Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002815.1 Hibiscus syriacus cultivar Beakdansim tig00005793_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: 117695
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3410 original size:15 final size:15
Alignment explanation
Indices: 3390--3419 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3380 CCACCTGCCC
3390 GTTCAGCATCCTTAA
1 GTTCAGCATCCTTAA
3405 GTTCAGCATCCTTAA
1 GTTCAGCATCCTTAA
3420 ATAGCCAGAA
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:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (15 bp):
GTTCAGCATCCTTAA
Found at i:10671 original size:29 final size:29
Alignment explanation
Indices: 10628--10694 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
10618 TATGTTTTTA
10628 CCCCCTAAAATTTTACAAGTTCAAGTTCG
1 CCCCCTAAAATTTTACAAGTTCAAGTTCG
* * *
10657 TCCCCTGAAATTTTATAAGTTCAAGTTCG
1 CCCCCTAAAATTTTACAAGTTCAAGTTCG
10686 CCCCCTAAA
1 CCCCCTAAA
10695 CTTAAAATCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.31
Consensus pattern (29 bp):
CCCCCTAAAATTTTACAAGTTCAAGTTCG
Found at i:11744 original size:199 final size:198
Alignment explanation
Indices: 11400--11798 Score: 717
Period size: 199 Copynumber: 2.0 Consensus size: 198
11390 ATCTAGCCCC
*
11400 ATTATGGATTAGGATCCACTAATATTGTGTAAAATTCTCTTAATTTTATATCTTTTTATGATCGT
1 ATTATGGATTAGGATCCACTAATATTGTGTAAAATTCTCTTAATTTTACATCTTTTTATGATCGT
*
11465 TTGGGTTGAAAGAAATTATTTTTTAATAAATATATTCTCATTCTCTAATGTTAATTTTTATTTTT
66 TTGGGTTGAAAGAAATTATTTTTTAATAAATACATTCTCATTCTCTAATGTTAATTTTTATTTTT
*
11530 AATGATAAAATAAGTTCACTTAGTTGAAGGCTTGAAAAGGTTGATGAAGAAAATAAGAGAGAAAT
131 AATGATAAAATAAGTTAACTTAGTTGAAGGCTTGAAAAGGTTGATGAAGAAAATAAGAGAGAAAT
11595 AAA
196 AAA
*
11598 ATTAGTGGATTAGGATCCATTAATATTGTGTAAAATTCTCTTAATTTTACATCTTTTTATGATCG
1 ATTA-TGGATTAGGATCCACTAATATTGTGTAAAATTCTCTTAATTTTACATCTTTTTATGATCG
* *
11663 TTTGGGTTGAGAGAAATTATTTTTTAATAAATACATTCTCATTTTCTAATGTTAATTTTTATTTT
65 TTTGGGTTGAAAGAAATTATTTTTTAATAAATACATTCTCATTCTCTAATGTTAATTTTTATTTT
**
11728 TAATGATAAAATAAGTTAACTTAGTTGAAGGCTTGAAAAGGTTGATGAAGAAGGTAAGAGAGAAA
130 TAATGATAAAATAAGTTAACTTAGTTGAAGGCTTGAAAAGGTTGATGAAGAAAATAAGAGAGAAA
11793 TAAA
195 TAAA
11797 AT
1 AT
11799 GAGAGGGACC
Statistics
Matches: 192, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
198 4 0.02
199 188 0.98
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (198 bp):
ATTATGGATTAGGATCCACTAATATTGTGTAAAATTCTCTTAATTTTACATCTTTTTATGATCGT
TTGGGTTGAAAGAAATTATTTTTTAATAAATACATTCTCATTCTCTAATGTTAATTTTTATTTTT
AATGATAAAATAAGTTAACTTAGTTGAAGGCTTGAAAAGGTTGATGAAGAAAATAAGAGAGAAAT
AAA
Found at i:24534 original size:29 final size:29
Alignment explanation
Indices: 24499--24580 Score: 119
Period size: 29 Copynumber: 2.8 Consensus size: 29
24489 AAACTAAATT
* * *
24499 GATGTCATTACTTACGTCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
24528 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
24557 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
24581 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:27072 original size:27 final size:26
Alignment explanation
Indices: 27034--27110 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 26
27024 TCATTTAAAT
27034 TTATTATTATTATTAAA-T-TTATTA
1 TTATTATTATTATTAAATTATTATTA
27058 TTATTATTATTATTAAA-TATTATTA
1 TTATTATTATTATTAAATTATTATTA
*
27083 TTAGTATATTATTATTAAATAATTATTA
1 TTA-T-TATTATTATTAAATTATTATTA
27111 CAAACCCATT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
24 18 0.38
25 9 0.19
26 1 0.02
27 13 0.27
28 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTATTATTATTATTAAATTATTATTA
Found at i:27110 original size:3 final size:3
Alignment explanation
Indices: 27034--27099 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
27024 TCATTTAAAT
* *
27034 TTA TTA TTA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
27080 TTA TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
27100 AATAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 3 0.06
3 48 0.89
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:27505 original size:16 final size:16
Alignment explanation
Indices: 27484--27518 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
27474 CGGAGAGACA
27484 AAAAACA-GAAAAGAAG
1 AAAAACAGGAAAA-AAG
27500 AAAAACAGGAAAAAAG
1 AAAAACAGGAAAAAAG
27516 AAA
1 AAA
27519 GAAAGAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAACAGGAAAAAAG
Found at i:27522 original size:20 final size:19
Alignment explanation
Indices: 27492--27531 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
27482 CAAAAAACAG
27492 AAAAGAAGAAA-AACAGGAA
1 AAAAGAAGAAAGAA-AGGAA
27511 AAAAGAAAGAAAGAAAGGAA
1 AAAAG-AAGAAAGAAAGGAA
27531 A
1 A
27532 GCTTACCGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 12 0.63
21 2 0.11
ACGTcount: A:0.75, C:0.03, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAAAGAAAGGAA
Found at i:28388 original size:20 final size:21
Alignment explanation
Indices: 28351--28391 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
28341 GAATTTTTTC
**
28351 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
28372 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
28392 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:29071 original size:20 final size:21
Alignment explanation
Indices: 29048--29099 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
29038 AGAAATTAAA
29048 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
29068 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
29090 -ATT-ATTTATT
1 AATTCATTTATT
29100 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:33483 original size:2 final size:2
Alignment explanation
Indices: 33476--33503 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33466 TTATCCTTTA
33476 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
33504 CCTTTGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36204 original size:84 final size:84
Alignment explanation
Indices: 36102--36503 Score: 551
Period size: 84 Copynumber: 4.7 Consensus size: 84
36092 GAACAAATGT
36102 AATGTGCTCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGG-ACAGAACC
1 AATGTGCT-CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-A-AACC
36165 AATTATTGAATTTGGAAAGATG
63 AATTATTGAATTTGGAAAGATG
*
36187 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
36252 TATTGAATTTGGGAAGATG
66 TATTGAATTTGGAAAGATG
*
36271 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
* *
36336 CATTGAATTT-GAGAGATG
66 TATTGAATTTGGAAAGATG
* * *
36354 AATGTGCTCATAGCGTCTTCTGGAAGTGTTATTTGAGTTATCTGGTCTGGTTTGGTATGAAACCA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA--AAA-C-
36419 CATAATCAATCATTGAATTTGG-AAGATG
62 C--AAT---T-ATTGAATTTGGAAAGATG
* * * *
36447 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATTTGATTTGGTA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
36504 TGAACTCCAA
Statistics
Matches: 284, Mismatches: 20, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
83 59 0.21
84 138 0.49
85 16 0.06
86 2 0.01
87 1 0.00
89 3 0.01
93 64 0.23
94 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (84 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
TATTGAATTTGGAAAGATG
Found at i:36501 original size:93 final size:88
Alignment explanation
Indices: 36102--36551 Score: 529
Period size: 84 Copynumber: 5.1 Consensus size: 88
36092 GAACAAATGT
*
36102 AATGTGCTCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGG-ACAGAACC
1 AATGTGCT-CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATA-AACC
36165 AAT---T-ATTGAATTTGGAAAGATG
64 AATCAATCATTGAATTTGG-AAGATG
*
36187 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-AAACCAG
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCAA
36251 T---T-ATTGAATTTGGGAAGATG
66 TCAATCATTGAATTT-GGAAGATG
*
36271 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-AAA-C--
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCAA
36332 -CAATCATTGAATTT-GAGAGATG
66 TCAATCATTGAATTTGGA-AGATG
* * *
36354 AATGTGCTCATAGCGTCTTCTGGAAGTGTTATTTGAGTTATCTGGTCTGGTTTGGTATGAAACCA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-AAA-C-
36419 CATAATCAATCATTGAATTTGGAAGATG
63 C--AATCAATCATTGAATTTGGAAGATG
* * * * *
36447 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATTTGATTTGGTATGAACTCC
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-AA-ACC
* *
36512 AAAATCAATCATTGGATTTGAAAGATG
64 --AATCAATCATTGAATTTGGAAGATG
*
36539 AATTTGCTCATAG
1 AATGTGCTCATAG
36552 TAGAAATAAG
Statistics
Matches: 326, Mismatches: 19, Indels: 33
0.86 0.05 0.09
Matches are distributed among these distances:
82 2 0.01
83 60 0.18
84 132 0.40
85 18 0.06
86 1 0.00
88 1 0.00
92 36 0.11
93 74 0.23
94 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (88 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATAAACCAA
TCAATCATTGAATTTGGAAGATG
Found at i:36503 original size:176 final size:169
Alignment explanation
Indices: 36102--36503 Score: 562
Period size: 176 Copynumber: 2.3 Consensus size: 169
36092 GAACAAATGT
* *
36102 AATGTGCTCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-ACAGAACCA
1 AATGTACT-CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGTACAGAACCA
* *
36166 ATTATTGAATTTGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTG
65 ATCATTGAATTTGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTG
*
36231 ATCTGGTTTGGTAAAACCAGTTATTGAATTTGGGAAGATG
130 ATCTGGTTTGGTAAAACCAATTATTGAATTTGGGAAGATG
36271 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-A-AACCA
1 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGGTACAGAACCA
* *
36334 ATCATTGAATTT-GAGAGATGAATGTGCTCATAGCGTCTTCTGGAAGTGTTATTTGAGTTATCTG
65 ATCATTGAATTTGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTG
*
36398 GTCTGGTTTGGTATGAAACCACATAATCAATCATTGAATTT-GGAAGATG
130 ATCTGGTTTGGTA--AAA-C-C--AAT---T-ATTGAATTTGGGAAGATG
* *
36447 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATTTGATTTGGTA
1 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG-TTTGGTA
36504 TGAACTCCAA
Statistics
Matches: 210, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
167 61 0.29
168 56 0.27
169 16 0.08
170 2 0.01
171 1 0.00
173 2 0.01
175 1 0.00
176 62 0.30
177 9 0.04
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (169 bp):
AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGGTACAGAACCAA
TCATTGAATTTGGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGA
TCTGGTTTGGTAAAACCAATTATTGAATTTGGGAAGATG
Found at i:40180 original size:77 final size:77
Alignment explanation
Indices: 39838--40500 Score: 956
Period size: 76 Copynumber: 8.4 Consensus size: 77
39828 CTATTTCTCA
39838 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
39903 AA-CCTTCGGGT
66 AAGCCTTAGGGT
39914 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
39978 AATCCTTCGGGT
66 AAGCCTTAGGGT
39990 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
40054 AAGCCTTCGGGT
66 AAGCCTTAGGGT
40066 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40131 AAGCCTTAGGGT
66 AAGCCTTAGGGT
40143 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40208 AAGCCTTAGGGT
66 AAGCCTTAGGGT
40220 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
40285 AAGCCTTAGGGT
66 AAGCCTTAGGGT
*********
40297 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAAAAAAAAAAAAAAAAAAAAAGCCTTTG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-----------AAAAAGCCTTCGGGAG-CTTT-
* *
40362 GGAGTTTTTTGATATTTACAAAAGCCTTAGGGT
53 --------TTGATGTTTTCAAAAGCCTTAGGGT
40395 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
40459 AAGCCTTCGAGT
66 AAGCCTTAGGGT
40471 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
40501 TCAACATTTC
Statistics
Matches: 538, Mismatches: 26, Indels: 46
0.88 0.04 0.08
Matches are distributed among these distances:
75 3 0.01
76 251 0.47
77 207 0.38
86 4 0.01
87 7 0.01
88 7 0.01
89 4 0.01
98 55 0.10
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (77 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AAGCCTTAGGGT
Found at i:40335 original size:1 final size:1
Alignment explanation
Indices: 40329--40354 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
40319 TGATGTTTCC
40329 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
40355 GCCTTTGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40386 original size:175 final size:174
Alignment explanation
Indices: 40175--40500 Score: 589
Period size: 175 Copynumber: 1.9 Consensus size: 174
40165 TGATGTTTCC
* *
40175 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTG
1 AAAAAGCCTTCGGGAGCTTTTTGATATTTACAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTG
*
40240 CATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAGCCTTAGGGTCATCTGTA
66 CATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-AAAGCCTTAGAGTCATCTGTA
40305 AGTCCTTCAGTGCATGATGTTTCCAAAAAAAAAAAAAAAAAAAAA
130 AGTCCTTCAGTGCATGATGTTTCCAAAAAAAAAAAAAAAAAAAAA
* *
40350 AAAAAGCCTTTGGGAGTTTTTTGATATTTACAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTG
1 AAAAAGCCTTCGGGAGCTTTTTGATATTTACAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTG
*
40415 CATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGAGTCATCTGTAA
66 CATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGAGTCATCTGTAA
40480 GTCCTTCAGTGCATGATGTTT
131 GTCCTTCAGTGCATGATGTTT
40501 TCAACATTTC
Statistics
Matches: 145, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
174 41 0.28
175 104 0.72
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (174 bp):
AAAAAGCCTTCGGGAGCTTTTTGATATTTACAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTG
CATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGAGTCATCTGTAA
GTCCTTCAGTGCATGATGTTTCCAAAAAAAAAAAAAAAAAAAAA
Found at i:40421 original size:98 final size:98
Alignment explanation
Indices: 40252--40431 Score: 324
Period size: 98 Copynumber: 1.8 Consensus size: 98
40242 TGATGTTTCC
* *
40252 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTG
1 AAAAAGCCTTCGGGAGCTTTTTGATATTTACAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTG
40317 CATGATGTTTCCAAAAAAAAAAAAAAAAAAAAA
66 CATGATGTTTCCAAAAAAAAAAAAAAAAAAAAA
* *
40350 AAAAAGCCTTTGGGAGTTTTTTGATATTTACAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTG
1 AAAAAGCCTTCGGGAGCTTTTTGATATTTACAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTG
40415 CATGATGTTTCCAAAAA
66 CATGATGTTTCCAAAAA
40432 GCCTTCGGGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 78 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (98 bp):
AAAAAGCCTTCGGGAGCTTTTTGATATTTACAAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTG
CATGATGTTTCCAAAAAAAAAAAAAAAAAAAAA
Found at i:40657 original size:15 final size:15
Alignment explanation
Indices: 40633--40665 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40623 TTTTTTTCAT
*
40633 TTAAATTTATTATTA
1 TTAAAATTATTATTA
40648 TTAAAATTATTATTA
1 TTAAAATTATTATTA
40663 TTA
1 TTA
40666 TTATTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAAATTATTATTA
Found at i:40711 original size:3 final size:3
Alignment explanation
Indices: 40639--40700 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
40629 TCATTTAAAT
** *
40639 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA -AA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
40684 TTA GTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
40701 AATAATTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 3 0.06
3 44 0.90
4 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:41105 original size:16 final size:16
Alignment explanation
Indices: 41084--41118 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41074 CGGAGAGACA
41084 AAAAACA-GAAAAGAAG
1 AAAAACAGGAAAA-AAG
41100 AAAAACAGGAAAAAAG
1 AAAAACAGGAAAAAAG
41116 AAA
1 AAA
41119 GAAAGAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAACAGGAAAAAAG
Found at i:41122 original size:20 final size:19
Alignment explanation
Indices: 41092--41131 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
41082 CAAAAAACAG
41092 AAAAGAAGAAA-AACAGGAA
1 AAAAGAAGAAAGAA-AGGAA
41111 AAAAGAAAGAAAGAAAGGAA
1 AAAAG-AAGAAAGAAAGGAA
41131 A
1 A
41132 GCTTACCGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 12 0.63
21 2 0.11
ACGTcount: A:0.75, C:0.03, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAGAAGAAAGAAAGGAA
Found at i:41907 original size:19 final size:18
Alignment explanation
Indices: 41883--41935 Score: 65
Period size: 16 Copynumber: 3.0 Consensus size: 18
41873 TAATTTAGTC
41883 ATTTATTTTATATGTTTTA
1 ATTTATTTTAT-TGTTTTA
41902 ATTTATTTTATTGTTTT-
1 ATTTATTTTATTGTTTTA
* *
41919 -TTTAATATATTGTTTTA
1 ATTTATTTTATTGTTTTA
41936 GTAGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 14 0.45
18 6 0.19
19 11 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.70
Consensus pattern (18 bp):
ATTTATTTTATTGTTTTA
Found at i:41986 original size:20 final size:21
Alignment explanation
Indices: 41949--41989 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41939 GAATTTTTTC
**
41949 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
41970 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
41990 ATATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:45144 original size:29 final size:29
Alignment explanation
Indices: 45108--45172 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
45098 TATGATAAAA
*
45108 AATCAATGTGACTATTGAACTTTAAATTG
1 AATCAATGTGACTACTGAACTTTAAATTG
45137 AATCAATGTGACTACTGAACTTTAAATTG
1 AATCAATGTGACTACTGAACTTTAAATTG
45166 AATCAAT
1 AATCAAT
45173 CAGACCACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (29 bp):
AATCAATGTGACTACTGAACTTTAAATTG
Found at i:46439 original size:22 final size:22
Alignment explanation
Indices: 46396--46439 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
46386 ATTATATTGT
*
46396 ATGAACAGTACCGTAAATAGTA
1 ATGAACAGTACCGTAAACAGTA
* *
46418 ATGAACTGTACCGTGAACAGTA
1 ATGAACAGTACCGTAAACAGTA
46440 CCGATTCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (22 bp):
ATGAACAGTACCGTAAACAGTA
Found at i:47167 original size:32 final size:31
Alignment explanation
Indices: 47041--47165 Score: 162
Period size: 31 Copynumber: 3.9 Consensus size: 31
47031 TATAATAATC
* * *
47041 TGTCCATATGTCCC-GATGAACATAGGTAAAC
1 TGTCCATATGTCCCAAAAG-ACATAGGTAAAT
*
47072 TGTCCATATGTCCCGAAAGACATAGGTAAAT
1 TGTCCATATGTCCCAAAAGACATAGGTAAAT
47103 TGTCCATATATGTCCCAAAAGACATAGGTAATAT
1 TGTCC--ATATGTCCCAAAAGACATAGGTAA-AT
*
47137 TGTTCATATGTCCCAAAAGACATAGGTAA
1 TGTCCATATGTCCCAAAAGACATAGGTAA
47166 TACCTCGACT
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
31 30 0.35
32 26 0.31
33 23 0.27
34 6 0.07
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (31 bp):
TGTCCATATGTCCCAAAAGACATAGGTAAAT
Found at i:48574 original size:10 final size:10
Alignment explanation
Indices: 48559--48594 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
48549 GGAGAGGAAG
48559 AAGAAGAAAT
1 AAGAAGAAAT
*
48569 AAGAAGAAAG
1 AAGAAGAAAT
48579 AAGAAG-AAT
1 AAGAAGAAAT
48588 AAGAAGA
1 AAGAAGA
48595 GAGTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (10 bp):
AAGAAGAAAT
Found at i:51657 original size:17 final size:17
Alignment explanation
Indices: 51635--51675 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
51625 TACATTTGAT
*
51635 TTTTTTATTT-TATTTTG
1 TTTTTTATTTGT-TTTTA
51652 TTTTTTATTTGTTTTTA
1 TTTTTTATTTGTTTTTA
51669 TTTTTTA
1 TTTTTTA
51676 CTCAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (17 bp):
TTTTTTATTTGTTTTTA
Found at i:54754 original size:26 final size:23
Alignment explanation
Indices: 54707--54754 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
54697 CTCTTATTCT
*
54707 TTATTCTTCTCTCCTAATCCAAC
1 TTATTCTTCTCTCCTAAACCAAC
54730 TTATTCTTTCTCTCTCTAGAACCAA
1 TTATTC-TTCTCTC-CTA-AACCAA
54755 ATTAAGCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 3 0.14
26 5 0.24
ACGTcount: A:0.23, C:0.31, G:0.02, T:0.44
Consensus pattern (23 bp):
TTATTCTTCTCTCCTAAACCAAC
Found at i:57286 original size:9 final size:9
Alignment explanation
Indices: 57272--57327 Score: 60
Period size: 9 Copynumber: 6.2 Consensus size: 9
57262 TTTTATCCAG
57272 TTTTATTAT
1 TTTTATTAT
57281 TTTTATTAT
1 TTTTATTAT
*
57290 TATTATTAT
1 TTTTATTAT
*
57299 TATTATTAT
1 TTTTATTAT
*
57308 TTATTAATAT
1 TT-TTATTAT
*
57318 TATTA-TAT
1 TTTTATTAT
57326 TT
1 TT
57328 ACAGGCCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
8 4 0.10
9 30 0.73
10 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTATTAT
Found at i:57289 original size:3 final size:3
Alignment explanation
Indices: 57274--57323 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
57264 TTATCCAGTT
* *
57274 TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
57320 TTA T
1 TTA T
57324 ATTTACAGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:58850 original size:17 final size:19
Alignment explanation
Indices: 58828--58863 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
58818 TTTTTAAATA
58828 TATAAA-TATAT-TATTTT
1 TATAAATTATATATATTTT
58845 TATAAATTATATATATTTT
1 TATAAATTATATATATTTT
58864 AAATTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATAAATTATATATATTTT
Found at i:58913 original size:134 final size:136
Alignment explanation
Indices: 58752--58997 Score: 383
Period size: 135 Copynumber: 1.8 Consensus size: 136
58742 TAATCATGTT
*
58752 TTAATATTTATTTTTTAATATTAAG-AAAGGGCAGTCTTAAAGCAACTAGATG-TCTATTTTCTG
1 TTAATATTTATTTTTCAATATTAAGAAAAGGGCAGTCTTAAAGCAACTAGATGTTC-ATTTTCTG
* * *
58815 ATATTTTTAAATATATAAATATATTATT-TTTATAAAT-TATATATATTTTAAATTACTAGATAA
65 ATATTTCTAAATAGATAAATATATT-TTATATATAAATATATATATATTTTAAATTACTAGATAA
58878 ATATTTTA
129 ATATTTTA
*
58886 TTAATATTTATTTTTCAATATTAAGAAAAGTGCAGTCTTAAAGCAACTAGATGTTCATTTTCTGA
1 TTAATATTTATTTTTCAATATTAAGAAAAGGGCAGTCTTAAAGCAACTAGATGTTCATTTTCTGA
* *
58951 TATTTCTAAATAGATAAATATCTTTTATATATATATATATATATATT
66 TATTTCTAAATAGATAAATATATTTTATATATAAATATATATATATT
58998 AATAGATTTT
Statistics
Matches: 101, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
134 26 0.26
135 63 0.62
136 12 0.12
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.47
Consensus pattern (136 bp):
TTAATATTTATTTTTCAATATTAAGAAAAGGGCAGTCTTAAAGCAACTAGATGTTCATTTTCTGA
TATTTCTAAATAGATAAATATATTTTATATATAAATATATATATATTTTAAATTACTAGATAAAT
ATTTTA
Found at i:60902 original size:3 final size:3
Alignment explanation
Indices: 60894--60918 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
60884 TTTCGGGCCT
60894 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
60919 GGGACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:63203 original size:2 final size:2
Alignment explanation
Indices: 63196--63253 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
63186 AAATTAAAAC
63196 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
63238 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
63254 AAGAAAACAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:77771 original size:3 final size:3
Alignment explanation
Indices: 77746--77813 Score: 77
Period size: 3 Copynumber: 22.3 Consensus size: 3
77736 AATAAGAAAC
* *
77746 AAT AAT AAAT AA- AAT AAT TAT AAT AAT AAT AAAT GAT AAT AAT AAAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT
77793 AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
77814 GTATATATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
2 4 0.07
3 43 0.77
4 9 0.16
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:77786 original size:13 final size:13
Alignment explanation
Indices: 77746--77813 Score: 90
Period size: 13 Copynumber: 5.5 Consensus size: 13
77736 AATAAGAAAC
77746 AATAATAAATAA-
1 AATAATAAATAAT
*
77758 AATAAT-TATAAT
1 AATAATAAATAAT
*
77770 AATAATAAATGAT
1 AATAATAAATAAT
77783 AATAATAAATAAT
1 AATAATAAATAAT
77796 AATAAT-AATAAT
1 AATAATAAATAAT
77808 -ATAATA
1 AATAATA
77814 GTATATATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.18
12 18 0.37
13 22 0.45
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:77786 original size:16 final size:16
Alignment explanation
Indices: 77746--77813 Score: 75
Period size: 16 Copynumber: 4.1 Consensus size: 16
77736 AATAAGAAAC
77746 AATAATAAATAAAATAAT
1 AATAAT-AAT-AAATAAT
*
77764 TATAATAAT-AATAAAT
1 AATAATAATAAAT-AAT
*
77780 GATAATAATAAATAAT
1 AATAATAATAAATAAT
77796 AATAATAATAATATAAT
1 AATAATAATAA-ATAAT
77813 A
1 A
77814 GTATATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
15 3 0.07
16 24 0.55
17 12 0.27
18 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (16 bp):
AATAATAATAAATAAT
Found at i:77819 original size:10 final size:10
Alignment explanation
Indices: 77746--77824 Score: 60
Period size: 9 Copynumber: 8.1 Consensus size: 10
77736 AATAAGAAAC
*
77746 AATAATAAAT
1 AATAATATAT
77756 AA-AATA-AT
1 AATAATATAT
*
77764 TATAATA-AT
1 AATAATATAT
77773 AATAA-ATGAT
1 AATAATAT-AT
*
77783 AATAATAAAT
1 AATAATATAT
77793 AATAATA-AT
1 AATAATATAT
77802 AATAATATAAT
1 AATAATAT-AT
*
77813 AGTATATATAT
1 AATA-ATATAT
77824 A
1 A
77825 TAAATATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
8 4 0.07
9 23 0.40
10 18 0.31
11 9 0.16
12 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (10 bp):
AATAATATAT
Found at i:77890 original size:38 final size:37
Alignment explanation
Indices: 77842--77928 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 37
77832 TTTAAAAAAC
*
77842 ATATAATATATAATTTCCAAAAATGCTTTAAAAAAATT
1 ATATATTATATAATTTCC-AAAATGCTTTAAAAAAATT
* * **
77880 ATATATTATAT-ATTTTCAAAATGGTTTTTAAAAATT
1 ATATATTATATAATTTCCAAAATGCTTTAAAAAAATT
77916 ATATATTATATAA
1 ATATATTATATAA
77929 ATGTTTTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 27 0.63
37 6 0.14
38 10 0.23
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (37 bp):
ATATATTATATAATTTCCAAAATGCTTTAAAAAAATT
Found at i:77957 original size:36 final size:36
Alignment explanation
Indices: 77874--78013 Score: 106
Period size: 36 Copynumber: 3.8 Consensus size: 36
77864 ATGCTTTAAA
* ** *
77874 AAAATTATATATTAT--ATATTTTCAAAATGGTTTTTA
1 AAAAGTATATATTATAAATATTTT-AAAAACG-TTTTC
* * * *
77910 AAAATTATATATTATATAAATGTTTTCATAACGTTTTC
1 AAAAGTATATA-T-TATAAATATTTTAAAAACGTTTTC
*
77948 AAAAGTATATATTATATATATTTTAAAAACGTTTTC
1 AAAAGTATATATTATAAATATTTTAAAAACGTTTTC
* *
77984 AAAAACTATATATTATATAAT-TTTCAAAAA
1 -AAAAGTATATATTATA-AATATTTTAAAAA
78014 ATATATTTTC
Statistics
Matches: 84, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
36 31 0.37
37 25 0.30
38 19 0.23
39 3 0.04
40 6 0.07
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAAGTATATATTATAAATATTTTAAAAACGTTTTC
Found at i:77996 original size:28 final size:26
Alignment explanation
Indices: 77961--78065 Score: 72
Period size: 28 Copynumber: 3.9 Consensus size: 26
77951 AGTATATATT
*
77961 ATATATATTTTAAAAACGTTTTCAAAA
1 ATATATATTATAAAAA-GTTTTCAAAA
*
77988 ACTATATATTAT-ATAA-TTTTCAAAA
1 A-TATATATTATAAAAAGTTTTCAAAA
* * *
78013 A-ATATATTTTCAAAATGGTTTTTTAAAA
1 ATATATATTAT-AAAA-AG-TTTTCAAAA
*
78041 ATTATATATTATATAAATGTTTTCA
1 A-TATATATTATA-AAAAGTTTTCA
78066 TAACGTTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
23 8 0.13
25 12 0.20
27 4 0.07
28 23 0.38
29 2 0.03
30 11 0.18
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (26 bp):
ATATATATTATAAAAAGTTTTCAAAA
Found at i:78023 original size:15 final size:16
Alignment explanation
Indices: 77998--78027 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
77988 ACTATATATT
77998 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
78014 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
78028 TGGTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:78053 original size:128 final size:127
Alignment explanation
Indices: 77887--78141 Score: 492
Period size: 128 Copynumber: 2.0 Consensus size: 127
77877 ATTATATATT
77887 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
77952 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
78014 ATATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAA
1 ATATATTTTCAAAATGG-TTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAA
*
78079 AGTATATATTATATATATTTTATAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
65 AGTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
78142 TATTTTAAAA
Statistics
Matches: 126, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
127 17 0.13
128 109 0.87
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (127 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
Found at i:78187 original size:38 final size:37
Alignment explanation
Indices: 78014--78216 Score: 157
Period size: 36 Copynumber: 5.4 Consensus size: 37
78004 TTTTCAAAAA
*
78014 ATATATTTTC-AAAATGGTTTTTTAAAAATTATATATTATAT
1 ATATATTTTCAAAAAT-G--TTTTAAAAACTATATA--ATAT
* * * * * * *
78055 AAATGTTTTC-ATAACGTTTTCAAAAGTATATATTAT
1 ATATATTTTCAAAAATGTTTTAAAAACTATATAATAT
* * *
78091 ATATATTTT-ATAAACGTTTTCAAAAACTATATATTAT
1 ATATATTTTCAAAAATGTTTT-AAAAACTATATAATAT
*
78128 ATA-ATTTTCAAAAATATTTTAAAAACTATATAATAT
1 ATATATTTTCAAAAATGTTTTAAAAACTATATAATAT
*
78164 ACATATTTTCAAAAAATGTTTT--AAACTATATATTATAT
1 ATATATTTTC-AAAAATGTTTTAAAAACTATATA--ATAT
*
78202 ATGTATTTTCAAAAA
1 ATATATTTTCAAAAA
78217 CAATTTGCAA
Statistics
Matches: 134, Mismatches: 21, Indels: 18
0.77 0.12 0.10
Matches are distributed among these distances:
36 50 0.37
37 36 0.27
38 36 0.27
40 1 0.01
41 11 0.08
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATATTTTCAAAAATGTTTTAAAAACTATATAATAT
Found at i:78190 original size:36 final size:37
Alignment explanation
Indices: 78071--78242 Score: 145
Period size: 37 Copynumber: 4.6 Consensus size: 37
78061 TTTCATAACG
* * * * **
78071 TTTTCAAAAGTATATATTATATATATTTT-ATAAACG
1 TTTTAAAAACTATATAATATATATATTTTCAAAAATA
*
78107 TTTTCAAAAACTATATATTATATA-ATTTTCAAAAATA
1 TTTT-AAAAACTATATAATATATATATTTTCAAAAATA
*
78144 TTTTAAAAACTATATAATATACATATTTTCAAAAA-A
1 TTTTAAAAACTATATAATATATATATTTTCAAAAATA
* * *
78180 TGTTT-TAAACTATATATTATATATGTATTTTCAAAAACA
1 T-TTTAAAAACTATATA--ATATATATATTTTCAAAAATA
* ** *
78219 ATTTGCAAACTATATGATATATAT
1 TTTTAAAAACTATATAATATATAT
78243 GTGTATATAT
Statistics
Matches: 114, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
36 38 0.33
37 46 0.40
38 20 0.18
39 10 0.09
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTTAAAAACTATATAATATATATATTTTCAAAAATA
Found at i:78970 original size:81 final size:80
Alignment explanation
Indices: 78863--79415 Score: 595
Period size: 81 Copynumber: 6.7 Consensus size: 80
78853 AAGTTGAATA
* * *
78863 TAATCGAACTCAAAGGTCTTTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
78928 CCTTGGAAGCTGAGTG
66 CCTTGG-AGCTGAGCG
****
78944 TAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
79009 CCTTGGAGCTGAGCG
66 CCTTGGAGCTGAGCG
* * *
79024 TAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCAAAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * *
79089 TGTGCCCTCGAAGCTGAGTG
62 TGTG-CCTTGGAGCTGAGCG
****
79109 TAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
79174 CCGTT-GAGCTGAGCG
66 CC-TTGGAGCTGAGCG
* * * * * * * * *
79189 TAGTCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGT
1 TAATCGAACTCAAAGGTC-TTTG---GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * *
79254 TATGCCCTTGAAGCTGAGTG
62 TGTG-CCTTGGAGCTGAGCG
* * * *
79274 TAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
79339 CCTTGGAGCTGAGCA
66 CCTTGGAGCTGAGCG
* * * * * *
79354 TAGTCGAACTCGAAGGTCTTGGTGGGCAGATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 TAATCGAACTCAAAGGTCTT--T-GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
79416 AGTTTGTTTA
Statistics
Matches: 386, Mismatches: 71, Indels: 28
0.80 0.15 0.06
Matches are distributed among these distances:
80 72 0.19
81 145 0.38
82 2 0.01
83 33 0.09
84 84 0.22
85 50 0.13
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (80 bp):
TAATCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCG
Found at i:79059 original size:165 final size:163
Alignment explanation
Indices: 78866--79415 Score: 775
Period size: 165 Copynumber: 3.4 Consensus size: 163
78856 TTGAATATAA
*
78866 TCGAACTCAAAGGTC-T--TTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCAAAGGTCTTGGTTAGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
78928 CCTTGGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
66 CCTT-GAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
78993 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
130 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * *
79027 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCAAAGGTC-TTGGTTAGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
*
79092 GCCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
65 G-CCTTGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
79157 ATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAG
129 ATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAG
* * * * * * * * *
79192 TCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTAT
1 TCGAACTCAAAGGTC-TTGGTTAGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
** *
79257 GCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCT
65 G-CCTTGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
* *
79322 ATACTGCAAATGATGTGCCTTGGAGCTGAGCATAG
129 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* ** * * * * *
79357 TCGAACTCGAAGGTCTTGGTGGGCAGATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 TCGAACTCAAAGGTCTTGGTTAGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAAT
79416 AGTTTGTTTA
Statistics
Matches: 351, Mismatches: 31, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
161 15 0.04
163 1 0.00
164 36 0.10
165 294 0.84
166 5 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (163 bp):
TCGAACTCAAAGGTCTTGGTTAGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
CCTTGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
Found at i:82446 original size:18 final size:19
Alignment explanation
Indices: 82406--82450 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
82396 AGTTAATGTG
*
82406 AATGCAATGAAAATAACAA
1 AATGCAAAGAAAATAACAA
82425 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAACAA
82443 AATGCAAA
1 AATGCAAA
82451 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:83101 original size:17 final size:17
Alignment explanation
Indices: 83075--83107 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
83065 TGCAAACGAT
*
83075 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
83092 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
83108 GGTTAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:84222 original size:13 final size:13
Alignment explanation
Indices: 84206--84233 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
84196 AAAGCGAATC
84206 AAAAAAATAAAAT
1 AAAAAAATAAAAT
84219 AAAAAAATAAAAT
1 AAAAAAATAAAAT
84232 AA
1 AA
84234 TAAAGTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:85506 original size:3 final size:3
Alignment explanation
Indices: 85481--85558 Score: 74
Period size: 3 Copynumber: 26.3 Consensus size: 3
85471 AATAAGAAAC
* *
85481 AAT AAT AAAT AA- AAT AAT TAT AAT AAT AAT AAT GAT AAT AAAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
*
85527 AAT AAT AAT -AT AAT AGT -AT AAT ATAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A
85559 TTTTAAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
2 7 0.11
3 46 0.74
4 9 0.15
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:85524 original size:33 final size:31
Alignment explanation
Indices: 85482--85558 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
85472 ATAAGAAACA
*
85482 ATAATAAATAAAATAATTATAATAATAATAAT
1 ATAATAAATAAAATAATAATAAT-ATAATAAT
*
85514 GATAATAAAT--AATAATAATAATATAATAGT
1 -ATAATAAATAAAATAATAATAATATAATAAT
*
85544 ATAATATATAAAATA
1 ATAATAAATAAAATA
85559 TTTTAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 8 0.21
30 7 0.18
31 15 0.38
33 9 0.23
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (31 bp):
ATAATAAATAAAATAATAATAATATAATAAT
Found at i:85528 original size:22 final size:21
Alignment explanation
Indices: 85463--85559 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 21
85453 AAAAAAACAA
* *
85463 AATAATTAA-ATAAGAAACAAT
1 AATAA-TAATATAATAAATAAT
* *
85484 AATAAATAAAATAAT-TATAAT
1 AAT-AATAATATAATAAATAAT
85505 AATAATAATGATAATAAATAAT
1 AATAATAAT-ATAATAAATAAT
*
85527 AATAATAATATAATAGTATAAT
1 AATAATAATATAATA-AATAAT
85549 ATATAA-AATAT
1 A-ATAATAATAT
85560 TTTAAAAAAC
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.08
21 24 0.38
22 31 0.48
23 4 0.06
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (21 bp):
AATAATAATATAATAAATAAT
Found at i:85547 original size:19 final size:22
Alignment explanation
Indices: 85482--85558 Score: 51
Period size: 19 Copynumber: 3.7 Consensus size: 22
85472 ATAAGAAACA
* *
85482 ATAATAAATAA-AATAATTATA
1 ATAATAAATAATAATAATAATG
*
85503 ATAAT-AATAATGATAATAA--
1 ATAATAAATAATAATAATAATG
85522 ATAAT-AATAATAAT-ATAATAG
1 ATAATAAATAATAATAATAAT-G
*
85543 TATAATATATAA-AATA
1 -ATAATAAATAATAATA
85559 TTTTAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
18 4 0.09
19 13 0.29
20 5 0.11
21 11 0.24
22 8 0.18
23 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (22 bp):
ATAATAAATAATAATAATAATG
Found at i:85648 original size:34 final size:33
Alignment explanation
Indices: 85559--85648 Score: 99
Period size: 33 Copynumber: 2.6 Consensus size: 33
85549 ATATAAAATA
**
85559 TTTTAAAAAACATATAATATAATTTCCAAAATGCT
1 TTTTAAAAATTATAT-ATAT-ATTTCCAAAATGCT
** * *
85594 TTAAAAAAATTATATATATATTTTCAAAATGGT
1 TTTTAAAAATTATATATATATTTCCAAAATGCT
85627 TTTTAAAAATTATATATTATAT
1 TTTTAAAAATTATATA-TATAT
85649 AAATGTTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 26 0.57
34 9 0.20
35 11 0.24
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (33 bp):
TTTTAAAAATTATATATATATTTCCAAAATGCT
Found at i:85649 original size:75 final size:76
Alignment explanation
Indices: 85570--85726 Score: 169
Period size: 75 Copynumber: 2.1 Consensus size: 76
85560 TTTAAAAAAC
* ** *
85570 ATATAATATAATTTCCAAAATGCTTT-AAAAAAAT-TA-TATATATATTTTCAAAATGGTTTTTA
1 ATATAATAT-ATTTCCAAAACGCTTTCAAAAAAATATATTATATATATTTT-AAAAACGTTTTCA
*
85632 AAAATTATATATT
64 AAAACTATATATT
* * * * **
85645 ATATAA-ATGTTTTCATAACGTTTTCAAAAGTATATATTATATATATTTTAAAAACGTTTTCAAA
1 ATATAATATATTTCCAAAACGCTTTCAAAAAAATATATTATATATATTTTAAAAACGTTTTCAAA
85709 AACTATATATT
66 AACTATATATT
85720 ATATAAT
1 ATATAAT
85727 TTTCAAAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
73 11 0.16
74 8 0.12
75 36 0.54
76 12 0.18
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (76 bp):
ATATAATATATTTCCAAAACGCTTTCAAAAAAATATATTATATATATTTTAAAAACGTTTTCAAA
AACTATATATT
Found at i:85679 original size:36 final size:36
Alignment explanation
Indices: 85627--85735 Score: 103
Period size: 37 Copynumber: 2.9 Consensus size: 36
85617 TCAAAATGGT
* * * * *
85627 TTTTAAAAATTATATATTATATAAATGTTTTCATAACG
1 TTTTCAAAAGTATATA-T-TATAAATATTTTAAAAACG
*
85665 TTTTCAAAAGTATATATTATATATATTTTAAAAACG
1 TTTTCAAAAGTATATATTATAAATATTTTAAAAACG
* *
85701 TTTTCAAAAACTATATATTATATAAT-TTTCAAAAA
1 TTTTC-AAAAGTATATATTATA-AATATTTTAAAAA
85736 ATATATTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
36 20 0.33
37 24 0.40
38 16 0.27
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTCAAAAGTATATATTATAAATATTTTAAAAACG
Found at i:85745 original size:15 final size:16
Alignment explanation
Indices: 85720--85749 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
85710 ACTATATATT
85720 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
85736 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
85750 TGGTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:85747 original size:127 final size:122
Alignment explanation
Indices: 85609--85857 Score: 419
Period size: 128 Copynumber: 2.0 Consensus size: 122
85599 AAAATTATAT
*
85609 ATATATTTTCAAAATGG-TTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAA
1 ATATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATATTTTCATAACGTTTTC-AA
85673 AGTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
65 AGTATATA-T-TATATATTTTAAAAACGTTTTC-AAAACTATATA-T-TATAATTTTCAAAAA
85736 ATATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATATTTTCATAACGTTTTCAAA
1 ATATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATATTTTCATAACGTTTTCAAA
*
85801 GTATATATTATATATTTTATAAACGTTTTCAAAACTATATATTATAATTTTCAAAAA
66 GTATATATTATATATTTTAAAAACGTTTTCAAAACTATATATTATAATTTTCAAAAA
85858 TATTTTAAAA
Statistics
Matches: 119, Mismatches: 2, Indels: 7
0.93 0.02 0.05
Matches are distributed among these distances:
122 15 0.13
123 1 0.01
124 11 0.09
125 21 0.18
126 1 0.01
127 27 0.23
128 43 0.36
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (122 bp):
ATATATTTTCAAAATGGTTTTTTAAAAATTATATATTATATAAATATTTTCATAACGTTTTCAAA
GTATATATTATATATTTTAAAAACGTTTTCAAAACTATATATTATAATTTTCAAAAA
Found at i:85845 original size:34 final size:34
Alignment explanation
Indices: 85779--85917 Score: 135
Period size: 34 Copynumber: 4.1 Consensus size: 34
85769 TATTATATAA
* *
85779 ATATTTTC-ATAACGTTTTCAAAGTATATATTAT
1 ATATTTTCAAAAACGTTTTCAAACTATATATTAT
*
85812 ATATTTT-ATAAACGTTTTCAAAACTATATATTAT
1 ATATTTTCAAAAACGTTTTC-AAACTATATATTAT
** * *
85846 A-ATTTTCAAAAATATTTTAAAAACTATA-ATATAC
1 ATATTTTCAAAAACGTTTT-CAAACTATATAT-TAT
*
85880 ATATTTTCAAAAAATGTTTT-AAACTATATATTAT
1 ATATTTTC-AAAAACGTTTTCAAACTATATATTAT
85914 ATAT
1 ATAT
85918 GTATTTTCAA
Statistics
Matches: 88, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
33 23 0.26
34 47 0.53
35 8 0.09
36 10 0.11
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (34 bp):
ATATTTTCAAAAACGTTTTCAAACTATATATTAT
Found at i:85954 original size:39 final size:38
Alignment explanation
Indices: 85881--85958 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 38
85871 ATAATATACA
*
85881 TATTTTCAAAAAATGTTTTAAACTATATATTATATATG
1 TATTTTCAAAAAATGTTGTAAACTATATATTATATATG
85919 TATTTTCAAAAACAAT-TTGTAAACTATATGA-TATATATG
1 TATTTTC-AAAA-AATGTTGTAAACTATAT-ATTATATATG
85958 T
1 T
85959 GTATATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
38 7 0.19
39 25 0.69
40 4 0.11
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (38 bp):
TATTTTCAAAAAATGTTGTAAACTATATATTATATATG
Found at i:88351 original size:4 final size:4
Alignment explanation
Indices: 88342--88388 Score: 85
Period size: 4 Copynumber: 11.5 Consensus size: 4
88332 AGGTTCTTTG
88342 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCTT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TT
88389 TTCCGCTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 38 0.90
5 4 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:90786 original size:16 final size:17
Alignment explanation
Indices: 90749--90789 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
90739 AATTAACTAA
90749 AATTTATA-AATAATAT
1 AATTTATATAATAATAT
* *
90765 ATTTTATATATTAA-AT
1 AATTTATATAATAATAT
90781 AATTTATAT
1 AATTTATAT
90790 TTTTTGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTATATAATAATAT
Found at i:92273 original size:31 final size:31
Alignment explanation
Indices: 92222--92289 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
92212 GTAAATCGAT
* *
92222 CATTTTGTTACTAATCGATAACGTTAGTGAC
1 CATTTTATTACAAATCGATAACGTTAGTGAC
* * *
92253 CATTTTATTACAAATTGATAATGTTGGTGAC
1 CATTTTATTACAAATCGATAACGTTAGTGAC
92284 CATTTT
1 CATTTT
92290 GTCACTTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (31 bp):
CATTTTATTACAAATCGATAACGTTAGTGAC
Found at i:104162 original size:64 final size:65
Alignment explanation
Indices: 104082--104222 Score: 189
Period size: 64 Copynumber: 2.2 Consensus size: 65
104072 AAGGAAAAAT
* * *
104082 AATTTATTTGAAAATTATTAACCGAAT-TAACTGA-ATTTTTTTCTTTAACCATTAATCGAATCG
1 AATTTATTTGAAAATTATTAACCGAATCAAACTAACATTTTTTTCTTTAA-CATTAATCGAACCG
104145 A
65 A
* *
104146 AATTTATTTGGAAATTATTAACCGAATCAAATTAATCGATTTTTTTCTTTAACATTAATCGAACC
1 AATTTATTTGAAAATTATTAACCGAATCAAACTAA-C-ATTTTTTTCTTTAACATTAATCGAACC
104211 GA
64 GA
104213 AA-TTATTTGA
1 AATTTATTTGA
104223 CCGTTAATCG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
64 26 0.39
65 4 0.06
66 7 0.10
67 16 0.24
68 14 0.21
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (65 bp):
AATTTATTTGAAAATTATTAACCGAATCAAACTAACATTTTTTTCTTTAACATTAATCGAACCGA
Found at i:104431 original size:95 final size:93
Alignment explanation
Indices: 104133--104453 Score: 462
Period size: 94 Copynumber: 3.4 Consensus size: 93
104123 TCTTTAACCA
* * *
104133 TTAATCGAATCGAAATTTATTTGGAAATTATTAACCGAATCAAATTAATCGATTTTTTTCTTTAA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATCGATTTTTTTCTTTAA
104198 CATTAATCGAACCGAAATTATTTGACCG
66 CATTAATCGAACCGAAATTATTTGACCG
* * * *
104226 TTAATCGAACCGAGATTTATTTGAAAATTATTAATCTAACCAAATTAATTGAGTTTTTTTCTTTA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATCGA-TTTTTTTCTTTA
* * *
104291 ACATTAAACGAACCGAAATTATTAGACAG
65 ACATTAATCGAACCGAAATTATTTGACCG
* * * * *
104320 GTAATCGAACCCAAATTTATTTGAAAATTATTAACCGAACCTAATCAACCGATTTTTTTTCTTTA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATCGA-TTTTTTTCTTTA
104385 ACTATTAATCGAACCGAAATTATTTGACCG
65 AC-ATTAATCGAACCGAAATTATTTGACCG
* *
104415 TTAATCGAATCTAAATTTATTTGAAAATTATTAACCGAA
1 TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAA
104454 TTAACCGAAT
Statistics
Matches: 200, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
93 45 0.22
94 95 0.47
95 60 0.30
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (93 bp):
TTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAATTAATCGATTTTTTTCTTTAA
CATTAATCGAACCGAAATTATTTGACCG
Found at i:105926 original size:16 final size:17
Alignment explanation
Indices: 105905--105936 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
105895 ACTATTCACG
105905 TGAATAGT-AAATTTTA
1 TGAATAGTGAAATTTTA
105921 TGAATAGTGAAATTTT
1 TGAATAGTGAAATTTT
105937 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (17 bp):
TGAATAGTGAAATTTTA
Found at i:114483 original size:32 final size:33
Alignment explanation
Indices: 114442--114523 Score: 114
Period size: 32 Copynumber: 2.5 Consensus size: 33
114432 GTGATGCTGA
114442 CTATACTATGCATTATCTGAATACAATACTGATT
1 CTAT-CTATGCATTATCTGAATACAATACTGATT
* *
114476 CT-TCTATGCATTATCTGAATGCAATATTGATT
1 CTATCTATGCATTATCTGAATACAATACTGATT
*
114508 CTAT-TGTGCATTATCT
1 CTATCTATGCATTATCT
114524 AAAAGCAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 40 0.91
33 2 0.05
34 2 0.05
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (33 bp):
CTATCTATGCATTATCTGAATACAATACTGATT
Found at i:114532 original size:32 final size:32
Alignment explanation
Indices: 114447--114535 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
114437 GCTGACTATA
*
114447 CTATGCATTATCTGAATA-CAATACTGATTCTT
1 CTATGCATTATCT-AAAAGCAATACTGATTCTT
* * *
114479 CTATGCATTATCTGAATGCAATATTGATTCTAT
1 CTATGCATTATCTAAAAGCAATACTGATTCT-T
*
114512 -TGTGCATTATCTAAAAGCAATACT
1 CTATGCATTATCTAAAAGCAATACT
114536 AACTTTATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
31 1 0.02
32 45 0.96
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (32 bp):
CTATGCATTATCTAAAAGCAATACTGATTCTT
Done.