Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002720.1 Hibiscus syriacus cultivar Beakdansim tig00005612_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: 242320
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:343 original size:2 final size:2
Alignment explanation
Indices: 336--387 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
326 TATAGAGTAC
336 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
376 AT AT AT AT AT AT
1 AT AT AT AT AT AT
388 TTGTAATTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:370 original size:25 final size:25
Alignment explanation
Indices: 336--387 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
326 TATAGAGTAC
336 ATATATATATATTATATATATATAT
1 ATATATATATATTATATATATATAT
361 ATATATATATATTATATATATATAT
1 ATATATATATATTATATATATATAT
386 AT
1 AT
388 TTGTAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATATATATATATTATATATATATAT
Found at i:2045 original size:16 final size:16
Alignment explanation
Indices: 2019--2055 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2009 TCTACTAAAG
2019 CATGATTGGGTAGATAT
1 CATG-TTGGGTAGATAT
2036 CATGTTGGGTAGATAT
1 CATGTTGGGTAGATAT
2052 -ATGT
1 CATGT
2056 GAATAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 12 0.60
17 4 0.20
ACGTcount: A:0.27, C:0.05, G:0.30, T:0.38
Consensus pattern (16 bp):
CATGTTGGGTAGATAT
Found at i:11954 original size:13 final size:12
Alignment explanation
Indices: 11938--12005 Score: 82
Period size: 13 Copynumber: 5.2 Consensus size: 12
11928 AAAAATAATG
11938 AAAAAATGAAATA
1 AAAAAATGAAA-A
11951 AAAAAATGAAAA
1 AAAAAATGAAAA
11963 AGAAAAATGAAAA
1 A-AAAAATGAAAA
*
11976 AGAAAAATGAATGA
1 A-AAAAATGAA-AA
11990 AAAAAATGGAAAA
1 AAAAAAT-GAAAA
12003 AAA
1 AAA
12006 GAAGGGTTCA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
12 2 0.04
13 43 0.86
14 5 0.10
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.10
Consensus pattern (12 bp):
AAAAAATGAAAA
Found at i:11967 original size:6 final size:7
Alignment explanation
Indices: 11934--11986 Score: 60
Period size: 7 Copynumber: 7.9 Consensus size: 7
11924 TTGAAAAAAT
11934 AATGAAAA
1 AATG-AAA
11942 AATGAAA
1 AATGAAA
11949 TAA--AAA
1 -AATGAAA
11955 AATGAAA
1 AATGAAA
11962 AA-GAAA
1 AATGAAA
11968 AATGAAA
1 AATGAAA
11975 AA-GAAA
1 AATGAAA
11981 AATGAA
1 AATGAA
11987 TGAAAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
5 2 0.05
6 15 0.38
7 17 0.43
8 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.11
Consensus pattern (7 bp):
AATGAAA
Found at i:11994 original size:26 final size:25
Alignment explanation
Indices: 11927--12005 Score: 92
Period size: 26 Copynumber: 3.2 Consensus size: 25
11917 ATTTTGCTTG
11927 AAAAAAT-AATG-AAAAAATGAAATA
1 AAAAAATGAATGAAAAAAATGAAA-A
*
11951 AAAAAATGAA-AAAGAAAAATGAAAA
1 AAAAAATGAATGAA-AAAAATGAAAA
*
11976 AGAAAAATGAATGAAAAAAATGGAAA
1 A-AAAAATGAATGAAAAAAATGAAAA
12002 AAAA
1 AAAA
12006 GAAGGGTTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
24 7 0.15
25 8 0.17
26 30 0.64
27 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (25 bp):
AAAAAATGAATGAAAAAAATGAAAA
Found at i:13049 original size:55 final size:55
Alignment explanation
Indices: 12964--13695 Score: 1090
Period size: 55 Copynumber: 13.3 Consensus size: 55
12954 AGATTTCCCA
* *
12964 ACGATTATTGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
*
13019 GCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
13074 ACGATTGTTGAAAATTGTTCGAGTCTTATACTCTATGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
13129 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
13184 ACGATTGTTGAAAATTGTTCGAGTCTTATACTCTATGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
13239 ACGACTGTTGAAGATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
13294 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
13349 ACGATTGATGAAAATTGTTCGAGTCTTATACTCTCTGCAA-AAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTG-AAGAAATAGGGAGCAGAC
* * * *
13404 ACGACTGTTGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGACCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
13459 ACGACTGTTGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
13514 ACGATTGATGAAGATTGTTCAAGTCTTATACTCTCTGAA-AGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGAC
* *
13569 ACGATTGATGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * *
13624 AAGATTTGTTGAAGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAACAGAC
1 ACGA-TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
*
13680 ACGATTGATGAAGATT
1 ACGATTGTTGAAGATT
13696 CTTCAAGTTC
Statistics
Matches: 619, Mismatches: 53, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
54 2 0.00
55 564 0.91
56 53 0.09
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:13785 original size:55 final size:53
Alignment explanation
Indices: 13689--13845 Score: 192
Period size: 55 Copynumber: 2.9 Consensus size: 53
13679 CACGATTGAT
* * *
13689 GAAGATTCTTCAAGTTC-CTACTCCCTAAGAAAGAGGGAGTGAACCCGTTGACA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAGTGAACCCGTTG-CA
* *
13742 GAAGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGAAGTGAACTCGTTTGCA
1 GAAGATTGTTCGAGTTCTATACTCCCT-AAGAAAGAGGGAGTGAACCCG-TTGCA
* * * *
13797 GAAAATTGTTCGAGTCCTATACTCCCTAA-AATGAGGGAGCGAACCCGTT
1 GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAGTGAACCCGTT
13846 TTCCGAATAT
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
52 2 0.02
53 29 0.32
54 10 0.11
55 46 0.51
56 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (53 bp):
GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAGTGAACCCGTTGCA
Found at i:16024 original size:2 final size:2
Alignment explanation
Indices: 16017--16102 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
16007 TATAGAGTAC
16017 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
16059 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
16101 AT
1 AT
16103 TGTAATTATA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18215 original size:6 final size:6
Alignment explanation
Indices: 18204--18262 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
18194 AAATAACTTG
* * *
18204 AAAAGA AAAAGA TAAAGA AAATA-A AAAGGA ATAAA-A AGAAAAA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAA-AGA AAAAGA A-AAAGA A-AAAGA AAAAGA
18253 AAAAGA AAAA
1 AAAAGA AAAA
18263 AAATAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 38 0.88
7 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (6 bp):
AAAAGA
Found at i:18238 original size:10 final size:10
Alignment explanation
Indices: 18217--18280 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
18207 AGAAAAAGAT
18217 AAAGAAAATAA
1 AAAG-AAATAA
*
18228 AAAGGAATAA
1 AAAGAAATAA
*
18238 AAAGAAAAAA
1 AAAGAAATAA
*
18248 AAAGAAAAAGA
1 AAAGAAATA-A
*
18259 AAAAAAATAA
1 AAAGAAATAA
*
18269 TAAATAAATAA
1 -AAAGAAATAA
18280 A
1 A
18281 TATGAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
10 24 0.53
11 21 0.47
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (10 bp):
AAAGAAATAA
Found at i:18317 original size:5 final size:5
Alignment explanation
Indices: 18307--18369 Score: 53
Period size: 5 Copynumber: 12.6 Consensus size: 5
18297 GAAGATAAAG
*
18307 AAAAT AAAAT AAAAAT AAAA- AATAA- AAAAT AAAAT AAAGAG AAGAA-
1 AAAAT AAAAT -AAAAT AAAAT AA-AAT AAAAT AAAAT AAA-AT AA-AAT
18353 AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAA
18370 TCAGATAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
4 10 0.20
5 30 0.60
6 9 0.18
7 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:18324 original size:20 final size:19
Alignment explanation
Indices: 18209--18364 Score: 75
Period size: 20 Copynumber: 7.6 Consensus size: 19
18199 ACTTGAAAAG
*
18209 AAAAAGATAAAGAAAATAA
1 AAAAAAATAAAGAAAATAA
*
18228 AAAGGAATAA-AAAGAAAAAAA
1 AAA--AA-AATAAAGAAAATAA
* *
18249 AAGAAAAAGAAAAAAAATAA
1 AA-AAAAATAAAGAAAATAA
* * *
18269 TAAATAAATAAATATGAATAA
1 -AAAAAAATAAAGA-AAATAA
18290 ATGAAACGAAGATAAAGAAAATAA
1 A--AAA--AA-ATAAAGAAAATAA
18314 AATAAAAAT-AA-AAAATAAA
1 AA-AAAAATAAAGAAAAT-AA
* *
18333 AAATAAAATAAAGAGAAGAA
1 AAA-AAAATAAAGAAAATAA
18353 AAAATAAATAAA
1 AAAA-AAATAAA
18365 ATAAATCAGA
Statistics
Matches: 106, Mismatches: 13, Indels: 35
0.69 0.08 0.23
Matches are distributed among these distances:
18 6 0.06
19 17 0.16
20 36 0.34
21 26 0.25
22 5 0.05
23 2 0.02
24 8 0.08
25 6 0.06
ACGTcount: A:0.77, C:0.01, G:0.10, T:0.13
Consensus pattern (19 bp):
AAAAAAATAAAGAAAATAA
Found at i:18329 original size:7 final size:7
Alignment explanation
Indices: 18312--18340 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
18302 TAAAGAAAAT
18312 AAAAT-A
1 AAAATAA
18318 AAAATAA
1 AAAATAA
18325 AAAATAA
1 AAAATAA
18332 AAAATAA
1 AAAATAA
18339 AA
1 AA
18341 TAAAGAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:18330 original size:13 final size:12
Alignment explanation
Indices: 18301--18344 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
18291 TGAAACGAAG
18301 ATAAAGAAAATAAA
1 ATAAA-AAAA-AAA
18315 ATAAAAATAAAAA
1 ATAAAAA-AAAAA
*
18328 ATAAAAAATAAA
1 ATAAAAAAAAAA
18340 ATAAA
1 ATAAA
18345 GAGAAGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 9 0.32
13 12 0.43
14 7 0.25
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (12 bp):
ATAAAAAAAAAA
Found at i:18335 original size:25 final size:25
Alignment explanation
Indices: 18288--18369 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
18278 AAATATGAAT
* * * *
18288 AAATGAAACGAAGATAAAGAAAATA
1 AAATAAAAAGAAGAAAAAAAAAATA
*
18313 AAATAAAAATAA-AAAATAAAAAATA
1 AAATAAAAAGAAGAAAA-AAAAAATA
* *
18338 AAATAAAGAGAAGAAAAAATAAATA
1 AAATAAAAAGAAGAAAAAAAAAATA
18363 AAATAAA
1 AAATAAA
18370 TCAGATAAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
24 3 0.06
25 40 0.85
26 4 0.09
ACGTcount: A:0.77, C:0.01, G:0.09, T:0.13
Consensus pattern (25 bp):
AAATAAAAAGAAGAAAAAAAAAATA
Found at i:18379 original size:28 final size:26
Alignment explanation
Indices: 18298--18390 Score: 93
Period size: 25 Copynumber: 3.6 Consensus size: 26
18288 AAATGAAACG
* *
18298 AAGATAAAGAAAATAAAATAAAA-AT
1 AAGAAAAAAAAAATAAAATAAAAGAT
*
18323 AA-AAAATAAAAAATAAAAT-AAAGAG
1 AAGAAAA-AAAAAATAAAATAAAAGAT
*
18348 AAGAAAAAATAAATAAAATAAATCAGAT
1 AAGAAAAAAAAAATAAAATAAA--AGAT
*
18376 AAGAAAAAAATAATA
1 AAGAAAAAAAAAATA
18391 TTAAAGAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
24 6 0.11
25 27 0.49
26 6 0.11
28 16 0.29
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.15
Consensus pattern (26 bp):
AAGAAAAAAAAAATAAAATAAAAGAT
Found at i:18654 original size:27 final size:29
Alignment explanation
Indices: 18624--18686 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
18614 AACACTAAAA
18624 ATATAA-A-AAAT-AAATAAATATATATAT
1 ATATAATATAAATGAAA-AAATATATATAT
*
18651 ATATAATATATATGAAAAAATATATATA-
1 ATATAATATAAATGAAAAAATATATATAT
18679 ATAATAAT
1 AT-ATAAT
18687 TAATAATAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 6 0.19
28 3 0.10
29 19 0.61
30 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (29 bp):
ATATAATATAAATGAAAAAATATATATAT
Found at i:19771 original size:2 final size:2
Alignment explanation
Indices: 19764--19813 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
19754 ATAAAATTTA
19764 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19805 AT AT -T AT AT
1 AT AT AT AT AT
19814 GGACGAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20862 original size:22 final size:23
Alignment explanation
Indices: 20819--20863 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
20809 TGATTACAAA
20819 TATAAATAAAATTCATTCACATT
1 TATAAATAAAATTCATTCACATT
*
20842 TATAAATAAAATT-GTTCACATT
1 TATAAATAAAATTCATTCACATT
20864 CTTTGAGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (23 bp):
TATAAATAAAATTCATTCACATT
Found at i:23246 original size:16 final size:16
Alignment explanation
Indices: 23225--23276 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
23215 ACTAGTTAGA
23225 TTGAGAGATTGGGTGC
1 TTGAGAGATTGGGTGC
** **
23241 TTGAGA-A-TGCTTTA
1 TTGAGAGATTGGGTGC
23255 TTGAGAGATTGGGTGC
1 TTGAGAGATTGGGTGC
23271 TTGAGA
1 TTGAGA
23277 ATGGACCTTG
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 15 0.58
ACGTcount: A:0.23, C:0.06, G:0.37, T:0.35
Consensus pattern (16 bp):
TTGAGAGATTGGGTGC
Found at i:31712 original size:27 final size:27
Alignment explanation
Indices: 31658--31713 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
31648 CCGTCATCAC
* *
31658 CACTTTGAACTTGAAACTTCATAGCAT
1 CACTTTGAACTTGAAACTTCACAACAT
*
31685 CACTTTGAACTTGAAAGTTCACAACAT
1 CACTTTGAACTTGAAACTTCACAACAT
31712 CA
1 CA
31714 AGATCTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTTCACAACAT
Found at i:32329 original size:2 final size:2
Alignment explanation
Indices: 32324--32363 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
32314 TTCGTCTCAT
32324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32364 GTTTAAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32432 original size:39 final size:41
Alignment explanation
Indices: 32347--32451 Score: 130
Period size: 41 Copynumber: 2.6 Consensus size: 41
32337 ATATATATAT
*
32347 ATATATATATATATATAG-TTTAAAAACATTTTTAAAAAGAC
1 ATATATATA-ATATATAGTTTTTAAAACATTTTTAAAAAGAC
* *
32388 GTATATATAATATATAGTTTTTAAAACATTTTT-GAAA-AC
1 ATATATATAATATATAGTTTTTAAAACATTTTTAAAAAGAC
32427 ATATATAT--TATATAGTTTTTGAAAA
1 ATATATATAATATATAGTTTTT-AAAA
32452 TATATATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
37 12 0.21
38 4 0.07
39 9 0.16
40 11 0.19
41 22 0.38
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.43
Consensus pattern (41 bp):
ATATATATAATATATAGTTTTTAAAACATTTTTAAAAAGAC
Found at i:32460 original size:67 final size:67
Alignment explanation
Indices: 32389--32521 Score: 153
Period size: 67 Copynumber: 2.0 Consensus size: 67
32379 TAAAAAGACG
* *
32389 TATATATAAT-ATATAGTTTTTAAAACATTTTTGAAAACATATATATTATATA-GTTTTTGAAAA
1 TATATATAATAAT-TAGTTTTTAAAACATTTTAG-AAACATATATATTACATATGTTTTTGAAAA
32452 TATA
64 TATA
* ** * ***
32456 TATATATTATAATTTTTTTTTAAAATATTTTAGAAGTTTATATATTACATATGTTTTTGAAAATA
1 TATATATAATAATTAGTTTTTAAAACATTTTAGAAACATATATATTACATATGTTTTTGAAAATA
32521 T
66 T
32522 TTTTATTTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
66 14 0.25
67 39 0.71
68 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.50
Consensus pattern (67 bp):
TATATATAATAATTAGTTTTTAAAACATTTTAGAAACATATATATTACATATGTTTTTGAAAATA
TA
Found at i:32466 original size:26 final size:26
Alignment explanation
Indices: 32415--32472 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
32405 TTTTTAAAAC
32415 ATTTTTGAAAACATATATATTATATA
1 ATTTTTGAAAACATATATATTATATA
* *
32441 GTTTTTGAAAATATATATA-TATTATA
1 ATTTTTGAAAACATATATATTA-TATA
32467 ATTTTT
1 ATTTTT
32473 TTTTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (26 bp):
ATTTTTGAAAACATATATATTATATA
Found at i:32473 original size:28 final size:29
Alignment explanation
Indices: 32427--32483 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
32417 TTTTGAAAAC
32427 ATATATATTATA-TAGTTTTTGAAAATAT
1 ATATATATTATATTAGTTTTTGAAAATAT
* *
32455 ATATATATTATAATT-TTTTTTTAAAATAT
1 ATATATATTAT-ATTAGTTTTTGAAAATAT
32484 TTTAGAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
29 13 0.52
30 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
ATATATATTATATTAGTTTTTGAAAATAT
Found at i:32530 original size:6 final size:6
Alignment explanation
Indices: 32519--32599 Score: 53
Period size: 6 Copynumber: 13.2 Consensus size: 6
32509 TTTTTGAAAA
* *
32519 TATTTT TATTTT TATTATT TATTAT TATTAT TA-TTT TA-TTT TATTTAT
1 TATTTT TATTTT TATT-TT TATTTT TATTTT TATTTT TATTTT TATTT-T
*
32567 T-TTATGT TA-TTT TATTCCT TATTTT TATGTTT T
1 TATT-T-T TATTTT TATT-TT TATTTT TAT-TTT T
32600 GTTTGTTGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
5 12 0.19
6 29 0.47
7 21 0.34
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (6 bp):
TATTTT
Found at i:32541 original size:19 final size:19
Alignment explanation
Indices: 32519--32579 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
32509 TTTTTGAAAA
32519 TATTTTTATTTTTATTATT
1 TATTTTTATTTTTATTATT
* *
32538 TATTATTATTATTA-T-TT
1 TATTTTTATTTTTATTATT
32555 TA-TTTTATTTATT-TTATGT
1 TATTTTTATTT-TTATTAT-T
32574 TATTTT
1 TATTTT
32580 ATTCCTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
16 6 0.18
17 7 0.21
18 2 0.06
19 15 0.45
20 3 0.09
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (19 bp):
TATTTTTATTTTTATTATT
Found at i:32545 original size:10 final size:9
Alignment explanation
Indices: 32522--32582 Score: 65
Period size: 9 Copynumber: 6.8 Consensus size: 9
32512 TTGAAAATAT
32522 TTTTATTT-
1 TTTTATTTA
32530 TTATTATTTA
1 TT-TTATTTA
32540 TTATTA-TTA
1 TT-TTATTTA
*
32549 TTAT-TTTA
1 TTTTATTTA
32557 TTTTATTTA
1 TTTTATTTA
32566 TTTTATGTTA
1 TTTTAT-TTA
32576 TTTTATT
1 TTTTATT
32583 CCTTATTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
8 9 0.20
9 22 0.48
10 15 0.33
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:32549 original size:16 final size:16
Alignment explanation
Indices: 32519--32563 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
32509 TTTTTGAAAA
*
32519 TATTT-TTATTTTTAT
1 TATTTATTATTATTAT
32534 TATTTATTATTATTAT
1 TATTTATTATTATTAT
32550 TATTTTATT-TTATT
1 TA-TTTATTATTATT
32564 TATTTTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 16 0.59
17 6 0.22
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTTATTATTATTAT
Found at i:35639 original size:19 final size:19
Alignment explanation
Indices: 35605--35649 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
35595 ATTTAGACAT
35605 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
35623 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
35642 TTTGCATT
1 TTTGCATT
35650 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:39540 original size:165 final size:165
Alignment explanation
Indices: 39041--39816 Score: 1083
Period size: 165 Copynumber: 4.7 Consensus size: 165
39031 TTTTTAAACA
* * *
39041 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGGGTTCGATTATAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
* * * * * * *
39106 TCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAA
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCCG-CGACCAAAA
*
39170 GACCTTTGAGTTCGACTACGCTCAGCTCAACGGCAC
130 GACCTTCGAGTTCGACTACGCTCAGCTCAACGGCAC
** * **
39206 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTATGC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
* * * * * * ** * * * *
39271 TCAGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTATAGAAGGGTTGTCTGCCAACAAAAG
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCCGCGACCAAAAG
*
39335 ACCTTTGAGTTCGACTACGCTCAGCTCAACGGCAC
131 ACCTTCGAGTTCGACTACGCTCAGCTCAACGGCAC
* * *
39370 ATCATTTCCAGTATAGCTTAAGTCGAGAAGGGCTATCTGTCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
*
39435 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCCGTGACCAAAAG
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCCGCGACCAAAAG
39500 ACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCAC
131 ACCTTCGAGTTCGACTACGCTCAGCT-CAACGGCAC
39535 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
* * *
39600 TCAACTTCGAGGTCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCCGTGACCAAAAG
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCCGCGACCAAAAG
39665 ACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCAC
131 ACCTTCGAGTTCGACTACGCTCAGCT-CAACGGCAC
*
39700 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGTCAAAGACCCCCGAGTTCGATTACAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
* * * * * * * * *
39765 TCAACTTCGAGGTCATATCGTTTACAACATAGCCCAAGGCAAGAAGAGTTAT
66 TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
39817 TTGTCAATAA
Statistics
Matches: 557, Mismatches: 51, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
163 3 0.01
164 142 0.25
165 409 0.73
166 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (165 bp):
ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACAC
TCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCCGCGACCAAAAG
ACCTTCGAGTTCGACTACGCTCAGCTCAACGGCAC
Found at i:40334 original size:2 final size:2
Alignment explanation
Indices: 40329--40385 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
40319 TTTTCGTCTC
40329 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
40371 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
40386 GTTTAAAAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40425 original size:39 final size:39
Alignment explanation
Indices: 40369--40459 Score: 130
Period size: 39 Copynumber: 2.3 Consensus size: 39
40359 ATATATATAT
*
40369 ATATATATATATATATAG-TTTAAAAACATTTTTAAAAAG
1 ATATATATATATATATAGTTTTAAAAACA-TTTTAAAAAC
* * *
40408 ATGTATATATATATATAGTTTTTAAAACATTTTGAAAAC
1 ATATATATATATATATAGTTTTAAAAACATTTTAAAAAC
40447 ATATATATATATA
1 ATATATATATATA
40460 GTTTTTTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.80
40 9 0.20
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (39 bp):
ATATATATATATATATAGTTTTAAAAACATTTTAAAAAC
Found at i:40469 original size:26 final size:24
Alignment explanation
Indices: 40437--40499 Score: 85
Period size: 23 Copynumber: 2.6 Consensus size: 24
40427 TTTTAAAACA
40437 TTTTGAAAACATATATATATATAGTT
1 TTTTGAAAA-ATATATAT-TATAGTT
40463 TTTTG-AAAATATATATTATAGTT
1 TTTTGAAAAATATATATTATAGTT
*
40486 TTTTTAAAAA-ATAT
1 TTTTGAAAAATATAT
40500 TTTAGAAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
23 15 0.43
24 12 0.34
25 3 0.09
26 5 0.14
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
TTTTGAAAAATATATATTATAGTT
Found at i:40548 original size:3 final size:3
Alignment explanation
Indices: 40542--40574 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
40532 AAATATTTTT
40542 TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40575 TATTTTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:40552 original size:14 final size:14
Alignment explanation
Indices: 40535--40603 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 14
40525 TTTTTGAAAA
40535 TATTTTTTTATTAT
1 TATTTTTTTATTAT
*
40549 TATTATTATTATTATTT
1 TATT-TTTTTATTA--T
40566 TATTTTATTTATT-T
1 TATTTT-TTTATTAT
*
40580 TATGTTATTTTATTCCT
1 TAT-TT-TTTTATT-AT
40597 TATTTTT
1 TATTTTT
40604 ATGTTTTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
14 8 0.18
15 18 0.40
16 5 0.11
17 14 0.31
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (14 bp):
TATTTTTTTATTAT
Found at i:40576 original size:9 final size:9
Alignment explanation
Indices: 40535--40593 Score: 61
Period size: 9 Copynumber: 6.4 Consensus size: 9
40525 TTTTTGAAAA
40535 TATTT-TTT
1 TATTTATTT
40543 TA-TTATTAT
1 TATTTATT-T
40552 TA-TTATTAT
1 TATTTATT-T
40561 TATTTTATTT
1 TA-TTTATTT
40571 TATTTATTT
1 TATTTATTT
40580 TATGTTATTT
1 TAT-TTATTT
40590 TATT
1 TATT
40594 CCTTATTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
7 2 0.04
8 4 0.09
9 23 0.50
10 12 0.26
11 5 0.11
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (9 bp):
TATTTATTT
Found at i:46188 original size:30 final size:30
Alignment explanation
Indices: 46152--46217 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
46142 CTCCTTGTGG
46152 GCTTGCACGCTTGGGCCTCCCACCGAGTCT
1 GCTTGCACGCTTGGGCCTCCCACCGAGTCT
46182 GCTTGCACGCTTGGGCCTCCCACCGAGTCT
1 GCTTGCACGCTTGGGCCTCCCACCGAGTCT
46212 GCTTGC
1 GCTTGC
46218 TGGGTTAGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.09, C:0.39, G:0.27, T:0.24
Consensus pattern (30 bp):
GCTTGCACGCTTGGGCCTCCCACCGAGTCT
Found at i:46382 original size:16 final size:16
Alignment explanation
Indices: 46363--46396 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
46353 AACTAAAAAT
46363 AAAAAAT-ATGTTTTAA
1 AAAAAATCAT-TTTTAA
46379 AAAAAATCATTTTTAA
1 AAAAAATCATTTTTAA
46395 AA
1 AA
46397 CTATATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (16 bp):
AAAAAATCATTTTTAA
Found at i:46480 original size:34 final size:33
Alignment explanation
Indices: 46404--46554 Score: 194
Period size: 34 Copynumber: 4.3 Consensus size: 33
46394 AAACTATATA
*
46404 ATATATATATTTTCAAAAATTATTTTCAAAACTAT
1 ATATATATATTTTCAAAAATTGTTTTCAAAAC--T
46439 ATAATATATATGTTTTCAAAAATTGATTTTCAAAACT
1 AT-ATATATA--TTTTCAAAAATTG-TTTTCAAAACT
*
46476 ATATAATATATTTTCAAAAATCGTTTTCAAAACT
1 ATAT-ATATATTTTCAAAAATTGTTTTCAAAACT
*
46510 ATATAATATATTTTGAAAAATTGTTTTCAAAACT
1 ATAT-ATATATTTTCAAAAATTGTTTTCAAAACT
46544 ATAATATATAT
1 AT-ATATATAT
46555 ATATATATAT
Statistics
Matches: 106, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
34 51 0.48
35 16 0.15
36 9 0.08
37 8 0.08
38 12 0.11
39 10 0.09
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (33 bp):
ATATATATATTTTCAAAAATTGTTTTCAAAACT
Found at i:46509 original size:73 final size:68
Alignment explanation
Indices: 46404--46556 Score: 209
Period size: 73 Copynumber: 2.2 Consensus size: 68
46394 AAACTATATA
*
46404 ATAT-ATATATTTTCAAAAATTATTTTCAAAACTATATAATATATATGTTTTCAAAAATTGATTT
1 ATATAATATATTTTCAAAAATCATTTTCAAAACTATAT-A-ATATA--TTTTCAAAAATTG-TTT
46468 TCAAAACT
61 TCAAAACT
* *
46476 ATATAATATATTTTCAAAAATCGTTTTCAAAACTATATAATATATTTTGAAAAATTGTTTTCAAA
1 ATATAATATATTTTCAAAAATCATTTTCAAAACTATATAATATATTTTCAAAAATTGTTTTCAAA
46541 ACT
66 ACT
46544 ATAATATATATAT
1 AT-ATA-ATATAT
46557 ATATATATAT
Statistics
Matches: 75, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
68 13 0.17
69 15 0.20
70 6 0.08
71 5 0.07
72 5 0.07
73 31 0.41
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (68 bp):
ATATAATATATTTTCAAAAATCATTTTCAAAACTATATAATATATTTTCAAAAATTGTTTTCAAA
ACT
Found at i:46554 original size:2 final size:2
Alignment explanation
Indices: 46543--46608 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
46533 TTTTCAAAAC
46543 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46584 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
46609 CTTCAAAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46636 original size:38 final size:36
Alignment explanation
Indices: 46592--46760 Score: 180
Period size: 40 Copynumber: 4.4 Consensus size: 36
46582 TATATATATA
46592 TATATATATATATATATCTTCAAAAAAATGTTTTCAAAAC
1 TATATAT-TATATATATCTTC---AAAATGTTTTCAAAAC
* *
46632 TATATATTATATATATGTTTTCAAAATGTTTTAAAAAAAC
1 TATATATTATATATA--TCTTCAAAATGTTTT--CAAAAC
* *
46672 TATATATTATATATATTTTCAAAATATTTTCAAACAC
1 TATATATTATATATATCTTCAAAATGTTTTCAAA-AC
46709 TATATATTATATATATGCTTTCAAAATGTTTTCAAAA-
1 TATATATTATATATAT-C-TTCAAAATGTTTTCAAAAC
*
46746 -ACATATTATATATAT
1 TATATATTATATATAT
46761 ATATATATAT
Statistics
Matches: 115, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
36 17 0.15
37 18 0.16
38 25 0.22
39 24 0.21
40 27 0.23
41 4 0.03
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (36 bp):
TATATATTATATATATCTTCAAAATGTTTTCAAAAC
Found at i:46715 original size:77 final size:81
Alignment explanation
Indices: 46592--46810 Score: 268
Period size: 77 Copynumber: 2.7 Consensus size: 81
46582 TATATATATA
* *
46592 TATATATATATATATATCTTCAAAAAAATGTTTTCAAAACTATATATTATATATATGTTTTCAAA
1 TATATATATATATATATTTTC--AAAAATGTTTTCAAAACTATATATTATATATATGCTTTCAAA
46657 ATGTTTT-AAAAA-A-AC
64 ATGTTTTCAAAAACATAC
*
46672 TATATAT-TATATATATTTTC-AAAATATTTTCAAACACTATATATTATATATATGCTTTCAAAA
1 TATATATATATATATATTTTCAAAAATGTTTTCAAA-ACTATATATTATATATATGCTTTCAAAA
*
46735 TGTTTTCAAAAACATAT
65 TGTTTTCAAAAACATAC
* * *
46752 TATATATATATATATATATATCTAAAATGTTTTAAAAAAACTATATATATTATATATAT
1 TATATATATATATATAT-TTTCAAAAATGTTTT--CAAAAC--TATATATTATATATAT
46811 ATATATTCAA
Statistics
Matches: 121, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
76 13 0.11
77 33 0.27
78 5 0.04
79 13 0.11
80 15 0.12
81 9 0.07
82 3 0.02
83 9 0.07
84 2 0.02
85 3 0.02
86 16 0.13
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (81 bp):
TATATATATATATATATTTTCAAAAATGTTTTCAAAACTATATATTATATATATGCTTTCAAAAT
GTTTTCAAAAACATAC
Found at i:47423 original size:20 final size:22
Alignment explanation
Indices: 47386--47433 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
47376 AATTAAATCC
47386 ATATTTTTATTGAATAAAAATA
1 ATATTTTTATTGAATAAAAATA
*
47408 ATATTTTT-TT-AATAAATATA
1 ATATTTTTATTGAATAAAAATA
*
47428 CTATTT
1 ATATTT
47434 CGTGTTGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 14 0.58
21 2 0.08
22 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTGAATAAAAATA
Found at i:49995 original size:26 final size:26
Alignment explanation
Indices: 49958--50027 Score: 122
Period size: 26 Copynumber: 2.7 Consensus size: 26
49948 GTTTTTATCC
49958 CTTAAAATTTTATAAGTTATTTCCTA
1 CTTAAAATTTTATAAGTTATTTCCTA
* *
49984 TTTAAAATTTTATAAGTTATTTTCTA
1 CTTAAAATTTTATAAGTTATTTCCTA
50010 CTTAAAATTTTATAAGTT
1 CTTAAAATTTTATAAGTT
50028 CACCCCTCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (26 bp):
CTTAAAATTTTATAAGTTATTTCCTA
Found at i:50735 original size:58 final size:59
Alignment explanation
Indices: 50634--50748 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 59
50624 TTGACTATTT
* * * *
50634 GGCGTTGTTTTATTAAGTCATTCGATTATTAAAAGTTAAAAAAT-TATCCCTCGACTATA
1 GGCGTTGCTTTATTAAGTCATCCGACTATTAAAAGTTAAAAAATATA-CACTCGACTATA
* *
50693 GGCGTTGCTTTGTTAAGTC-TCCGACTATTAAAAGTTACAAAATATACACTCGACTA
1 GGCGTTGCTTTATTAAGTCATCCGACTATTAAAAGTTAAAAAATATACACTCGACTA
50749 ATCATATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
58 30 0.61
59 19 0.39
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.36
Consensus pattern (59 bp):
GGCGTTGCTTTATTAAGTCATCCGACTATTAAAAGTTAAAAAATATACACTCGACTATA
Found at i:53913 original size:2 final size:2
Alignment explanation
Indices: 53906--53931 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53896 AGGTCATTCG
53906 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
53932 GAAAATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54572 original size:21 final size:22
Alignment explanation
Indices: 54532--54573 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
54522 ATAATAATAA
54532 ATATTACATATAATGCTCCTATT
1 ATATTACATATAAT-CTCCTATT
*
54555 ATATTATATATAAT-TCCTA
1 ATATTACATATAATCTCCTA
54574 CTACAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATTACATATAATCTCCTATT
Found at i:67824 original size:2 final size:2
Alignment explanation
Indices: 67739--67812 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
67729 TCATATAGTT
67739 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67781 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67813 GAGGTTATAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:68211 original size:14 final size:14
Alignment explanation
Indices: 68189--68239 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
68179 TCCATTTACA
68189 TTAGGGTTTAATGT
1 TTAGGGTTTAATGT
*
68203 TTAGTGTTT-ATGGT
1 TTAGGGTTTAAT-GT
** *
68217 TTAAAGTTTAAAGT
1 TTAGGGTTTAATGT
68231 TTAGGGTTT
1 TTAGGGTTT
68240 CTATAAACTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
13 2 0.07
14 26 0.90
15 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (14 bp):
TTAGGGTTTAATGT
Found at i:68232 original size:21 final size:21
Alignment explanation
Indices: 68189--68239 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
68179 TCCATTTACA
* **
68189 TTAGGGTTTAATGTTTAGTGT
1 TTAGGGTTTAAAGTTTAAAGT
*
68210 TTATGGTTTAAAGTTTAAAGT
1 TTAGGGTTTAAAGTTTAAAGT
68231 TTAGGGTTT
1 TTAGGGTTT
68240 CTATAAACTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (21 bp):
TTAGGGTTTAAAGTTTAAAGT
Found at i:68338 original size:19 final size:19
Alignment explanation
Indices: 68314--68374 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
68304 TAATTTACTT
68314 TATATAGTTTATATATATA
1 TATATAGTTTATATATATA
68333 TATATAGTTTATATATACTA
1 TATATAGTTTATATATA-TA
* * *
68353 TACATGGTTTATATATACA
1 TATATAGTTTATATATATA
68372 TAT
1 TAT
68375 TATATAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 20 0.54
20 17 0.46
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (19 bp):
TATATAGTTTATATATATA
Found at i:68362 original size:20 final size:20
Alignment explanation
Indices: 68317--68370 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
68307 TTTACTTTAT
*
68317 ATAGTTTATATATA-TATAT
1 ATAGTTTATATATACTATAC
68336 ATAGTTTATATATACTATAC
1 ATAGTTTATATATACTATAC
*
68356 ATGGTTTATATATAC
1 ATAGTTTATATATAC
68371 ATATTATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (20 bp):
ATAGTTTATATATACTATAC
Found at i:68697 original size:21 final size:21
Alignment explanation
Indices: 68665--68717 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
68655 TTACATTAGG
*
68665 GTTT-GTGATTTAGGGTTTAAT
1 GTTTAGTG-TTTAGGGTTTAAA
*
68686 GTTTAGTGTTTATGGTTTAAA
1 GTTTAGTGTTTAGGGTTTAAA
*
68707 GTTTAGAGTTT
1 GTTTAGTGTTT
68718 CTATAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (21 bp):
GTTTAGTGTTTAGGGTTTAAA
Found at i:68806 original size:2 final size:2
Alignment explanation
Indices: 68801--68851 Score: 50
Period size: 2 Copynumber: 25.0 Consensus size: 2
68791 TTATATAGTT
** *
68801 TA TA TA TA TA TA TA TA TA GG T- TA TA TA TA TA TA TA GTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
68843 TA TA CTA TA
1 TA TA -TA TA
68852 CATGGTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
1 1 0.02
2 37 0.90
3 3 0.07
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:68814 original size:17 final size:17
Alignment explanation
Indices: 68805--68851 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
68795 ATAGTTTATA
68805 TATATATATATATAGGT
1 TATATATATATATAGGT
*
68822 TATATATATATATAGTT
1 TATATATATATATAGGT
68839 TATATATACTATA
1 TATATATA-TATA
68852 CATGGTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (17 bp):
TATATATATATATAGGT
Found at i:68846 original size:21 final size:21
Alignment explanation
Indices: 68792--68835 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
68782 TAATTTACTT
*
68792 TATATAGTTTATATATATATA
1 TATATAGGTTATATATATATA
68813 TATATAGGTTATATATATATA
1 TATATAGGTTATATATATATA
68834 TA
1 TA
68836 GTTTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TATATAGGTTATATATATATA
Found at i:68870 original size:497 final size:497
Alignment explanation
Indices: 68325--70169 Score: 2616
Period size: 495 Copynumber: 3.6 Consensus size: 497
68315 ATATAGTTTA
*
68325 TATATATATATATAGTTTATATATACTATACATGGTTTATATATACATATTATATAAAATTATTT
1 TATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATTATTT
68390 AATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAA
66 AATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAA
*
68455 TTAGTATGTCACATTGCATATTATTTGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTT
131 TTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTT
*
68520 GCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCTCATTTATTTTGTTGTT
196 GCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTT
*
68585 ATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCATTATATATATACATTAGTGTTAG
261 ATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTATATATATACATTAGTGTTAG
68650 TCCATTTACATTAGGGTTTGTGATTTAGGGTTTAATGTTTAGTGTTTATGGTTTAAAGTTTAGAG
326 TCCATTTACATTAGGGTTTGTGATTTAGGGTTTAATGTTTAGTGTTTATGGTTTAAAGTTTAGAG
68715 TTTCTATAAACTATATAATTTATTACTTTATATAGTTTATGCATAATGTTTCTATAAACTATATA
391 TTTCTATAAACTATATAATTTATTACTTTATATAGTTTATGCATAATGTTTCTATAAACTATATA
68780 AGTAATTTACTTTATATAGTTTATATATATATATATATAGGT
456 AGTAATTTACTTTATATAGTTTATATATATATATATATAGGT
68822 TATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATT-TAT
1 TATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATTAT-T
68886 TAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATA
65 TAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATA
*
68951 ATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATTTCATATTAATTTCATT
130 ATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATT
69016 TGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGT
195 TGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGT
* * *
69081 TATGAATAAGTAATAATAAAACTAAAAAATAAGTCCATTCGCATTAGAGCTAGTCCATTTACATT
260 TATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATT--A--TA-T--ATATACATT
* * * * * ** * *** *
69146 AATTTACATAGGCCCA-ATACATAAGTCCACTCTT-TTA-TTACAAATATATATGCATTAGTGCT
318 AGTGT---TA-GTCCATTTACATTAG---GGT-TTGTGATTTA-GGGT-T-TA---A-T-GT-TT
* * * * * * * *
69208 AGTCCATTTATATTAGGGTTTAATA-TTTAGTGTTTATGGTTTAAAGTTTA-AAGTTTA-AAGTT
366 AGT---GTT-TA-T--GGTTTAA-AGTTTAGAG-TT-T-CTATAAACTATATAA-TTTATTACTT
* * * * * *
69270 TAGGGTTTAGGGTTTCTATGAACTATATAATTTATTACTTTATA-TAGTTTATGCATAATGTT--
419 TA---TATA--G-TT-TATG--C---ATAATGT-TT-CTATAAACTA-TATAAG--TAAT-TTAC
* * * * * * *
69332 TCTATAAACTATATAAGTAATTTACTTTATATAGTTT
466 TTTATATAGTTTAT-A-T-ATATA-TATATATAG-GT
* *
69369 ATATATATATATATAGTTTATATATACTATGCATGGTTTATATATACATATTATATAAAATTATT
1 -TATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATTATT
69434 TAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATA
65 TAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATA
**
69499 ATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTCTTACATGTCATATTAATTTCATT
130 ATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATT
*
69564 TTCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGT
195 TGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGT
*
69629 TATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCATTATATATATACATTAGTGTTA
260 TATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTATATATATACATTAGTGTTA
69694 GTCCATTTACATTAGGGTTTGTGATTTAGGGTTTAATGTTTAGTGTTTATGGTTTAAAGTTTAGA
325 GTCCATTTACATTAGGGTTTGTGATTTAGGGTTTAATGTTTAGTGTTTATGGTTTAAAGTTTAGA
69759 GTTTCTATAAACTATATAATTTATTACTTTATATAGTTTATGCATAATGTTTCTATAAACTATAT
390 GTTTCTATAAACTATATAATTTATTACTTTATATAGTTTATGCATAATGTTTCTATAAACTATAT
69824 AAGTAATTTACTTTATATAGTTTATATATATATATATATAGG-
455 AAGTAATTTACTTTATATAGTTTATATATATATATATATAGGT
69866 T-TATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATTATTT
1 TATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATTATTT
69930 AATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAA
66 AATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAA
*
69995 TTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATTTCATATTAATTTCATTT
131 TTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTT
70060 GCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTT
196 GCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTT
*
70125 ATGAATAAGTAATAATAAAACCAAAAAATAAGTTCATTTGCATTA
261 ATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTA
70170 GTGTTGTCCA
Statistics
Matches: 1185, Mismatches: 92, Indels: 144
0.83 0.06 0.10
Matches are distributed among these distances:
495 295 0.25
496 2 0.00
497 295 0.25
499 9 0.01
500 4 0.00
501 5 0.00
502 6 0.01
503 10 0.01
504 20 0.02
505 4 0.00
506 6 0.01
507 9 0.01
508 4 0.00
509 4 0.00
510 4 0.00
511 7 0.01
512 4 0.00
513 1 0.00
515 4 0.00
516 1 0.00
517 14 0.01
518 12 0.01
519 3 0.00
520 13 0.01
521 2 0.00
522 3 0.00
523 3 0.00
524 2 0.00
525 13 0.01
526 3 0.00
527 12 0.01
528 14 0.01
529 1 0.00
530 4 0.00
532 1 0.00
533 4 0.00
534 7 0.01
535 4 0.00
536 4 0.00
537 4 0.00
538 9 0.01
539 6 0.01
540 4 0.00
541 20 0.02
542 10 0.01
543 6 0.01
544 5 0.00
545 4 0.00
546 9 0.01
547 1 0.00
548 293 0.25
549 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.44
Consensus pattern (497 bp):
TATATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATTATTT
AATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAA
TTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTT
GCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTT
ATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTATATATATACATTAGTGTTAG
TCCATTTACATTAGGGTTTGTGATTTAGGGTTTAATGTTTAGTGTTTATGGTTTAAAGTTTAGAG
TTTCTATAAACTATATAATTTATTACTTTATATAGTTTATGCATAATGTTTCTATAAACTATATA
AGTAATTTACTTTATATAGTTTATATATATATATATATAGGT
Found at i:69256 original size:7 final size:7
Alignment explanation
Indices: 69246--69271 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
69236 AGTGTTTATG
69246 GTTTAAA
1 GTTTAAA
69253 GTTTAAA
1 GTTTAAA
69260 GTTTAAA
1 GTTTAAA
69267 GTTTA
1 GTTTA
69272 GGGTTTAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (7 bp):
GTTTAAA
Found at i:69256 original size:14 final size:14
Alignment explanation
Indices: 69239--69278 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
69229 AATATTTAGT
*
69239 GTTTATGGTTTAAA
1 GTTTAAGGTTTAAA
*
69253 GTTTAAAGTTTAAA
1 GTTTAAGGTTTAAA
*
69267 GTTTAGGGTTTA
1 GTTTAAGGTTTA
69279 GGGTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
GTTTAAGGTTTAAA
Found at i:69409 original size:20 final size:20
Alignment explanation
Indices: 69362--69415 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
69352 TTTACTTTAT
*
69362 ATAGTTTATATATA-TATAT
1 ATAGTTTATATATACTATAC
*
69381 ATAGTTTATATATACTATGC
1 ATAGTTTATATATACTATAC
*
69401 ATGGTTTATATATAC
1 ATAGTTTATATATAC
69416 ATATTATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (20 bp):
ATAGTTTATATATACTATAC
Found at i:69430 original size:548 final size:519
Alignment explanation
Indices: 67765--70429 Score: 2727
Period size: 497 Copynumber: 5.1 Consensus size: 519
67755 TATATATATA
* * * * *
67765 TATATA-TATATATA-TATATATATATATATATATATATATATATATATAGAGGTTATATAT-CT
1 TATATAGTTTATATAGTTTATATATATATATATATAGATATATATATATATAGTTTATATATACT
67827 ATACATGGTTTATACATACATATTATAT--AA-TA-TT-AT----TTAATAAAATTATTTAAATG
66 ATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATG
67883 TAAATTA-ACTAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATAT
131 TAAATTATA-TAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATAT
* *
67947 GGTTCATAAATAGTAGTACATGTCATATTAATTTCAATTGCATAATTAGTATTTTAGTTGCATGT
195 GGTTCATAAATAGTAGTACATTTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGT
* *
68012 TAGGTTAATTCACATTAATAACCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACTAAAA
260 TAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAA
*
68077 AATAAGTCTATTTGCATTAGAGCTAGTCCATTTACATTAGTTTACATAGGCCCAATACATAAGCC
325 AATAAGTCCATTTGCATTAGA-CTAGTCCATTTACATTAGTTTACATA-GCCCAATACATAAG-C
*
68142 CACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTACATTAGGG-TT-TA---A-T
387 CACTCTTTTATTACAAATATATATGCATTAGTGCTAGT-CATTTATATTAGGGTTTATATTTAGT
*
68201 GTTTAGTGTTTAT-GGTTTAAAGTTT-AA----A-GTTTAGGGTTTCTATAAACTATATAATTTA
451 GTTTA-TGTTTATAAGTTTAAAGTTTAAAGTTTAGGTTTAGGGTTTCTATAAACTATATAA-TTA
68259 TTACTT
514 TTACTT
68265 TATATAGTTTATGCATAATGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATAT
1 TATATAGTTTAT--AT-A-G--T-T-T--A-TATAT-A-T-A--TA---TATATAG---ATATAT
*
68330 ATATATATAGTTTATATATACTATACATGGTTTATATATACATATTATATAAAATTATTTAATAA
44 ATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAA
68395 AATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGT
109 AATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGT
* *
68460 ATGTCACATTGCATATTATTTGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATA
174 ATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATTTCATATTAATTTCATTTGCATA
*
68525 ATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCTCATTTATTTTGTTGTTATGAA
239 ATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAA
* * *
68590 TAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCATT--A-TA-T--ATATACATTAGTGT--
304 TAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTAGACTAGTCCATTTACATTAGTTTAC
* * * ** * *** * * * **
68647 -TAGTCCATTTACATTAG--GGT-TTGTGATTTA-GGGTTTA-ATG-TTTAGTGTTTA-TGGTTT
369 ATAGCCCA-ATACATAAGCCACTCTT-TTA-TTACAAATATATATGCATTAGTG-CTAGTCATTT
* * * ** * * * * * * * * ** **
68704 AAAGTTTAGAGTTTCTATAAACTATATA-ATTTATTACTTT--A---TATAGTTTATGCATAATG
430 ATA--TTAGGGTTTATATTTAGTGTTTATGTTTATAAGTTTAAAGTTTAAAGTTTAGGTTTAGGG
*
68763 TTTCTATAAACTATATAAGTA--A---
493 TTTCTATAAACTATATAATTATTACTT
* *
68785 T-T-TACTTTATATAGTTTATATATATATATATATAGGTTATATATATATATAGTTTATATATAC
1 TATATAGTTTATATAGTTTATATATATATATATATA-GATATATATATATATAGTTTATATATAC
68848 TATACATGGTTTATACATACATATTATATAAAATT-TATTAATAAAATTAATAAAATTATTTAAA
65 TATACATGGTTTATACATACATATTATATAAAATTAT-TTAATAAAATTAATAAAATTATTTAAA
68912 TGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATA
129 TGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATA
68977 TGGTTCATAAATAGTAGTACATTTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATG
194 TGGTTCATAAATAGTAGTACATTTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATG
*
69042 TTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACTAAA
259 TTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAA
* *
69107 AAATAAGTCCATTCGCATTAGAGCTAGTCCATTTACATTAATTTACATAGGCCCAATACATAAGT
324 AAATAAGTCCATTTGCATTAGA-CTAGTCCATTTACATTAGTTTACATA-GCCCAATACATAAG-
69172 CCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTAATATTTA
386 CCACTCTTTTATTACAAATATATATGCATTAGTGCTAGT-CATTTATATTAGGGTTT-ATATTTA
*
69237 GTGTTTATGGTTTA-AAGTTTAAAGTTTAAAGTTTAGGGTTTAGGGTTTCTATGAACTATATAAT
449 GTGTTTAT-GTTTATAAGTTTAAAGTTTAAAGTTTA-GGTTTAGGGTTTCTATAAACTATATAA-
69301 TTATTACTT
511 TTATTACTT
69310 TATATAGTTTATGCATAATGTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATAT
1 TATATAGTTTAT--AT-A-G--T-T-T--A-TATAT-A-T-A--TA---TATATAG---ATATAT
* *
69375 ATATATATAGTTTATATATACTATGCATGGTTTATATATACATATTATATAAAATTATTTAATAA
44 ATATATATAGTTTATATATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAA
69440 AATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGT
109 AATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGT
** * *
69505 ATGTCACATTGCATATTATATGGTTCATAAATAGTCTTACATGTCATATTAATTTCATTTTCATA
174 ATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATTTCATATTAATTTCATTTGCATA
69570 ATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAA
239 ATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAA
* * *
69635 TAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCATT--A-TA-T--ATATACATTAGTGT--
304 TAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTAGACTAGTCCATTTACATTAGTTTAC
* * * ** * *** * * * **
69692 -TAGTCCATTTACATTAG--GGT-TTGTGATTTA-GGGTTTA-ATG-TTTAGTGTTTA-TGGTTT
369 ATAGCCCA-ATACATAAGCCACTCTT-TTA-TTACAAATATATATGCATTAGTG-CTAGTCATTT
* * * ** * * * * * * * * ** **
69749 AAAGTTTAGAGTTTCTATAAACTATATA-ATTTATTACTTT--A---TATAGTTTATGCATAATG
430 ATA--TTAGGGTTTATATTTAGTGTTTATGTTTATAAGTTTAAAGTTTAAAGTTTAGGTTTAGGG
*
69808 TTTCTATAAACTATATAAGTA--A---
493 TTTCTATAAACTATATAATTATTACTT
* *
69830 T-T-TACTTTATATAGTTTATATATATATATATATAGGT-TATATATATATAGTTTATATATACT
1 TATATAGTTTATATAGTTTATATATATATATATATAGATATATATATATATAGTTTATATATACT
69892 ATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATG
66 ATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATG
69957 TAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATG
131 TAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATG
70022 GTTCATAAATAGTAGTACATTTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTT
196 GTTCATAAATAGTAGTACATTTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTT
70087 AGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAA
261 AGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAA
* *
70152 ATAAGTTCATTTGCATTAGTGTTGTCCATTTACATTAGTGCTGTCCATTTATATTAGTTTACATA
326 ATAAGTCCATTTGCATTA-----G-------AC--TA-----GTCCATTTACATTAGTTTACAT-
* *
70217 AACCCAATACATAAACCCACTCTTTTATTACAAATATATATGCATTAGTGCTAGTTCATTTATAT
371 AGCCCAATACAT-AAGCCACTCTTTTATTACAAATATATATGCATTAGTGCTAG-TCATTTATAT
* * *
70282 TAGGGTTTATGATTTAGGGTTTAATGTTTAGTATTTATGGTTTAAAGTTTAGAGTTTATGATTTA
434 TAGGGTTTAT-ATTTAGTGTTT-ATGTTTA-TA---A--GTTTAAAGTTTAAAGTTTA-GGTTTA
* *
70347 GGGTTTCTATAAATTATATAAGTAATTTACTT
490 GGGTTTCTATAAACTATATAA-TTA-TTACTT
* ** *
70379 TATATAGTTTATATA-TATATAGGTATATATATATAG-TTTATATATACTATA
1 TATATAGTTTATATAGTTTATATATATATATATATAGATATATATATA-TATA
70430 CATGGTTTAT
Statistics
Matches: 1789, Mismatches: 189, Indels: 323
0.78 0.08 0.14
Matches are distributed among these distances:
495 294 0.16
496 2 0.00
497 295 0.16
499 14 0.01
500 7 0.00
501 6 0.00
502 5 0.00
503 2 0.00
504 14 0.01
505 2 0.00
506 2 0.00
507 19 0.01
508 7 0.00
509 4 0.00
510 9 0.01
511 17 0.01
512 20 0.01
513 14 0.01
514 7 0.00
515 4 0.00
516 5 0.00
518 30 0.02
519 30 0.02
520 28 0.02
521 15 0.01
522 6 0.00
523 13 0.01
524 42 0.02
525 42 0.02
526 54 0.03
527 45 0.03
528 13 0.01
529 12 0.01
530 10 0.01
531 6 0.00
532 10 0.01
533 16 0.01
534 240 0.13
535 8 0.00
536 6 0.00
537 5 0.00
538 15 0.01
539 1 0.00
540 1 0.00
541 20 0.01
542 20 0.01
543 4 0.00
544 2 0.00
545 1 0.00
546 8 0.00
548 293 0.16
549 3 0.00
550 27 0.02
551 14 0.01
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (519 bp):
TATATAGTTTATATAGTTTATATATATATATATATAGATATATATATATATAGTTTATATATACT
ATACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATG
TAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATG
GTTCATAAATAGTAGTACATTTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTT
AGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAA
ATAAGTCCATTTGCATTAGACTAGTCCATTTACATTAGTTTACATAGCCCAATACATAAGCCACT
CTTTTATTACAAATATATATGCATTAGTGCTAGTCATTTATATTAGGGTTTATATTTAGTGTTTA
TGTTTATAAGTTTAAAGTTTAAAGTTTAGGTTTAGGGTTTCTATAAACTATATAATTATTACTT
Found at i:69742 original size:21 final size:21
Alignment explanation
Indices: 69710--69762 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
69700 TTACATTAGG
*
69710 GTTT-GTGATTTAGGGTTTAAT
1 GTTTAGTG-TTTAGGGTTTAAA
*
69731 GTTTAGTGTTTATGGTTTAAA
1 GTTTAGTGTTTAGGGTTTAAA
*
69752 GTTTAGAGTTT
1 GTTTAGTGTTT
69763 CTATAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (21 bp):
GTTTAGTGTTTAGGGTTTAAA
Found at i:69857 original size:15 final size:15
Alignment explanation
Indices: 69852--69894 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
69842 AGTTTATATA
69852 TATATATATATAGGT
1 TATATATATATAGGT
*
69867 TATATATATATAGTT
1 TATATATATATAGGT
69882 TATATATACTATA
1 TATATATA-TATA
69895 CATGGTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (15 bp):
TATATATATATAGGT
Found at i:69863 original size:21 final size:21
Alignment explanation
Indices: 69837--69878 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
69827 TAATTTACTT
*
69837 TATATAGTTTATATATATATA
1 TATATAGGTTATATATATATA
69858 TATATAGGTTATATATATATA
1 TATATAGGTTATATATATATA
69879 GTTTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TATATAGGTTATATATATATA
Found at i:70187 original size:19 final size:19
Alignment explanation
Indices: 70159--70209 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
70149 AAAATAAGTT
* *
70159 CATTTGCATTAGTGTTGTC
1 CATTTACATTAGTGCTGTC
70178 CATTTACATTAGTGCTGTC
1 CATTTACATTAGTGCTGTC
*
70197 CATTTATATTAGT
1 CATTTACATTAGT
70210 TTACATAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (19 bp):
CATTTACATTAGTGCTGTC
Found at i:70229 original size:13 final size:13
Alignment explanation
Indices: 70211--70235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
70201 TATATTAGTT
70211 TACATAAACCCAA
1 TACATAAACCCAA
70224 TACATAAACCCA
1 TACATAAACCCA
70236 CTCTTTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (13 bp):
TACATAAACCCAA
Found at i:70339 original size:21 final size:20
Alignment explanation
Indices: 70286--70346 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
70276 TTATATTAGG
* *
70286 GTTTATGATTTAGGGTTTAAT
1 GTTTA-GATTTATGGTTTAAA
70307 GTTTAGTATTTATGGTTTAAA
1 GTTTAG-ATTTATGGTTTAAA
*
70328 GTTTAGAGTTTATGATTTA
1 GTTTAGA-TTTATGGTTTA
70347 GGGTTTCTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.06
21 33 0.94
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.52
Consensus pattern (20 bp):
GTTTAGATTTATGGTTTAAA
Found at i:70405 original size:14 final size:13
Alignment explanation
Indices: 70388--70424 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
70378 TTATATAGTT
70388 TATATATATATAGG
1 TATATATATATA-G
70402 TATATATATATAG
1 TATATATATATAG
*
70415 TTTATATATA
1 TATATATATA
70425 CTATACATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (13 bp):
TATATATATATAG
Found at i:70699 original size:25 final size:24
Alignment explanation
Indices: 70671--70740 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
70661 TAATATAAAT
70671 TATAATTTATAAACTATATATTTTA
1 TATAATTTATAAA-TATATATTTTA
* * *
70696 TATAGTTTATACATATATAGTTTA
1 TATAATTTATAAATATATATTTTA
* *
70720 TATATATATATATATATATAT
1 TATA-ATTTATAAATATATAT
70741 AAGTAATTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
24 14 0.38
25 23 0.62
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (24 bp):
TATAATTTATAAATATATATTTTA
Found at i:70723 original size:17 final size:15
Alignment explanation
Indices: 70694--70729 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
70684 CTATATATTT
70694 TATATAGTTTATACA
1 TATATAGTTTATACA
*
70709 TATATAGTTTATATA
1 TATATAGTTTATACA
70724 TATATA
1 TATATA
70730 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:70758 original size:2 final size:2
Alignment explanation
Indices: 70596--70741 Score: 60
Period size: 2 Copynumber: 75.0 Consensus size: 2
70586 TCTCTCTCTC
* *
70596 TA TA TA TA TA TA TA -A TC TA TA GA T- TA CT- TA TA T- TA GT- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA
* * * *
70635 TA CA TA CA TA CA TA TA TA TA CTA TA T- TA -A TA TA AA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
70675 -A TT TA TA AA CTA TA TA T- TT TA TA TA GTT TA TA CA TA TA TA GTT
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA
70718 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
70742 AGTAATTAGA
Statistics
Matches: 105, Mismatches: 23, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
1 10 0.10
2 88 0.84
3 7 0.07
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:70980 original size:19 final size:20
Alignment explanation
Indices: 70944--70981 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
70934 AAATTTTCTA
70944 TTCTCTCTAAATTTCCCAAT
1 TTCTCTCTAAATTTCCCAAT
70964 TTCTCTCTAAA-TTCCCAA
1 TTCTCTCTAAATTTCCCAA
70982 ATAAAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCTCTCTAAATTTCCCAAT
Found at i:71565 original size:23 final size:23
Alignment explanation
Indices: 71531--71590 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
71521 TGAATATATA
*
71531 TATATATATATATAAATTATAGTT
1 TATAAATATATAT-AATTATAGTT
**
71555 TATAAACTATATATTTTTATAGTT
1 TATAAA-TATATATAATTATAGTT
*
71579 TATACATATATA
1 TATAAATATATA
71591 GTTTACATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 6 0.19
24 18 0.58
25 7 0.23
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (23 bp):
TATAAATATATATAATTATAGTT
Found at i:71624 original size:13 final size:13
Alignment explanation
Indices: 71572--71702 Score: 77
Period size: 13 Copynumber: 9.2 Consensus size: 13
71562 TATATATTTT
71572 TATAGTTTATACATA
1 TATAGTTTAT--ATA
*
71587 TATAGTTTACATA
1 TATAGTTTATATA
*
71600 TATATTTTATATA
1 TATAGTTTATATA
*
71613 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
71628 CATA-ATT-TATA
1 TATAGTTTATATA
71639 TATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
71657 TATAGTTTATAATACAAA
1 TATAGTTTAT-AT----A
71675 TATAGTTTATATA
1 TATAGTTTATATA
71688 TATAGTTTATATA
1 TATAGTTTATATA
71701 TA
1 TA
71703 AACTTATATT
Statistics
Matches: 93, Mismatches: 10, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
11 6 0.06
12 1 0.01
13 37 0.40
14 3 0.03
15 21 0.23
16 2 0.02
17 5 0.05
18 18 0.19
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:71677 original size:18 final size:18
Alignment explanation
Indices: 71638--71685 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
71628 CATAATTTAT
* *
71638 ATATAGCTTATAATAATT
1 ATATAGTTTATAATAATA
71656 ATATAGTTTATAATACA-A
1 ATATAGTTTATAATA-ATA
71674 ATATAGTTTATA
1 ATATAGTTTATA
71686 TATATAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (18 bp):
ATATAGTTTATAATAATA
Found at i:71838 original size:16 final size:16
Alignment explanation
Indices: 71817--71866 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
71807 CTTTTGTGTT
*
71817 TTTTAATTTATTTCAA
1 TTTTAATGTATTTCAA
*
71833 TTTTAA-GTATTTCAC
1 TTTTAATGTATTTCAA
71848 TTTTATATGTA-TTCAA
1 TTTTA-ATGTATTTCAA
71864 TTT
1 TTT
71867 AGCCCTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (16 bp):
TTTTAATGTATTTCAA
Found at i:71845 original size:15 final size:17
Alignment explanation
Indices: 71825--71866 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
71815 TTTTTTAATT
71825 TATTTCAATTTTA-A-G
1 TATTTCAATTTTATATG
*
71840 TATTTCACTTTTATATG
1 TATTTCAATTTTATATG
71857 TA-TTCAATTT
1 TATTTCAATTT
71867 AGCCCTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 12 0.52
16 8 0.35
17 3 0.13
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.57
Consensus pattern (17 bp):
TATTTCAATTTTATATG
Found at i:72836 original size:35 final size:35
Alignment explanation
Indices: 72772--72865 Score: 113
Period size: 35 Copynumber: 2.7 Consensus size: 35
72762 ACCATGGAAA
*
72772 AAACATAAAACTTAAAAGTCCATGA-TACATAAACC
1 AAACATAAAACTTAAAAGTCCA-AATTACATAAACC
*
72807 AAACATAGAAA-TTAGAAA-TCCAAATTACATAATCC
1 AAACATA-AAACTTA-AAAGTCCAAATTACATAAACC
*
72842 AAAGATAAAACTTAAAAGTCCAAA
1 AAACATAAAACTTAAAAGTCCAAA
72866 AAAATAGAGC
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
34 7 0.14
35 38 0.75
36 6 0.12
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.20
Consensus pattern (35 bp):
AAACATAAAACTTAAAAGTCCAAATTACATAAACC
Found at i:73001 original size:40 final size:40
Alignment explanation
Indices: 72947--73036 Score: 155
Period size: 40 Copynumber: 2.3 Consensus size: 40
72937 TGTTAGGGTG
*
72947 AATAA-TTAGGGAAAAAAGAGATCTAGTATGTTTGGGCGA
1 AATAATTTGGGGAAAAAAGAGATCTAGTATGTTTGGGCGA
*
72986 AATAATTTGGGGAAAAAAGAGATCTAGTATGTTTGGGTGA
1 AATAATTTGGGGAAAAAAGAGATCTAGTATGTTTGGGCGA
73026 AATAATTTGGG
1 AATAATTTGGG
73037 AATTGGGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 5 0.10
40 43 0.90
ACGTcount: A:0.39, C:0.03, G:0.29, T:0.29
Consensus pattern (40 bp):
AATAATTTGGGGAAAAAAGAGATCTAGTATGTTTGGGCGA
Found at i:79482 original size:20 final size:20
Alignment explanation
Indices: 79442--79480 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
79432 TATTACAGGA
*
79442 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCCACAAAAG
79462 ATTTCATGGCCTCCACAAA
1 ATTT-ATGGCCTCCACAAA
79481 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCCACAAAAG
Found at i:80509 original size:64 final size:63
Alignment explanation
Indices: 80441--80584 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 63
80431 ATGCACATAC
*
80441 AGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-
1 AGTGCATCGATGCATCCAA--TAAAAA-AAAACATCGAATAGGATTTATGCATCGATGCAT-AGT
80504 G-
62 GT
* * * *
80505 AGTGCATCGATGCATCCCCAATAAATACAAACATCTAATAGGATTTATGCATCGATGCATGGTGT
1 AGTGCATCGATGCAT--CCAATAAAAAAAAACATCGAATAGGATTTATGCATCGATGCATAGTGT
80570 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
80585 ACCTCCATTA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
63 1 0.01
64 47 0.67
65 20 0.29
67 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (63 bp):
AGTGCATCGATGCATCCAATAAAAAAAAACATCGAATAGGATTTATGCATCGATGCATAGTGT
Found at i:81270 original size:103 final size:103
Alignment explanation
Indices: 81045--81262 Score: 384
Period size: 103 Copynumber: 2.1 Consensus size: 103
81035 GTAGAGGGTC
*
81045 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
81110 TTGATCCTTGGCATATGTATATGATTTTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
81148 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
81213 TTGAT-CTCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCT-TAGCATATGTATATGATTCTTAAGGAATGA
81251 TATGTGGTCCTT
1 TATGTGGTCCTT
81263 ATGGACATTA
Statistics
Matches: 110, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
102 2 0.02
103 108 0.98
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:81328 original size:23 final size:23
Alignment explanation
Indices: 81277--81341 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
81267 ACATTATTAT
81277 ATGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
** *
81300 GCGGCACT-CTGGTGCAATTTTAC
1 ATGGCACTAC-GGTGCAATTCTAC
* *
81323 ATGGCACTTCGGTGTAATT
1 ATGGCACTACGGTGCAATT
81342 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:86324 original size:269 final size:269
Alignment explanation
Indices: 85845--86392 Score: 1078
Period size: 269 Copynumber: 2.0 Consensus size: 269
85835 AATTCACGCC
85845 TTAAGTTATTCTCATGAAAGATAAAATCACGATGGTCAGGACTGTTCATCGTACATCAAGTCCAT
1 TTAAGTTATTCTCATGAAAGATAAAATCACGATGGTCAGGACTGTTCATCGTACATCAAGTCCAT
*
85910 GACAATAGAGCAATAAAAATCCAGAACCAAGGCGATGGTTCCATCTCTAAGGTGAACAGGTAGAG
66 GACAATAGAGCAATAAAAATCCAGAACCAAGACGATGGTTCCATCTCTAAGGTGAACAGGTAGAG
85975 GCTAAAGGAGTACAAAGTATCCCCAGTCATGTGCGACAAACTGGCATCGATGGCACATGATGCTC
131 GCTAAAGGAGTACAAAGTATCCCCAGTCATGTGCGACAAACTGGCATCGATGGCACATGATGCTC
86040 AAGAGTTTGCCTTACTTACTTGAACAAAATTCGTTGCCTAAGCAACACAAATTTGAATTTTGTAC
196 AAGAGTTTGCCTTACTTACTTGAACAAAATTCGTTGCCTAAGCAACACAAATTTGAATTTTGTAC
86105 ATAAATAAA
261 ATAAATAAA
86114 TTAAGTTATTCTCATGAAAGATAAAATCACGATGGTCAGGACTGTTCATCGTACATCAAGTCCAT
1 TTAAGTTATTCTCATGAAAGATAAAATCACGATGGTCAGGACTGTTCATCGTACATCAAGTCCAT
86179 GACAATAGAGCAATAAAAATCCAGAACCAAGACGATGGTTCCATCTCTAAGGTGAACAGGTAGAG
66 GACAATAGAGCAATAAAAATCCAGAACCAAGACGATGGTTCCATCTCTAAGGTGAACAGGTAGAG
86244 GCTAAAGGAGTACAAAGTATCCCCAGTCATGTGCGACAAACTGGCATCGATGGCACATGATGCTC
131 GCTAAAGGAGTACAAAGTATCCCCAGTCATGTGCGACAAACTGGCATCGATGGCACATGATGCTC
*
86309 AAGAGTTTGCCTTACTTACTTGAACAAAATTCGTTGTCTAAGCAACACAAATTTGAATTTTGTAC
196 AAGAGTTTGCCTTACTTACTTGAACAAAATTCGTTGCCTAAGCAACACAAATTTGAATTTTGTAC
86374 ATAAATAAA
261 ATAAATAAA
86383 TTAAGTTATT
1 TTAAGTTATT
86393 TTCTGCTTTC
Statistics
Matches: 277, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
269 277 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (269 bp):
TTAAGTTATTCTCATGAAAGATAAAATCACGATGGTCAGGACTGTTCATCGTACATCAAGTCCAT
GACAATAGAGCAATAAAAATCCAGAACCAAGACGATGGTTCCATCTCTAAGGTGAACAGGTAGAG
GCTAAAGGAGTACAAAGTATCCCCAGTCATGTGCGACAAACTGGCATCGATGGCACATGATGCTC
AAGAGTTTGCCTTACTTACTTGAACAAAATTCGTTGCCTAAGCAACACAAATTTGAATTTTGTAC
ATAAATAAA
Found at i:96268 original size:2 final size:2
Alignment explanation
Indices: 96261--96294 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
96251 TTAAATCACA
96261 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
96295 TATGCCCACA
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:98886 original size:2 final size:2
Alignment explanation
Indices: 98879--98907 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
98869 CAAGTTGAAC
98879 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
98908 TGTAACACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:100928 original size:2 final size:2
Alignment explanation
Indices: 100921--100952 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
100911 TGATTCAGTC
100921 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
100953 CAATTCCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:106041 original size:15 final size:15
Alignment explanation
Indices: 106021--106050 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
106011 GGAGCATTTC
106021 AATTCTATGCTTACA
1 AATTCTATGCTTACA
106036 AATTCTATGCTTACA
1 AATTCTATGCTTACA
106051 CTAGTAGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
AATTCTATGCTTACA
Found at i:108784 original size:169 final size:169
Alignment explanation
Indices: 108505--108841 Score: 674
Period size: 169 Copynumber: 2.0 Consensus size: 169
108495 AATGAGATCA
108505 CGATCATGGACAATGGGGGAACATTTTCGGACAGGCAGTTGTTTTTCGGTGGGCCGTTGGAAGAG
1 CGATCATGGACAATGGGGGAACATTTTCGGACAGGCAGTTGTTTTTCGGTGGGCCGTTGGAAGAG
108570 GGGTTGTTTTTGGTGAGTCCGAGAAAGGATGATAATGGCACGGGGAAGAGCGGAGTTTTCGAAGA
66 GGGTTGTTTTTGGTGAGTCCGAGAAAGGATGATAATGGCACGGGGAAGAGCGGAGTTTTCGAAGA
108635 AGTGATGGAAGGGCTGTATTATGGGACAAAAGAGAGCGC
131 AGTGATGGAAGGGCTGTATTATGGGACAAAAGAGAGCGC
108674 CGATCATGGACAATGGGGGAACATTTTCGGACAGGCAGTTGTTTTTCGGTGGGCCGTTGGAAGAG
1 CGATCATGGACAATGGGGGAACATTTTCGGACAGGCAGTTGTTTTTCGGTGGGCCGTTGGAAGAG
108739 GGGTTGTTTTTGGTGAGTCCGAGAAAGGATGATAATGGCACGGGGAAGAGCGGAGTTTTCGAAGA
66 GGGTTGTTTTTGGTGAGTCCGAGAAAGGATGATAATGGCACGGGGAAGAGCGGAGTTTTCGAAGA
108804 AGTGATGGAAGGGCTGTATTATGGGACAAAAGAGAGCG
131 AGTGATGGAAGGGCTGTATTATGGGACAAAAGAGAGCG
108842 TGGGGTGTGC
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 168 1.00
ACGTcount: A:0.26, C:0.12, G:0.39, T:0.24
Consensus pattern (169 bp):
CGATCATGGACAATGGGGGAACATTTTCGGACAGGCAGTTGTTTTTCGGTGGGCCGTTGGAAGAG
GGGTTGTTTTTGGTGAGTCCGAGAAAGGATGATAATGGCACGGGGAAGAGCGGAGTTTTCGAAGA
AGTGATGGAAGGGCTGTATTATGGGACAAAAGAGAGCGC
Found at i:112901 original size:18 final size:19
Alignment explanation
Indices: 112878--112914 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
112868 TCAGTAATCC
112878 TATTCCC-TGGTAATCTTT
1 TATTCCCATGGTAATCTTT
112896 TATTCCCATTGGTAATCTT
1 TATTCCCA-TGGTAATCTT
112915 ACATTCTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTT
Found at i:112995 original size:17 final size:17
Alignment explanation
Indices: 112973--113008 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
112963 ACCGTTAGAA
*
112973 CACTTAGTGCATCGGTG
1 CACTTAGTGCATCGATG
112990 CACTTAGTGCATCGATG
1 CACTTAGTGCATCGATG
113007 CA
1 CA
113009 TAAAATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (17 bp):
CACTTAGTGCATCGATG
Found at i:113066 original size:19 final size:19
Alignment explanation
Indices: 113042--113111 Score: 124
Period size: 19 Copynumber: 3.7 Consensus size: 19
113032 CAAGCCTGGA
113042 GTGCATCGATGCATGGTCT
1 GTGCATCGATGCATGGTCT
113061 GTGCATCGATGCATGGTCT
1 GTGCATCGATGCATGGTCT
*
113080 GTGCATCGATGCATGG-CA
1 GTGCATCGATGCATGGTCT
113098 GTGCATCGATGCAT
1 GTGCATCGATGCAT
113112 CAATGAGTGC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 15 0.30
19 35 0.70
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (19 bp):
GTGCATCGATGCATGGTCT
Found at i:113122 original size:38 final size:38
Alignment explanation
Indices: 113040--113131 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 38
113030 AACAAGCCTG
* **
113040 GAGTGCATCGATGCATGGTCTGTGCATCGATGCATGGT
1 GAGTGCATCGATGCATGGTCAGTGCATCGATGCATAAT
**
113078 CTGTGCATCGATGCATGG-CAGTGCATCGATGCATCAAT
1 GAGTGCATCGATGCATGGTCAGTGCATCGATGCAT-AAT
*
113116 GAGTGCATCGGTGCAT
1 GAGTGCATCGATGCAT
113132 CTTTTCACAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
37 15 0.33
38 30 0.67
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.27
Consensus pattern (38 bp):
GAGTGCATCGATGCATGGTCAGTGCATCGATGCATAAT
Found at i:114872 original size:3 final size:3
Alignment explanation
Indices: 114864--114892 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
114854 TAAAATTAGT
114864 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
114893 TTTAATGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:117498 original size:3 final size:3
Alignment explanation
Indices: 117490--117532 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
117480 GGTCGAAAAA
*
117490 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
117533 ACAATTGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:127355 original size:20 final size:20
Alignment explanation
Indices: 127319--127356 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
127309 ATCCTATTCC
**
127319 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
127339 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
127357 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:129314 original size:3 final size:3
Alignment explanation
Indices: 129306--129331 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
129296 TAAAATTAGT
129306 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
129332 TTTAATGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:131932 original size:3 final size:3
Alignment explanation
Indices: 131924--131963 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
131914 GGTCGAAAAA
*
131924 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
131964 ACAATTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:138424 original size:36 final size:37
Alignment explanation
Indices: 138350--138475 Score: 134
Period size: 37 Copynumber: 3.5 Consensus size: 37
138340 AGATTGTTTC
* * * * *
138350 TCTCGAAAAA-AAATGTCGTCTCGCTAGAGATAATTT
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATTT
*
138386 T-TCTTAAAAATC-AATTTTGTCTCGCTTGAGACAGTTT
1 TCTC-TAAAAA-CAAATTTTGTCTCGCTTGAGACAATTT
138423 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATTT
1 TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATTT
* *
138460 T-TCTCAAAATAAATTT
1 TCTCTAAAAACAAATTT
138476 CATCTTACTT
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
35 2 0.03
36 20 0.26
37 52 0.68
38 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (37 bp):
TCTCTAAAAACAAATTTTGTCTCGCTTGAGACAATTT
Found at i:138487 original size:36 final size:37
Alignment explanation
Indices: 138384--138498 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 37
138374 TAGAGATAAT
** * *
138384 TTTTCT-TAAAAATC-AATTTTGTCTCGCTTGAGACAG
1 TTTTCTCTAAAAA-CAAATTTCATCTCACTTGAGACAA
** *
138420 TTTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
1 TTTTCTCTAAAAACAAATTTCATCTCACTTGAGACAA
* * * **
138457 TTTT-TCTCAAAATAAATTTCATCTTACTTGAGATGA
1 TTTTCTCTAAAAACAAATTTCATCTCACTTGAGACAA
138493 TTTTCT
1 TTTTCT
138499 GCAAATTTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
36 35 0.52
37 32 0.48
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (37 bp):
TTTTCTCTAAAAACAAATTTCATCTCACTTGAGACAA
Found at i:138825 original size:29 final size:29
Alignment explanation
Indices: 138767--138842 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
138757 GAGACATTTC
* *
138767 CCCTTGAAATACAAATTTTGAAATTGTTT
1 CCCTTAAAACACAAATTTTGAAATTGTTT
* *
138796 CCCTTAAAACACAAATCTTTG-AGTTTTTT
1 CCCTTAAAACACAAAT-TTTGAAATTGTTT
*
138825 CTCTTAAAACA-AAATTTT
1 CCCTTAAAACACAAATTTT
138843 ATCTCTCTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 3 0.07
28 4 0.10
29 30 0.73
30 4 0.10
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.41
Consensus pattern (29 bp):
CCCTTAAAACACAAATTTTGAAATTGTTT
Found at i:139228 original size:131 final size:134
Alignment explanation
Indices: 138991--139347 Score: 341
Period size: 131 Copynumber: 2.7 Consensus size: 134
138981 AAACTATTAT
* * * * *** * * *
138991 CCTTAAAGATGGCCAACCGTCCTCATCACGTATGAATTGTGTCATCC-CATGACCAGACCTCCTC
1 CCTTAAAGATGGCCAGCCATCCTCATCACATAGGAACCATGTCATCCAC-CGACCAAACTTCCTC
*
139055 ATCACGTAGGAGTCATGTCACCCCTAGATAACCAGTTGTCCTCATCACATAGGAACCGTGTTAT-
65 ATCACGTAGGAGTCATGTCACCCCTAGATAACCAGTCGTCCTCATCACATAGGAACCGTGTTATC
139119 A-ATC-
130 ACA-CA
* * *
139123 CC-TAAAGATGGCCTGCCATCCTTATCACATAGGAACCATGTCATCTACCGACCAAACTTCCTCA
1 CCTTAAAGATGGCCAGCCATCCTCATCACATAGGAACCATGTCATCCACCGACCAAACTTCCTCA
* * * * *** *
139187 TCATGTAGGAG-CCTTTCCACCTCTAGATAACCAGTCGTCCTCATCGTGTAGGAACTGTGTTATC
66 TCACGTAGGAGTCATGT-CACCCCTAGATAACCAGTCGTCCTCATCACATAGGAACCGTGTTATC
139251 ACACA
130 ACACA
* * *** * *
139256 CCTTAAAGATGGCCAGTCGTCCTCATCGTGTAGGAACCATGTCATCCATCGACCATA-TCTCCTC
1 CCTTAAAGATGGCCAGCCATCCTCATCACATAGGAACCATGTCATCCACCGACCAAACT-TCCTC
* * *
139320 ATCACGTAGCAGTCGTGTCACCCTTAGA
65 ATCACGTAGGAGTCATGTCACCCCTAGA
139348 CGACCATAAT
Statistics
Matches: 179, Mismatches: 38, Indels: 14
0.77 0.16 0.06
Matches are distributed among these distances:
130 3 0.02
131 97 0.54
132 5 0.03
133 4 0.02
134 67 0.37
135 3 0.02
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (134 bp):
CCTTAAAGATGGCCAGCCATCCTCATCACATAGGAACCATGTCATCCACCGACCAAACTTCCTCA
TCACGTAGGAGTCATGTCACCCCTAGATAACCAGTCGTCCTCATCACATAGGAACCGTGTTATCA
CACA
Found at i:139540 original size:3 final size:3
Alignment explanation
Indices: 139532--139578 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
139522 GTCGAAAAAA
*
139532 TAT TAT TAT TATT TAT TAT TAT T-T CTAT TAT CAT TAT T-T TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT
139577 TA
1 TA
139579 ACATTTGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 3 0.08
3 31 0.82
4 4 0.11
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:141108 original size:5 final size:5
Alignment explanation
Indices: 141098--141123 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
141088 CTCTTTTCAC
141098 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
141124 CTCTGTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:142203 original size:6 final size:6
Alignment explanation
Indices: 142189--142235 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
142179 CTGTTCTTCC
*
142189 GGAAAT GGAAGT GGAAGT GGAAGT GGAAGT GGAAGT GGAAGT GGAAG
1 GGAAGT GGAAGT GGAAGT GGAAGT GGAAGT GGAAGT GGAAGT GGAAG
142236 AAGAAAGACG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.49, T:0.15
Consensus pattern (6 bp):
GGAAGT
Found at i:144500 original size:19 final size:19
Alignment explanation
Indices: 144476--144515 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
144466 CAACCAATAA
*
144476 AATTTATTCATCTTAAAAT
1 AATTTATTCATCTCAAAAT
144495 AATTTATTCATCTCAAAAT
1 AATTTATTCATCTCAAAAT
144514 AA
1 AA
144516 CTACCCACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTATTCATCTCAAAAT
Found at i:149370 original size:90 final size:89
Alignment explanation
Indices: 149254--149428 Score: 289
Period size: 90 Copynumber: 2.0 Consensus size: 89
149244 TCTCGAATAT
* *
149254 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCCTAATATGATTA
1 TTAAATTCAATTAATTAAATAAAGATTTAATTAATTTGAAATAATAAAAAT-CCTAATATGATTA
*
149318 GGGTAACTTGGATATAAAAGGATTA
65 GGGTAACTTAGATATAAAAGGATTA
149343 TTAAATTCTAATTAATTAAATAAAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGATTA
1 TTAAATTC-AATTAATTAAATAAAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGATTA
*
149408 GGGTAACTTAGTTATAAAAGG
65 GGGTAACTTAGATATAAAAGG
149429 GTATGTTAGG
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
89 7 0.09
90 68 0.85
91 5 0.06
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATAAAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGATTAG
GGTAACTTAGATATAAAAGGATTA
Found at i:151743 original size:16 final size:16
Alignment explanation
Indices: 151696--151746 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
151686 TATTACGACC
*
151696 TGTTTTCAACCTGACC
1 TGTTTTCAACCTGACT
* * *
151712 TGTTATGAACATGACT
1 TGTTTTCAACCTGACT
151728 TGTTTTCAACCTGACT
1 TGTTTTCAACCTGACT
151744 TGT
1 TGT
151747 AAATGATCTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (16 bp):
TGTTTTCAACCTGACT
Found at i:151761 original size:32 final size:32
Alignment explanation
Indices: 151696--151763 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
151686 TATTACGACC
* *
151696 TGTTTTCAACCTGACCTGTTATGAACATGACT
1 TGTTTTCAACCTGACCTGTAATGAACATAACT
* *
151728 TGTTTTCAACCTGACTTGTAAATGATC-TAACT
1 TGTTTTCAACCTGACCTGT-AATGAACATAACT
151760 TGTT
1 TGTT
151764 ATTGACTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (32 bp):
TGTTTTCAACCTGACCTGTAATGAACATAACT
Found at i:151817 original size:16 final size:16
Alignment explanation
Indices: 151778--151818 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
151768 ACTTGATATG
151778 ATAT-TTACCTGACTT
1 ATATATTACCTGACTT
*
151793 A-ACATTTACCTGACTT
1 ATATA-TTACCTGACTT
151809 ATATATTACC
1 ATATATTACC
151819 ATTGATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
14 1 0.05
15 1 0.05
16 17 0.81
17 2 0.10
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (16 bp):
ATATATTACCTGACTT
Found at i:156479 original size:2 final size:2
Alignment explanation
Indices: 156472--156702 Score: 81
Period size: 2 Copynumber: 113.5 Consensus size: 2
156462 TAATAAATTA
*
156472 AT AT AT AT TT AT AT AT ACT A- AT GA- ACT AT AT ACT AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT -AT A-T AT AT A-T AT AT AT AT
* * * *
156513 TT AT AT AA ACT AT AT AGT TT AT AT AT ACT A- AT AA ACT AT AT A-
1 AT AT AT AT A-T AT AT A-T AT AT AT AT A-T AT AT AT A-T AT AT AT
* *
156555 AT AT AT AGT TT AT AT AT AGT AT AT A- AT AT AGT TT AT AT AT A-
1 AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
* * * ** * *
156596 AT -T CAT AT AT AC ACT AC AT A- AT TT AT AT GC A- AT AT AT AA AA
1 AT AT -AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
156637 AT -T AT AA AT AT AA ACT AT AT AGT TT AT AT CAT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT -AT AT AT AT AT AT
156679 AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
156703 ATTGTTTTAA
Statistics
Matches: 170, Mismatches: 31, Indels: 56
0.66 0.12 0.22
Matches are distributed among these distances:
1 12 0.07
2 137 0.81
3 21 0.12
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:156502 original size:51 final size:51
Alignment explanation
Indices: 156472--156581 Score: 157
Period size: 51 Copynumber: 2.1 Consensus size: 51
156462 TAATAAATTA
*
156472 ATATATATTTATATATACTAATGAACTATATACTATATAATTTATATAAACT
1 ATATA-ATTTATATATACTAATAAACTATATACTATATAATTTATATAAACT
* * * * *
156524 ATATAGTTTATATATACTAATAAACTATATAATATATAGTTTATATATAGT
1 ATATAATTTATATATACTAATAAACTATATACTATATAATTTATATAAACT
156575 ATATAAT
1 ATATAAT
156582 ATAGTTTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 46 0.90
52 5 0.10
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (51 bp):
ATATAATTTATATATACTAATAAACTATATACTATATAATTTATATAAACT
Found at i:156524 original size:18 final size:18
Alignment explanation
Indices: 156498--156693 Score: 104
Period size: 18 Copynumber: 10.7 Consensus size: 18
156488 ACTAATGAAC
156498 TATATACTATATAATTTA
1 TATATACTATATAATTTA
* *
156516 TATAAACTATATAGTTTA
1 TATATACTATATAATTTA
**
156534 TATATACTA-ATAAACTA
1 TATATACTATATAATTTA
*
156551 TATA-A-TATATAGTTTA
1 TATATACTATATAATTTA
*
156567 TATATAGTATATAA--TA
1 TATATACTATATAATTTA
*
156583 TAGTTTA-TATATAATTCATA
1 TA-TATACTATATAATT--TA
* *
156603 TATACACTACATAATTTA
1 TATATACTATATAATTTA
*
156621 TATGCAATA-TATAAAAATTATAAA
1 TAT---ATACTAT-ATAATT-T--A
* *
156645 TATAAACTATATAGTTTA
1 TATATACTATATAATTTA
*
156663 TATCATA-TATATATATATA
1 TAT-ATACTATATA-ATTTA
156682 TATATA-TATATA
1 TATATACTATATA
156694 TATATTATAA
Statistics
Matches: 136, Mismatches: 23, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
15 2 0.01
16 21 0.15
17 13 0.10
18 54 0.40
19 10 0.07
20 15 0.11
21 13 0.10
22 4 0.03
24 4 0.03
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (18 bp):
TATATACTATATAATTTA
Found at i:156555 original size:9 final size:9
Alignment explanation
Indices: 156481--156555 Score: 50
Period size: 9 Copynumber: 8.8 Consensus size: 9
156471 AATATATATT
*
156481 TATATATAC
1 TATATAAAC
*
156490 TA-ATGAAC
1 TATATAAAC
156498 TATAT--AC
1 TATATAAAC
**
156505 TATATAATT
1 TATATAAAC
156514 TATATAAAC
1 TATATAAAC
***
156523 TATATAGTT
1 TATATAAAC
*
156532 TATATATAC
1 TATATAAAC
156541 TA-ATAAAC
1 TATATAAAC
156549 TATATAA
1 TATATAA
156556 TATATAGTTT
Statistics
Matches: 49, Mismatches: 13, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
7 7 0.14
8 13 0.27
9 29 0.59
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (9 bp):
TATATAAAC
Found at i:156571 original size:11 final size:11
Alignment explanation
Indices: 156555--156606 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
156545 AAACTATATA
156555 ATATATAGTTT
1 ATATATAGTTT
*
156566 ATATATAGTAT
1 ATATATAGTTT
156577 ATAATATAGTTT
1 AT-ATATAGTTT
* *
156589 ATATATAATTC
1 ATATATAGTTT
156600 ATATATA
1 ATATATA
156607 CACTACATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
11 26 0.72
12 10 0.28
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (11 bp):
ATATATAGTTT
Found at i:157786 original size:25 final size:25
Alignment explanation
Indices: 157758--157819 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
157748 ATGTATGCTT
*
157758 ATAATTCAAGACAATTAATCACAAC
1 ATAATTCAAGACAATCAATCACAAC
* *
157783 ATAATTCATGACAATCAATCATAAC
1 ATAATTCAAGACAATCAATCACAAC
* *
157808 GTAATTTAAGAC
1 ATAATTCAAGAC
157820 TGTTTATTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.27
Consensus pattern (25 bp):
ATAATTCAAGACAATCAATCACAAC
Done.