Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006968.1 Hibiscus syriacus cultivar Beakdansim tig00017942_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: 68578
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2225 original size:28 final size:29
Alignment explanation
Indices: 2194--2250 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2184 AGTTGAATAG
2194 CTCATAAAGT-TATATAAAAAAACATCAA
1 CTCATAAAGTGTATATAAAAAAACATCAA
*
2222 CTCATAAAGTGTATATAAAAAGACATCAA
1 CTCATAAAGTGTATATAAAAAAACATCAA
2251 TTTCTGCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (29 bp):
CTCATAAAGTGTATATAAAAAAACATCAA
Found at i:6436 original size:26 final size:26
Alignment explanation
Indices: 6406--6457 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6396 CAATGTATAT
6406 CAAAATTCCAATGATCACATTAAAAC
1 CAAAATTCCAATGATCACATTAAAAC
6432 CAAAATTCCAATGATCACATTAAAAC
1 CAAAATTCCAATGATCACATTAAAAC
6458 AAATCAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.04, T:0.23
Consensus pattern (26 bp):
CAAAATTCCAATGATCACATTAAAAC
Found at i:8054 original size:27 final size:25
Alignment explanation
Indices: 7983--8056 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 25
7973 TAAATACAAT
*
7983 AAATAATATTATTTATCATAAAATTTA
1 AAATAAT-TTATTTATTAT-AAATTTA
*
8010 ATATAA--TATTT-TTA-AAATATTA
1 AAATAATTTATTTATTATAAAT-TTA
8032 AAATAATTTATTTATTATTAAATTT
1 AAATAATTTATTTATTA-TAAATTT
8057 TATTTTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
21 4 0.11
22 8 0.21
23 2 0.05
24 10 0.26
25 3 0.08
26 2 0.05
27 9 0.24
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (25 bp):
AAATAATTTATTTATTATAAATTTA
Found at i:8071 original size:14 final size:13
Alignment explanation
Indices: 8042--8080 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
8032 AAATAATTTA
8042 TTTATTATTAAAT
1 TTTATTATTAAAT
*
8055 TTTATTTTTATAAT
1 TTTATTATTA-AAT
*
8069 TTTATTAATAAA
1 TTTATTATTAAA
8081 AATATTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATTATTAAAT
Found at i:8250 original size:27 final size:27
Alignment explanation
Indices: 8220--8300 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
8210 TATTATATTA
8220 TATTAATATTAAATATATAAATAATAT
1 TATTAATATTAAATATATAAATAATAT
*
8247 TATTAATTATT-AATA-ATTTAATAATAT
1 TATTAA-TATTAAATATA-TAAATAATAT
** *
8274 TATTTCTATGAAAT-TAATAAATAATAT
1 TATTAATATTAAATAT-ATAAATAATAT
8301 AAATTTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
26 4 0.09
27 35 0.80
28 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTAATATTAAATATATAAATAATAT
Found at i:9900 original size:14 final size:14
Alignment explanation
Indices: 9881--9927 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
9871 GCGAGAGCAT
*
9881 CCGAGGTCATCCGA
1 CCGAGGCCATCCGA
*
9895 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
9909 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
9923 GCGAG
1 CCGAG
9928 CTATGCGAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.21, C:0.36, G:0.34, T:0.09
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:10627 original size:29 final size:29
Alignment explanation
Indices: 10594--10658 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
10584 TCGAGTCTTT
10594 CAACTATTAAAAGTTATAAAATGATCCCC
1 CAACTATTAAAAGTTATAAAATGATCCCC
10623 CAACTATTAAAAGTTATAAAATGATCCCC
1 CAACTATTAAAAGTTATAAAATGATCCCC
10652 CAACTAT
1 CAACTAT
10659 AAGAAGATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.28
Consensus pattern (29 bp):
CAACTATTAAAAGTTATAAAATGATCCCC
Found at i:18721 original size:348 final size:348
Alignment explanation
Indices: 18084--18788 Score: 1367
Period size: 348 Copynumber: 2.0 Consensus size: 348
18074 TTTGTAATCG
18084 TTTCCTTGCTACCTGATGCACTTGTATTTTCTTCATTCTTTTGGATCTGCTGGTTCTTTTCTACG
1 TTTCCTTGCTACCTGATGCACTTGTATTTTCTTCATTCTTTTGGATCTGCTGGTTCTTTTCTACG
18149 TGCTCCACACTAGTGGTAGCATCCTTTTGCTGGTTTTCTTCCATTGAATTTAACTTCATAACATC
66 TGCTCCACACTAGTGGTAGCATCCTTTTGCTGGTTTTCTTCCATTGAATTTAACTTCATAACATC
18214 ATTTTCGATTGCTTTACTGCCTTCTGATATGCTCACATTTTTCTTCTTTTGCCTTTTCCTCTGGA
131 ATTTTCGATTGCTTTACTGCCTTCTGATATGCTCACATTTTTCTTCTTTTGCCTTTTCCTCTGGA
18279 CCTCAGAAGTATTATTTGCTTTTCTTGTCTTCAGGAACTTCATGGCCACTGACTTTGCAACATCA
196 CCTCAGAAGTATTATTTGCTTTTCTTGTCTTCAGGAACTTCATGGCCACTGACTTTGCAACATCA
*
18344 GATTTGGCCTTCGATAAATTTGAGCTTTTCTTTTCAGATGGTTCTGATCTTGCCAAGTCTACTGT
261 GATTTGGCCTTCGATAAATTTGAGCTTTTCTTTTCAGATGGCTCTGATCTTGCCAAGTCTACTGT
18409 AGGGTCAGCTTCATCTTTGTTAT
326 AGGGTCAGCTTCATCTTTGTTAT
18432 TTTCCTTGCTACCTGATGCACTTGTATTTTCTTCATTCTTTTGGATCTGCTGGTTCTTTTCTACG
1 TTTCCTTGCTACCTGATGCACTTGTATTTTCTTCATTCTTTTGGATCTGCTGGTTCTTTTCTACG
*
18497 TGCTCCACACTCGTGGTAGCATCCTTTTGCTGGTTTTCTTCCATTGAATTTAACTTCATAACATC
66 TGCTCCACACTAGTGGTAGCATCCTTTTGCTGGTTTTCTTCCATTGAATTTAACTTCATAACATC
18562 ATTTTCGATTGCTTTACTGCCTTCTGATATGCTCACATTTTTCTTCTTTTGCCTTTTCCTCTGGA
131 ATTTTCGATTGCTTTACTGCCTTCTGATATGCTCACATTTTTCTTCTTTTGCCTTTTCCTCTGGA
18627 CCTCAGAAGTATTATTTGCTTTTCTTGTCTTCAGGAACTTCATGGCCACTGACTTTGCAACATCA
196 CCTCAGAAGTATTATTTGCTTTTCTTGTCTTCAGGAACTTCATGGCCACTGACTTTGCAACATCA
18692 GATTTGGCCTTCGATAAATTTGAGCTTTTCTTTTCAGATGGCTCTGATCTTGCCAAGTCTACTGT
261 GATTTGGCCTTCGATAAATTTGAGCTTTTCTTTTCAGATGGCTCTGATCTTGCCAAGTCTACTGT
* *
18757 GGGGTCAGCTTCATTTTTGTTAT
326 AGGGTCAGCTTCATCTTTGTTAT
18780 TTT-CTTGCT
1 TTTCCTTGCT
18789 CCATAGCTGA
Statistics
Matches: 353, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
347 6 0.02
348 347 0.98
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.45
Consensus pattern (348 bp):
TTTCCTTGCTACCTGATGCACTTGTATTTTCTTCATTCTTTTGGATCTGCTGGTTCTTTTCTACG
TGCTCCACACTAGTGGTAGCATCCTTTTGCTGGTTTTCTTCCATTGAATTTAACTTCATAACATC
ATTTTCGATTGCTTTACTGCCTTCTGATATGCTCACATTTTTCTTCTTTTGCCTTTTCCTCTGGA
CCTCAGAAGTATTATTTGCTTTTCTTGTCTTCAGGAACTTCATGGCCACTGACTTTGCAACATCA
GATTTGGCCTTCGATAAATTTGAGCTTTTCTTTTCAGATGGCTCTGATCTTGCCAAGTCTACTGT
AGGGTCAGCTTCATCTTTGTTAT
Found at i:28779 original size:22 final size:22
Alignment explanation
Indices: 28754--28804 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
28744 CACCACAGCT
*
28754 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
28776 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
28798 CGTAGAA
1 CGTAGAA
28805 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:28805 original size:22 final size:22
Alignment explanation
Indices: 28762--28806 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
28752 CTCGTATAAA
28762 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
28784 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
28806 T
1 T
28807 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:29067 original size:30 final size:31
Alignment explanation
Indices: 29026--29085 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
29016 TAGACATAGT
*
29026 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
29056 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
29086 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:29142 original size:29 final size:29
Alignment explanation
Indices: 29100--29171 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
29090 TTTTCTGCAT
**
29100 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
29129 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
29158 ATTCATGTCATGTA
1 ATTCATGTCATGTA
29172 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:29592 original size:68 final size:67
Alignment explanation
Indices: 29474--29625 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 67
29464 TTTTTCTCAT
* * * *
29474 GGGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAA-ATCATATACGA
29539 TGA
65 TGA
* * * *
29542 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
29607 GA
66 GA
*
29609 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
29626 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 27 0.36
68 48 0.64
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
GA
Found at i:29635 original size:21 final size:21
Alignment explanation
Indices: 29605--29647 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29595 ATCATATTCG
* *
29605 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
29626 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
29647 T
1 T
29648 AATCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:29637 original size:67 final size:67
Alignment explanation
Indices: 29475--29647 Score: 206
Period size: 68 Copynumber: 2.6 Consensus size: 67
29465 TTTTCTCATG
* * *
29475 GGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCC-CCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
*
29540 GAG
65 GAA
* * * *
29543 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
29607 GAA
65 GAA
* *
29610 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
29648 AATCCAGAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
65 6 0.07
67 39 0.42
68 45 0.49
69 2 0.02
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATG
AA
Found at i:35691 original size:22 final size:22
Alignment explanation
Indices: 35674--35740 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
35664 CTCGTATAAA
35674 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
35696 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
35718 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
35740 T
1 T
35741 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:36001 original size:30 final size:31
Alignment explanation
Indices: 35960--36019 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
35950 TAGACATAGT
*
35960 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
35990 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
36020 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:36076 original size:29 final size:29
Alignment explanation
Indices: 36034--36105 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
36024 TTTTCTGCAT
**
36034 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
36063 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
36092 ATTCATGTCATGTA
1 ATTCATGTCATGTA
36106 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:36526 original size:68 final size:67
Alignment explanation
Indices: 36408--36559 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 67
36398 TTTTTCTCAT
* * * *
36408 GGGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAA-ATCATATACGA
36473 TGA
65 TGA
* * * *
36476 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTT
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
36541 GA
66 GA
*
36543 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
36560 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 27 0.36
68 48 0.64
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATCATATACGAT
GA
Found at i:36569 original size:21 final size:21
Alignment explanation
Indices: 36539--36581 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
36529 ATCATATTCG
* *
36539 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
36560 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
36581 T
1 T
36582 AATCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:36571 original size:67 final size:67
Alignment explanation
Indices: 36409--36581 Score: 206
Period size: 68 Copynumber: 2.6 Consensus size: 67
36399 TTTTCTCATG
* * *
36409 GGGGAATCGGTTCCTCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTTCC-CCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
*
36474 GAG
65 GAA
* * * *
36477 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGAT
36541 GAA
65 GAA
* *
36544 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
36582 AATCCAGAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
65 6 0.07
67 39 0.42
68 45 0.49
69 2 0.02
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAATATCATATACGATG
AA
Found at i:37780 original size:105 final size:105
Alignment explanation
Indices: 37573--37795 Score: 261
Period size: 105 Copynumber: 2.1 Consensus size: 105
37563 GATTGTCCAT
* * * * * *
37573 AAGGACCACATA-TAAATTCCTTTAGAACCATATACATATACCAAAGATCAAGTAAGTGTCTCAA
1 AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAAGACCAAATAAGTGTCGCAA
37637 AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
66 AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
* * * * *
37677 AAGGACCACGTAGAAAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATATGTGTCGC-A
1 AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAAGACCAAATAAGTGTCGCAA
* * * * * *
37741 AAGTACCTCATAGATGTTCCATAGGATACCTATATGTCCCG
66 AAG-ACCTCATACATGCTCCAAAGAATACATATACGTCCCG
*
37782 AAGGACCGCGTAGA
1 AAGGACCACGTAGA
37796 CCCTCGACTC
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
104 15 0.15
105 84 0.85
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (105 bp):
AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAAGACCAAATAAGTGTCGCAA
AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
Found at i:40028 original size:12 final size:12
Alignment explanation
Indices: 40013--40067 Score: 83
Period size: 12 Copynumber: 4.6 Consensus size: 12
40003 GTTATTTAAA
40013 CGGGTATTGGGC
1 CGGGTATTGGGC
*
40025 CGGGTATTGGGT
1 CGGGTATTGGGC
40037 CGGGTATTGGGC
1 CGGGTATTGGGC
* *
40049 CGGGAATCGGGC
1 CGGGTATTGGGC
40061 CGGGTAT
1 CGGGTAT
40068 ATATATATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.11, C:0.16, G:0.49, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:40072 original size:2 final size:2
Alignment explanation
Indices: 40065--40164 Score: 57
Period size: 2 Copynumber: 52.5 Consensus size: 2
40055 TCGGGCCGGG
* * * *
40065 TA TA TA TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
40106 TA TA TT TT TT TA TT TA AA T- TA AA TT TA T- TA -A TA 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
*
40144 TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA T
40165 TTATTTTTAT
Statistics
Matches: 73, Mismatches: 20, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
1 5 0.07
2 68 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40120 original size:33 final size:33
Alignment explanation
Indices: 40065--40152 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
40055 TCGGGCCGGG
*
40065 TATATATATATATATATATATTTAAATTAAATA
1 TATAAATATATATATATATATTTAAATTAAATA
* * * *
40098 TATAAATATATATTTTTTTATTTAAATTAAATT
1 TATAAATATATATATATATATTTAAATTAAATA
*
40131 TATTAATATTATATATATATAT
1 TATAAATA-TATATATATATAT
40153 ATATATAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 35 0.78
34 10 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TATAAATATATATATATATATTTAAATTAAATA
Found at i:42010 original size:18 final size:19
Alignment explanation
Indices: 41989--42037 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
41979 AAGTTGCTCG
*
41989 AAAAAGAAAAAA-ACA-GA
1 AAAAAAAAAAAAGACATGA
42006 AAAAAATAAAAAAGACATGA
1 AAAAAA-AAAAAAGACATGA
42026 AAGAAAAAAAAA
1 AA-AAAAAAAAA
42038 TAGAAAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.19
18 6 0.22
19 3 0.11
20 9 0.33
21 4 0.15
ACGTcount: A:0.82, C:0.04, G:0.10, T:0.04
Consensus pattern (19 bp):
AAAAAAAAAAAAGACATGA
Found at i:42011 original size:19 final size:20
Alignment explanation
Indices: 41988--42037 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
41978 AAAGTTGCTC
41988 GAAAAAGAAAAAAACA-GAAA
1 GAAAAA-AAAAAAACATGAAA
*
42008 -AAAATAAAAAAGACATGAAA
1 GAAAA-AAAAAAAACATGAAA
42028 GAAAAAAAAA
1 GAAAAAAAAA
42038 TAGAAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 12 0.46
20 10 0.38
21 4 0.15
ACGTcount: A:0.80, C:0.04, G:0.12, T:0.04
Consensus pattern (20 bp):
GAAAAAAAAAAAACATGAAA
Found at i:45655 original size:51 final size:50
Alignment explanation
Indices: 45532--45655 Score: 167
Period size: 51 Copynumber: 2.4 Consensus size: 50
45522 TAGCAGTAAA
*
45532 GCGCCCCCTGACTCGTGTTATATGCTGATTTGGCGTCACGTGGGGTATAGC
1 GCGCCCCCTGAC-CGTGCTATATGCTGATTTGGCGTCACGTGGGGTATAGC
* ** * *
45583 GCACCCCCTGTACCGCCCTATATGTTGATTTGGCGTCAGGTGGGGTATAGC
1 GCGCCCCCTG-ACCGTGCTATATGCTGATTTGGCGTCACGTGGGGTATAGC
45634 GCGCCCCCTGAACCGTGCTATA
1 GCGCCCCCTG-ACCGTGCTATA
45656 CCTGTGTAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
51 60 0.97
52 2 0.03
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (50 bp):
GCGCCCCCTGACCGTGCTATATGCTGATTTGGCGTCACGTGGGGTATAGC
Found at i:47595 original size:21 final size:21
Alignment explanation
Indices: 47528--47595 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
47518 CATTTATCAA
47528 TATTCCATAAGCTCGTAAGCT
1 TATTCCATAAGCTCGTAAGCT
** * * * *
47549 TATTTTACAATCTAC-TTACCAT
1 TATTCCATAAGCT-CGTAAGC-T
47571 TATTCCATAAGCTCGTAAGCT
1 TATTCCATAAGCTCGTAAGCT
47592 TATT
1 TATT
47596 TTACCAATAT
Statistics
Matches: 32, Mismatches: 12, Indels: 6
0.64 0.24 0.12
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (21 bp):
TATTCCATAAGCTCGTAAGCT
Found at i:47624 original size:44 final size:43
Alignment explanation
Indices: 47528--48399 Score: 1360
Period size: 44 Copynumber: 20.0 Consensus size: 43
47518 CATTTATCAA
* *
47528 TATTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
*
47571 TATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCAT
*
47615 TATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTCACCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCAT
*
47659 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTATCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
*
47702 T-TTTCCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCAT
1 TATTT--CATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
*
47746 TATTTCATAAGCTCGTAAGCTTATTTTACCAATAAACTTACCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCAT
47790 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
*
47833 T-TTTCCCATAAGCTCGTAAGCTTATTTTACATTATACTTACCAT
1 TATTT--CATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
*
47877 TATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTATCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCAT
47921 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
*
47964 T-TTTCCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCAT
1 TATTT--CATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
*
48008 TATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCAT
48052 TATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCAT
48096 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
*
48139 T-TTTCCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCAT
1 TATTT--CATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
* * *
48183 TATTCCATAAGCTCGTAAGCTTATTTTACATTATACTTTCCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
* *
48226 TATTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCAT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
* *
48269 TATTCCATAAGCTCGTAAGCTTATTTTACAATATACTTACTAT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
* *
48312 T-TTTCCATAAGCCCGTAAGCTTATTTTACCAATATACTTACTAT
1 TATTT-CATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCAT
48356 T-TTTCCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
1 TATTT-CATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
48399 T
1 T
48400 GTATCTATAT
Statistics
Matches: 779, Mismatches: 32, Indels: 36
0.92 0.04 0.04
Matches are distributed among these distances:
42 14 0.02
43 311 0.40
44 444 0.57
45 10 0.01
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (43 bp):
TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
Found at i:47679 original size:131 final size:130
Alignment explanation
Indices: 47528--48399 Score: 1430
Period size: 131 Copynumber: 6.7 Consensus size: 130
47518 CATTTATCAA
* * *
47528 TATTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATTATTCCATAAGCTCGTAAGCTT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTTTCCATAAGCTCGTAAGCTT
*
47593 ATTTTACCAATATACTTACCATTATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTCACCA
66 ATTTTA-CAATATACTTACCATTATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA
47658 T
130 T
*
47659 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTATCATTTTTCCCATAAGCTCGTAAGCT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTTT-CCATAAGCTCGTAAGCT
* *
47724 TATTTTACAATCTACTTACCATTATTTCATAAGCTCGTAAGCTTATTTTACCAATAAACTTACCA
65 TATTTTACAATATACTTACCATTATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA
47789 T
130 T
47790 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTTTCCCATAAGCTCGTAAGCT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTTT-CCATAAGCTCGTAAGCT
* *
47855 TATTTTACATTATACTTACCATTATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTATCA
65 TATTTTACAATATACTTACCATTATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA
47920 T
130 T
47921 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTTTCCCATAAGCTCGTAAGCT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTTT-CCATAAGCTCGTAAGCT
* *
47986 TATTTTACAATCTACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA
65 TATTTTACAATATACTTACCATTATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA
48051 T
130 T
48052 TATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTT-CATAAGCTCGTAAGC
1 TATTTCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCATT-TTTCCATAAGCTCGTAAGC
*
48116 TTATTTTACAATATACTTACCATT-TTTCCCATAAGCTCGTAAGCTTATTTTA-CAATCTACTTA
64 TTATTTTACAATATACTTACCATTATTT--CATAAGCTCGTAAGCTTATTTTACCAATATACTTA
48179 CCAT
127 CCAT
* * * *
48183 TATTCCATAAGCTCGTAAGCTTATTTTACATTATACTTTCCATTATTCCATAAGCTCGTAAGCTT
1 TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTTTCCATAAGCTCGTAAGCTT
* * *
48248 ATTTTACAATCTACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACTAT
66 ATTTTACAATATACTTACCATTATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
* *
48312 T-TTTCCATAAGCCCGTAAGCTTATTTTACCAATATACTTACTATTTTTCCATAAGCTCGTAAGC
1 TATTT-CATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCATTTTTCCATAAGCTCGTAAGC
48376 TTATTTTACAATATACTTACCATT
64 TTATTTTACAATATACTTACCATT
48400 GTATCTATAT
Statistics
Matches: 698, Mismatches: 34, Indels: 19
0.93 0.05 0.03
Matches are distributed among these distances:
128 2 0.00
129 61 0.09
130 108 0.15
131 461 0.66
132 63 0.09
133 3 0.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (130 bp):
TATTTCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTTTCCATAAGCTCGTAAGCTT
ATTTTACAATATACTTACCATTATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
Found at i:47845 original size:175 final size:173
Alignment explanation
Indices: 47530--48399 Score: 1403
Period size: 175 Copynumber: 5.0 Consensus size: 173
47520 TTTATCAATA
*
47530 TTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATTATTCCATAAGCTCGTAAGCTTAT
1 TTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATTATTTCATAAGCTCGTAAGCTTAT
*
47595 TTTACCAATATACTTACCATTATTT-CATAAGCTCGTAAGCTTATTTTACCAATATACTCACCAT
66 TTTA-CAATATACTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCAT
*
47659 TATTT-CATAAGCTCGTAAGCTTATTTTACAATATACTTATCATT-T
128 T-TTTCCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTAT
47704 TTCCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATTATTTCATAAGCTCGTAAGCTTA
1 TT-CCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATTATTTCATAAGCTCGTAAGCTTA
*
47769 TTTTACCAATAAACTTACCATTATTT-CATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
65 TTTTA-CAATATACTTACCATT-TTTCCATAAGCTCGTAAGCTTATTTTACAATATACTTACCAT
*
47833 TTTTCCCATAAGCTCGTAAGCTTATTTTACATTATACTTACCATTAT
128 TTTT-CCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTAT
* *
47880 TT-CATAAGCTCGTAAGCTTATTTTACCAATATACTTATCATTATTTCATAAGCTCGTAAGCTTA
1 TTCCATAAGCTCGTAAGCTTATTTTA-CAATCTACTTACCATTATTTCATAAGCTCGTAAGCTTA
*
47944 TTTTACAATATACTTACCATTTTTCCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATT
65 TTTTACAATATACTTACCATTTTT-CCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATT
*
48009 ATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTAT
129 TTTCCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCATTAT
*
48055 TT-CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTTCATAAGCTCGTAAGCTTA
1 TTCCATAAGCTCGTAAGCTTATTTTA-CAATCTACTTACCATTATTTCATAAGCTCGTAAGCTTA
*
48119 TTTTACAATATACTTACCATTTTTCCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATT
65 TTTTACAATATACTTACCATTTTT-CCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATT
* * *
48184 ATTCCATAAGCTCGTAAGCTTATTTTACATTATACTTTCCATTA-
129 TTTCCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTAT
*
48228 TTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATTATTCCATAAGCTCGTAAGCTTAT
1 TTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATTATTTCATAAGCTCGTAAGCTTAT
* * *
48293 TTTACAATATACTTACTATTTTTCCATAAGCCCGTAAGCTTATTTTACCAATATACTTACTATTT
66 TTTACAATATACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTA-CAATATACTTACCATTT
48358 TTCCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATT
130 TTCCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATT
48400 GTATCTATAT
Statistics
Matches: 663, Mismatches: 23, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
172 23 0.03
173 121 0.18
174 117 0.18
175 399 0.60
176 3 0.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (173 bp):
TTCCATAAGCTCGTAAGCTTATTTTACAATCTACTTACCATTATTTCATAAGCTCGTAAGCTTAT
TTTACAATATACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTTT
TCCATAAGCTCGTAAGCTTATTTTACAATATACTTACCATTAT
Found at i:48250 original size:21 final size:21
Alignment explanation
Indices: 48225--48293 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
48215 ATACTTTCCA
48225 TTATTCCATAAGCTCGTAAGC
1 TTATTCCATAAGCTCGTAAGC
** * * * *
48246 TTATTTTACAATCTAC-TTACC
1 TTATTCCATAAGCT-CGTAAGC
48267 ATTATTCCATAAGCTCGTAAGC
1 -TTATTCCATAAGCTCGTAAGC
48289 TTATT
1 TTATT
48294 TTACAATATA
Statistics
Matches: 33, Mismatches: 12, Indels: 6
0.65 0.24 0.12
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.41
Consensus pattern (21 bp):
TTATTCCATAAGCTCGTAAGC
Found at i:48729 original size:176 final size:176
Alignment explanation
Indices: 48434--49306 Score: 1534
Period size: 176 Copynumber: 5.0 Consensus size: 176
48424 ATCCATAAAT
* * **
48434 TCCATAT-GAAATTCATAC-CATATGTATGATTCTTTTACCATTTTTAGCACATATAATGCCCTA
1 TCCATATGGAAATACATACACTTA-GTATGATTCCCTTACCA-TTTTAGCACATATAATGCCCTA
* * * **
48497 TATGGAAATCCATATATTCATTATGATTTCCTTAACGTTTTAGCACACTTAGTGCTCCATATTGA
64 TTTGGAAATCCATATATTCAATATGATTTCCTTAACATTTTAGCACACAAAGTGCTCCATATTGA
* *
48562 AATCCATACACTTAATATGATTTCTTATCATTTTAGCACATTCAGTGC
129 AATCCATACACTTAGTATGATTTCTTATCGTTTTAGCACATTCAGTGC
*
48610 TCCATATGGAAATACATACACTTAGTATGACTCCCTTACCATTTTAGCACATATAATGCCCTATT
1 TCCATATGGAAATACATACACTTAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATT
48675 TGGAAATCCATATATTCAATATGATTTCCTTAACATTTTAGCACACAAAGTGCTCCATATTGAAA
66 TGGAAATCCATATATTCAATATGATTTCCTTAACATTTTAGCACACAAAGTGCTCCATATTGAAA
48740 TCCATACACTTAGTATGATTTCTTATCGTTTTAGCACATTCAGTGC
131 TCCATACACTTAGTATGATTTCTTATCGTTTTAGCACATTCAGTGC
*
48786 TCCATATGGAAATACATACACTTAGTATGACTCCCTTACCATTTTAGCACATATAATGCCCTATT
1 TCCATATGGAAATACATACACTTAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATT
48851 TGGAAATCCATATATTCAATATGATTTCCTTAACATTTTAGCACACAAAGTGCTCCATATTGAAA
66 TGGAAATCCATATATTCAATATGATTTCCTTAACATTTTAGCACACAAAGTGCTCCATATTGAAA
48916 TCCATACACTTAGTATGATTTCTTATCGTTTTAGCACATTCAGTGC
131 TCCATACACTTAGTATGATTTCTTATCGTTTTAGCACATTCAGTGC
*
48962 TCCATATGGAAATACATACACTTAGTATGATTCTCTTACCATTTTAGCACATATAATGCCCTATT
1 TCCATATGGAAATACATACACTTAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATT
*
49027 TGGAAATCCATGTATTCAATATGATTTCCTTAACATTTTAGCACACAAAGTGCTCCATATTGAAA
66 TGGAAATCCATATATTCAATATGATTTCCTTAACATTTTAGCACACAAAGTGCTCCATATTGAAA
49092 TCCATACACTTAGTATGATTTCTTATCGTTTTAGCACATTCAGTGC
131 TCCATACACTTAGTATGATTTCTTATCGTTTTAGCACATTCAGTGC
*
49138 TCCATATGGTAATACATACACTTAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATT
1 TCCATATGGAAATACATACACTTAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATT
**
49203 TGGAAATCCATATATTCAATATGATTTCCTTAACATTTTAGCACACTTAGTGCTCCATATTGAAA
66 TGGAAATCCATATATTCAATATGATTTCCTTAACATTTTAGCACACAAAGTGCTCCATATTGAAA
* *
49268 TCCATACACTTAGTATGATTTCTTATCATTTTTGCACAT
131 TCCATACACTTAGTATGATTTCTTATCGTTTTAGCACAT
49307 ATAATGCCAT
Statistics
Matches: 673, Mismatches: 22, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
176 646 0.96
177 24 0.04
178 3 0.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.37
Consensus pattern (176 bp):
TCCATATGGAAATACATACACTTAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATT
TGGAAATCCATATATTCAATATGATTTCCTTAACATTTTAGCACACAAAGTGCTCCATATTGAAA
TCCATACACTTAGTATGATTTCTTATCGTTTTAGCACATTCAGTGC
Found at i:49680 original size:19 final size:19
Alignment explanation
Indices: 49634--49707 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
49624 TTTTGGCCCT
*
49634 TATGCATCGATGCA-TTCTA
1 TATGCATCGATGCACTGC-A
49653 TAGTGCATCGATGCACTGCA
1 TA-TGCATCGATGCACTGCA
49673 TATGCATCGATGCACTGCA
1 TATGCATCGATGCACTGCA
49692 TATGCATCGATGCACT
1 TATGCATCGATGCACT
49708 TATTGTATTC
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 35 0.67
20 15 0.29
21 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (19 bp):
TATGCATCGATGCACTGCA
Found at i:55259 original size:17 final size:18
Alignment explanation
Indices: 55216--55256 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
55206 AAATTATTTT
55216 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
55233 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
55251 ATTAAA
1 AGTAAA
55257 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:55316 original size:10 final size:10
Alignment explanation
Indices: 55297--55326 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
55287 CCTTAAACGA
*
55297 GAGAGTATTT
1 GAGAGAATTT
55307 GAGAGAATTT
1 GAGAGAATTT
55317 GAGAGAATTT
1 GAGAGAATTT
55327 AGTATGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:55551 original size:49 final size:48
Alignment explanation
Indices: 55448--55571 Score: 124
Period size: 49 Copynumber: 2.5 Consensus size: 48
55438 GATAAATAGG
* * * * * *
55448 TATAGCGCGGAGCAGGGGGCGCGCTATAGCCACGTGTAACCCAGTCAGCG
1 TATAGCGCGG-GTA-GGGGCGCGCTATACCCACGTGGAACCAAATCAGCA
*
55498 TATAGCGCGGTGTAGGGG-GCGCTATACCCCACGTGGCACCAAATCAGCA
1 TATAGCGCGG-GTAGGGGCGCGCTATA-CCCACGTGGAACCAAATCAGCA
55547 TATAGCGCGGGTCAGGGGACGCGCT
1 TATAGCGCGGGT-AGGGG-CGCGCT
55572 TTACTGCTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
48 10 0.16
49 35 0.56
50 12 0.19
51 5 0.08
ACGTcount: A:0.22, C:0.27, G:0.35, T:0.15
Consensus pattern (48 bp):
TATAGCGCGGGTAGGGGCGCGCTATACCCACGTGGAACCAAATCAGCA
Found at i:55645 original size:30 final size:29
Alignment explanation
Indices: 55583--55645 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
55573 TACTGCTACG
* *
55583 GGTGTTAGATCGAAAAATATAATTTGACC
1 GGTGTTAGATCGAAAAATATAATATCACC
*
55612 GGTGTTAGATCGATAAATAT-ATCGATCACC
1 GGTGTTAGATCGAAAAATATAAT--ATCACC
55642 GGTG
1 GGTG
55646 ATTTTTCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.07
29 19 0.66
30 8 0.28
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (29 bp):
GGTGTTAGATCGAAAAATATAATATCACC
Found at i:55900 original size:2 final size:2
Alignment explanation
Indices: 55893--55917 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55883 GATAAAAGTT
55893 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
55918 TTAAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56460 original size:2 final size:2
Alignment explanation
Indices: 56448--56793 Score: 242
Period size: 2 Copynumber: 178.5 Consensus size: 2
56438 AGTATCGTAT
*
56448 TA TA TA GTA TA TA TA -A TA TA -A TA TT TA TA TA -A TA TA TA GTA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
56489 T- TA TA TA CTA TG T- TA TA T- TA T- TA TA TA GTA TA GTA T- TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA
*
56527 TA GTA T- TA TA -A TA TA TA T- TA TA T- TA TA T- TA TA TG T- TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56564 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
* *
56606 T- TA T- TA TA GTA TA GTA TA TA TT TA TA TGG TA TA TA TA TA T-
1 TA TA TA TA TA -TA TA -TA TA TA TA TA TA T-A TA TA TA TA TA TA
* * *
56646 TA TA T- TA -A TA T- TA TA TG TA TA TA TA GTG TG 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
* *
56686 TA TA T- TA TA GTA TA TA TA TA TA TA TA TA TT TG TA TA GTA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
56729 TA T- TA TA TA T- TA TA TA T- TA TT TA TA GTA T- TA TT TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
56767 CTA TA TA TT TA T- TA TA TGA TA TGA TA T
1 -TA TA TA TA TA TA TA TA T-A TA T-A TA T
56794 TATTATTATT
Statistics
Matches: 280, Mismatches: 21, Indels: 86
0.72 0.05 0.22
Matches are distributed among these distances:
1 27 0.10
2 223 0.80
3 30 0.11
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56534 original size:43 final size:40
Alignment explanation
Indices: 56411--56809 Score: 251
Period size: 43 Copynumber: 9.8 Consensus size: 40
56401 AATACAATAT
* * * *
56411 TATA-TTATATTATATATTATTTTATAGAGTATCGTATTATA
1 TATATTTATATTATATA-TATATTATATATTAT-ATATTATA
* *
56452 TAGTATATATAATATA-ATAT-TTATATAATATATAGTATTATA
1 TA-TATTTATATTATATATATATTATAT-AT-TATA-TATTATA
*
56494 TACTATGTTATATTAT-TATATAGTATAGTATTATAGTATTATAA
1 TA-TAT-TTATATTATATATATATTATA-TATTATA-TATTAT-A
*
56538 TATATATTATATTATATTATATGTTATATA-TATATA-TATA
1 TATAT-TTATATTATA-TATATATTATATATTATATATTATA
*
56578 TATATATATA-TATATATATATATATATATTATTATAGTATAGTA
1 TATATTTATATTATATATATAT-TATATATTA-TATA-T-TA-TA
56622 TATATTTATATGGTATATATATA-T-TATATTA-ATATTATA
1 TATATTTATAT--TATATATATATTATATATTATATATTATA
* * *
56661 TGTATATATAGTGTGTATATATA-TATATATTATAGTATATATA
1 TATATTTATA-T-TATATATATATTATATATTATA-TAT-TATA
* *
56704 TATATATATATT-TGTATAGTA-TATATATTATATATTATA
1 TATATTTATATTATATATA-TATTATATATTATATATTATA
* * *
56743 TATTATTTATAGTAT-TATTTATTACTATA-TATTTATTATA
1 TA-TATTTATATTATATATATATTA-TATATTATATATTATA
*
56783 TGATA-TGATATTAT-TAT-TATTAT-TATT
1 T-ATATTTATATTATATATATATTATATATT
56810 TTCATTTTTT
Statistics
Matches: 298, Mismatches: 26, Indels: 72
0.75 0.07 0.18
Matches are distributed among these distances:
36 2 0.01
37 8 0.03
38 15 0.05
39 45 0.15
40 59 0.20
41 31 0.10
42 27 0.09
43 61 0.20
44 29 0.10
45 11 0.04
47 10 0.03
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (40 bp):
TATATTTATATTATATATATATTATATATTATATATTATA
Found at i:56594 original size:45 final size:45
Alignment explanation
Indices: 56407--56788 Score: 312
Period size: 45 Copynumber: 8.4 Consensus size: 45
56397 ATACAATACA
* *
56407 ATAT-TATATTATATTATATATTAT-TTTATAGAGTATCGTAT-TAT
1 ATATATATATTATATTATATATTATATATATATA-TAT-GTATATAT
* *
56451 ATAGTATATATAATATAATAT-TTATATA-ATATATA-GTAT-TAT
1 ATA-TATATATTATATTATATATTATATATATATATATGTATATAT
* *
56493 ATA-CTATGTTATATTAT-TA-TATAGTATAGTAT-TATAGTATTATAAT
1 ATATATATATTATATTATATATTATA-TATA-TATATAT-GTA-TAT-AT
* *
56539 ATATATTATATTATATTATATGTTATATATATATATATATATATAT
1 ATATA-TATATTATATTATATATTATATATATATATATGTATATAT
* *
56585 ATATATATATATATATATATATTATTATAGTATAGTATATATTTATATGGT
1 ATATATATAT-TATAT-TATA-TATTATA-TATA-TATATATGTATAT-AT
* *
56636 ATATATATATTATATTA-ATATTATATGTATATATAGTGTGTATAT
1 ATATATATATTATATTATATATTATATATATATATA-TGTATATAT
* *
56681 ATATATATATTATAGTATATA-TATATATATATATTTGTATAGTAT
1 ATATATATATTATATTATATATTATATATATATATATGTATA-TAT
* *
56726 ATATAT-TA-TATATTATATATTATTTATAGTAT-TATTTAT-TACT
1 ATATATATATTATATTATATATTATATATA-TATATATGTATATA-T
* *
56769 ATATATTTATTATATGATAT
1 ATATATATATTATATTATAT
56789 GATATTATTA
Statistics
Matches: 279, Mismatches: 28, Indels: 61
0.76 0.08 0.17
Matches are distributed among these distances:
39 5 0.02
40 12 0.04
41 3 0.01
42 15 0.05
43 20 0.07
44 27 0.10
45 71 0.25
46 42 0.15
47 14 0.05
48 24 0.09
49 14 0.05
50 21 0.08
51 11 0.04
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (45 bp):
ATATATATATTATATTATATATTATATATATATATATGTATATAT
Found at i:56689 original size:112 final size:112
Alignment explanation
Indices: 56407--56783 Score: 355
Period size: 112 Copynumber: 3.3 Consensus size: 112
56397 ATACAATACA
* *
56407 ATAT-TATATTATATTATATATTAT-TT-TATAGAGTATCGTAT-TATATAGTATATATA-ATAT
1 ATATATATATTATATTATATATTATATTATATATAGTGT-GTATATATATA-TATATATATATAT
* *
56467 AATATTTATATAATATATAGTATTATATACTATGTTATATTAT-TATATAGTATAGT
64 -ATATATATAT-ATATATA-TATTAT-TA-TA-G-TATATTATATATTTA-TATAGT
* *
56523 AT-TATAGTATTATAATATATATTATATTATATTATA-TGTTATATATATATATATATATATATA
1 ATATATA-TATTATATTATATATTATATTATA-TATAGTG-TGTATATATATATATATATATATA
* *
56586 TATATATATATATATATATATTATTATAGTATAGTATATATTTATATGGT
63 TATATATATATATATATATATTATTATAGTATATTATATATTTATATAGT
56636 ATATATATATTATATTA-ATATTATATGTATATATAGTGTGTATATATATATATAT-TATAGTAT
1 ATATATATATTATATTATATATTATAT-TATATATAGTGTGTATATATATATATATATATA-TAT
* * * *
56699 ATATATATATATATATTTGTATAGTATA-TATATTATATA-TTATATATT
64 ATATATATATATATATATAT-TATTATAGTATATTATATATTTATATAGT
* *
56747 ATTTATAGTATTATTTATTACTATATATTTATTATAT
1 ATATATA-TATTA--TATTA-TATAT-TATATTATAT
56784 GATATGATAT
Statistics
Matches: 223, Mismatches: 18, Indels: 40
0.79 0.06 0.14
Matches are distributed among these distances:
111 17 0.08
112 65 0.29
113 35 0.16
114 15 0.07
115 3 0.01
116 15 0.07
117 27 0.12
118 9 0.04
119 23 0.10
120 14 0.06
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.53
Consensus pattern (112 bp):
ATATATATATTATATTATATATTATATTATATATAGTGTGTATATATATATATATATATATATAT
ATATATATATATATATATTATTATAGTATATTATATATTTATATAGT
Found at i:56764 original size:16 final size:16
Alignment explanation
Indices: 56407--56783 Score: 103
Period size: 17 Copynumber: 23.8 Consensus size: 16
56397 ATACAATACA
56407 ATATTATATTATAT--T
1 ATATT-TATTATATAGT
*
56422 ATATATTATTTTATAG-
1 ATAT-TTATTATATAGT
*
56438 AGTATCGTATTATATAGT
1 A-TAT-TTATTATATAGT
* *
56456 ATATATAATATAATA-T
1 ATATTTATTAT-ATAGT
* * *
56472 TTATATAATATATAGT
1 ATATTTATTATATAGT
*
56488 AT-TATA-TACTAT-GT
1 ATATTTATTA-TATAGT
56502 -TATATTATTATATAGT
1 ATAT-TTATTATATAGT
*
56518 ATA-GTA-T-TATAGT
1 ATATTTATTATATAGT
* * *
56531 AT-TATAATATATATT
1 ATATTTATTATATAGT
56546 ATATTATATTATAT-GT
1 ATATT-TATTATATAGT
*
56562 -TATATA-TATATA-T
1 ATATTTATTATATAGT
*
56575 ATATATA-TATATA-T
1 ATATTTATTATATAGT
*
56589 ATATATA-TATATA-T
1 ATATTTATTATATAGT
56603 ATA-TTATTATAGTA-T
1 ATATTTATTATA-TAGT
* *
56618 AGTATATATTTATATGGT
1 A-TATTTA-TTATATAGT
56636 ATATATATATTATAT--T
1 ATAT-T-TATTATATAGT
56652 AATATTATATGTATATA-T
1 -ATATT-TAT-TATATAGT
* *
56670 AGTGTGTATATATATA-T
1 A-TATTTAT-TATATAGT
56687 ATATTATAGTATATATA-T
1 ATATT-TA-T-TATATAGT
*
56705 ATATATATATTTGTATAGT
1 ATAT-T-TA-TTATATAGT
* *
56724 ATATATATTATATATT
1 ATATTTATTATATAGT
56740 ATATATTATT-TATAGT
1 ATAT-TTATTATATAGT
*
56756 ATTATTTATTA-CTA-T
1 A-TATTTATTATATAGT
56771 ATATTTATTATAT
1 ATATTTATTATAT
56784 GATATGATAT
Statistics
Matches: 288, Mismatches: 34, Indels: 80
0.72 0.08 0.20
Matches are distributed among these distances:
13 19 0.07
14 52 0.18
15 45 0.16
16 60 0.21
17 65 0.23
18 35 0.12
19 12 0.04
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.53
Consensus pattern (16 bp):
ATATTTATTATATAGT
Found at i:57027 original size:2 final size:2
Alignment explanation
Indices: 57016--57180 Score: 96
Period size: 2 Copynumber: 88.5 Consensus size: 2
57006 ATTGTTTTTT
*
57016 TA TA TGA TA TA TA T- TA TG T- TA TA T- TA T- TA TA TA GTA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
57056 TT TA TA T- TA TA -A AA T- TA TA TA GTA TA T- TA T- TA TA GTA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* *
57094 TT TA -A TA TA TA T- TA TA T- TA TA TG T- 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
*
57132 TA TA T- TA GTA TA TA TA TT TA T- TA TA TA TA TA T- TA TA T- TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57171 TA GTA TA TA T
1 TA -TA TA TA T
57181 TTGAAAATAT
Statistics
Matches: 131, Mismatches: 8, Indels: 48
0.70 0.04 0.26
Matches are distributed among these distances:
1 18 0.14
2 101 0.77
3 12 0.09
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (2 bp):
TA
Found at i:57037 original size:5 final size:5
Alignment explanation
Indices: 57015--57178 Score: 91
Period size: 5 Copynumber: 33.2 Consensus size: 5
57005 TATTGTTTTT
* * *
57015 TTATA TGATA -TATA TTATG TTATA TTAT- TATATA GTATA -TAT- TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA T-TATA TTATA TTATA TTATA
* * *
57062 TTATA --AAA TTATA -TAGTA -TATTA TTATA GTATT TTA-A TATATA
1 TTATA TTATA TTATA TTA-TA TTA-TA TTATA TTATA TTATA T-TATA
57105 TTATA TTATA TGT-TA -TATA TATATA TATATA TTAGTA TATATA TT-TA
1 TTATA TTATA T-TATA TTATA T-TATA T-TATA TTA-TA T-TATA TTATA
*
57152 TTATA TATATA TTATA TTATA GTATA T
1 TTATA T-TATA TTATA TTATA TTATA T
57179 ATTTGAAAAT
Statistics
Matches: 126, Mismatches: 14, Indels: 38
0.71 0.08 0.21
Matches are distributed among these distances:
3 3 0.02
4 19 0.15
5 75 0.60
6 27 0.21
7 2 0.02
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (5 bp):
TTATA
Found at i:57048 original size:10 final size:10
Alignment explanation
Indices: 57023--57181 Score: 94
Period size: 11 Copynumber: 14.8 Consensus size: 10
57013 TTTTATATGA
57023 TATATATTAT
1 TATATATTAT
57033 GT-TATATTAT
1 -TATATATTAT
*
57043 TATATAGTA-
1 TATATATTAT
*
57052 TATATTTATAT
1 TATATAT-TAT
*
57063 TATAAAATTAT
1 TAT-ATATTAT
57074 ATAGTATATTAT
1 -TA-TATATTAT
57086 TATAGTATT-T
1 TATA-TATTAT
57096 TA-ATATATAT
1 TATATAT-TAT
*
57106 TATATTATATGT
1 TATA-TAT-TAT
57118 TATATATATAT
1 TATATAT-TAT
57129 ATATATATTAGT
1 -TATATATTA-T
57141 ATATATATTTAT
1 -TATATA-TTAT
57153 TATATATATAT
1 TATATAT-TAT
*
57164 TATAT-TATAG
1 TATATAT-TAT
57174 TATATATT
1 TATATATT
57182 TGAAAATATT
Statistics
Matches: 123, Mismatches: 9, Indels: 33
0.75 0.05 0.20
Matches are distributed among these distances:
8 3 0.02
9 8 0.07
10 35 0.28
11 37 0.30
12 36 0.29
13 4 0.03
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (10 bp):
TATATATTAT
Found at i:57072 original size:28 final size:29
Alignment explanation
Indices: 57015--57178 Score: 117
Period size: 28 Copynumber: 5.6 Consensus size: 29
57005 TATTGTTTTT
* *
57015 TTATAT-G-ATATATATTATGTTATATTA
1 TTATATAGTATATATATTATATTATAATA
*
57042 TTATATAGTATATAT-TTATATTATAAAA
1 TTATATAGTATATATATTATATTATAATA
* **
57070 TTATATAGTATAT-TATTATAGTATTTTA
1 TTATATAGTATATATATTATATTATAATA
* *
57098 ATATATATTATATTATATGT-TATATATATATA
1 TTATATAGTATA-TATAT-TATAT-TATA-ATA
57130 TATATATTAGTATATATATT-TATTAT-ATA
1 T-TATA-TAGTATATATATTATATTATAATA
*
57159 TATATTATATTATAGTATAT
1 T-TA-TATAGTATA-TATAT
57179 ATTTGAAAAT
Statistics
Matches: 110, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
27 7 0.06
28 43 0.39
29 20 0.18
30 12 0.11
31 7 0.06
32 6 0.05
33 9 0.08
34 6 0.05
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (29 bp):
TTATATAGTATATATATTATATTATAATA
Found at i:57179 original size:23 final size:23
Alignment explanation
Indices: 57022--57181 Score: 102
Period size: 23 Copynumber: 6.8 Consensus size: 23
57012 TTTTTATATG
*
57022 ATATATATTATGTTATATTAT--T
1 ATATATA-TATATTATATTATAGT
**
57044 ATATAGTATATATTTATATTATAAA
1 ATATA-TATATA-TTATATTATAGT
57069 AT-TATATAGTA-TATTATTATAGT
1 ATATATATA-TATTA-TATTATAGT
*
57092 ATTTTAATATATATTATATTATATGT
1 A-TAT-ATATATATTATATTATA-GT
57118 -TATATATATA-TATATATATTAGT
1 ATATATATATATTATAT-TA-TAGT
* *
57141 ATATATATTTATTATATATATATT
1 ATATATATATATTATAT-TATAGT
57165 ATAT-TATAGTA-TATATT
1 ATATATATA-TATTATATT
57182 TGAAAATATT
Statistics
Matches: 114, Mismatches: 8, Indels: 32
0.74 0.05 0.21
Matches are distributed among these distances:
22 16 0.14
23 42 0.37
24 27 0.24
25 20 0.18
26 9 0.08
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
ATATATATATATTATATTATAGT
Found at i:58307 original size:5 final size:5
Alignment explanation
Indices: 58286--58407 Score: 80
Period size: 5 Copynumber: 24.6 Consensus size: 5
58276 TAATAACTTA
* *
58286 ATAAT ATAA- ATACT ATAAT AT-AT AATAAT ATACT AT-AT ATAAT ATATACT
1 ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATA-A-T
* *
58336 ATACA- AT-AT ATAAT ATACT AT-AT ATAAT AATACACT AT-AT ATTAT
1 ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT -ATA-A-T ATAAT ATAAT
*
58381 ATAAT ATAAT AT-AT ATACT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
58408 TAACATAAAC
Statistics
Matches: 93, Mismatches: 10, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
3 1 0.01
4 20 0.22
5 57 0.61
6 6 0.06
7 8 0.09
8 1 0.01
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:58311 original size:7 final size:7
Alignment explanation
Indices: 58286--58410 Score: 109
Period size: 7 Copynumber: 17.6 Consensus size: 7
58276 TAATAACTTA
58286 ATAATAT
1 ATAATAT
58293 A-AATACT
1 ATAATA-T
58300 ATAATAT
1 ATAATAT
58307 ATAATAAT
1 ATAAT-AT
58315 ATACTATAT
1 ATA--ATAT
58324 ATAATAT
1 ATAATAT
*
58331 ATACTAT
1 ATAATAT
*
58338 ACAATAT
1 ATAATAT
58345 ATAATAT
1 ATAATAT
58352 ACT-ATAT
1 A-TAATAT
58359 ATAATA-
1 ATAATAT
58365 ATACACTAT
1 ATA-A-TAT
*
58374 ATATTAT
1 ATAATAT
58381 AT-A-AT
1 ATAATAT
58386 ATAATAT
1 ATAATAT
58393 AT-ATACT
1 ATAATA-T
58400 ATAATAT
1 ATAATAT
58407 ATAA
1 ATAA
58411 CATAAACGGG
Statistics
Matches: 98, Mismatches: 6, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
5 4 0.04
6 12 0.12
7 57 0.58
8 15 0.15
9 8 0.08
10 2 0.02
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:64083 original size:2 final size:2
Alignment explanation
Indices: 64076--64108 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
64066 AGAAGAGTTT
64076 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
64109 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:64391 original size:28 final size:29
Alignment explanation
Indices: 64360--64416 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
64350 TATATTTTAA
64360 TATTTTTGA-TAAAAGTATT-ATATAAAAT
1 TATTTTTGATTAAAA-TATTAATATAAAAT
* *
64388 TATTTTTTATTAAAATATTAATATTAAAT
1 TATTTTTGATTAAAATATTAATATAAAAT
64417 ACTACTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (29 bp):
TATTTTTGATTAAAATATTAATATAAAAT
Found at i:68346 original size:199 final size:204
Alignment explanation
Indices: 67734--68509 Score: 963
Period size: 195 Copynumber: 3.8 Consensus size: 204
67724 ATTTAAGAAT
* * * *
67734 TAAATTGAACAATATGAAATTACAAATAAAATTTAAATAAATTAAACAACACACATTGATGAGAG
1 TAAATTGAAAAATATGAAATTAAAAATAAAATTTAAATATATTAAACAACACA-A---A--AGGG
*
67799 ATCAAATCGAAATAATTTTAAATTGTGAGG-TGAAATTAATACAAAAAAGTACTAAATTATACCC
60 ATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACTC
* *
67863 ATTTAAAAAGTTATGGGCCAATTTAAAAAATATAATTAAGTAATAAGTATGGATCAATTTCATAT
125 ATTTAAAAAGTTAT-GGCCAATTT-AAAAA-ATAA--AAGTAATAAGTATGGGTCAATTTCAGAT
*
67928 GCAAATAAAAGTTGGAGGAC
185 GCAAATAAAATTTGGAGGAC
* * * *** **
67948 TAAATTGAACAAATATGAAATTACAAATAAAATTT-AATA-A-CACAC-ATTGATGAGGGATCAA
1 TAAATTGAA-AAATATGAAATTAAAAATAAAATTTAAATATATTAAACAACACAAAAGGGATCAA
*
68009 ATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC-C-TATT
65 ATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACTCAT-TT
* *
68072 AAAAAGTTATGGTCAATTT--AAAAT---AGTAATAAGTATGGGTCAATTTCAGATGAAAATAAA
129 AAAAAGTTATGGCCAATTTAAAAAATAAAAGTAATAAGTATGGGTCAATTTCAGATGCAAATAAA
68132 ATTTGGAGGAC
194 ATTTGGAGGAC
68143 TAAATTGAATAAATATGAAATTAAAAATAAAAATTTAAATATA-TAAAC-ACACAAAAGGGATC-
1 TAAATTGAA-AAATATGAAATTAAAAAT-AAAATTTAAATATATTAAACAACACAAAAGGGATCA
* *
68205 AATCAAAATAA-TTTAAATT-TGAGGTTG-AATTAATACAAAAAAGTA-TTAATTATACTCATTT
64 AATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACTCATTT
* *
68266 AAAAAGTTATGAGCCAATTTAAAAAATAAAAGTAAGAA-TATGGGTCAATTTCAGGTGCAAATAA
129 AAAAAGTTATG-GCCAATTTAAAAAATAAAAGTAATAAGTATGGGTCAATTTCAGATGCAAATAA
68330 AATTTGGAGGAC
193 AATTTGGAGGAC
68342 TAAATTGAAAAATAT-AAATTATAAAATAAAATTTAAATATATTAAACAACACAAAA-GGATCAA
1 TAAATTGAAAAATATGAAATTA-AAAATAAAATTTAAATATATTAAACAACACAAAAGGGATCAA
*
68405 ATCGAAATAATTTTAAATT-TGAGGTTGAAATTAATACAAAAATGTACTAAA-TATACTCATTTA
65 ATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACTCATTTA
68468 AAAAGTTATGGACCAATTATAAATAGAA-AATAAGTAATAAGT
130 AAAAGTTATGG-CCAATT-TAAA-A-AATAA-AAGTAATAAGT
68510 TGAGAAAAAA
Statistics
Matches: 500, Mismatches: 35, Indels: 63
0.84 0.06 0.11
Matches are distributed among these distances:
193 9 0.02
194 32 0.06
195 84 0.17
196 15 0.03
197 39 0.08
198 34 0.07
199 63 0.13
200 26 0.05
201 48 0.10
202 7 0.01
203 3 0.01
204 19 0.04
205 46 0.09
206 32 0.06
211 2 0.00
212 3 0.01
213 1 0.00
214 13 0.03
215 24 0.05
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.30
Consensus pattern (204 bp):
TAAATTGAAAAATATGAAATTAAAAATAAAATTTAAATATATTAAACAACACAAAAGGGATCAAA
TCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACTCATTTAA
AAAGTTATGGCCAATTTAAAAAATAAAAGTAATAAGTATGGGTCAATTTCAGATGCAAATAAAAT
TTGGAGGAC
Done.