Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015246.1 Kokia drynarioides strain JFW-HI SEQ_130291, 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: 194553
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 645 characters in sequence are not A, C, G, or T
Found at i:4803 original size:17 final size:17
Alignment explanation
Indices: 4783--4824 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
4773 CTCCCTTGAC
*
4783 CTTTAACCTTCCATCTT
1 CTTTAACCTTCCATATT
*
4800 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
4817 CTTGTAAC
1 CTT-TAAC
4825 TACTTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:4808 original size:24 final size:24
Alignment explanation
Indices: 4763--4810 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4753 ATGGATGTTC
* *
4763 AACCTTTCATCTCCCTTGACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
* *
4787 AACCTTCCATCTTCTTTAACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
4811 CATATTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.02, T:0.44
Consensus pattern (24 bp):
AACCTTCCATCTCCCTTAACCTTT
Found at i:10135 original size:31 final size:30
Alignment explanation
Indices: 10100--10170 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
10090 CATGAGTTAT
10100 AATTTTAATTTCTATATTT-TCCGAATTAGTA
1 AATTTTAATTTCTATATTTGT-CGAATT-GTA
* *
10131 AATTTTAATTTTTATATTTGTCGAATTTTA
1 AATTTTAATTTCTATATTTGTCGAATTGTA
10161 ATATTTTAAT
1 A-ATTTTAAT
10171 CTCGATTCGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 3 0.08
31 32 0.89
32 1 0.03
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (30 bp):
AATTTTAATTTCTATATTTGTCGAATTGTA
Found at i:15416 original size:29 final size:29
Alignment explanation
Indices: 15383--15471 Score: 92
Period size: 31 Copynumber: 3.0 Consensus size: 29
15373 TTGTTTTAAT
15383 GTGCAATTGTATACAT-AAACTTTAATTTG
1 GTGCAATT-TATACATGAAACTTTAATTTG
*
15412 GTGCAA-TTATACACGTGAAACTCTAATTGTG
1 GTGCAATTTATACA--TGAAACTTTAATT-TG
* *
15443 GTTCAAATTTATACTTGAAACTTTAATTT
1 GTGC-AATTTATACATGAAACTTTAATTT
15472 TGATTTAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
27 6 0.12
28 1 0.02
29 7 0.14
30 11 0.22
31 17 0.34
32 2 0.04
33 6 0.12
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (29 bp):
GTGCAATTTATACATGAAACTTTAATTTG
Found at i:30361 original size:63 final size:63
Alignment explanation
Indices: 30231--30362 Score: 165
Period size: 63 Copynumber: 2.1 Consensus size: 63
30221 ATACCCTTTG
* * * ** * *
30231 TCTCGAGATATCCAAACATCGAAACTAAATTAAGAAAATATGGGAGACATGTCTTGATATCAG
1 TCTCGAGACATCCAAACATCGAAACTAAATTAAGAAAATAGGGGAGACATGTATCAATACCAA
* ** *
30294 TCTCGAGACATCCTAACATCGAAGTTAAATTAAGACAATAGGGGAGACATGTATCAATACCAA
1 TCTCGAGACATCCAAACATCGAAACTAAATTAAGAAAATAGGGGAGACATGTATCAATACCAA
30357 TCTCGA
1 TCTCGA
30363 TATATGAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.24
Consensus pattern (63 bp):
TCTCGAGACATCCAAACATCGAAACTAAATTAAGAAAATAGGGGAGACATGTATCAATACCAA
Found at i:34205 original size:3 final size:3
Alignment explanation
Indices: 34197--34224 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
34187 CCCCAAATCT
34197 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
34225 ATTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:47615 original size:13 final size:13
Alignment explanation
Indices: 47578--47622 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
47568 TAATAGGTCG
*
47578 AAATTTTTTTTA-
1 AAATTTTGTTTAT
47590 AAATATTTG-TTAT
1 AAAT-TTTGTTTAT
47603 AAATTTTGTTTAT
1 AAATTTTGTTTAT
47616 AAATTTT
1 AAATTTT
47623 ATGATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (13 bp):
AAATTTTGTTTAT
Found at i:51345 original size:6 final size:6
Alignment explanation
Indices: 51334--51377 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
51324 ACATAACCTT
*
51334 CATACA CATACA CATACA CGTACA CATACA CAT--A CATACA CATA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATA
51378 TACTTAATTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.12
6 30 0.88
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.18
Consensus pattern (6 bp):
CATACA
Found at i:53001 original size:24 final size:24
Alignment explanation
Indices: 52974--53022 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
52964 AAATTTCAAA
52974 ATATTTATAAAAATT-TCAAAATTT
1 ATATTTATAAAAATTAT-AAAATTT
* *
52998 ATATTTTTAAAAGTTATAAAATTT
1 ATATTTATAAAAATTATAAAATTT
53022 A
1 A
53023 AAAACATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
ATATTTATAAAAATTATAAAATTT
Found at i:59184 original size:13 final size:13
Alignment explanation
Indices: 59166--59194 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
59156 CCCGATGCGT
59166 ACCAAAGGGAAGA
1 ACCAAAGGGAAGA
59179 ACCAAAGGGAAGA
1 ACCAAAGGGAAGA
59192 ACC
1 ACC
59195 GTGACATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.21, G:0.28, T:0.00
Consensus pattern (13 bp):
ACCAAAGGGAAGA
Found at i:61137 original size:58 final size:58
Alignment explanation
Indices: 61067--61178 Score: 224
Period size: 58 Copynumber: 1.9 Consensus size: 58
61057 CATTGCGAGA
61067 AGGAATATCACTGATAACATTGTCATCGCTCAGGAAGTTATCCACTCAATGAAAGGTC
1 AGGAATATCACTGATAACATTGTCATCGCTCAGGAAGTTATCCACTCAATGAAAGGTC
61125 AGGAATATCACTGATAACATTGTCATCGCTCAGGAAGTTATCCACTCAATGAAA
1 AGGAATATCACTGATAACATTGTCATCGCTCAGGAAGTTATCCACTCAATGAAA
61179 AGTTGTAAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (58 bp):
AGGAATATCACTGATAACATTGTCATCGCTCAGGAAGTTATCCACTCAATGAAAGGTC
Found at i:64638 original size:29 final size:29
Alignment explanation
Indices: 64603--64743 Score: 104
Period size: 29 Copynumber: 4.8 Consensus size: 29
64593 TTTCGTGGTC
64603 AAAAATGGGATTTTTAGAAGTTTGGGGGT
1 AAAAATGGGATTTTTAGAAGTTTGGGGGT
* *
64632 AAAAAT-GAATTTTTTTAGAAGTTTTGGGGTT
1 AAAAATGGGA--TTTTTAGAAG-TTTGGGGGT
* * * *
64663 AAAAATGAGATTTTTGGAAGTTCGGGGGC
1 AAAAATGGGATTTTTAGAAGTTTGGGGGT
**** * * *
64692 AAAAACAAAATTTTTGGAAGTCTCGGGGT
1 AAAAATGGGATTTTTAGAAGTTTGGGGGT
* *
64721 CCAAAATGGGTTTTTTAGAAGTT
1 -AAAAATGGGATTTTTAGAAGTT
64744 CGAAGGTAAA
Statistics
Matches: 84, Mismatches: 23, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
28 2 0.02
29 34 0.40
30 33 0.39
31 14 0.17
32 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAAATGGGATTTTTAGAAGTTTGGGGGT
Found at i:64649 original size:30 final size:32
Alignment explanation
Indices: 64613--64677 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
64603 AAAAATGGGA
64613 TTTTTAGAAG-TTTGGGGGTAAAAATGA-ATT
1 TTTTTAGAAGTTTTGGGGGTAAAAATGAGATT
*
64643 TTTTTAGAAGTTTTGGGGTTAAAAATGAGATT
1 TTTTTAGAAGTTTTGGGGGTAAAAATGAGATT
64675 TTT
1 TTT
64678 GGAAGTTCGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 10 0.31
31 16 0.50
32 6 0.19
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.45
Consensus pattern (32 bp):
TTTTTAGAAGTTTTGGGGGTAAAAATGAGATT
Found at i:64683 original size:30 final size:30
Alignment explanation
Indices: 64603--64684 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
64593 TTTCGTGGTC
*
64603 AAAAATGGGATTTTTAGAAG-TTTGGGGGT
1 AAAAATGAGATTTTTAGAAGTTTTGGGGGT
*
64632 AAAAATGA-ATTTTTTTAGAAGTTTTGGGGTT
1 AAAAATGAGA--TTTTTAGAAGTTTTGGGGGT
*
64663 AAAAATGAGATTTTTGGAAGTT
1 AAAAATGAGATTTTTAGAAGTT
64685 CGGGGGCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
28 1 0.02
29 7 0.15
30 21 0.46
31 16 0.35
32 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (30 bp):
AAAAATGAGATTTTTAGAAGTTTTGGGGGT
Found at i:64736 original size:59 final size:59
Alignment explanation
Indices: 64599--64768 Score: 187
Period size: 59 Copynumber: 2.9 Consensus size: 59
64589 GAAATTTCGT
* * ** * * *
64599 GGTCAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGAATTTTTTTAGAAGTTTTGG
1 GGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAA-CAAAATTTTTGGAAGTCTCGG
* * * *
64659 GGTTAAAAATGAGATTTTTGGAAGTTCGGGGGCAAAAACAAAATTTTTGGAAGTCTCGG
1 GGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAACAAAATTTTTGGAAGTCTCGG
* * ** *
64718 GGTCCAAAATGGGTTTTTTAGAAGTTCGAAGGTAAAAACAGAATTTTTGGA
1 GGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAACAAAATTTTTGGA
64769 CAGTTTAGGA
Statistics
Matches: 90, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
59 57 0.63
60 33 0.37
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.33
Consensus pattern (59 bp):
GGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAACAAAATTTTTGGAAGTCTCGG
Found at i:66557 original size:17 final size:17
Alignment explanation
Indices: 66537--66615 Score: 95
Period size: 17 Copynumber: 4.6 Consensus size: 17
66527 TAAATAGATT
* *
66537 TAAAATTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
66554 TAAATTTAAATTTTAAG
1 TAAATTTAAATTTAAAA
**
66571 TAAATTTAAGCTTAAAA
1 TAAATTTAAATTTAAAA
*
66588 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
66605 TAAATTTAAAT
1 TAAATTTAAAT
66616 CCTATTGGGC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:67294 original size:206 final size:206
Alignment explanation
Indices: 66940--67401 Score: 570
Period size: 206 Copynumber: 2.2 Consensus size: 206
66930 CTGGTTTCAC
* * * * ** **
66940 TGATTTGGTCTTCTTCTCCGTATCTCATCAGGAAGATG-GTCGCGTCACTTGTTTTGATCCACTT
1 TGATTTGGTCTTTTTCTCAGTATCTCATCAGGAAGATGACT-GCATCGTTTGTTTAAATCCACTT
* * * *
67004 TTCTGTACCTCATCAGGAAGACGGATTTGGATCACTTCTTCGCATCTCATGAGGAAGCTAACCAC
65 CTCTGCACCTCATCAGGAAGACGAATTTGGATCACTTCTTCGCATCTCATCAGGAAGCTAACCAC
* * *
67069 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGTTGGGGTTCGAAGATTTGCTCATAT
130 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACAT
*
67134 CGAGCGTGGGTT
195 CGAGCATGGGTT
* *
67146 TGATTTGGTCTTTTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTAAATTCGCTTC
1 TGATTTGGTCTTTTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTAAATCCACTTC
* * * * *
67211 TCTGCATCTTATCAGGAAGACGAATTTGG-TCCACTTC-TCAGTATCTTATCAGGAAGCTAACCT
66 TCTGCACCTCATCAGGAAGACGAATTTGGAT-CACTTCTTC-GCATCTCATCAGGAAGCTAACCA
* * * * * *
67274 TTTTGTTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACA
129 CTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACA
67339 TCGAGCATGGGTT
194 TCGAGCATGGGTT
* * * * *
67352 TGATTTGATCTTTTTCTCAATATTTCATCAGAAAGATGACCGCATCGTTT
1 TGATTTGGTCTTTTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTT
67402 TGTAGATAAT
Statistics
Matches: 219, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
205 3 0.01
206 215 0.98
207 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (206 bp):
TGATTTGGTCTTTTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTAAATCCACTTC
TCTGCACCTCATCAGGAAGACGAATTTGGATCACTTCTTCGCATCTCATCAGGAAGCTAACCACT
TTATTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGATTCGAAGATTTGCTCACATC
GAGCATGGGTT
Found at i:78290 original size:23 final size:23
Alignment explanation
Indices: 78256--78305 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
78246 TAATTTAACT
78256 AAAT-TTTAAAAGTTAAGAGCTA
1 AAATGTTTAAAAGTTAAGAGCTA
*
78278 AAATGTTTAAAAGTTGAGAGCTA
1 AAATGTTTAAAAGTTAAGAGCTA
78301 AAATG
1 AAATG
78306 ACCCCAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.48, C:0.04, G:0.18, T:0.30
Consensus pattern (23 bp):
AAATGTTTAAAAGTTAAGAGCTA
Found at i:85477 original size:57 final size:57
Alignment explanation
Indices: 85389--85504 Score: 178
Period size: 57 Copynumber: 2.0 Consensus size: 57
85379 AAGGAGTTGT
* * *
85389 TTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAATATTTAGTTTTAG
1 TTATGAGTGTTATTTAAGAATAAAATTATATTCGGGTTTAAAAATATTTAGGTTTAG
* * *
85446 TTATGAGTGTTTTTTAAGAATGAAATTATATTCGGGTTTAAAAATATTTGGGTTTAG
1 TTATGAGTGTTATTTAAGAATAAAATTATATTCGGGTTTAAAAATATTTAGGTTTAG
85503 TT
1 TT
85505 TGTTGATGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (57 bp):
TTATGAGTGTTATTTAAGAATAAAATTATATTCGGGTTTAAAAATATTTAGGTTTAG
Found at i:85665 original size:9 final size:9
Alignment explanation
Indices: 85653--85678 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
85643 TATTCGGTTT
85653 ATTCGAATA
1 ATTCGAATA
85662 ATTCGAATA
1 ATTCGAATA
85671 ATTCGAAT
1 ATTCGAAT
85679 TCGAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (9 bp):
ATTCGAATA
Found at i:85709 original size:23 final size:24
Alignment explanation
Indices: 85671--85721 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
85661 AATTCGAATA
*
85671 ATTCGAATTCGAAAATTAAACTCG
1 ATTCGAACTCGAAAATTAAACTCG
85695 ATTCGAACTCG-AAATTAAACTCG
1 ATTCGAACTCGAAAATTAAACTCG
85718 ATTC
1 ATTC
85722 ATTTAACTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (24 bp):
ATTCGAACTCGAAAATTAAACTCG
Found at i:87379 original size:9 final size:9
Alignment explanation
Indices: 87350--87393 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
87340 TAAAACATAA
87350 ATTTTACAAT
1 ATTTTA-AAT
87360 ATTTATAAAT
1 ATTT-TAAAT
*
87370 ATTTTGAAT
1 ATTTTAAAT
87379 ATTTTAAAAT
1 ATTTT-AAAT
87389 ATTTT
1 ATTTT
87394 TTTTTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 9 0.30
10 19 0.63
11 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:87381 original size:19 final size:19
Alignment explanation
Indices: 87357--87393 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
87347 TAAATTTTAC
87357 AATA-TTTATAAATATTTTG
1 AATATTTTA-AAATATTTTG
87376 AATATTTTAAAATATTTT
1 AATATTTTAAAATATTTT
87394 TTTTTTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
AATATTTTAAAATATTTTG
Found at i:91674 original size:14 final size:14
Alignment explanation
Indices: 91655--91688 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
91645 ATCCCTGCCA
91655 ACCCCTTTGGGTTC
1 ACCCCTTTGGGTTC
91669 ACCCCTTTGGGTTC
1 ACCCCTTTGGGTTC
91683 ACCCCT
1 ACCCCT
91689 ATGTAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.18, T:0.32
Consensus pattern (14 bp):
ACCCCTTTGGGTTC
Found at i:102272 original size:38 final size:38
Alignment explanation
Indices: 102221--102300 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
102211 TTCAAAGCAA
102221 TAAAGTGGTATCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGGTATCCAGTACCTCATCGAATCTATCCGAAG
102259 TAAAGTGGTATCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGGTATCCAGTACCTCATCGAATCTATCCGAAG
102297 TAAA
1 TAAA
102301 ATAATGACGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (38 bp):
TAAAGTGGTATCCAGTACCTCATCGAATCTATCCGAAG
Found at i:102451 original size:18 final size:18
Alignment explanation
Indices: 102428--102464 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
102418 ACAATTCTTA
102428 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
102446 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
102464 T
1 T
102465 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:119735 original size:22 final size:24
Alignment explanation
Indices: 119697--119740 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
119687 TGAATGTTTG
119697 AGTAAAAATATTAAA-TTAATTTA
1 AGTAAAAATATTAAATTTAATTTA
*
119720 AGTAAAAA-ATTGAATTTAATT
1 AGTAAAAATATTAAATTTAATT
119741 AGTGATTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (24 bp):
AGTAAAAATATTAAATTTAATTTA
Found at i:124095 original size:6 final size:6
Alignment explanation
Indices: 124084--124122 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
124074 TGATCAAAAT
* * *
124084 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
124123 TATAAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:126750 original size:110 final size:111
Alignment explanation
Indices: 126384--126811 Score: 417
Period size: 109 Copynumber: 3.9 Consensus size: 111
126374 GTTACTTGCT
* * * * *
126384 CATGGATATGTGGATATAACCTCGAAACATGAAAAATGTTAGAAAATCTGA-TGATATTC-AGGC
1 CATGGATATGAGGATATGACCTTGAAACATGAAAAATGTTAGAAAATCCGACTGATATTCGACGC
** * * *
126447 CCACATTATATCTGACACTTACAAGTAGGTTACTAAGTTTAATACGACA
66 ATAC-TTATATCGGACACTTACAAGTAGGTTACTAGGTTTAAT--GAGA
* * * *
126496 CATGGATATGTA-GATATGA-CTTCGAAACATGAAAAAATG-TAGAAAA-ACTAATGGTATTCGG
1 CATGGATATG-AGGATATGACCTT-GAAACATG-AAAAATGTTAGAAAATCCGACTGATATTC-G
* ** * *
126557 ACCCATACTTATATCTAACACTTACAAGTAGATTACTAGGTTTAATGCGA
62 ACGCATACTTATATCGGACACTTACAAGTAGGTTACTAGGTTTAATGAGA
* *
126607 -ATGGATATGCGAATATGACCTTGAAACATGAAAAAT-TTAGAAAATCCGACT-ATATTCGTACG
1 CATGGATATGAGGATATGACCTTGAAACATGAAAAATGTTAGAAAATCCGACTGATATTCG-ACG
* * *
126669 CATACTTGTATCGGACACTTACAAGTAGGTTACTAGGCTTAATGTGA
65 CATACTTATATCGGACACTTACAAGTAGGTTACTAGGTTTAATGAGA
* * * * *
126716 CATGGATATGAGGATATGACCTTGAAACATGAAAAATGTAAAAAAATCGGACT-ATGTTCGCACA
1 CATGGATATGAGGATATGACCTTGAAACATGAAAAATGTTAGAAAATCCGACTGATATTCG-ACG
* * *
126780 CATACTTGTATCGGACCCTTACAAATAGGTTA
65 CATACTTATATCGGACACTTACAAGTAGGTTA
126812 ATTTTGTGTA
Statistics
Matches: 264, Mismatches: 39, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
108 1 0.00
109 61 0.23
110 60 0.23
111 58 0.22
112 38 0.14
113 42 0.16
114 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (111 bp):
CATGGATATGAGGATATGACCTTGAAACATGAAAAATGTTAGAAAATCCGACTGATATTCGACGC
ATACTTATATCGGACACTTACAAGTAGGTTACTAGGTTTAATGAGA
Found at i:126803 original size:220 final size:221
Alignment explanation
Indices: 126385--126803 Score: 485
Period size: 222 Copynumber: 1.9 Consensus size: 221
126375 TTACTTGCTC
* * * * *
126385 ATGGATATGTGGATATAACCTCGAAACATGAAAAATGTTAGAAAATCTGATGATATTCAGGCCCA
1 ATGGATATGCGAATATAACCTCGAAACATGAAAAATGTTAGAAAATCCGATGATATTCACGCACA
* *
126450 CATTATATCTGACACTTACAAGTAGGTTACTAAGTTTAATACGACACATGGATATGTAGATATGA
66 CATTATATCGGACACTTACAAGTAGGTTACTAAGCTTAATA-GACACATGGATATGTAGATATGA
* * * * * *
126515 CTTCGAAACATGAAAAAATGTAGAAAAACTAATGGTATTCGGACCCATACTTATATCTAACACTT
130 CTTCGAAACATGAAAAAATGTAAAAAAACGAATGATATTCGCACACATACTTATATCGAACACTT
126580 ACAAGTAGATTACTAGGTTTAATGCGA
195 ACAAGTAGATTACTAGGTTTAATGCGA
* *
126607 ATGGATATGCGAATATGACCTTGAAACATGAAAAAT-TTAGAAAATCCGACT-ATATTCGTACGC
1 ATGGATATGCGAATATAACCTCGAAACATGAAAAATGTTAGAAAATCCGA-TGATATTC--ACGC
* * * **
126670 ATAC-TTGTATCGGACACTTACAAGTAGGTTACTAGGCTTAAT-GTGACATGGATATG-AGGATA
63 ACACATTATATCGGACACTTACAAGTAGGTTACTAAGCTTAATAGACACATGGATATGTA-GATA
* * * *
126732 TGACCTT-GAAACATG-AAAAATGTAAAAAAATCGGACT-ATGTTCGCACACATACTTGTATCGG
127 TGA-CTTCGAAACATGAAAAAATGTAAAAAAA-C-GAATGATATTCGCACACATACTTATATCGA
*
126794 ACCCTTACAA
189 ACACTTACAA
126804 ATAGGTTAAT
Statistics
Matches: 165, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
219 15 0.09
220 55 0.33
221 23 0.14
222 67 0.41
223 5 0.03
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (221 bp):
ATGGATATGCGAATATAACCTCGAAACATGAAAAATGTTAGAAAATCCGATGATATTCACGCACA
CATTATATCGGACACTTACAAGTAGGTTACTAAGCTTAATAGACACATGGATATGTAGATATGAC
TTCGAAACATGAAAAAATGTAAAAAAACGAATGATATTCGCACACATACTTATATCGAACACTTA
CAAGTAGATTACTAGGTTTAATGCGA
Found at i:131857 original size:23 final size:23
Alignment explanation
Indices: 131831--131878 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
131821 ACGGGTGTGC
*
131831 ATGTATTCGTTTTTGAGCTTTGA
1 ATGTATTCGTTTTCGAGCTTTGA
131854 ATGTATTCGTTTTCGAGCTTTGA
1 ATGTATTCGTTTTCGAGCTTTGA
131877 AT
1 AT
131879 ATAATGAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.10, G:0.21, T:0.50
Consensus pattern (23 bp):
ATGTATTCGTTTTCGAGCTTTGA
Found at i:135153 original size:3 final size:3
Alignment explanation
Indices: 135147--135191 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
135137 CAACAACAAC
* * * *
135147 AAT AAT AAT AAT AAT AAT ATT ACT ACT ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
135192 TAGCATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:136052 original size:3 final size:3
Alignment explanation
Indices: 136044--136077 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
136034 CGAAGATGTT
136044 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
136078 TTGGTATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:137523 original size:2 final size:2
Alignment explanation
Indices: 137511--137541 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
137501 ATAGATTTTA
*
137511 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
137542 ATTACTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:148328 original size:15 final size:15
Alignment explanation
Indices: 148308--148361 Score: 74
Period size: 15 Copynumber: 3.6 Consensus size: 15
148298 TAAAATTCTC
148308 GAATCATTTCAATTT
1 GAATCATTTCAATTT
148323 GAATCATTTCAATTT
1 GAATCATTTCAATTT
*
148338 GAATCAAGTT-AATTT
1 GAATC-ATTTCAATTT
*
148353 GAATTATTT
1 GAATCATTT
148362 ATCATTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
14 3 0.09
15 29 0.83
16 3 0.09
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.46
Consensus pattern (15 bp):
GAATCATTTCAATTT
Found at i:150735 original size:29 final size:29
Alignment explanation
Indices: 150684--150741 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
150674 TTTGAAAGGT
* *
150684 TAATGATCAAATTTAACATAAAAAATAAA
1 TAATGACCAAATTGAACATAAAAAATAAA
*
150713 TAATGACCAAATTGACACA-AAAATATAAA
1 TAATGACCAAATTGA-ACATAAAAAATAAA
150742 CATTGAGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.24
Consensus pattern (29 bp):
TAATGACCAAATTGAACATAAAAAATAAA
Found at i:151370 original size:20 final size:19
Alignment explanation
Indices: 151326--151367 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
151316 GAACTTTTTG
151326 AAAAGAAAATTAGACAAAA
1 AAAAGAAAATTAGACAAAA
151345 AAAAGAAAATTAGACAAAA
1 AAAAGAAAATTAGACAAAA
151364 AAAA
1 AAAA
151368 AGATACTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.76, C:0.05, G:0.10, T:0.10
Consensus pattern (19 bp):
AAAAGAAAATTAGACAAAA
Found at i:153852 original size:15 final size:15
Alignment explanation
Indices: 153832--153862 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
153822 TTTATATAAT
*
153832 TTTTTGAATTTTTTA
1 TTTTTGAATATTTTA
153847 TTTTTGAATATTTTA
1 TTTTTGAATATTTTA
153862 T
1 T
153863 AAATTTTAAA
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:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTTTGAATATTTTA
Found at i:159661 original size:23 final size:23
Alignment explanation
Indices: 159617--159682 Score: 105
Period size: 23 Copynumber: 2.8 Consensus size: 23
159607 GCGCGCGCTT
*
159617 TGATTAGCACTGAGGTGTGCTCTC
1 TGATTAGCACTG-TGTGTGCTCTC
159641 TGATTAGCACTGTGTGTGCTCTC
1 TGATTAGCACTGTGTGTGCTCTC
*
159664 TGATTAGCACTTTGTGTGC
1 TGATTAGCACTGTGTGTGC
159683 ACAGTACTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 28 0.70
24 12 0.30
ACGTcount: A:0.15, C:0.20, G:0.27, T:0.38
Consensus pattern (23 bp):
TGATTAGCACTGTGTGTGCTCTC
Found at i:159718 original size:23 final size:23
Alignment explanation
Indices: 159688--159777 Score: 78
Period size: 23 Copynumber: 3.9 Consensus size: 23
159678 TGTGCACAGT
159688 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
* *
159711 ACTTTGTGTGCTCTCTGTTGCCCAGC
1 ACTTTGTGTACTCTCTGTT---TAGC
* *
159737 ACTTATGTG--CTCTCTATTTAGT
1 ACTT-TGTGTACTCTCTGTTTAGC
*
159759 ACTTCG-GTACTCTCTGTTT
1 ACTTTGTGTACTCTCTGTTT
159778 GTTCCGTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 15 0.28
23 18 0.33
25 8 0.15
26 7 0.13
27 4 0.07
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:162818 original size:38 final size:37
Alignment explanation
Indices: 162758--162836 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
162748 AATTAATAAT
*
162758 ATTCATGTATAATTTCTTTTTAGAATTGCACCAAATCAAA
1 ATTCATG-ATAATTCCTTTTTAGAA-TG-ACCAAATCAAA
*
162798 ATTCATG-TAATTCCTTTTTAGAATGACTAAATCAAA
1 ATTCATGATAATTCCTTTTTAGAATGACCAAATCAAA
162834 ATT
1 ATT
162837 TTATCACTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 13 0.35
37 2 0.05
38 15 0.41
40 7 0.19
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (37 bp):
ATTCATGATAATTCCTTTTTAGAATGACCAAATCAAA
Found at i:167757 original size:43 final size:43
Alignment explanation
Indices: 167708--167795 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
167698 TTTACCTGTT
*
167708 ATAAAGAGGTGATTCTTATACACTTATCTGTTATAGTGAGATA
1 ATAAAGAGGTGATTCGTATACACTTATCTGTTATAGTGAGATA
*
167751 ATAAAGAGGTGATTCGTATACACTTGTCTGTTATAGTGAGATA
1 ATAAAGAGGTGATTCGTATACACTTATCTGTTATAGTGAGATA
167794 AT
1 AT
167796 CGTTGTAAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.36
Consensus pattern (43 bp):
ATAAAGAGGTGATTCGTATACACTTATCTGTTATAGTGAGATA
Found at i:171567 original size:3 final size:3
Alignment explanation
Indices: 171559--171596 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
171549 ACTAATTCAT
171559 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
171597 TGATAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:179743 original size:13 final size:13
Alignment explanation
Indices: 179727--179757 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
179717 CTTCTTGCAT
179727 GGGTTTCTTTGAA
1 GGGTTTCTTTGAA
179740 GGGTTTCTTTGAA
1 GGGTTTCTTTGAA
179753 GGGTT
1 GGGTT
179758 AATTGCACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.06, G:0.35, T:0.45
Consensus pattern (13 bp):
GGGTTTCTTTGAA
Found at i:191666 original size:2 final size:2
Alignment explanation
Indices: 191661--191694 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
191651 ATTATATATA
191661 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
191695 AATTCATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:193658 original size:96 final size:96
Alignment explanation
Indices: 193474--193665 Score: 253
Period size: 96 Copynumber: 2.0 Consensus size: 96
193464 CTTTTGCAAA
**
193474 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCG
1 AAGGATATTTGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCG
* * ** *
193539 GAATCGAAGATAAGGGTACATTGCCTCGATT
66 AAACCGAAGATAAAAGAACATTGCCTCGATT
* * *
193570 AAGGGTATTTGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTC
1 AAGGATATTTGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTC
*
193634 GAAACCCGAA-ATAAAAGAATATTGCCTCGATT
65 GAAA-CCGAAGATAAAAGAACATTGCCTCGATT
193666 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
95 1 0.01
96 78 0.94
97 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (96 bp):
AAGGATATTTGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCG
AAACCGAAGATAAAAGAACATTGCCTCGATT
Done.