 TTTATTTTATTTAT-ATTTTAT
* *
46599 TTTATTTTGTTTCTATTTTAT
1 TTTATTTTATTTATATTTTAT
46620 TTT
1 TTT
46623 TACTATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTATTTTATTTATATTTTAT
Found at i:46639 original size:15 final size:15
Alignment explanation
Indices: 46612--46685 Score: 71
Period size: 15 Copynumber: 4.8 Consensus size: 15
46602 ATTTTGTTTC
*
46612 TATTTTATT-TTTAC
1 TATTTTATTATTTAT
*
46626 TATTTTTTTATTTAT
1 TATTTTATTATTTAT
46641 TATTTACTATTATATTAT
1 TATTT--TATTAT-TTAT
46659 TATTTATATTA-TTAT
1 TATTT-TATTATTTAT
*
46674 TATTTTTTTATT
1 TATTTTATTATT
46686 GATTTTATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
14 12 0.24
15 19 0.38
17 10 0.20
18 9 0.18
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTTATTATTTAT
Found at i:46660 original size:18 final size:17
Alignment explanation
Indices: 46633--46677 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
46623 TACTATTTTT
46633 TTAT-TTATTATTTACTA
1 TTATATTATTATTTA-TA
46650 TTATATTATTATTTATA
1 TTATATTATTATTTATA
46667 TTATTATTATT
1 TTA-TATTATT
46678 TTTTTATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATATTATTATTTATA
Found at i:47753 original size:56 final size:56
Alignment explanation
Indices: 47693--47813 Score: 158
Period size: 56 Copynumber: 2.2 Consensus size: 56
47683 TAAAGTTTCT
* *
47693 AAAATAAAAATTTTC-AAAAACATTTTG-GGAGAAAGTTGAAAGTGTC-AATTTCCCTG
1 AAAATAAAAA-GTTCAAAAAACATTTTGAGGA-AAAGTTGAAAGTATCAAATTT-CCTG
* *
47749 AAAATAAAAAGTTCAAAAAATATTTTGAGGAAAAGTTGAAAGTATCAAATTTCCTT
1 AAAATAAAAAGTTCAAAAAACATTTTGAGGAAAAGTTGAAAGTATCAAATTTCCTG
47805 AAAATAAAA
1 AAAATAAAA
47814 TTTCTAAAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
55 3 0.05
56 47 0.81
57 8 0.14
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (56 bp):
AAAATAAAAAGTTCAAAAAACATTTTGAGGAAAAGTTGAAAGTATCAAATTTCCTG
Found at i:47856 original size:65 final size:68
Alignment explanation
Indices: 47786--47923 Score: 185
Period size: 69 Copynumber: 2.1 Consensus size: 68
47776 AGGAAAAGTT
* *
47786 GAAAGTATCAAATTTCCTT-AAAATAAAATTTCT-AAAATAAAAA-AGTC-CAGAAAATATATTT
1 GAAAGTATCAAATTTCCTTGAAAATAAAATTTCTAAAAATAAAAATA-TCAAAAAAAATATATTT
47847 TTAG
65 TTAG
* * *
47851 GAAAGTATCAATTTTTCTTGAAAATAAAATTTTTAAAAATAAAAATTATCAAAAAAAATATATTT
1 GAAAGTATCAAATTTCCTTGAAAATAAAATTTCTAAAAATAAAAA-TATCAAAAAAAATATATTT
47916 TTAG
65 TTAG
47920 GAAA
1 GAAA
47924 AGTTGGAAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
65 17 0.27
66 13 0.21
67 10 0.16
68 2 0.03
69 21 0.33
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (68 bp):
GAAAGTATCAAATTTCCTTGAAAATAAAATTTCTAAAAATAAAAATATCAAAAAAAATATATTTT
TAG
Found at i:48002 original size:60 final size:62
Alignment explanation
Indices: 47883--48006 Score: 153
Period size: 60 Copynumber: 2.0 Consensus size: 62
47873 AATAAAATTT
* * * **
47883 TTAAAAATAAAAATTATCAAAAAAAATATATTTTTAGGAAAAGTTGGAAGTACCAATTTTCC
1 TTAAAAAGAAAAATTATCAAAAAAAATACATTTTAAGGAAAAGTTAAAAGTACCAATTTTCC
* * * *
47945 TTAAAAAGAAAAATTATC-CAGAAAA-ACATTTTAAGGAAGAGTTAAAAGTATCAATTTTCC
1 TTAAAAAGAAAAATTATCAAAAAAAATACATTTTAAGGAAAAGTTAAAAGTACCAATTTTCC
48005 TT
1 TT
48007 GTACAAAAGC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 31 0.58
61 5 0.09
62 17 0.32
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (62 bp):
TTAAAAAGAAAAATTATCAAAAAAAATACATTTTAAGGAAAAGTTAAAAGTACCAATTTTCC
Found at i:50336 original size:5 final size:5
Alignment explanation
Indices: 50321--50362 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
50311 GGAATTCTTA
50321 ATTTT -TTTT ATTTT ATTTTT ATTTT AATGTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT A-TTTT ATTTT -AT-TTT ATTTT ATTTT
50363 TTTAAATGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 4 0.12
5 17 0.52
6 9 0.27
7 3 0.09
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:50534 original size:118 final size:116
Alignment explanation
Indices: 50409--50928 Score: 432
Period size: 117 Copynumber: 4.4 Consensus size: 116
50399 ATATATATAT
*
50409 ATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCT-TTGAAAATAAAAAATTTCTAAAAAATAT
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTCTT-AAAATAAAAAATTTCTAAAAAATAT
* * * *
50473 TTTTAAAGAAAAGTTGAAAGAATCAATTTTTCATGAAAACAAAATTTTAAAAAA
65 TTTTAAGGAAAAGTT-AAAGTATCAA-TTTTCTTGAAAATAAAATTTTAAAAAA
50527 ATATTTTT-AGGGAAAAGTTGAAAGTATCAA-TTTCTCTTGAAAATAAAAAAGTTT-TAAAAAAA
1 ATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCTCTT-AAAATAAAAAA-TTTCT-AAAAAA
* * * * *
50589 TTATTTTCAGGGAAAAATTAAAAGTATTAA--TCCTTGAAAATAAAATTTCT-AAAAA
62 -TATTTTTAAGGAAAAGTT-AAAGTATCAATTTTCTTGAAAATAAAATTT-TAAAAAA
* * *
50644 ATATTTTTGAGGAAAATTTGGAAGTATCAATTTTC-CTTTAAAAT--AAAATTTC-AAGAAAAAA
1 ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTC-TTAAAATAAAAAATTTCTAA-AAAATA
* * *
50705 GTATTTTGAGGAAAAGTTAAAGTATCAATTTTCTTTAAAATATAATTTTCAAAAAA
64 -T-TTTTAAGGAAAAGTTAAAGTATCAATTTTCTTGAAAATAAAATTTT-AAAAAA
* *
50761 A-ATATTTTAAGGAAAAGTTAAAAGTATCAATTTT-TCTTAAAAT--AAAATTT-TAAAAAA-AT
1 ATAT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCTCTTAAAATAAAAAATTTCTAAAAAATAT
* * * * *
50820 GCATTTTAGGGAAAATTTAGAAGTACCAATTTTCATTTTTTAAAA-AAATTTTGTAAAGAAA
65 ---TTTTAAGGAAAAGTTA-AAGTATCAATTTTC----TTGAAAATAAAATTT-TAAA-AAA
* *
50881 A-ACGTTTTAAGGAAAAGTTGAAAGTATCAATTTT-TCTTAAAATAAAAA
1 ATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTCTTAAAATAAAAA
50929 CTTCCAAATG
Statistics
Matches: 336, Mismatches: 34, Indels: 60
0.78 0.08 0.14
Matches are distributed among these distances:
113 4 0.01
114 18 0.05
115 34 0.10
116 46 0.14
117 91 0.27
118 50 0.15
119 17 0.05
120 73 0.22
122 3 0.01
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.36
Consensus pattern (116 bp):
ATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTCTTAAAATAAAAAATTTCTAAAAAATATT
TTTAAGGAAAAGTTAAAGTATCAATTTTCTTGAAAATAAAATTTTAAAAAA
Found at i:50543 original size:58 final size:58
Alignment explanation
Indices: 50421--50927 Score: 427
Period size: 58 Copynumber: 8.6 Consensus size: 58
50411 ATTTTTGAGA
**
50421 AAAAGTTGAAAGTATCAA-TTTTCTTTGAAAATAAAAAATTTCT-AAAAAATATTTTTAAAG
1 AAAAGTTGAAAGTATCAATTTTTC-TTGAAAAT--AAAATTT-TAAAAAAATATTTTTAGGG
* * *
50481 AAAAGTTGAAAGAATCAATTTTTCATGAAAACAAAATTTTAAAAAAATATTTTTAGGG
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTAAAAAAATATTTTTAGGG
* *
50539 AAAAGTTGAAAGTATCAATTTCTCTTGAAAATAAAAAAGTTTTAAAAAAATTATTTTCAGGG
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAAT--AAAA-TTTTAAAAAAA-TATTTTTAGGG
* * * *
50601 AAAAATTAAAAGTATTAA---TCCTTGAAAATAAAATTTCT-AAAAAATATTTTT-GAGG
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTT-TAAAAAAATATTTTTAG-GG
* * * * * *
50656 AAAATTTGGAAGTATCAATTTTCCTTTAAAATAAAATTTCAAGAAAAAAGTATTTTGA-GG
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTT-TA-AAAAAA-TATTTTTAGGG
* * *
50716 AAAAGTT-AAAGTATCAA-TTTTCTTTAAAATATAATTTTCAAAAAAA-ATATTTTAAGG
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTT-AAAAAAATAT-TTTTAGGG
*
50773 AAAAGTTAAAAGTATCAATTTTTCTT-AAAATAAAATTTTAAAAAAATGCA-TTTTAGGG
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTAAAAAAAT--ATTTTTAGGG
* * * * * * *
50831 AAAA-TTTAGAAGTACCAATTTTCATTTTTTAAAA-AAATTTTGTAAAGAAAA-ACGTTTTAAGG
1 AAAAGTTGA-AAGTATCAA-TTT--TTCTTGAAAATAAAATTT-TAAA-AAAATA-TTTTTAGGG
50893 AAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAAA
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAA
50928 ACTTCCAAAT
Statistics
Matches: 373, Mismatches: 40, Indels: 69
0.77 0.08 0.14
Matches are distributed among these distances:
54 1 0.00
55 24 0.06
56 13 0.03
57 31 0.08
58 132 0.35
59 35 0.09
60 43 0.12
61 35 0.09
62 52 0.14
63 7 0.02
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (58 bp):
AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTAAAAAAATATTTTTAGGG
Found at i:50753 original size:17 final size:18
Alignment explanation
Indices: 50721--50754 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
50711 TGAGGAAAAG
*
50721 TTAAAGTATCAATTTTCT
1 TTAAAATATCAATTTTCT
50739 TTAAAATAT-AATTTTC
1 TTAAAATATCAATTTTC
50755 AAAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (18 bp):
TTAAAATATCAATTTTCT
Found at i:50899 original size:120 final size:116
Alignment explanation
Indices: 50665--50927 Score: 327
Period size: 120 Copynumber: 2.2 Consensus size: 116
50655 GAAAATTTGG
* * *
50665 AAGTATCAATTTTCCTTTAAAATAAAATTTCAAGAAAAAAGTATTTTGAGGAAAAGTTAAAGTAT
1 AAGTATCAATTTTTC-TTAAAATAAAATTTCAAGAAAAAAGCATTTTGAGGAAAAGTTAAAGTAC
*
50730 CAATTTTCTTTAAAATATAATTTTCAAAAAAAATATTTTAAGGAAAAGTTAA
65 CAATTTTCTTTAAAATATAATTTTCAAAAAAAACATTTTAAGGAAAAGTTAA
* * *
50782 AAGTATCAATTTTTCTTAAAATAAAATTTTAA-AAAAATGCATTTT-AGGGAAAATTTAGAAGTA
1 AAGTATCAATTTTTCTTAAAATAAAATTTCAAGAAAAAAGCATTTTGA-GGAAAAGTTA-AAGTA
* * *
50845 CCAATTTTCATTTTTTAAAA-A-AATTTTGTAAAGAAAAACGTTTTAAGGAAAAGTTGA
64 CCAATTTTC----TTTAAAATATAATTTT-CAAA-AAAAACATTTTAAGGAAAAGTTAA
50902 AAGTATCAATTTTTCTTAAAATAAAA
1 AAGTATCAATTTTTCTTAAAATAAAA
50928 ACTTCCAAAT
Statistics
Matches: 128, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
114 1 0.01
115 20 0.16
116 29 0.23
117 14 0.11
118 6 0.05
119 4 0.03
120 54 0.42
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.37
Consensus pattern (116 bp):
AAGTATCAATTTTTCTTAAAATAAAATTTCAAGAAAAAAGCATTTTGAGGAAAAGTTAAAGTACC
AATTTTCTTTAAAATATAATTTTCAAAAAAAACATTTTAAGGAAAAGTTAA
Found at i:55514 original size:5 final size:5
Alignment explanation
Indices: 55492--55565 Score: 53
Period size: 5 Copynumber: 14.0 Consensus size: 5
55482 AAATTTCTCA
* * *
55492 AAAAT AAAAC CAAA- AAAAT AAAAT AAAAT GAGCTAA- AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -A--AAAT AAAAT AAAAT
55538 AAAAT CAAAAAT AAAAT AAAAAT AAAAT
1 AAAAT --AAAAT AAAAT -AAAAT AAAAT
55566 GGAAAAAGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
4 5 0.09
5 37 0.66
6 7 0.12
7 5 0.09
8 2 0.04
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:55553 original size:22 final size:22
Alignment explanation
Indices: 55503--55565 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
55493 AAATAAAACC
* *
55503 AAAAAAATAAAATAAAATGAGC
1 AAAAAAATAAAATAAAATCAGA
*
55525 TAAAAAATAAAATAAAATCA-A
1 AAAAAAATAAAATAAAATCAGA
55546 AAATAAAATAAAAATAAAAT
1 AAA-AAAAT-AAAATAAAAT
55566 GGAAAAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.06
22 23 0.66
23 10 0.29
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (22 bp):
AAAAAAATAAAATAAAATCAGA
Found at i:55571 original size:12 final size:11
Alignment explanation
Indices: 55528--55565 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
55518 AATGAGCTAA
55528 AAAAT-AAAAT
1 AAAATAAAAAT
55538 AAAATCAAAAAT
1 AAAAT-AAAAAT
55550 AAAATAAAAAT
1 AAAATAAAAAT
55561 AAAAT
1 AAAAT
55566 GGAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 5 0.19
11 11 0.42
12 10 0.38
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:56453 original size:3 final size:3
Alignment explanation
Indices: 56445--56484 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
56435 AAGGAAAAGG
56445 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
56485 CATACTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:65935 original size:101 final size:98
Alignment explanation
Indices: 65704--65935 Score: 217
Period size: 101 Copynumber: 2.4 Consensus size: 98
65694 AATTCCATAT
* * ** *
65704 TTAAATTCT--CCATTCATTTAGTAGG-ATTAAAATTTTTCTTTTCTCAAAAATTCATATGAAAT
1 TTAAATTCTCCCCAATCATTTAGTAGGAATAAAAATTTTAATTTTCACAAAAATTCATATGAAAT
* * * *
65766 TCTCCAATCATTTGGTTTAAATTCACATTCAAGA
66 TCTCCAATAATTTGG-TTAAATCCAAATTCAAAA
* * *
65800 TTTAATTC-CTCCCAATCATTT-GATA-GAATTAAAAATTTTAATTTTCACAAAAAATTTATTTT
1 TTAAATTCTC-CCCAATCATTTAG-TAGGAA-TAAAAATTTTAATTTTCAC-AAAAATTCA-TAT
*
65862 GAAATTCTCCAATAATTTGG-TAGAATCCATAATTTAAAA
61 GAAATTCTCCAATAATTTGGTTA-AATCCA-AATTCAAAA
*
65901 TTAAATTCTCCCCAATCATTTAGTAGGAAAAAAAA
1 TTAAATTCTCCCCAATCATTTAGTAGGAATAAAAA
65936 CTATTTTTTA
Statistics
Matches: 108, Mismatches: 15, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
96 7 0.06
97 2 0.02
98 12 0.11
99 17 0.16
100 13 0.12
101 52 0.48
102 5 0.05
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.40
Consensus pattern (98 bp):
TTAAATTCTCCCCAATCATTTAGTAGGAATAAAAATTTTAATTTTCACAAAAATTCATATGAAAT
TCTCCAATAATTTGGTTAAATCCAAATTCAAAA
Found at i:67560 original size:4 final size:4
Alignment explanation
Indices: 67553--67597 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
67543 AAATGAATGA
* * *
67553 AAAT AAAT AAAT TAAC AAAT AAAC AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
67598 TGAACCTAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:69695 original size:22 final size:21
Alignment explanation
Indices: 69663--69724 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
69653 TTCCAATCAC
69663 TTTTTCATTTTTTCATTTTTCA
1 TTTTT-ATTTTTTCATTTTTCA
* *
69685 TTTTTATTTTTTTATTTTTTTA
1 TTTTTATTTTTTCA-TTTTTCA
69707 TTTTTA-TTTTTCATTTTT
1 TTTTTATTTTTTCATTTTT
69725 TTCTCTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 5 0.14
21 14 0.39
22 17 0.47
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTATTTTTTCATTTTTCA
Found at i:69709 original size:29 final size:29
Alignment explanation
Indices: 69663--69744 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
69653 TTCCAATCAC
* *
69663 TTTTTCATTTTTTCATTTTTCATTTTT-AT
1 TTTTTTATTTTTTTATTTTT-ATTTTTCAT
69692 TTTTTTATTTTTTTATTTTTATTTTTCAT
1 TTTTTTATTTTTTTATTTTTATTTTTCAT
* *
69721 TTTTTT-CTCTTTT-TTTTTATTTTT
1 TTTTTTATTTTTTTATTTTTATTTTT
69745 TTTTCAAGCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.23
28 11 0.23
29 26 0.54
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (29 bp):
TTTTTTATTTTTTTATTTTTATTTTTCAT
Found at i:69725 original size:22 final size:19
Alignment explanation
Indices: 69670--69748 Score: 77
Period size: 21 Copynumber: 3.9 Consensus size: 19
69660 CACTTTTTCA
* *
69670 TTTTTTCATTTTTCATTTTTA
1 TTTTTTTATTTTT--TTTTTT
69691 TTTTTTTATTTTTTTATTTT
1 TTTTTTTATTTTTTT-TTTT
* *
69711 TATTTTTCATTTTTTTCTCTT
1 T-TTTTTTATTTTTTT-TTTT
69732 TTTTTTTATTTTTTTTT
1 TTTTTTTATTTTTTTTT
69749 CAAGCATAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 3 0.06
20 17 0.35
21 29 0.59
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTATTTTTTTTTTT
Found at i:69743 original size:7 final size:7
Alignment explanation
Indices: 69663--69745 Score: 66
Period size: 7 Copynumber: 11.9 Consensus size: 7
69653 TTCCAATCAC
*
69663 TTTTTCA
1 TTTTTTA
69670 TTTTTTCA
1 TTTTTT-A
*
69678 TTTTTCA
1 TTTTTTA
69685 -TTTTTA
1 TTTTTTA
69691 TTTTTTTA
1 -TTTTTTA
69699 TTTTTT-
1 TTTTTTA
69705 TATTTTTA
1 T-TTTTTA
*
69713 TTTTTCA
1 TTTTTTA
69720 TTTTTT-
1 TTTTTTA
*
69726 TCTCTTT-
1 T-TTTTTA
69733 TTTTTTA
1 TTTTTTA
69740 TTTTTT
1 TTTTTT
69746 TTTCAAGCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
6 11 0.18
7 38 0.61
8 13 0.21
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTA
Found at i:69743 original size:8 final size:8
Alignment explanation
Indices: 69685--69746 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
69675 TCATTTTTCA
69685 TTTTTATT
1 TTTTTATT
69693 TTTTTATT
1 TTTTTATT
69701 TTTTTA--
1 TTTTTATT
69707 TTTTTATT
1 TTTTTATT
69715 TTTCATT-TT
1 TTT--TTATT
*
69724 TTTCTCTTTT
1 TTT-T-TATT
69734 TTTTTATT
1 TTTTTATT
69742 TTTTT
1 TTTTT
69747 TTCAAGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
6 6 0.13
8 26 0.57
9 7 0.15
10 7 0.15
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTATT
Found at i:80149 original size:55 final size:56
Alignment explanation
Indices: 80063--80205 Score: 229
Period size: 55 Copynumber: 2.6 Consensus size: 56
80053 TCTTGTGTAG
80063 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT-GAAATTT-ATTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-TTTTTTGGAAATTTGATTTTAA
* *
80118 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATTTTTTTGGAAATTTGTTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTGGAAATTTGATTTTAA
*
80174 GGAAAATTG-TACTTTCAACTTTTCCCTAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA
80206 CAAAAATTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
54 6 0.07
55 61 0.74
56 15 0.18
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (56 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTGGAAATTTGATTTTAA
Found at i:80478 original size:54 final size:53
Alignment explanation
Indices: 80345--80675 Score: 335
Period size: 48 Copynumber: 6.4 Consensus size: 53
80335 GAAAAAACTT
*
80345 AACTTTTCCTCAAAAT-TTTTTTTGAAATTTATTTTAAGAAAATTGATACTTTC
1 AACTTTT-CTCAAAATATTTTTTTGAAATTTATTTTAAGGAAATTGATACTTTC
*
80398 AAC-TTTCTCAAAATA-TTTTTT---A-TTATTTCTAAGGAAATTGATA-TGTC
1 AACTTTTCTCAAAATATTTTTTTGAAATTTATTT-TAAGGAAATTGATACTTTC
* *
80445 AACTTTTCTCAAATCTATTTTTTTGAAATTTATTTTAA-GAAAATGATA-TTTC
1 AACTTTTCTCAAA-ATATTTTTTTGAAATTTATTTTAAGGAAATTGATACTTTC
* *
80497 AAC----CTCAAGAACATTTTTTTGAAATTTTGTTTTAAGGAAATTGATACTTTC
1 AACTTTTCTCAA-AATATTTTTTTGAAA-TTTATTTTAAGGAAATTGATACTTTC
*
80548 AA------TCAAAAAATTTTTTTGAAATTTAATTTTAAGGAAAATTGATACTTTC
1 AACTTTTCTCAAAATATTTTTTTGAAATTT-ATTTTAAGG-AAATTGATACTTTC
*
80597 AACTTTTCCCAAAA-ATATTTTTTGAAATTTATTTTAAGGAAAATTGATACTTTC
1 AACTTTTCTCAAAATAT-TTTTTTGAAATTTATTTTAAGG-AAATTGATACTTTC
*
80651 AACTTTTCCCAAAAATATATTTTTT
1 AACTTTTCTC-AAAATAT-TTTTTT
80676 TTGGAAATTT
Statistics
Matches: 242, Mismatches: 12, Indels: 45
0.81 0.04 0.15
Matches are distributed among these distances:
47 15 0.06
48 62 0.26
49 32 0.13
50 15 0.06
51 20 0.08
52 18 0.07
53 7 0.03
54 42 0.17
55 22 0.09
56 9 0.04
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (53 bp):
AACTTTTCTCAAAATATTTTTTTGAAATTTATTTTAAGGAAATTGATACTTTC
Found at i:80712 original size:6 final size:6
Alignment explanation
Indices: 80703--80755 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
80693 AAGAAAATGA
* * *
80703 AAAAAT AAAAGT AAATAT AAAGATAA AAAAAT AAAAAT AAAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAA-A-AT AAAAAT AAAAAT -AAAAAT AAAAAT
80754 AA
1 AA
80756 GATAAGAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 27 0.71
7 7 0.18
8 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:80749 original size:27 final size:26
Alignment explanation
Indices: 80696--80755 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
80686 TTATTTAAAG
* * *
80696 AAAATGAAAAAATAAAAGTAAATATA
1 AAAATAAAAAAATAAAAATAAAAATA
*
80722 AAGATAAAAAAATAAAAATAAAAAATA
1 AAAATAAAAAAATAAAAAT-AAAAATA
80749 AAAATAA
1 AAAATAA
80756 GATAAGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (26 bp):
AAAATAAAAAAATAAAAATAAAAATA
Done.