Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014566.1 Kokia drynarioides strain JFW-HI SEQ_129605, 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: 309119
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 110 characters in sequence are not A, C, G, or T
Found at i:3535 original size:22 final size:21
Alignment explanation
Indices: 3509--3554 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
3499 ATTCACATGT
3509 TTTCTTACTCATTTTCCTTTTG
1 TTTC-TACTCATTTTCCTTTTG
*
3531 TTTCTGCTCATTTTCCTTTTG
1 TTTCTACTCATTTTCCTTTTG
3552 TTT
1 TTT
3555 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.07, C:0.22, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTCTACTCATTTTCCTTTTG
Found at i:18048 original size:22 final size:22
Alignment explanation
Indices: 18022--18069 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
18012 CAACAATTTA
*
18022 AATT-ACTTTTAGTTGCACTGAC
1 AATTAACTTTTA-TTACACTGAC
*
18044 AATTAACTTTTATTACATTGAC
1 AATTAACTTTTATTACACTGAC
18066 AATT
1 AATT
18070 TTAATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (22 bp):
AATTAACTTTTATTACACTGAC
Found at i:26247 original size:21 final size:21
Alignment explanation
Indices: 26217--26263 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
26207 GATTTGTTGA
* * *
26217 AAGGATAAAAAGAGGAAGCGC
1 AAGGACAAAAAGAAGAAGCAC
26238 AAGGACAAAAAGAAGAAGCAC
1 AAGGACAAAAAGAAGAAGCAC
26259 AAGGA
1 AAGGA
26264 GAAAGGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.57, C:0.11, G:0.30, T:0.02
Consensus pattern (21 bp):
AAGGACAAAAAGAAGAAGCAC
Found at i:30084 original size:47 final size:47
Alignment explanation
Indices: 30010--30104 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
30000 GAAAAGAAAA
*
30010 ATTAGTAGAAATAAAAGAATCCTGAGTAAGAAAACATATGGATAGTG
1 ATTAATAGAAATAAAAGAATCCTGAGTAAGAAAACATATGGATAGTG
30057 ATTAATAGAAATAAAAGAATCCTGAGTAAGAAAACATATGGATAGTG
1 ATTAATAGAAATAAAAGAATCCTGAGTAAGAAAACATATGGATAGTG
30104 A
1 A
30105 AAAATTATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (47 bp):
ATTAATAGAAATAAAAGAATCCTGAGTAAGAAAACATATGGATAGTG
Found at i:36052 original size:30 final size:30
Alignment explanation
Indices: 36018--36084 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
36008 CTTAGAAGTT
36018 TCATGCTCAAAAATTAAAAATTCCTCATCA
1 TCATGCTCAAAAATTAAAAATTCCTCATCA
*
36048 TCATGCTCAAAAATTGAAAATTCCTCATCA
1 TCATGCTCAAAAATTAAAAATTCCTCATCA
36078 TCATGCT
1 TCATGCT
36085 AAACTTATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (30 bp):
TCATGCTCAAAAATTAAAAATTCCTCATCA
Found at i:48765 original size:18 final size:18
Alignment explanation
Indices: 48744--48779 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
48734 TATCATTAAG
48744 TTAGAAAATGTAAAAACT
1 TTAGAAAATGTAAAAACT
48762 TTAGAAAATGTAAAAACT
1 TTAGAAAATGTAAAAACT
48780 AAGTATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (18 bp):
TTAGAAAATGTAAAAACT
Found at i:64376 original size:26 final size:26
Alignment explanation
Indices: 64347--64404 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
64337 GATAGATCTT
**
64347 TAAAACCATGGAAAGAAAACAAATTG
1 TAAAACCATACAAAGAAAACAAATTG
* * *
64373 TAAAACTATACAAAGAAAACGAATTT
1 TAAAACCATACAAAGAAAACAAATTG
64399 TAAAAC
1 TAAAAC
64405 TGAAACAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.59, C:0.12, G:0.10, T:0.19
Consensus pattern (26 bp):
TAAAACCATACAAAGAAAACAAATTG
Found at i:68581 original size:82 final size:82
Alignment explanation
Indices: 68444--68601 Score: 307
Period size: 82 Copynumber: 1.9 Consensus size: 82
68434 GTACCGTGAC
68444 CATCTCTGACATGAAGTACACGATATGGACCATCTGAGCATCATCCCGTGGCGGTGCATCATCTT
1 CATCTCTGACATGAAGTACACGATATGGACCATCTGAGCATCATCCCGTGGCGGTGCATCATCTT
68509 TCATACTACCTGAGCAT
66 TCATACTACCTGAGCAT
*
68526 CATCTCTGACATGAAGTACACGATGTGGACCATCTGAGCATCATCCCGTGGCGGTGCATCATCTT
1 CATCTCTGACATGAAGTACACGATATGGACCATCTGAGCATCATCCCGTGGCGGTGCATCATCTT
68591 TCATACTACCT
66 TCATACTACCT
68602 AGATCGCGAT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (82 bp):
CATCTCTGACATGAAGTACACGATATGGACCATCTGAGCATCATCCCGTGGCGGTGCATCATCTT
TCATACTACCTGAGCAT
Found at i:69567 original size:15 final size:15
Alignment explanation
Indices: 69535--69566 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
69525 GAGTTGTTTG
69535 AAAGAATAAAAATAA
1 AAAGAATAAAAATAA
69550 AAAG-ATAAAAATAA
1 AAAGAATAAAAATAA
69564 AAA
1 AAA
69567 AAAGTTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAGAATAAAAATAA
Found at i:80600 original size:18 final size:18
Alignment explanation
Indices: 80549--80600 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
80539 CATTGATCTC
**
80549 CTTTATTTTATTTTATTT
1 CTTTATTTTATTTTAAGT
80567 CTTTATTTTCTATTTTAAGT
1 CTTTA-TTT-TATTTTAAGT
80587 -TTTACTTTTATTTT
1 CTTTA-TTTTATTTT
80601 TGGTTGTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 11 0.38
19 10 0.34
20 8 0.28
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (18 bp):
CTTTATTTTATTTTAAGT
Found at i:90973 original size:18 final size:17
Alignment explanation
Indices: 90952--90999 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 17
90942 TTGTATGACT
90952 GCATCTGGGTCTGTGATC
1 GCATCT-GGTCTGTGATC
90970 GCATCTGGTCATGTGATC
1 GCATCTGGTC-TGTGATC
*
90988 ACATCTGGTCTG
1 GCATCTGGTCTG
91000 GTTGCACGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.15, C:0.23, G:0.29, T:0.33
Consensus pattern (17 bp):
GCATCTGGTCTGTGATC
Found at i:104471 original size:27 final size:28
Alignment explanation
Indices: 104423--104480 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
104413 CGTACATTGG
* *
104423 AATTTAGTTTTAGCTTTAAC-TTAGATT
1 AATTTAGTTTTAGATTAAACTTTAGATT
104450 AATTTAG-TTTAGATTAATACTTTAGATT
1 AATTTAGTTTTAGATTAA-ACTTTAGATT
104478 AAT
1 AAT
104481 ATCCTTCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 8 0.30
27 9 0.33
28 10 0.37
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.50
Consensus pattern (28 bp):
AATTTAGTTTTAGATTAAACTTTAGATT
Found at i:104475 original size:13 final size:13
Alignment explanation
Indices: 104443--104481 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
104433 TAGCTTTAAC
*
104443 TTAGATTAATTTAGT
1 TTAGATTAA--TACT
104458 TTAGATTAATACT
1 TTAGATTAATACT
104471 TTAGATTAATA
1 TTAGATTAATA
104482 TCCTTCACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.61
15 9 0.39
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (13 bp):
TTAGATTAATACT
Found at i:113079 original size:23 final size:21
Alignment explanation
Indices: 113053--113095 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
113043 TTTTGTCACT
113053 ATTCACTTATTTTCTTACTCATG
1 ATTCACTTA-TTTC-TACTCATG
**
113076 ATTCTTTTATTTCTACTCAT
1 ATTCACTTATTTCTACTCAT
113096 TTTTCTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTCACTTATTTCTACTCATG
Found at i:113094 original size:21 final size:22
Alignment explanation
Indices: 113063--113104 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
113053 ATTCACTTAT
113063 TTTCTTACTCATGATTCTTTTA
1 TTTCTTACTCATGATTCTTTTA
**
113085 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATGATTCTTTT
113105 CTTTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTA
Found at i:125679 original size:17 final size:17
Alignment explanation
Indices: 125657--125690 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
125647 TGAGTTCACC
125657 GTTTTAATGTGACTCGA
1 GTTTTAATGTGACTCGA
125674 GTTTTAATGTGACTCGA
1 GTTTTAATGTGACTCGA
125691 ATCTTCCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (17 bp):
GTTTTAATGTGACTCGA
Found at i:132826 original size:20 final size:21
Alignment explanation
Indices: 132801--132847 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
132791 GTCATTGCAA
*
132801 TTTTTACTTTTACTT-TTTGC
1 TTTTTACTTTTACTTGTTTCC
* *
132821 TTTTTATTTTTATTTGTTTCC
1 TTTTTACTTTTACTTGTTTCC
132842 TTTTTA
1 TTTTTA
132848 ATTTATGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTTACTTTTACTTGTTTCC
Found at i:147794 original size:17 final size:17
Alignment explanation
Indices: 147772--147804 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
147762 ACTATTTCAG
147772 ATAATTTTTATTTTTGA
1 ATAATTTTTATTTTTGA
*
147789 ATAATTTTTGTTTTTG
1 ATAATTTTTATTTTTG
147805 GTTTTAGACT
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:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (17 bp):
ATAATTTTTATTTTTGA
Found at i:153819 original size:2 final size:2
Alignment explanation
Indices: 153814--153841 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
153804 TCTTTTTTTC
153814 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
153842 TTTAAGGAAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:163070 original size:26 final size:23
Alignment explanation
Indices: 163018--163062 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
163008 ATTCCTAAAT
163018 TGGAGAGAAAAGGAAGGTGAGAGA
1 TGGAGAGAAAAGG-AGGTGAGAGA
163042 TGGAGAGATAAAGG-GGTGAGA
1 TGGAGAGA-AAAGGAGGTGAGA
163063 TAGAATGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 8 0.40
25 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.47, T:0.11
Consensus pattern (23 bp):
TGGAGAGAAAAGGAGGTGAGAGA
Found at i:171881 original size:27 final size:27
Alignment explanation
Indices: 171830--171881 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
171820 TTTTGAACAA
*
171830 TTTAATTTTTTTTGTTTTTTCTATTCT
1 TTTAATTTTTTTTGTTTCTTCTATTCT
171857 TTTAACTTTCTTTTT-TTTCTT-TATT
1 TTTAA-TTT-TTTTTGTTTCTTCTATT
171882 TTTCATTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.41
28 8 0.36
29 5 0.23
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.77
Consensus pattern (27 bp):
TTTAATTTTTTTTGTTTCTTCTATTCT
Found at i:175101 original size:2 final size:2
Alignment explanation
Indices: 175094--175120 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
175084 TTTTAAAAAG
175094 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
175121 GCTGCATGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:175585 original size:15 final size:15
Alignment explanation
Indices: 175565--175595 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
175555 TAATATTTCA
175565 TTTTCTTTTCTCTTT
1 TTTTCTTTTCTCTTT
*
175580 TTTTCTTTTTTCTTT
1 TTTTCTTTTCTCTTT
175595 T
1 T
175596 CTTTTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTCTTTTCTCTTT
Found at i:176204 original size:17 final size:17
Alignment explanation
Indices: 176184--176222 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
176174 GATAATGTAG
176184 ATGCAACGACAATAAAA
1 ATGCAACGACAATAAAA
* * *
176201 ATGCAATGACATTAATA
1 ATGCAACGACAATAAAA
176218 ATGCA
1 ATGCA
176223 GGTACAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (17 bp):
ATGCAACGACAATAAAA
Found at i:181089 original size:81 final size:81
Alignment explanation
Indices: 180991--181141 Score: 230
Period size: 81 Copynumber: 1.9 Consensus size: 81
180981 CCCCCTAAAA
* * * *
180991 TGATAAAATTTTTATTTAATCTTTTAAAATTTGTATTTTTACTATCATAAAAATAACAATTTAAC
1 TGATAAAATTTTGATTTAATCCTTTAAAAATTATATTTTTACTATCATAAAAATAACAATTTAAC
181056 TTCGATCTTTTAATCC
66 TTCGATCTTTTAATCC
* * * *
181072 TGATAAAATTTTGATTTAATCCTTTAAAAATTATATTTTTATTATCATAAAAATTATAATTTAAT
1 TGATAAAATTTTGATTTAATCCTTTAAAAATTATATTTTTACTATCATAAAAATAACAATTTAAC
181137 TTCGA
66 TTCGA
181142 CTTCCTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 62 1.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (81 bp):
TGATAAAATTTTGATTTAATCCTTTAAAAATTATATTTTTACTATCATAAAAATAACAATTTAAC
TTCGATCTTTTAATCC
Found at i:189177 original size:32 final size:33
Alignment explanation
Indices: 189141--189204 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
189131 GCACTTATAT
**
189141 TTAATGAATGTA-TTAGAGTAGATGCATTTAGC
1 TTAATGAATGTATTTAGAAAAGATGCATTTAGC
* *
189173 TTAATTAATGTATTTAGAAAAGATGTATTTAG
1 TTAATGAATGTATTTAGAAAAGATGCATTTAG
189205 TAGTCATGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.41
Consensus pattern (33 bp):
TTAATGAATGTATTTAGAAAAGATGCATTTAGC
Found at i:212432 original size:132 final size:132
Alignment explanation
Indices: 212194--212436 Score: 362
Period size: 132 Copynumber: 1.8 Consensus size: 132
212184 GATTTTTGGA
* *
212194 ATTACATGTTATATGGGTACTGGTCTTACATGTCCTATCGATGGCTGAGATCCGACATTTGTTGC
1 ATTACAGGTTATATGAGTACTGGTCTTACATGTCCTATCGATGGCTGAGATCCGACATTTGTTGC
* * *
212259 AGATTTTCCACAGCTCGTGTGAGTAGCATCGTGTAGCTTAACATCTTTACCCACAGCTCATGTGA
66 AGATTCTCCACAACTCGTGTGAGCAGCATCGTGTAGCTTAACATCTTTACCCACAGCTCATGTGA
212324 GC
131 GC
* * * *
212326 ATTACAGGTTATATGAGTACTGGTCTTAGATGTCTTA-CTGATGGTTGAGATCTGACATTTGTTG
1 ATTACAGGTTATATGAGTACTGGTCTTACATGTCCTATC-GATGGCTGAGATCCGACATTTGTTG
* * *
212390 CGGATTCTCCACAACTCGTGTGAGCAGCATTGTGTAGTTTAACATCT
65 CAGATTCTCCACAACTCGTGTGAGCAGCATCGTGTAGCTTAACATCT
212437 CAACCTACAA
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
131 1 0.01
132 97 0.99
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (132 bp):
ATTACAGGTTATATGAGTACTGGTCTTACATGTCCTATCGATGGCTGAGATCCGACATTTGTTGC
AGATTCTCCACAACTCGTGTGAGCAGCATCGTGTAGCTTAACATCTTTACCCACAGCTCATGTGA
GC
Found at i:216794 original size:30 final size:29
Alignment explanation
Indices: 216747--217071 Score: 244
Period size: 30 Copynumber: 11.1 Consensus size: 29
216737 TCTCTGAACA
* * *
216747 TTCCAAAAATCATATTTTGACCCTCAAACC
1 TTCCAAAAATTACATTTTTACCCTCAAA-C
* * *
216777 TTCCTAAAATTTCATTTTTACCCTTAAAC
1 TTCCAAAAATTACATTTTTACCCTCAAAC
* * * * *
216806 TTTCCACAAATCACAATTTGACCCTCGAAC
1 -TTCCAAAAATTACATTTTTACCCTCAAAC
*
216836 TT--AAAAATTACATTTTTACCCTCAAAAT
1 TTCCAAAAATTACATTTTTACCCTC-AAAC
** * *
216864 TTTTAAAAATTTCATTTTTTCCCTCAAAC
1 TTCCAAAAATTACATTTTTACCCTCAAAC
** **
216893 TTCTCAAAAATTACATTTTTGTCCTTGAAC
1 TTC-CAAAAATTACATTTTTACCCTCAAAC
**
216923 TTCCAAAAATTACATTTTTACCCTTGAAC
1 TTCCAAAAATTACATTTTTACCCTCAAAC
* * * * *
216952 TTCAAAAAATCACATTTTAATCATCAACAC
1 TTCCAAAAATTACATTTTTACCCTCAA-AC
* * * *
216982 TTTTCAAAAATTACATTTTTTCCTTCGAAC
1 -TTCCAAAAATTACATTTTTACCCTCAAAC
*
217012 TTCC-AAAATTACGTTTTTACCCT-AAAC
1 TTCCAAAAATTACATTTTTACCCTCAAAC
* *
217039 TTTCCCAAAATTACATTTTTACCCCTAAAAC
1 -TTCCAAAAATTACATTTTTA-CCCTCAAAC
217070 TT
1 TT
217072 TCCTAAATTA
Statistics
Matches: 231, Mismatches: 53, Indels: 22
0.75 0.17 0.07
Matches are distributed among these distances:
27 20 0.09
28 24 0.10
29 69 0.30
30 95 0.41
31 23 0.10
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.38
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCCTCAAAC
Found at i:216959 original size:117 final size:116
Alignment explanation
Indices: 216767--217062 Score: 328
Period size: 117 Copynumber: 2.5 Consensus size: 116
216757 CATATTTTGA
* * * * *
216767 CCCTCAAACCTTCCTAAAATTTCATTTTTACCCTTAAACTTTCCACAAATCACAATTTGACCCTC
1 CCCTCAAA-CTTCC-AAAATTACATTTTTA-CCTTAAACTTTCCAAAAATTACATTTTTACCCTC
* * * * *
216832 GAACTT-AAAAATTACATTTTTACCCTCAA-AATTTTTAAAAATTTCATTTTTT
63 GAACTTAAAAAATCACATTTTAACCATCAACAATTTTCAAAAATTACATTTTTT
* * *
216884 CCCTCAAACTTCTCAAAAATTACATTTTTGTCCTTGAAC-TTCCAAAAATTACATTTTTACCCTT
1 CCCTCAAACTTC-C-AAAATTACATTTTT-ACCTTAAACTTTCCAAAAATTACATTTTTACCCTC
* *
216948 GAACTTCAAAAAATCACATTTTAATCATCAACACTTTTCAAAAATTACATTTTTT
63 GAACTT-AAAAAATCACATTTTAACCATCAACAATTTTCAAAAATTACATTTTTT
* * * * *
217003 CCTTCGAACTTCCAAAATTACGTTTTTACCCTAAACTTTCCCAAAATTACATTTTTACCC
1 CCCTCAAACTTCCAAAATTACATTTTTACCTTAAACTTTCCAAAAATTACATTTTTACCC
217063 CTAAAACTTT
Statistics
Matches: 150, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
116 36 0.24
117 64 0.43
118 20 0.13
119 30 0.20
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (116 bp):
CCCTCAAACTTCCAAAATTACATTTTTACCTTAAACTTTCCAAAAATTACATTTTTACCCTCGAA
CTTAAAAAATCACATTTTAACCATCAACAATTTTCAAAAATTACATTTTTT
Found at i:217049 original size:88 final size:88
Alignment explanation
Indices: 216838--217040 Score: 243
Period size: 89 Copynumber: 2.3 Consensus size: 88
216828 CCTCGAACTT
* * ** ** * *
216838 AAAAATTACATTTTTACCCTCAAAATTTTTAAAAATTTCATTTT-TTCCCTCAAACTTCTCAAAA
1 AAAAATTACATTTTTACCCT-TAAACTTCAAAAAATCACATTTTAAT-CATCAAACTTCTCAAAA
216902 ATTACATTTTTGTCCTTGAACTTCC
64 ATTACATTTTTGTCCTTGAACTTCC
* *
216927 AAAAATTACATTTTTACCCTTGAACTTCAAAAAATCACATTTTAATCATCAACACTTTTCAAAAA
1 AAAAATTACATTTTTACCCTTAAACTTCAAAAAATCACATTTTAATCATCAA-ACTTCTCAAAAA
216992 TTACATTTTT-TCCTTCGAACTTCC
65 TTACATTTTTGTCCTT-GAACTTCC
*
217016 -AAAATTACGTTTTTACCC-TAAACTT
1 AAAAATTACATTTTTACCCTTAAACTT
217041 TCCCAAAATT
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
87 6 0.06
88 43 0.43
89 50 0.51
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.40
Consensus pattern (88 bp):
AAAAATTACATTTTTACCCTTAAACTTCAAAAAATCACATTTTAATCATCAAACTTCTCAAAAAT
TACATTTTTGTCCTTGAACTTCC
Found at i:217059 original size:89 final size:89
Alignment explanation
Indices: 216830--217059 Score: 265
Period size: 88 Copynumber: 2.6 Consensus size: 89
216820 AATTTGACCC
* * ** * *
216830 TCGAACTT-AAAAATTACATTTTTACCCTCAAAATTTTTAAAAATTTCATTTTT-TCCCTCAAAC
1 TCGAACTTCCAAAATTACATTTTTACCCT-AAACTTTCAAAAAATTACATTTTTATCCATCAAAC
216893 TTCTCAAAAATTACATTTTTGTCCT
65 TTCTCAAAAATTACATTTTTGTCCT
* * *
216918 T-GAACTTCCAAAAATTACATTTTTACCCTTGAAC-TTCAAAAAATCACATTTTAAT-CATCAAC
1 TCGAACTTCC-AAAATTACATTTTTACCC-TAAACTTTCAAAAAATTACATTTTTATCCATCAA-
*
216980 ACTTTTCAAAAATTACATTTTT-TCCT
63 ACTTCTCAAAAATTACATTTTTGTCCT
* **
217006 TCGAACTTCCAAAATTACGTTTTTACCCTAAACTTTCCCAAAATTACATTTTTA
1 TCGAACTTCCAAAATTACATTTTTACCCTAAACTTTCAAAAAATTACATTTTTA
217060 CCCCTAAAAC
Statistics
Matches: 119, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
87 10 0.08
88 58 0.49
89 50 0.42
90 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (89 bp):
TCGAACTTCCAAAATTACATTTTTACCCTAAACTTTCAAAAAATTACATTTTTATCCATCAAACT
TCTCAAAAATTACATTTTTGTCCT
Found at i:217312 original size:19 final size:19
Alignment explanation
Indices: 217288--217328 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
217278 AACTTTAATA
217288 TTAA-TTGCATAGCTCATAT
1 TTAATTTGCAT-GCTCATAT
*
217307 TTAATTTGCATGCTCATTT
1 TTAATTTGCATGCTCATAT
217326 TTA
1 TTA
217329 TCCCTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.49
Consensus pattern (19 bp):
TTAATTTGCATGCTCATAT
Found at i:224517 original size:25 final size:25
Alignment explanation
Indices: 224487--224537 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
224477 AACCATTTGT
224487 ACATACCCAATAAACAAAATTAATC
1 ACATACCCAATAAACAAAATTAATC
224512 ACATACCCAATAAACAAAATTAATC
1 ACATACCCAATAAACAAAATTAATC
224537 A
1 A
224538 TTCTTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.24, G:0.00, T:0.20
Consensus pattern (25 bp):
ACATACCCAATAAACAAAATTAATC
Found at i:229090 original size:39 final size:39
Alignment explanation
Indices: 229045--229715 Score: 352
Period size: 39 Copynumber: 17.2 Consensus size: 39
229035 TTTTGATCCT
229045 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
* *
229084 TTACCCCGAGCCTAGGGCAGATTGCAGCCATTC-G---ATCTC
1 TTACCCCGAGCTTGGGGCAGA-T-CA-CCA-TCAGCCAATCTC
** *
229123 TTACCTAGAGCTTAGGGCAGATCACCATCAGCCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
* ** ** * ** *
229162 TTACCCCGAGCCTGGGGTGGATTGCAATCATTCGATCTC
1 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
* * *
229201 TTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTT
1 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
* * * * ** * * *
229240 TTACCCCAATCATAGGGCAGAT-TGCAACCGTCCGATCTC
1 TTACCCCGAGCTTGGGGCAGATCACCATCAG-CCAATCTC
* * * * **
229279 TTACCCCGAGCTT-AGACTAAATCATCATCAGTAAATCTC
1 TTACCCCGAGCTTGGGGC-AGATCACCATCAGCCAATCTC
* * * * * * ** * *
229318 TTA-CCCGAGCCTAGGGTAGATTACAACCATTCGATCTT
1 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
* * *
229356 TTAGCCCGAGCTTGGGGCAGATCACCATTAAG-AAATCTC
1 TTACCCCGAGCTTGGGGCAGATCACCA-TCAGCCAATCTC
* ** * * ** * *
229395 TTACCCCGAGCCTGGGGCAGATTGCAACCATTCGATCTT
1 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
* * *
229434 TTACCCCGAGCCTGGGGCAGATCACCATTAGCAAATCTC
1 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
* *
229473 TTACCCCGATCATGGGGCAGATTGCAGCCATTC-G---ATCTC
1 TTACCCCGAGCTTGGGGCAGA-T-CA-CCA-TCAGCCAATCTC
* * *
229512 TTACTCCAAG-TCTGGGGTAGATCACCATCAGCCAATCTC
1 TTACCCCGAGCT-TGGGGCAGATCACCATCAGCCAATCTC
* * * ** **** *
229551 TTACCCCAAGCTTGAGGCAAAT-TGCAGTCATTTGATCTT
1 TTACCCCGAGCTTGGGGCAGATCACCA-TCAGCCAATCTC
* * **
229590 TTACCCCAAGCGTAAGGCAGATCACCATCAGCCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
*
229629 TTACCCCGAGCTTGGGGCAGATTGCAGCCATTC-G---ATCTT
1 TTACCCCGAGCTTGGGGCAGA-T-CA-CCA-TCAGCCAATCTC
* *
229668 TTACCCCGAGCGTGGGGCAGATCATCATCAGCCAATCTC
1 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
229707 TTACCCCGA
1 TTACCCCGA
229716 TCATAGGGCA
Statistics
Matches: 466, Mismatches: 131, Indels: 70
0.70 0.20 0.10
Matches are distributed among these distances:
35 6 0.01
36 11 0.02
37 6 0.01
38 35 0.08
39 374 0.80
40 11 0.02
41 6 0.01
42 12 0.03
43 5 0.01
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (39 bp):
TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTC
Found at i:229134 original size:78 final size:78
Alignment explanation
Indices: 229045--229741 Score: 728
Period size: 78 Copynumber: 8.9 Consensus size: 78
229035 TTTTGATCCT
*
229045 TTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCA
1 TTACCCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCA
229110 GCCATTCGATCTC
66 GCCATTCGATCTC
* * * **
229123 TTACCTAGAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGTGGATTGCA
1 TTACCCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCA
**
229188 ATCATTCGATCTC
66 GCCATTCGATCTC
* * * * *
229201 TTACCCCA-AGCCTGGGGCAGATCACCATCAGCCAATCTTTTACCCCAATCATAGGGCAGATTGC
1 TTA-CCCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGC
* * *
229265 AACCGTCCGATCTC
65 AGCCATTCGATCTC
* * * * * ** * *
229279 TTACCCCGAGCTT-AGACTAAATCATCATCAGTAAATCTCTTA-CCCGAGCCTAGGGTAGATTAC
1 TTACCCAGAGCTTGGGGC-AGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGC
* *
229342 AACCATTCGATCTT
65 AGCCATTCGATCTC
* * *
229356 TTAGCCC-GAGCTTGGGGCAGATCACCATTAAG-AAATCTCTTACCCCGAGCCTGGGGCAGATTG
1 TTA-CCCAGAGCTTGGGGCAGATCACCA-TCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTG
* *
229419 CAACCATTCGATCTT
64 CAGCCATTCGATCTC
* * * * * * *
229434 TTACCCCGAGCCTGGGGCAGATCACCATTAGCAAATCTCTTACCCCGATCATGGGGCAGATTGCA
1 TTACCCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCA
229499 GCCATTCGATCTC
66 GCCATTCGATCTC
* * * *
229512 TTACTCCA-AG-TCTGGGGTAGATCACCATCAGCCAATCTCTTACCCCAAG-CTTGAGGCAAATT
1 TTAC-CCAGAGCT-TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAG-GGCAGATT
* * *
229574 GCAGTCATTTGATCTT
63 GCAGCCATTCGATCTC
* ** * *
229590 TTACCCCA-AGCGTAAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTGC
1 TTA-CCCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGC
*
229654 AGCCATTCGATCTT
65 AGCCATTCGATCTC
* * * * * *
229668 TTACCCCGAGCGTGGGGCAGATCATCATCAGCCAATCTCTTACCCCGATCATAGGGCAGATTACA
1 TTACCCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCA
*
229733 GTCATTCGA
66 GCCATTCGA
229742 AGCAATAAAG
Statistics
Matches: 519, Mismatches: 84, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
77 69 0.13
78 442 0.85
79 8 0.02
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.25
Consensus pattern (78 bp):
TTACCCAGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGGCAGATTGCA
GCCATTCGATCTC
Found at i:230181 original size:17 final size:17
Alignment explanation
Indices: 230142--230179 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
230132 AAACCCATTC
*
230142 TTAAATTTACTTTAAGT
1 TTAAATTTACTTTAAAT
230159 TTAAATTTA-TTTAAAT
1 TTAAATTTACTTTAAAT
230175 TTAAA
1 TTAAA
230180 ATAAATAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTACTTTAAAT
Found at i:232023 original size:30 final size:29
Alignment explanation
Indices: 231878--232474 Score: 477
Period size: 29 Copynumber: 20.2 Consensus size: 29
231868 CTTAGAAGGT
* *
231878 CCCTAAACTTTCAAAAAAT-CATATTTTAAC
1 CCCTAAACTTCCAAAAATTACAT-TTTT-AC
* * *
231908 CCCTCAACCTTTCC-AAAATTTCATTTTGAC
1 CCCT-AAAC-TTCCAAAAATTACATTTTTAC
* * * *
231938 CCTTAAAGTTTCCAAAAATCACATTTTAAAACC
1 CCCTAAA-CTTCCAAAAATTACATTTT--TA-C
* *
231971 CCCTAAACTT-CATAAAAATACATTCTTAC
1 CCCTAAACTTCCA-AAAATTACATTTTTAC
*
232000 CCCTAAACTTCTTAAAAATTACATTTTTAC
1 CCCTAAACTTC-CAAAAATTACATTTTTAC
* ** * *
232030 CCCTAAATTTCTTGAAAACTA-ATTTTT-G
1 CCCTAAACTTC-CAAAAATTACATTTTTAC
* *
232058 TCCTCAAACTTCCAAAAATTTCATTTTTAC
1 CCCT-AAACTTCCAAAAATTACATTTTTAC
* * *
232088 CCTTAAACTTCCAAAAATCACATTTTAAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* * *
232117 CCCTAAGCTTCTCAAAAATTATATTTTTGC
1 CCCTAAACTTC-CAAAAATTACATTTTTAC
*
232147 CCCCAAACTTCC-AAAATTACATTTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
** * * *
232175 TAAC-AAACTTCTAAAAATCACA-TTTTAA
1 -CCCTAAACTTCCAAAAATTACATTTTTAC
* *
232203 CCCTCGAACTTCTTAAAAATTACATTTTTAC
1 CCCT-AAACTTC-CAAAAATTACATTTTTAC
*
232234 CCCTAAACTTCCAAAAATCACATTTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
232263 CCCTAAACTTCTCAAAAATTACATTTTTAC
1 CCCTAAACTTC-CAAAAATTACATTTTTAC
* *
232293 CCCTATACTTCCAAAAATCACATTTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
* *
232322 CCCTAAACTTCTCAAAAATTATATTTTT-G
1 CCCTAAACTTC-CAAAAATTACATTTTTAC
*
232351 CCCTCAAACTTCC-AAAATCACATTTTTA-
1 CCCT-AAACTTCCAAAAATTACATTTTTAC
*
232379 CCCTCAAACTTCACAAAAAATTACATTTTTTGC
1 CCCT-AAACTTC-C-AAAAATTACA-TTTTTAC
232412 CTCC-AAACTTCC-AAAATTA-AGTTTTTAC
1 C-CCTAAACTTCCAAAAATTACA-TTTTTAC
* * *
232440 CCC-GAACTTCCCAAAATGACATTTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTAC
232468 CCCTAAA
1 CCCTAAA
232475 AGTTTTTAAA
Statistics
Matches: 459, Mismatches: 74, Indels: 69
0.76 0.12 0.11
Matches are distributed among these distances:
27 10 0.02
28 82 0.18
29 152 0.33
30 142 0.31
31 32 0.07
32 31 0.07
33 8 0.02
34 2 0.00
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTAC
Found at i:232162 original size:59 final size:59
Alignment explanation
Indices: 231878--232474 Score: 510
Period size: 59 Copynumber: 10.1 Consensus size: 59
231868 CTTAGAAGGT
* * * * * * *
231878 CCCTAAACTTTCAAAAAATCATATTTTAACCCCTCAACCTT-TCCAAAATTTCATTTTGAC
1 CCCTAAAC-TTCCAAAAATCACATTTTTACCCCT-AAACTTCTCAAAAATTACATTTTTAC
* * * *
231938 CCTTAAAGTTTCCAAAAATCACATTTTAAAACCCCCTAAACTTCAT-AAAAA-TACATTCTTAC
1 CCCTAAA-CTTCCAAAAATCACATTTT--TA-CCCCTAAACTTC-TCAAAAATTACATTTTTAC
* * * ** * *
232000 CCCTAAACTTCTTAAAAATTACATTTTTACCCCTAAATTTCTTGAAAACTA-ATTTTT-G
1 CCCTAAACTTC-CAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATTACATTTTTAC
* ** * * *
232058 TCCTCAAACTTCCAAAAATTTCATTTTTACCCTTAAACTTC-CAAAAATCACATTTTAAC
1 CCCT-AAACTTCCAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATTACATTTTTAC
* * * * *
232117 CCCTAAGCTTCTCAAAAATTATATTTTTGCCCCCAAACTTC-C-AAAATTACATTTTTAC
1 CCCTAAACTTC-CAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATTACATTTTTAC
** * * * *
232175 TAAC-AAACTTCTAAAAATCACA-TTTTAACCCTCGAACTTCTTAAAAATTACATTTTTAC
1 -CCCTAAACTTCCAAAAATCACATTTTTACCCCT-AAACTTCTCAAAAATTACATTTTTAC
232234 CCCTAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATTACATTTTTAC
1 CCCTAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATTACATTTTTAC
* * *
232293 CCCTATACTTCCAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATTATATTTTT-G
1 CCCTAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATTACATTTTTAC
* *
232351 CCCTCAAACTTCC-AAAATCACATTTTTA-CCCTCAAACTTCACAAAAAATTACATTTTTTGC
1 CCCT-AAACTTCCAAAAATCACATTTTTACCCCT-AAACTTCTC-AAAAATTACA-TTTTTAC
* * * *
232412 CTCC-AAACTTCC-AAAATTA-AGTTTTTACCCC-GAACTTC-CCAAAATGACATTTTTAC
1 C-CCTAAACTTCCAAAAATCACA-TTTTTACCCCTAAACTTCTCAAAAATTACATTTTTAC
232468 CCCTAAA
1 CCCTAAA
232475 AGTTTTTAAA
Statistics
Matches: 442, Mismatches: 67, Indels: 60
0.78 0.12 0.11
Matches are distributed among these distances:
55 2 0.00
56 17 0.04
57 31 0.07
58 89 0.20
59 191 0.43
60 59 0.13
61 7 0.02
62 36 0.08
63 9 0.02
64 1 0.00
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (59 bp):
CCCTAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATTACATTTTTAC
Found at i:232491 original size:205 final size:204
Alignment explanation
Indices: 231878--232474 Score: 606
Period size: 205 Copynumber: 2.9 Consensus size: 204
231868 CTTAGAAGGT
* * * *
231878 CCCTAAACTTTCAAAAAATCATATTTTAACCCCTCAACCTT-TCCAAAATT-TCA-TTTTGACCC
1 CCCTAAAC-TTCCAAAAATCACATTTTAACCCCT-AAACTTCTCAAAAATTAT-ATTTTTG-CCC
** * * ** *
231940 TTAAAGTTTCCAAAAATCACATTTTAAAACCCCCTAAACTTCATAAAAAT-ACATTCTTACCCCT
62 CCAAA-CTTCC-AAAATCACATTTT--TACCAAC-AAACTTCA-AAAAATCACATT-TTAACCCT
* ** **
232004 -AAACTTCTTAAAAATTACATTTTTACCCCTAAATTTCTTGAAAA-CTA-ATTTTT-GTCCTCAA
120 CAAACTTC-TAAAAATTACATTTTTACCCCTAAACTTC-CAAAAATC-ACATTTTTACCCCT-AA
*
232065 ACTTC-CAAAAATTTCATTTTTAC
181 ACTTCTCAAAAATTACATTTTTAC
* *
232088 CCTTAAACTTCCAAAAATCACATTTTAACCCCTAAGCTTCTCAAAAATTATATTTTTGCCCCCAA
1 CCCTAAACTTCCAAAAATCACATTTTAACCCCTAAACTTCTCAAAAATTATATTTTTGCCCCCAA
* * * *
232153 ACTTCCAAAATTACATTTTTACTAACAAACTTCTAAAAATCACATTTTAACCCTCGAACTTCTTA
66 ACTTCCAAAATCACATTTTTACCAACAAACTTCAAAAAATCACATTTTAACCCTCAAACTTC-TA
232218 AAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATT
130 AAAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATT
232283 ACATTTTTAC
195 ACATTTTTAC
* * *
232293 CCCTATACTTCCAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATTATATTTTTGCCCTCAA
1 CCCTAAACTTCCAAAAATCACATTTTAACCCCTAAACTTCTCAAAAATTATATTTTTGCCCCCAA
** * ***
232358 ACTTCCAAAATCACATTTTTACCCTCAAACTTCACAAAAAATTACATTTTTTGCCTCCAAACTTC
66 ACTTCCAAAATCACATTTTTACCAACAAACTT--CAAAAAATCACATTTTAACCCT-CAAACTTC
* * * *
232423 -CAAAATTA-AGTTTTTACCCC-GAACTTCCCAAAATGACATTTTTACCCCTAAA
128 TAAAAATTACA-TTTTTACCCCTAAACTTCCAAAAATCACATTTTTACCCCTAAA
232475 AGTTTTTAAA
Statistics
Matches: 333, Mismatches: 41, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
203 18 0.05
204 61 0.18
205 141 0.42
206 17 0.05
207 29 0.09
208 16 0.05
209 38 0.11
210 13 0.04
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (204 bp):
CCCTAAACTTCCAAAAATCACATTTTAACCCCTAAACTTCTCAAAAATTATATTTTTGCCCCCAA
ACTTCCAAAATCACATTTTTACCAACAAACTTCAAAAAATCACATTTTAACCCTCAAACTTCTAA
AAATTACATTTTTACCCCTAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCTCAAAAATTA
CATTTTTAC
Found at i:246301 original size:31 final size:31
Alignment explanation
Indices: 246266--246328 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
246256 AAAAAAAAAC
*
246266 TTTAACAACTCAATGACTTAAATAAAAACTT
1 TTTAACAACTCAATAACTTAAATAAAAACTT
* ** * *
246297 TTTAATAGTTCAATAACTTAACTGAAAACTT
1 TTTAACAACTCAATAACTTAAATAAAAACTT
246328 T
1 T
246329 CGGATAGTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (31 bp):
TTTAACAACTCAATAACTTAAATAAAAACTT
Found at i:246746 original size:28 final size:27
Alignment explanation
Indices: 246715--246800 Score: 79
Period size: 26 Copynumber: 3.1 Consensus size: 27
246705 AGGCTTGCTC
246715 ATATTATTTTTTATTTTTTAAAATATTT
1 ATATTATTTTTTATTTTTTAAAAT-TTT
* *
246743 ATATTA--TTTTAATATTTAATAATTTT
1 ATATTATTTTTTATTTTTTAA-AATTTT
* *
246769 ATA-CATTTTTTATTTATTGAAAATTTTT
1 ATATTATTTTTTATTT-TTTAAAA-TTTT
246797 ATAT
1 ATAT
246801 AGTCATCTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
25 1 0.02
26 17 0.37
27 11 0.24
28 17 0.37
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (27 bp):
ATATTATTTTTTATTTTTTAAAATTTT
Found at i:246758 original size:17 final size:16
Alignment explanation
Indices: 246736--246769 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
246726 TATTTTTTAA
*
246736 AATATTTATATTATTTT
1 AATATTTA-ATAATTTT
246753 AATATTTAATAATTTT
1 AATATTTAATAATTTT
246769 A
1 A
246770 TACATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATATTTAATAATTTT
Found at i:249444 original size:13 final size:13
Alignment explanation
Indices: 249422--249473 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
249412 AAGGTTTGAG
*
249422 GTTTGGGGTTCAA
1 GTTTGAGGTTCAA
*
249435 GTTTGAGGTTCGA
1 GTTTGAGGTTCAA
* * *
249448 GTTTGAGATTTAGG
1 GTTTGAGGTTCA-A
249462 GTTTGAGGTTCA
1 GTTTGAGGTTCA
249474 TAGTAAAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.17, C:0.06, G:0.37, T:0.40
Consensus pattern (13 bp):
GTTTGAGGTTCAA
Found at i:263125 original size:52 final size:52
Alignment explanation
Indices: 263028--263266 Score: 329
Period size: 52 Copynumber: 4.6 Consensus size: 52
263018 TTCCCATTTA
* *
263028 ATACTCACGATGACACAAAGTCATCGGACCTTA-AATCCGTAAAAGGA-TCTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGT-AAAGGATTC-AT
* * * *
263080 ATGCTCAGGATAACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
263132 ATGCTCACAATGACACATAGACATTGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
263184 ATACTCATGATGACACATAGTTATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
263236 ATACTCACGATGACACATAGTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
263267 TTTTCATTTA
Statistics
Matches: 164, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
52 155 0.95
53 9 0.05
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:265081 original size:15 final size:16
Alignment explanation
Indices: 265049--265082 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
265039 ATAATTGGTC
*
265049 CTTCAATTATATTAAA
1 CTTCAATTATAATAAA
265065 CTTCAATTA-AATAAA
1 CTTCAATTATAATAAA
265080 CTT
1 CTT
265083 TATTTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (16 bp):
CTTCAATTATAATAAA
Found at i:265857 original size:11 final size:11
Alignment explanation
Indices: 265841--265877 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
265831 GTGGTGGTCA
*
265841 CGATGGTGGTT
1 CGATGGTGGTG
265852 CGATGGTGGTG
1 CGATGGTGGTG
*
265863 CGGTGGTGGTG
1 CGATGGTGGTG
265874 CGAT
1 CGAT
265878 TAACTAATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.08, C:0.11, G:0.51, T:0.30
Consensus pattern (11 bp):
CGATGGTGGTG
Found at i:267596 original size:42 final size:42
Alignment explanation
Indices: 267545--267628 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
267535 AATTTAAATA
267545 ATGGGACTCGATTCGAGAAACAAATTTTTTAAACAATTTTAT
1 ATGGGACTCGATTCGAGAAACAAATTTTTTAAACAATTTTAT
* *
267587 ATGGGACTCGATTCGAGAAATAAATTTTTTAAATAATTTTAT
1 ATGGGACTCGATTCGAGAAACAAATTTTTTAAACAATTTTAT
267629 TATAAGTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (42 bp):
ATGGGACTCGATTCGAGAAACAAATTTTTTAAACAATTTTAT
Found at i:267970 original size:7 final size:7
Alignment explanation
Indices: 267958--267994 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
267948 TCCCTTCCAG
267958 CTCTCAC
1 CTCTCAC
267965 CTCTCAC
1 CTCTCAC
267972 CTCTCAC
1 CTCTCAC
267979 CTCTCAC
1 CTCTCAC
267986 CTCTCAC
1 CTCTCAC
267993 CT
1 CT
267995 TCTTTTCCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.14, C:0.57, G:0.00, T:0.30
Consensus pattern (7 bp):
CTCTCAC
Found at i:272373 original size:3 final size:3
Alignment explanation
Indices: 272358--272393 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
272348 CTTTATAATA
272358 ATT ATT -TT CATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
272394 TATCGAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:279879 original size:17 final size:17
Alignment explanation
Indices: 279857--279889 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
279847 TAATAAAAAT
279857 ATAATTT-TATTATTTAA
1 ATAATTTATA-TATTTAA
279874 ATAATTTATATATTTA
1 ATAATTTATATATTTA
279890 TAATTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATAATTTATATATTTAA
Found at i:281084 original size:15 final size:15
Alignment explanation
Indices: 281064--281099 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
281054 ATCAGATGAA
*
281064 GAAGAAACTTCTTTT
1 GAAGAAACTTCTTCT
281079 GAAGAAACTTCTTCT
1 GAAGAAACTTCTTCT
281094 GAAGAA
1 GAAGAA
281100 TTATCTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (15 bp):
GAAGAAACTTCTTCT
Found at i:298791 original size:21 final size:21
Alignment explanation
Indices: 298765--298810 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
298755 TGCCGAGACT
298765 ATAAATTCTACAAAA-AATAGA
1 ATAAATTCTACAAAAGAA-AGA
* *
298786 ATAAATTTTGCAAAAGAAAGA
1 ATAAATTCTACAAAAGAAAGA
298807 ATAA
1 ATAA
298811 CTACACATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.24
Consensus pattern (21 bp):
ATAAATTCTACAAAAGAAAGA
Found at i:300190 original size:17 final size:17
Alignment explanation
Indices: 300170--300202 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
300160 CTTAAATCAA
300170 TTTTTT-AAAAAGTAATT
1 TTTTTTGAAAAA-TAATT
300187 TTTTTTGAAAAATAAT
1 TTTTTTGAAAAATAAT
300203 ACTAAAGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
TTTTTTGAAAAATAATT
Found at i:300500 original size:15 final size:15
Alignment explanation
Indices: 300480--300531 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
300470 ATTTTTTGGA
300480 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* ** *
300495 TTATATTTAAAAAAA
1 TTATATTTTAATTAT
* *
300510 TTATGTTTTTATTAT
1 TTATATTTTAATTAT
300525 TTATATT
1 TTATATT
300532 AATGTGTTGT
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:300697 original size:19 final size:20
Alignment explanation
Indices: 300656--300697 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
300646 TTTTCAGCAA
*
300656 TTTAATTTTTTTTATGTTGT
1 TTTAATTTTTTTTATGTTAT
*
300676 TTTAATTTTTTTTCT-TTAT
1 TTTAATTTTTTTTATGTTAT
300695 TTT
1 TTT
300698 CTATTCTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTAATTTTTTTTATGTTAT
Found at i:305878 original size:20 final size:20
Alignment explanation
Indices: 305828--305878 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
305818 CGAAAAATGA
*
305828 TTTTTGAAAAATGAATTACT
1 TTTTTGAAAAATAAATTACT
*
305848 TTTGTGAAAAATAAATTACT
1 TTTTTGAAAAATAAATTACT
305868 TTTTTGGAAAA
1 TTTTT-GAAAA
305879 GTTAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (20 bp):
TTTTTGAAAAATAAATTACT
Found at i:308267 original size:12 final size:12
Alignment explanation
Indices: 308226--308277 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
308216 GGCACGCAAT
*
308226 GAAAGGGGAAGG
1 GAAAGGGGAAGA
* *
308238 GGAAGGGGAAGG
1 GAAAGGGGAAGA
*
308250 GGAAGGGGAAGA
1 GAAAGGGGAAGA
*
308262 GAAAGGAGAAGGA
1 GAAAGGGGAA-GA
308275 GAA
1 GAA
308278 TGAGAAGAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
12 30 0.86
13 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (12 bp):
GAAAGGGGAAGA
Found at i:308267 original size:18 final size:18
Alignment explanation
Indices: 308226--308283 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
308216 GGCACGCAAT
*
308226 GAAAGGGGAAGGGGAAGG
1 GAAAGGGGAAGGGGAAGA
*
308244 GGAAGGGGAAGGGGAAGA
1 GAAAGGGGAAGGGGAAGA
* *
308262 GAAAGGAGAAGGAGAATGA
1 GAAAGGGGAAGGGGAA-GA
308281 GAA
1 GAA
308284 GAGCTTGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 29 0.85
19 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.53, T:0.02
Consensus pattern (18 bp):
GAAAGGGGAAGGGGAAGA
Found at i:308277 original size:6 final size:6
Alignment explanation
Indices: 308228--308260 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
308218 CACGCAATGA
308228 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAG
308261 AGAAAGGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:308434 original size:14 final size:14
Alignment explanation
Indices: 308401--308427 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
308391 CAATGGACTG
308401 AAAAACTTTTACAA
1 AAAAACTTTTACAA
308415 AAAAACTTTTACA
1 AAAAACTTTTACA
308428 GGTAAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAACTTTTACAA
Done.