Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009459.1 Kokia drynarioides strain JFW-HI SEQ_124166, 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: 95375
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:6691 original size:30 final size:29
Alignment explanation
Indices: 6656--7023 Score: 331
Period size: 30 Copynumber: 12.4 Consensus size: 29
6646 TTTTTTGTTT
6656 AAAAATTACATTTTAACCCTCAAACTTTC
1 AAAAATTACATTTTAACCCTCAAACTTTC
* * *
6685 AAAAAATCACATTTTAACTCTCGAACTTTGC
1 -AAAAATTACATTTTAACCCTCAAACTTT-C
* *
6716 AAAAATCACATTTTAACCCTCGAACTTTGC
1 AAAAATTACATTTTAACCCTCAAACTTT-C
* * *
6746 AAAAATTACATTTTGACCATTAAAC-TTC
1 AAAAATTACATTTTAACCCTCAAACTTTC
*
6774 TTAAAATTACATTTTAACCCTCAAAC-TTC
1 -AAAAATTACATTTTAACCCTCAAACTTTC
6803 ATAAAATTACATTTTAACCC-CTAAACTTTCC
1 A-AAAATTACATTTTAACCCTC-AAACTTT-C
*
6834 AAAAATTACATTTTAACCCTTAAAC-TTC
1 AAAAATTACATTTTAACCCTCAAACTTTC
* *
6862 ATAACATTACATTTTAACCCTTAAACTTTC
1 A-AAAATTACATTTTAACCCTCAAACTTTC
* *
6892 TAAAAATTACATTTTGACCC-CTACAC-TTC
1 -AAAAATTACATTTTAACCCTC-AAACTTTC
*
6921 ACAAAATTATATTTTAA-CCTCAAACTTTTC
1 A-AAAATTACATTTTAACCCTCAAAC-TTTC
* * * *
6951 CAAAGTTACATTTTTTACTCC-CAAACTTCC
1 AAAAATTACA-TTTTAAC-CCTCAAACTTTC
* * *
6981 CAAAATTACGTTTTGACCC-CAAACTTATC
1 AAAAATTACATTTTAACCCTCAAACTT-TC
7010 AAAAATTACCATTT
1 AAAAATTA-CATTT
7024 GCCCCTAAAC
Statistics
Matches: 284, Mismatches: 34, Indels: 40
0.79 0.09 0.11
Matches are distributed among these distances:
28 19 0.07
29 111 0.39
30 143 0.50
31 9 0.03
32 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCTCAAACTTTC
Found at i:6801 original size:59 final size:59
Alignment explanation
Indices: 6655--7023 Score: 342
Period size: 59 Copynumber: 6.2 Consensus size: 59
6645 CTTTTTTGTT
* * * **
6655 TAAAAATTACATTTTAACCCTCAAACTTTCAAAAAATCACATTTTAACTCTCGAACTTTGC
1 TAAAAATTACATTTTAACCCTCAAAC-TTCATAAAATTACATTTTAACCCTTAAACTTT-C
* * * *
6716 -AAAAATCACATTTTAACCCTCGAACTTTGCA-AAAATTACATTTTGACCATTAAAC-TTC
1 TAAAAATTACATTTTAACCCTCAAAC-TT-CATAAAATTACATTTTAACCCTTAAACTTTC
* *
6774 TTAAAATTACATTTTAACCCTCAAACTTCATAAAATTACATTTTAACCCCTAAACTTTC
1 TAAAAATTACATTTTAACCCTCAAACTTCATAAAATTACATTTTAACCCTTAAACTTTC
* * *
6833 CAAAAATTACATTTTAACCCTTAAACTTCATAACATTACATTTTAACCCTTAAACTTTC
1 TAAAAATTACATTTTAACCCTCAAACTTCATAAAATTACATTTTAACCCTTAAACTTTC
* * * * *
6892 TAAAAATTACATTTTGACCC-CTACACTTCACAAAATTATATTTTAA-CCTCAAACTTT-
1 TAAAAATTACATTTTAACCCTC-AAACTTCATAAAATTACATTTTAACCCTTAAACTTTC
* * * ** * * *
6949 TCCAAAGTTACATTTTTTACTCC-CAAACTTCCCAAAATTACGTTTTGACCC-CAAACTTATC
1 T-AAAAATTACA-TTTTAAC-CCTCAAACTTCATAAAATTACATTTTAACCCTTAAACTT-TC
7010 -AAAAATTACCATTT
1 TAAAAATTA-CATTT
7024 GCCCCTAAAC
Statistics
Matches: 259, Mismatches: 37, Indels: 26
0.80 0.11 0.08
Matches are distributed among these distances:
57 3 0.01
58 42 0.16
59 160 0.62
60 52 0.20
61 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (59 bp):
TAAAAATTACATTTTAACCCTCAAACTTCATAAAATTACATTTTAACCCTTAAACTTTC
Found at i:7028 original size:28 final size:27
Alignment explanation
Indices: 6982--7061 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 27
6972 CAAACTTCCC
**
6982 AAAATTACGTTTTGACCCCAAACTTATC-A
1 AAAATTACCATTTG-CCCCAAAC--ATCAA
7011 AAAATTACCATTTGCCCCTAAACATCAA
1 AAAATTACCATTTGCCCC-AAACATCAA
7039 AAAATTACCATTTAGCTCCCAAA
1 AAAATTACCATTT-GC-CCCAAA
7062 TTTCCAAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
27 3 0.07
28 18 0.40
29 21 0.47
30 3 0.07
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.28
Consensus pattern (27 bp):
AAAATTACCATTTGCCCCAAACATCAA
Found at i:8009 original size:319 final size:320
Alignment explanation
Indices: 7431--8015 Score: 677
Period size: 319 Copynumber: 1.8 Consensus size: 320
7421 CCTTTAAAAC
* * *
7431 CGAGGCAATATCCTTTTCGTGTGAAAATCTCAAAAAATCGTGCCCTAACATGCGGGGTGTGATTT
1 CGAGGCAATATCCTTTTCGTGTGAAAATCTCAAAAAACCATGCCCTAACATGCGAGGTGTGATTT
* * *
7496 TTCGTATAATCTGCACAATCAAATATCCTCTTCTAAACTTTTCAAATCCCCTTTAATTTTGAGAT
66 TTCGTATAATCTGCACAATCAAATATCCTCTTCTAAAATTTTCAAATCCCCTTCAATTTTGAAAT
*
7561 TCCGAGAATGTCATGCCCTAACGTGTTGGACACGACTTCAATTCTCCGAGAAATTCAAAACACAC
131 TCCGAGAACGTCATGCCCTAACGTGTTGGACACGACTTCAATTCTCCGAGAAATTCAAAACACAC
* * ** * *
7626 GGGCATTTTCTTCAAATTTAATTATTGAAAATCACGTGAAATAAGTTATGTGTCCGAGGATCGTA
196 GGGCATTTTCTTCAAATATAATTATTGAAAATCAC-TGAAATAAGTTATGAGAACAAAGATCGTA
7691 TCTTAAACTTAATTCAAAACTTTGAGTTCTCAAAAAATATACAAATAATTTAAAACAAGAA
260 TCTTAAACTTAATTCAAAACTTTGAGTTCTCAAAAAATATACAAATAATTTAAAACAAGAA
* * * * *
7752 CGAGGCAATATTC-TTTCGTGTGAAAA-CTTCAAAAAACCATGTCGTAACGTGCTAGGTGTGA-T
1 CGAGGCAATATCCTTTTCGTGTGAAAATC-TCAAAAAACCATGCCCTAACATGCGAGGTGTGATT
* * * * **
7814 TTTCGTATAAT-TCGCGCGAT-GAATATCTTCTT-TAAAATCTTTCAAAATGTCCTTCAATTTTG
65 TTTCGTATAATCT-GCACAATCAAATATCCTCTTCTAAAAT-TTTC-AAATCCCCTTCAATTTTG
* * *
7876 AAAGTT-CGAGAACGT-AGTGCTCTAACGTGTTGGACATGACTTTCAATTCTCCGAGAAATTCGA
127 AAA-TTCCGAGAACGTCA-TGCCCTAACGTGTTGGACACGAC-TTCAATTCTCCGAGAAATTCAA
* * * * * * ** *
7939 AACGCACGGACGGTTTT-TCTCAAATATGATTTTTGAAAATCA-TGCAATATTTTCTGAGAACAA
189 AACACACGGGC-ATTTTCT-TCAAATATAATTATTGAAAATCACTGAAATAAGTTATGAGAACAA
*
8002 AGATCGTATTTTAA
252 AGATCGTATCTTAA
8016 GTTTTATTCG
Statistics
Matches: 218, Mismatches: 37, Indels: 20
0.79 0.13 0.07
Matches are distributed among these distances:
317 5 0.02
318 16 0.07
319 89 0.41
320 72 0.33
321 36 0.17
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (320 bp):
CGAGGCAATATCCTTTTCGTGTGAAAATCTCAAAAAACCATGCCCTAACATGCGAGGTGTGATTT
TTCGTATAATCTGCACAATCAAATATCCTCTTCTAAAATTTTCAAATCCCCTTCAATTTTGAAAT
TCCGAGAACGTCATGCCCTAACGTGTTGGACACGACTTCAATTCTCCGAGAAATTCAAAACACAC
GGGCATTTTCTTCAAATATAATTATTGAAAATCACTGAAATAAGTTATGAGAACAAAGATCGTAT
CTTAAACTTAATTCAAAACTTTGAGTTCTCAAAAAATATACAAATAATTTAAAACAAGAA
Found at i:10584 original size:19 final size:19
Alignment explanation
Indices: 10560--10647 Score: 149
Period size: 19 Copynumber: 4.6 Consensus size: 19
10550 GGTCGTGTGC
*
10560 CCAGCCTGTGTGGCAGGGT
1 CCAGCCCGTGTGGCAGGGT
*
10579 CCAGCCCGTGTAGCAGGGT
1 CCAGCCCGTGTGGCAGGGT
10598 CCAGCCCGTGTGGCAGGGT
1 CCAGCCCGTGTGGCAGGGT
*
10617 TCAGCCCGTGTGGCAGGGT
1 CCAGCCCGTGTGGCAGGGT
10636 CCAGCCCGTGTG
1 CCAGCCCGTGTG
10648 ACTCTTAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.11, C:0.31, G:0.40, T:0.18
Consensus pattern (19 bp):
CCAGCCCGTGTGGCAGGGT
Found at i:12001 original size:27 final size:26
Alignment explanation
Indices: 11971--12033 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 26
11961 TTTATCGAGG
11971 TATTAATTTATCAATAAATGAATATTT
1 TATTAATTTATCAATAAATGAATA-TT
* *
11998 TATTAATTTATCGATAAATTAATATT
1 TATTAATTTATCAATAAATGAATATT
*
12024 TACTAATTTA
1 TATTAATTTA
12034 GAGAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 11 0.33
27 22 0.67
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (26 bp):
TATTAATTTATCAATAAATGAATATT
Found at i:12184 original size:35 final size:35
Alignment explanation
Indices: 12142--12212 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
12132 TGTATCAAAG
12142 TTAATTGGTTCATGTAACAAAAAAAAAAGAGTTAA
1 TTAATTGGTTCATGTAACAAAAAAAAAAGAGTTAA
* *
12177 TTAATTGGTTCATGTAACCAAAAAAAAGGAGTTAA
1 TTAATTGGTTCATGTAACAAAAAAAAAAGAGTTAA
12212 T
1 T
12213 GGTTTCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (35 bp):
TTAATTGGTTCATGTAACAAAAAAAAAAGAGTTAA
Found at i:14577 original size:11 final size:11
Alignment explanation
Indices: 14561--14589 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
14551 CCAGCCTTGA
14561 AGAGAGAGGGG
1 AGAGAGAGGGG
14572 AGAGAGAGGGG
1 AGAGAGAGGGG
14583 AGAGAGA
1 AGAGAGA
14590 AGAGAGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (11 bp):
AGAGAGAGGGG
Found at i:15140 original size:30 final size:30
Alignment explanation
Indices: 14940--15155 Score: 190
Period size: 30 Copynumber: 7.3 Consensus size: 30
14930 TTTTACACCC
* * * *
14940 AAACTTCTCCAAAATTATATTTT-ACCTCT
1 AAACTTTTCTAAAATCATATTTTGACCCCT
* * *
14969 AAACTTTCCCAAAATCATAATTTGACCTCC-
1 AAACTTTTCTAAAATCATATTTTGACC-CCT
* * * *
14999 AAAC-TTCCTTAAAT-TTCATTTTGACCCTT
1 AAACTTTTCTAAAATCAT-ATTTTGACCCCT
* * *
15028 AAACTTTTC-AAAAACTTCATTTTAACCCCT
1 AAACTTTTCTAAAATCAT-ATTTTGACCCCT
* * *
15058 AAAATTTTCCAAAATCACATTTTGACCCCT
1 AAACTTTTCTAAAATCATATTTTGACCCCT
15088 AAACTTTTCTAAAATCATATTTTGACCCCT
1 AAACTTTTCTAAAATCATATTTTGACCCCT
* * *
15118 GAACTTTTCTAAAATCATATTTTAACCCTT
1 AAACTTTTCTAAAATCATATTTTGACCCCT
15148 AAACTTTT
1 AAACTTTT
15156 TCAAAACTAC
Statistics
Matches: 153, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
28 2 0.01
29 42 0.27
30 103 0.67
31 6 0.04
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.39
Consensus pattern (30 bp):
AAACTTTTCTAAAATCATATTTTGACCCCT
Found at i:15140 original size:90 final size:88
Alignment explanation
Indices: 14940--15183 Score: 237
Period size: 90 Copynumber: 2.7 Consensus size: 88
14930 TTTTACACCC
* * * * * *
14940 AAACTTCTCCAAAATTATATTTT-ACCTCTAAACTTTCCCAAAATCATAATTTGACCTCCAAACT
1 AAACTT-TTCAAAATCATATTTTAACCCCTAAACTTTTCCAAAATCACATTTTGACCTCCAAACT
* * *
15004 TCCTTAAATTTCATTTTGACCCTT
65 TCCTAAAATATCATTTTGACCCCT
* * *
15028 AAACTTTTCAAAAACTTCATTTTAACCCCTAAAATTTTCCAAAATCACATTTTGACC-CCTAAAC
1 AAACTTTTCAAAATCAT-ATTTTAACCCCTAAACTTTTCCAAAATCACATTTTGACCTCC-AAAC
*
15092 TTTTCTAAAATCAT-ATTTTGACCCCT
64 -TTCCTAAAAT-ATCATTTTGACCCCT
* * *
15118 GAACTTTTCTAAAATCATATTTTAACCCTTAAACTTTTTCAAAA-CTACATTTTGACCAT-CAAA
1 AAACTTTTC-AAAATCATATTTTAACCCCTAAACTTTTCCAAAATC-ACATTTTGACC-TCCAAA
15181 CTT
63 CTT
15184 TCCCAAAGTT
Statistics
Matches: 128, Mismatches: 19, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
87 7 0.05
88 13 0.10
89 35 0.27
90 65 0.51
91 8 0.06
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (88 bp):
AAACTTTTCAAAATCATATTTTAACCCCTAAACTTTTCCAAAATCACATTTTGACCTCCAAACTT
CCTAAAATATCATTTTGACCCCT
Found at i:15183 original size:60 final size:60
Alignment explanation
Indices: 15015--15205 Score: 199
Period size: 60 Copynumber: 3.2 Consensus size: 60
15005 CCTTAAATTT
* * *
15015 CATTTTGACCCTTAAACTTTTCAAAAACTTCATTTTAACCCCTAAAATTTTCCAAAATCA
1 CATTTTGACCCTTAAACTTTTCAAAAACTACATTTTGACCCCTAAACTTTTCCAAAATCA
* * * * *
15075 CATTTTGACCCCTAAACTTTTCTAAAA-TCATATTTTGACCCCTGAACTTTTCTAAAATCA
1 CATTTTGACCCTTAAACTTTTCAAAAACT-ACATTTTGACCCCTAAACTTTTCCAAAATCA
* * * * * *
15135 TATTTTAACCCTTAAACTTTTTC-AAAACTACATTTTGA-CCATCAAACTTTCCCAAAGTTA
1 CATTTTGACCCTTAAAC-TTTTCAAAAACTACATTTTGACCCCT-AAACTTTTCCAAAATCA
*
15195 CATTTTTACCC
1 CATTTTGACCC
15206 CCAAAAGTCT
Statistics
Matches: 107, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
59 4 0.04
60 97 0.91
61 6 0.06
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (60 bp):
CATTTTGACCCTTAAACTTTTCAAAAACTACATTTTGACCCCTAAACTTTTCCAAAATCA
Found at i:15200 original size:90 final size:90
Alignment explanation
Indices: 14958--15236 Score: 219
Period size: 90 Copynumber: 3.1 Consensus size: 90
14948 CCAAAATTAT
* * * * * ** **
14958 ATTTT-ACCTCTAAACTTTCCCAAAATCATAATTTGACCTCC-AAAC-TTCCTTAAATTTCATTT
1 ATTTTAACCCCTAAAATTTTCCAAAATCACATTTTGACC-CCTAAACTTTCCCAAAATCACATTT
* *
15020 TGACCCTTAAACTTTTCAAAAACTTC
65 TGACCCCTAAACTTTTCAAAAACATC
* * *
15046 ATTTTAACCCCTAAAATTTTCCAAAATCACATTTTGACCCCTAAACTTTTCTAAAATCATATTTT
1 ATTTTAACCCCTAAAATTTTCCAAAATCACATTTTGACCCCTAAACTTTCCCAAAATCACATTTT
* *
15111 GACCCCTGAACTTTTCTAAAATCAT-
66 GACCCCTAAACTTTTC-AAAAACATC
* * * * * *
15136 ATTTTAACCCTTAAACTTTTTCAAAA-CTACATTTTGA-CCATCAAACTTTCCCAAAGTTACATT
1 ATTTTAACCCCTAAAATTTTCCAAAATC-ACATTTTGACCCCT-AAACTTTCCCAAAATCACATT
* * ** * *
15199 TTTACCCCCAAAAGTCTCAAAAACTTC
64 TTGACCCCTAAACTTTTCAAAAACATC
15226 ATTTTTAACCC
1 A-TTTTAACCC
15237 TCTTTTTTCT
Statistics
Matches: 152, Mismatches: 31, Indels: 13
0.78 0.16 0.07
Matches are distributed among these distances:
88 7 0.05
89 42 0.28
90 88 0.58
91 15 0.10
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (90 bp):
ATTTTAACCCCTAAAATTTTCCAAAATCACATTTTGACCCCTAAACTTTCCCAAAATCACATTTT
GACCCCTAAACTTTTCAAAAACATC
Found at i:34956 original size:74 final size:74
Alignment explanation
Indices: 34871--35019 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
34861 CTATAGAACA
34871 ATATATTAAATTACATAATATATATAAAAATAATATATCATATAATTCGAAATGAACTGAACTAA
1 ATATATTAAATTACATAATATATATAAAAATAATATATCATATAATTCGAAATGAACTGAACTAA
34936 TTTAAGATT
66 TTTAAGATT
34945 ATATATTAAATTACATAATATATATAAAAATAATATATCATATAATTCGAAATGAACTGAACTAA
1 ATATATTAAATTACATAATATATATAAAAATAATATATCATATAATTCGAAATGAACTGAACTAA
35010 TTTAAGATT
66 TTTAAGATT
35019 A
1 A
35020 AATTTTTAAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (74 bp):
ATATATTAAATTACATAATATATATAAAAATAATATATCATATAATTCGAAATGAACTGAACTAA
TTTAAGATT
Found at i:39319 original size:15 final size:15
Alignment explanation
Indices: 39299--39334 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
39289 TGATCCCGAA
*
39299 ATCACTGTTTCTTAC
1 ATCACTGTTTCTGAC
39314 ATCACTGTTTCTGAC
1 ATCACTGTTTCTGAC
39329 ATCACT
1 ATCACT
39335 AAAAATCAAG
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:0.22, C:0.28, G:0.08, T:0.42
Consensus pattern (15 bp):
ATCACTGTTTCTGAC
Found at i:49551 original size:15 final size:15
Alignment explanation
Indices: 49528--49608 Score: 90
Period size: 15 Copynumber: 5.4 Consensus size: 15
49518 TAAGAACAAA
*
49528 AATCGTGAAATCCCT
1 AATCATGAAATCCCT
* *
49543 AATCATGAAATCTCA
1 AATCATGAAATCCCT
*
49558 AATCGTGAAATCCCT
1 AATCATGAAATCCCT
*
49573 AATGATGAAATCCCT
1 AATCATGAAATCCCT
** *
49588 AATTGTGAAATCCCA
1 AATCATGAAATCCCT
49603 AATCAT
1 AATCAT
49609 TTCAAAAATT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (15 bp):
AATCATGAAATCCCT
Found at i:49561 original size:30 final size:30
Alignment explanation
Indices: 49527--49608 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
49517 TTAAGAACAA
*
49527 AAATCGTGAAATCCCTAATCATGAAATCTC
1 AAATCGTGAAATCCCTAATCATGAAATCCC
*
49557 AAATCGTGAAATCCCTAATGATGAAATCCC
1 AAATCGTGAAATCCCTAATCATGAAATCCC
* * *
49587 TAATTGTGAAATCCCAAATCAT
1 AAATCGTGAAATCCCTAATCAT
49609 TTCAAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (30 bp):
AAATCGTGAAATCCCTAATCATGAAATCCC
Found at i:49715 original size:9 final size:9
Alignment explanation
Indices: 49703--49737 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
49693 ATGATTTGAA
49703 TGGTTCGAG
1 TGGTTCGAG
*
49712 TGGTTCGAA
1 TGGTTCGAG
*
49721 TGTTTCGAG
1 TGGTTCGAG
49730 TGGTTCGA
1 TGGTTCGA
49738 AGAAAAAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.14, C:0.11, G:0.37, T:0.37
Consensus pattern (9 bp):
TGGTTCGAG
Found at i:49716 original size:27 final size:27
Alignment explanation
Indices: 49686--49737 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
49676 GTAGAGGTTG
49686 GGTTCGAATGATTT-GAATGGTTCGAGT
1 GGTTCGAATG-TTTCGAATGGTTCGAGT
*
49713 GGTTCGAATGTTTCGAGTGGTTCGA
1 GGTTCGAATGTTTCGAATGGTTCGA
49738 AGAAAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.19, C:0.10, G:0.35, T:0.37
Consensus pattern (27 bp):
GGTTCGAATGTTTCGAATGGTTCGAGT
Found at i:49721 original size:18 final size:18
Alignment explanation
Indices: 49686--49738 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
49676 GTAGAGGTTG
* * *
49686 GGTTCGAATGATTTGAAT
1 GGTTCGAGTGGTTCGAAT
49704 GGTTCGAGTGGTTCGAAT
1 GGTTCGAGTGGTTCGAAT
*
49722 GTTTCGAGTGGTTCGAA
1 GGTTCGAGTGGTTCGAA
49739 GAAAAAATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.21, C:0.09, G:0.34, T:0.36
Consensus pattern (18 bp):
GGTTCGAGTGGTTCGAAT
Found at i:60391 original size:37 final size:37
Alignment explanation
Indices: 60350--60496 Score: 188
Period size: 37 Copynumber: 4.0 Consensus size: 37
60340 TGCATCTAAA
60350 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
* * *
60387 TATTCAGGTTATGTGTCTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
* ** *
60424 TATTCAGGCTTTGTAACTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
* * **
60461 TATTCAAGCTGTGTGCCTAG-AGGCTTCATGCCAGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
60497 AATTATAAAG
Statistics
Matches: 96, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
36 13 0.14
37 83 0.86
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCAGTG
Found at i:60432 original size:21 final size:21
Alignment explanation
Indices: 60408--60477 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 21
60398 TGTGTCTAGT
60408 AGGCTTTGTGCCGGTGTATTC
1 AGGCTTTGTGCCGGTGTATTC
** *
60429 AGGCTTTGTAAC----TAGT-
1 AGGCTTTGTGCCGGTGTATTC
60445 AGGCTTTGTGCCGGTGTATTC
1 AGGCTTTGTGCCGGTGTATTC
* *
60466 AAGCTGTGTGCC
1 AGGCTTTGTGCC
60478 TAGAGGCTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
16 10 0.28
17 3 0.08
20 3 0.08
21 20 0.56
ACGTcount: A:0.14, C:0.19, G:0.31, T:0.36
Consensus pattern (21 bp):
AGGCTTTGTGCCGGTGTATTC
Found at i:69550 original size:31 final size:31
Alignment explanation
Indices: 69491--69550 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
69481 CGCTGATTTT
*
69491 AATGAAAACTTTCAAATAGTTCAGTGACTTA
1 AATGAAAACTTTCAAATAGTTCAATGACTTA
** *
69522 AATGAAAACTTTTGAATATTTCAATGACT
1 AATGAAAACTTTCAAATAGTTCAATGACT
69551 ATTTTGTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (31 bp):
AATGAAAACTTTCAAATAGTTCAATGACTTA
Found at i:72224 original size:15 final size:15
Alignment explanation
Indices: 72204--72236 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
72194 AGAGTTTACA
72204 AATATA-ATTATAAAT
1 AATATATATT-TAAAT
72219 AATATATATTTAAAT
1 AATATATATTTAAAT
72234 AAT
1 AAT
72237 TACAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATATTTAAAT
Found at i:72674 original size:27 final size:28
Alignment explanation
Indices: 72634--72686 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
72624 AATTATGTGT
* *
72634 AAGTTTTTGTTTTGATCATTTAATTAAA
1 AAGTTTTTGATTTGATCATTGAATTAAA
*
72662 AAGTTTTT-ATTTGGTCATTGAATTA
1 AAGTTTTTGATTTGATCATTGAATTA
72687 TTAAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (28 bp):
AAGTTTTTGATTTGATCATTGAATTAAA
Found at i:72692 original size:30 final size:31
Alignment explanation
Indices: 72656--72734 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
72646 TGATCATTTA
* *
72656 ATTAAAAAGTTTTTATTT-GGTCATTGAATT
1 ATTAAAAAGTTTTTATTTAAGTCATTGAACT
* **
72686 ATTAAAAAATTTTCT-TTTAAGTTGTTGAACT
1 ATTAAAAAGTTTT-TATTTAAGTCATTGAACT
*
72717 ATTCAAAAGTTTTTATTT
1 ATTAAAAAGTTTTTATTT
72735 TAGTAACTGG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
30 16 0.41
31 23 0.59
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (31 bp):
ATTAAAAAGTTTTTATTTAAGTCATTGAACT
Found at i:76024 original size:18 final size:19
Alignment explanation
Indices: 75980--76025 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
75970 TGTAAAGTGT
75980 ACTACGAAGATGATGATGGA
1 ACTA-GAAGATGATGATGGA
* *
76000 AAT-GAAGATGGTG-TGGA
1 ACTAGAAGATGATGATGGA
76017 ACTAGAAGA
1 ACTAGAAGA
76026 ACATGAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 6 0.27
18 14 0.64
20 2 0.09
ACGTcount: A:0.41, C:0.07, G:0.33, T:0.20
Consensus pattern (19 bp):
ACTAGAAGATGATGATGGA
Found at i:78293 original size:26 final size:26
Alignment explanation
Indices: 78264--78314 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
78254 TTCAATAAAA
78264 TATTAAGAATATAAA-T-TAAAATTTAT
1 TATTAA-AATA-AAATTATAAAATTTAT
*
78290 TATTGAAATAAAATTATAAAATTTA
1 TATTAAAATAAAATTATAAAATTTA
78315 ATAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 3 0.14
25 5 0.23
26 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
TATTAAAATAAAATTATAAAATTTAT
Found at i:79104 original size:29 final size:31
Alignment explanation
Indices: 79062--79122 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 31
79052 TATAAATATT
*
79062 TTTAATAATATATTA-AAAATATTGTTTAAAA
1 TTTAATAATATATTATAAAATATT-ATTAAAA
*
79093 TTTAA-AAT-TATTATAAGATATTATTAAAA
1 TTTAATAATATATTATAAAATATTATTAAAA
79122 T
1 T
79123 ATTAGGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 12 0.44
30 10 0.37
31 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
TTTAATAATATATTATAAAATATTATTAAAA
Found at i:79117 original size:13 final size:11
Alignment explanation
Indices: 79042--79126 Score: 54
Period size: 12 Copynumber: 7.8 Consensus size: 11
79032 CATGATTTAA
*
79042 AAAATATTAAT
1 AAAATATTATT
*
79053 ATAAATATTTTT
1 A-AAATATTATT
79065 AATAATA-TATT
1 AA-AATATTATT
*
79076 AAAAATATTGTTT
1 -AAAATATT-ATT
79089 AAAAT-TTA--
1 AAAATATTATT
*
79097 AAATTATTA-T
1 AAAATATTATT
*
79107 AAGATATTATT
1 AAAATATTATT
79118 AAAATATTA
1 AAAATATTA
79127 GGCTTGTTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
10 7 0.12
11 20 0.35
12 21 0.37
13 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
AAAATATTATT
Found at i:79732 original size:3 final size:3
Alignment explanation
Indices: 79724--79764 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
79714 AGTACAATTT
*
79724 AAG AAG AAG AAG AAG AAG AAG AAG TAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
79765 AACCCTTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:86996 original size:19 final size:17
Alignment explanation
Indices: 86970--87015 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
86960 TTAAACACAC
86970 TATTAAAAT-TGAAATAAA
1 TATTAAAATAT-AAAT-AA
86988 TATTTAAAATATAAATAA
1 TA-TTAAAATATAAATAA
87006 TATTAAAATA
1 TATTAAAATA
87016 AATTATTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.31
18 6 0.23
19 11 0.42
20 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TATTAAAATATAAATAA
Found at i:87003 original size:15 final size:15
Alignment explanation
Indices: 86983--87024 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
86973 TAAAATTGAA
86983 ATAAATATTTAAAAT
1 ATAAATATTTAAAAT
86998 ATAAATAATATTAAAAT
1 ATAAAT-AT-TTAAAAT
*
87015 A-AATTATTTA
1 ATAAATATTTA
87025 GTGTTCACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 3 0.12
15 8 0.33
16 5 0.21
17 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATATTTAAAAT
Found at i:90803 original size:2 final size:2
Alignment explanation
Indices: 90796--90822 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
90786 ATAAATACAA
90796 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
90823 AACCTAGTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94156 original size:17 final size:17
Alignment explanation
Indices: 94128--94200 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
94118 TTGGAAATTG
94128 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
94144 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
94161 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
94178 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
94195 AATTTA
1 AATTTA
94201 AAAAGTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 5 0.10
17 45 0.90
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:94176 original size:7 final size:6
Alignment explanation
Indices: 94133--94202 Score: 60
Period size: 6 Copynumber: 12.2 Consensus size: 6
94123 AATTGAATTT
* *
94133 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
94179 ATTT-- ATTATAA AATTAA ATTTAA A
1 ATTTAA ATT-TAA ATTTAA ATTTAA A
94203 AAGTCCAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
4 7 0.13
5 5 0.10
6 34 0.65
7 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:95015 original size:8 final size:9
Alignment explanation
Indices: 94990--95014 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
94980 ATCTTTTTAA
94990 AAAAAAAAT
1 AAAAAAAAT
94999 AAAAAAAAT
1 AAAAAAAAT
95008 AAAAAAA
1 AAAAAAA
95015 TTAATAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Done.