Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014517.1 Kokia drynarioides strain JFW-HI SEQ_129556, 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: 207502
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:3631 original size:41 final size:41
Alignment explanation
Indices: 3540--3707 Score: 265
Period size: 41 Copynumber: 4.2 Consensus size: 41
3530 TGGAAGGACA
* *
3540 GCAGA-AACTAGTTAGTCAAACATGAAGCAG-TATA--AAT
1 GCAGAGAACTATTTAGTCAAGCATGAAGCAGATATATCAAT
3577 GCAGAGAACTATTTAGTCAAGCATGAAGCAGATATATCAAT
1 GCAGAGAACTATTTAGTCAAGCATGAAGCAGATATATCAAT
3618 GCAGAGAACTATTTAGTCAAGCATGAAGCAGATATATCAAT
1 GCAGAGAACTATTTAGTCAAGCATGAAGCAGATATATCAAT
*
3659 GCAGAGAACTATTTAGTCAAGCATGAAGCAGATA-ATAAAT
1 GCAGAGAACTATTTAGTCAAGCATGAAGCAGATATATCAAT
*
3699 GCAAAGAAC
1 GCAGAGAAC
3708 ATCATGCACA
Statistics
Matches: 123, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
37 5 0.04
38 23 0.19
39 4 0.03
40 13 0.11
41 78 0.63
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (41 bp):
GCAGAGAACTATTTAGTCAAGCATGAAGCAGATATATCAAT
Found at i:11318 original size:20 final size:19
Alignment explanation
Indices: 11293--11365 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 19
11283 GCTCGAGCTG
11293 AAAAAAACAATAGAAACAAC
1 AAAAAAACAATAGAAA-AAC
*
11313 AAAAAAATAATAGCAAAAAC
1 AAAAAAACAATAG-AAAAAC
* *
11333 AATACCAAAACATTAGGAATAAC
1 AA-A--AAAACAATA-GAAAAAC
11356 AAAAAAACAA
1 AAAAAAACAA
11366 CAAGATAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
20 23 0.53
21 4 0.09
22 1 0.02
23 14 0.33
24 1 0.02
ACGTcount: A:0.71, C:0.14, G:0.05, T:0.10
Consensus pattern (19 bp):
AAAAAAACAATAGAAAAAC
Found at i:13170 original size:23 final size:22
Alignment explanation
Indices: 13126--13170 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
13116 AGATGTGCTA
*
13126 TCAAATTTAGAAATTCAAGAGG
1 TCAAATTTAGAAATCCAAGAGG
* *
13148 TCAATTTTGAGAAATCCATGAGG
1 TCAAATTT-AGAAATCCAAGAGG
13171 GATGTGAAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (22 bp):
TCAAATTTAGAAATCCAAGAGG
Found at i:15483 original size:27 final size:26
Alignment explanation
Indices: 15453--15522 Score: 61
Period size: 28 Copynumber: 2.5 Consensus size: 26
15443 GTCCTTTCTA
*
15453 TTCAGTACTCACCACAAAAATTTTCCT
1 TTCAG-ACTCACCACAAAAACTTTCCT
*
15480 TTCAAAGACTCGA-CACAAAAGCTTTCCT
1 TTC--AGACTC-ACCACAAAAACTTTCCT
15508 TTCAGAGACTCACCA
1 TTC--AGACTCACCA
15523 TAAAGGCGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 4 0.11
28 29 0.81
29 3 0.08
ACGTcount: A:0.34, C:0.30, G:0.09, T:0.27
Consensus pattern (26 bp):
TTCAGACTCACCACAAAAACTTTCCT
Found at i:15496 original size:28 final size:28
Alignment explanation
Indices: 15465--15518 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
15455 CAGTACTCAC
*
15465 CACAAAAATTTTCCTTTCAAAGACTCGA
1 CACAAAAACTTTCCTTTCAAAGACTCGA
* *
15493 CACAAAAGCTTTCCTTTCAGAGACTC
1 CACAAAAACTTTCCTTTCAAAGACTC
15519 ACCATAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.09, T:0.28
Consensus pattern (28 bp):
CACAAAAACTTTCCTTTCAAAGACTCGA
Found at i:26929 original size:30 final size:29
Alignment explanation
Indices: 26873--26929 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
26863 TTTTCACAGG
*
26873 TGAAATGAGAAACAAAAAGAAGATTATGA
1 TGAAATGAGAAACAAAAAGAACATTATGA
* * *
26902 TGAAATTGAGGAACAAACAGCACATTAT
1 TGAAA-TGAGAAACAAAAAGAACATTAT
26930 TAAGAGAGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.53, C:0.09, G:0.19, T:0.19
Consensus pattern (29 bp):
TGAAATGAGAAACAAAAAGAACATTATGA
Found at i:28275 original size:15 final size:15
Alignment explanation
Indices: 28257--28291 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28247 ACAATTGAGA
28257 AAGAAAACAACAAGC
1 AAGAAAACAACAAGC
* *
28272 AAGAAAACAAGAATC
1 AAGAAAACAACAAGC
28287 AAGAA
1 AAGAA
28292 TCAAGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.14, G:0.14, T:0.03
Consensus pattern (15 bp):
AAGAAAACAACAAGC
Found at i:28812 original size:22 final size:22
Alignment explanation
Indices: 28779--28820 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
28769 TTAATTGCTT
28779 TTTTTGAAACATTTTGAAAACC
1 TTTTTGAAACATTTTGAAAACC
28801 TTTTT-AATACATTTTGAAAA
1 TTTTTGAA-ACATTTTGAAAA
28821 TTTAAGTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTTGAAACATTTTGAAAACC
Found at i:40778 original size:30 final size:30
Alignment explanation
Indices: 40711--40780 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
40701 AATTACGAGT
*
40711 TAAAAGAGATTTCACAATAATAAAAGAGAAT
1 TAAAA-AGATTTCACAATAATAAAAGAGAAG
** *
40742 TAAAAAGATTTCACTGTAATAAATGA-AAG
1 TAAAAAGATTTCACAATAATAAAAGAGAAG
40771 TACAAAAGAT
1 TA-AAAAGAT
40781 GAAGAGAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.12
30 25 0.74
31 5 0.15
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (30 bp):
TAAAAAGATTTCACAATAATAAAAGAGAAG
Found at i:44679 original size:227 final size:227
Alignment explanation
Indices: 44277--44735 Score: 641
Period size: 227 Copynumber: 2.0 Consensus size: 227
44267 CCATGATTGA
** *
44277 AAGACACTATGACATCATGATAAACAAGTGTAAGACCATAGTTGGACTATGACAACCTAGCTAAT
1 AAGACACTATGACATCATGATAAACAAGTACAAGACCATAGTTGGACTATGACAACCTAGCTAAC
* * * * * *
44342 CCGTCAAAACGGTAAACACGGGGAACACATGAGGTGTAAGATCATAGTTGGACTATGGCCACCAA
66 CCATCAAAACGATAAACACAGGGAACACATGAGCTGTAAGAACATAGTTGGACTATGACCACCAA
* ** * *
44407 GGTAGTTCGTCGGGATGACAAACACAAGGTTAAAATGAGTAAGACCATAGCTGAAAGATGTTATG
131 GGTAGTTCGTCAGGACAACAAACACAAGGTTAAAATGACTAAGACCATAGCTGAAAGATGCTATG
* * * *
44472 GCATCAAAATATGAATTGACGATAAAATGAGT
196 ACATCAAAAAATGAATTGACAATAAAACGAGT
* *
44504 AAGACACTATGACATCATGGTAAACAGGTACAAGACCATAGTTGGACTATGACAACCTAGCTAAC
1 AAGACACTATGACATCATGATAAACAAGTACAAGACCATAGTTGGACTATGACAACCTAGCTAAC
* * * *
44569 CCATCGAGATGATAAACATAGGGAACACATGAGCTGTAAGAACATAGTTGGACTATGACCACCAA
66 CCATCAAAACGATAAACACAGGGAACACATGAGCTGTAAGAACATAGTTGGACTATGACCACCAA
*** *
44634 GGTAG-TCTGTCAGGACAACAAACATGTGGTTAAAATGACTAAGACCTTAGCTGAAAGATGCTAT
131 GGTAGTTC-GTCAGGACAACAAACACAAGGTTAAAATGACTAAGACCATAGCTGAAAGATGCTAT
*
44698 GACATCAAAAAATGGATTGACAATAAAACGAGT
195 GACATCAAAAAATGAATTGACAATAAAACGAGT
44731 AAGAC
1 AAGAC
44736 CTTAGCTGAA
Statistics
Matches: 202, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
226 2 0.01
227 200 0.99
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (227 bp):
AAGACACTATGACATCATGATAAACAAGTACAAGACCATAGTTGGACTATGACAACCTAGCTAAC
CCATCAAAACGATAAACACAGGGAACACATGAGCTGTAAGAACATAGTTGGACTATGACCACCAA
GGTAGTTCGTCAGGACAACAAACACAAGGTTAAAATGACTAAGACCATAGCTGAAAGATGCTATG
ACATCAAAAAATGAATTGACAATAAAACGAGT
Found at i:54167 original size:42 final size:41
Alignment explanation
Indices: 54121--54199 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
54111 TAAAAAATAT
* *
54121 TTTTACAAAATAATTTTTTTATCTCAAAAATATTTTTTTTCA
1 TTTTACAAAATAA-TATTTTATCTCAAAAATACTTTTTTTCA
*** *
54163 TTTTATTTAATAATATTTTATTTCAAAAATACTTTTT
1 TTTTACAAAATAATATTTTATCTCAAAAATACTTTTT
54200 ATACCAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
41 21 0.68
42 10 0.32
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (41 bp):
TTTTACAAAATAATATTTTATCTCAAAAATACTTTTTTTCA
Found at i:58541 original size:80 final size:79
Alignment explanation
Indices: 58447--58607 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 79
58437 AGATCAACAA
*
58447 GAAAAAAAAAATGGATGGAAAAGTGGAAACTTATAGAGTCAGACTTGTAGTAAAAGGTTATACTT
1 GAAAAAAAAAATGGATGGAAAAGTGGAAACTTACAGAGTCAGACTTGTAGTAAAAGGTTATACTT
58512 AGAAATAAGGTATC
66 AGAAATAAGGTATC
58526 GAAAAAAAAATATGGATGGAAAAGTGGAAACTTACAGAGTCAGACTTGTAGTAAAAGGTTATACT
1 GAAAAAAAAA-ATGGATGGAAAAGTGGAAACTTACAGAGTCAGACTTGTAGTAAAAGGTTATACT
58591 TAGAAATAAGGTATC
65 TAGAAATAAGGTATC
58606 GA
1 GA
58608 TTATGAAAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 10 0.12
80 70 0.88
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.24
Consensus pattern (79 bp):
GAAAAAAAAAATGGATGGAAAAGTGGAAACTTACAGAGTCAGACTTGTAGTAAAAGGTTATACTT
AGAAATAAGGTATC
Found at i:65461 original size:15 final size:15
Alignment explanation
Indices: 65441--65505 Score: 60
Period size: 15 Copynumber: 4.0 Consensus size: 15
65431 ACTACAAAAC
65441 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
65456 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
65475 ATTTTATTATTAATAT
1 A-TTTATTATTAATAT
65491 ATTTA-TATTGAATAT
1 ATTTATTATT-AATAT
65506 TTTCAATGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
14 4 0.10
15 16 0.38
16 4 0.10
17 4 0.10
18 4 0.10
19 4 0.10
20 6 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:65552 original size:16 final size:16
Alignment explanation
Indices: 65521--65557 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
65511 ATGTGAATAA
65521 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
65537 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
65553 TATTA
1 TATTA
65558 AAATAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:69068 original size:23 final size:24
Alignment explanation
Indices: 69038--69159 Score: 155
Period size: 23 Copynumber: 5.3 Consensus size: 24
69028 ATATTAGCGC
69038 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGATTCAGCACTGTGTGT
*
69061 GCTTACTGATTC-GCACTATGTGT
1 GCTTACTGATTCAGCACTGTGTGT
*
69084 GCTTACTGATT-TGCACTGTGTGT
1 GCTTACTGATTCAGCACTGTGTGT
**
69107 GCTTACT-ATTTTGCACTGTGTGT
1 GCTTACTGATTCAGCACTGTGTGT
* *
69130 GCCTACTGATTTA-CACTGTGTGT
1 GCTTACTGATTCAGCACTGTGTGT
69153 GCTTACT
1 GCTTACT
69160 ATTTCCCCAG
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
22 3 0.03
23 80 0.89
24 7 0.08
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.42
Consensus pattern (24 bp):
GCTTACTGATTCAGCACTGTGTGT
Found at i:69105 original size:46 final size:46
Alignment explanation
Indices: 69050--69164 Score: 178
Period size: 46 Copynumber: 2.5 Consensus size: 46
69040 TTACTGTTCA
*
69050 GCACTGTGTGTGCTTACTGA-TTCGCACTATGTGTGCTTACTGATTT
1 GCACTGTGTGTGCTTACT-ATTTCGCACTATGTGTGCCTACTGATTT
* *
69096 GCACTGTGTGTGCTTACTATTTTGCACTGTGTGTGCCTACTGATTT
1 GCACTGTGTGTGCTTACTATTTCGCACTATGTGTGCCTACTGATTT
*
69142 ACACTGTGTGTGCTTACTATTTC
1 GCACTGTGTGTGCTTACTATTTC
69165 CCCAGCAGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 1 0.02
46 62 0.98
ACGTcount: A:0.15, C:0.20, G:0.23, T:0.43
Consensus pattern (46 bp):
GCACTGTGTGTGCTTACTATTTCGCACTATGTGTGCCTACTGATTT
Found at i:80475 original size:19 final size:21
Alignment explanation
Indices: 80435--80476 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
80425 AATAGAAAAA
80435 AGAGAAGAACAAGAGAACGAG
1 AGAGAAGAACAAGAGAACGAG
*
80456 AGAGAGGAA-AAGAGAA-GAG
1 AGAGAAGAACAAGAGAACGAG
80475 AG
1 AG
80477 TTGAGAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.57, C:0.05, G:0.38, T:0.00
Consensus pattern (21 bp):
AGAGAAGAACAAGAGAACGAG
Found at i:93331 original size:2 final size:2
Alignment explanation
Indices: 93324--93358 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
93314 ATGCTATTCT
* *
93324 TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
93359 TTTATATTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:94400 original size:2 final size:2
Alignment explanation
Indices: 94393--94418 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
94383 TTACATTTTC
94393 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
94419 GGGTGAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94587 original size:18 final size:18
Alignment explanation
Indices: 94552--94589 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
94542 TGAATTTTTG
*
94552 AATTCGAATAACTTGAAT
1 AATTCGAATAACTCGAAT
94570 AATTCGAATAAAC-CGAAT
1 AATTCGAAT-AACTCGAAT
94588 AA
1 AA
94590 AATTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAACTCGAAT
Found at i:99167 original size:10 final size:10
Alignment explanation
Indices: 99152--99198 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
99142 ATCAATTCGG
99152 TTAATTTTGA
1 TTAATTTTGA
*
99162 TTAATTTCGA
1 TTAATTTTGA
*
99172 TTCATTTTGA
1 TTAATTTTGA
* *
99182 CTAA-TTCGA
1 TTAATTTTGA
99191 TTAATTTT
1 TTAATTTT
99199 AATTTGGTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.55
Consensus pattern (10 bp):
TTAATTTTGA
Found at i:99191 original size:19 final size:19
Alignment explanation
Indices: 99145--99198 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
99135 ATATATTATC
* *
99145 AATTCGGTTAATTTTGATT
1 AATTCGATTAATTTTGACT
*
99164 AATTTCGATTCATTTTGACT
1 AA-TTCGATTAATTTTGACT
99184 AATTCGATTAATTTT
1 AATTCGATTAATTTT
99199 AATTTGGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (19 bp):
AATTCGATTAATTTTGACT
Found at i:99849 original size:5 final size:5
Alignment explanation
Indices: 99839--99864 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
99829 AGTCATATGA
99839 AGCCC AGCCC AGCCC AGCCC AGCCC A
1 AGCCC AGCCC AGCCC AGCCC AGCCC A
99865 ATCCCAAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
AGCCC
Found at i:103255 original size:2 final size:2
Alignment explanation
Indices: 103248--103274 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
103238 TTGCTTGATT
103248 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
103275 GTGCGCGCTC
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:107170 original size:19 final size:19
Alignment explanation
Indices: 107148--107206 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
107138 AAAAATATTT
107148 AAATTATTAAAATTTATAA
1 AAATTATTAAAATTTATAA
**
107167 AAATTAATTAAAA-ACATAA
1 AAATT-ATTAAAATTTATAA
107186 AAA-T-TTATAAATTTATAA
1 AAATTATTA-AAATTTATAA
107204 AAA
1 AAA
107207 ATAATTCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 3 0.09
17 3 0.09
18 8 0.24
19 12 0.36
20 7 0.21
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTATTAAAATTTATAA
Found at i:108977 original size:6 final size:6
Alignment explanation
Indices: 108966--108994 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
108956 AGATGTTCTT
108966 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
108995 AAGAGCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:119224 original size:21 final size:21
Alignment explanation
Indices: 119200--119240 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
119190 AAAATTTAAA
* *
119200 TTAAAAAAACATAAATAAAAT
1 TTAAAAAAACAAAAACAAAAT
119221 TTAAAAAAACAAAAACAAAA
1 TTAAAAAAACAAAAACAAAA
119241 GACCCTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (21 bp):
TTAAAAAAACAAAAACAAAAT
Found at i:119234 original size:26 final size:24
Alignment explanation
Indices: 119183--119240 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
119173 ATGCCACGTC
*
119183 AACAAAAAAAATTTAAATTAAAAA
1 AACAAAAAAAATTTAAATAAAAAA
*
119207 AACATAAATAAAATTTAAAAAAACAAA
1 AACA-AAA-AAAATTTAAATAAA-AAA
119234 AACAAAA
1 AACAAAA
119241 GACCCTAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 3 0.10
26 15 0.52
27 7 0.24
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (24 bp):
AACAAAAAAAATTTAAATAAAAAA
Found at i:139490 original size:33 final size:33
Alignment explanation
Indices: 139426--139490 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
139416 CATAGTTTGT
* * *
139426 TTACATGAATTCGCATGTGGTGAGTTTGCATCC
1 TTACATGAACTCGCATGTGATGAGTTCGCATCC
139459 TTACATGAACTCGCATGTGATG-GATTCGCATC
1 TTACATGAACTCGCATGTGATGAG-TTCGCATC
139491 ATCACTCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (33 bp):
TTACATGAACTCGCATGTGATGAGTTCGCATCC
Found at i:142238 original size:33 final size:33
Alignment explanation
Indices: 142152--142249 Score: 133
Period size: 33 Copynumber: 3.0 Consensus size: 33
142142 CATAGTTCGT
*
142152 TTACATGAGTTCGCATGTGGTGAGTTTACATCC
1 TTACATGAGTTCGCATGTGGTGAGTTTGCATCC
*
142185 TTACATGAGTTCGTATGTGGTGAGTTTGCATCC
1 TTACATGAGTTCGCATGTGGTGAGTTTGCATCC
* * * * *
142218 TTACATGAGCTCACACGTGGTGGGTTCGCATC
1 TTACATGAGTTCGCATGTGGTGAGTTTGCATC
142250 ATCACGCAAG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (33 bp):
TTACATGAGTTCGCATGTGGTGAGTTTGCATCC
Found at i:147205 original size:46 final size:46
Alignment explanation
Indices: 147120--147212 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 46
147110 TCAAGCCCTT
*
147120 TTCTTGTAATTTTTATGGATTTGAAGTCATGGGAGCTTGATTTAGC
1 TTCTTGTAATTTTTATGGATTTGAAGTCATGAGAGCTTGATTTAGC
147166 TTCTTGTAATTTTTTATGGATTTGAAGTCATGAGA-CTTGATTTAGC
1 TTCTTGTAA-TTTTTATGGATTTGAAGTCATGAGAGCTTGATTTAGC
147212 T
1 T
147213 AGTCCATGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 21 0.47
47 24 0.53
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.47
Consensus pattern (46 bp):
TTCTTGTAATTTTTATGGATTTGAAGTCATGAGAGCTTGATTTAGC
Found at i:159464 original size:31 final size:31
Alignment explanation
Indices: 159424--159482 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
159414 AAATGATCAT
*
159424 TGAATTATTCAAAAGTTTTCATTTAAGTTAC
1 TGAACTATTCAAAAGTTTTCATTTAAGTTAC
** *
159455 TGAACTATTCGGAAGTTTTTATTTAAGT
1 TGAACTATTCAAAAGTTTTCATTTAAGT
159483 CATTAAGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (31 bp):
TGAACTATTCAAAAGTTTTCATTTAAGTTAC
Found at i:161943 original size:31 final size:31
Alignment explanation
Indices: 161908--161993 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 31
161898 TAATAGCCAA
*
161908 GTGACTTAAATAAAAACTTTCGAATAGTTCG
1 GTGACTTAAATAAAAACTTTCAAATAGTTCG
* *
161939 GTGACTTAAATGAAAACTTTCAAATAGTTTG
1 GTGACTTAAATAAAAACTTTCAAATAGTTCG
* * * *
161970 ATGACTTAATTGAAACCTTTCAAA
1 GTGACTTAAATAAAAACTTTCAAA
161994 CAGTCCAGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (31 bp):
GTGACTTAAATAAAAACTTTCAAATAGTTCG
Found at i:169717 original size:3 final size:3
Alignment explanation
Indices: 169711--169772 Score: 115
Period size: 3 Copynumber: 20.3 Consensus size: 3
169701 CTACTACAAC
169711 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
169759 TAT TAT TAT ATAT T
1 TAT TAT TAT -TAT T
169773 TTGGTCCCTG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:200663 original size:30 final size:31
Alignment explanation
Indices: 200629--200692 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
200619 CAATGAATTA
200629 ATATTTTAAAATT-TAAAAATGT-TAAAAAAT
1 ATATTTTAAAATTATAAAAAT-TATAAAAAAT
*
200659 ATATTTTAAAATTATTAAAATTATAAAAAAT
1 ATATTTTAAAATTATAAAAATTATAAAAAAT
200690 ATA
1 ATA
200693 AAAAAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (31 bp):
ATATTTTAAAATTATAAAAATTATAAAAAAT
Found at i:200695 original size:40 final size:38
Alignment explanation
Indices: 200626--200705 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 38
200616 TTACAATGAA
* * *
200626 TTAATATTTTAAAATTTAAAAATGTTAAAAAATATATT
1 TTAAAATTTTAAAATTTAAAAATGATAAAAAAAATATT
200664 TTAAAATTATTAAAATTATAAAAAAT-ATAAAAAAAATATT
1 TTAAAATT-TTAAAATT-T-AAAAATGATAAAAAAAATATT
200704 TT
1 TT
200706 TTTAATATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 7 0.19
39 8 0.22
40 15 0.42
41 6 0.17
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (38 bp):
TTAAAATTTTAAAATTTAAAAATGATAAAAAAAATATT
Found at i:205697 original size:23 final size:24
Alignment explanation
Indices: 205671--205765 Score: 58
Period size: 23 Copynumber: 4.1 Consensus size: 24
205661 AAATTTATTA
205671 TAAGATTTAATTT-ATTTTAAATT
1 TAAGATTTAATTTAATTTTAAATT
**
205694 TAAG-TTTGTTTTAAATTTT-AATT
1 TAAGATTTAATTT-AATTTTAAATT
* **
205717 TAA-A-TTAAGTTTAAATTTACTTT
1 TAAGATTTAA-TTTAATTTTAAATT
* * *
205740 TAAAATTAAAATT-ATTTTAAATT
1 TAAGATTTAATTTAATTTTAAATT
205763 TAA
1 TAA
205766 AAAGTCCCAT
Statistics
Matches: 53, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
22 13 0.25
23 29 0.55
24 8 0.15
25 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (24 bp):
TAAGATTTAATTTAATTTTAAATT
Found at i:205722 original size:6 final size:6
Alignment explanation
Indices: 205658--205766 Score: 52
Period size: 6 Copynumber: 19.0 Consensus size: 6
205648 TAAATTCCCT
* * **
205658 TTTAAA TTT--A TTATAAGA TTT-AA TTT-AT TTTAAA TTTAAG TTT-GT
1 TTTAAA TTTAAA TT-TAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * ** *
205703 TTTAAA TTTTAA TTTAAA -TTAAG TTTAAA TTTACT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
205750 ATT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
205767 AAGTCCCATT
Statistics
Matches: 76, Mismatches: 19, Indels: 16
0.68 0.17 0.14
Matches are distributed among these distances:
4 3 0.04
5 19 0.25
6 50 0.66
7 1 0.01
8 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:205735 original size:29 final size:29
Alignment explanation
Indices: 205681--205766 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
205671 TAAGATTTAA
* **
205681 TTTATTTTAAATTTAAGTTT-GTTTTAAAT
1 TTTAATTTAAA-TTAAGTTTAAATTTAAAT
*
205710 TTTAATTTAAATTAAGTTTAAATTT-ACT
1 TTTAATTTAAATTAAGTTTAAATTTAAAT
* *
205738 TTTAAAATTAAAATT-ATTTTAAATTTAAA
1 TTT--AATTTAAATTAAGTTTAAATTTAAA
205767 AAGTCCCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
28 13 0.28
29 23 0.50
30 10 0.22
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTAATTTAAATTAAGTTTAAATTTAAAT
Found at i:205767 original size:17 final size:17
Alignment explanation
Indices: 205658--205766 Score: 112
Period size: 17 Copynumber: 6.4 Consensus size: 17
205648 TAAATTCCCT
*
205658 TTTAAATTTATTATAAGA
1 TTTAAATTTATTTTAA-A
205676 TTT-AATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
205692 TTTAAGTTTGTTTTAAA
1 TTTAAATTTATTTTAAA
* ** *
205709 TTTTAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
205726 TTTAAATTTACTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
205744 ATTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
205761 TTTAAA
1 TTTAAA
205767 AAGTCCCATT
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
16 4 0.05
17 54 0.74
18 15 0.21
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:206493 original size:3 final size:3
Alignment explanation
Indices: 206485--206529 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
206475 TTAAATGAAT
* * **
206485 TAA TAA TAA TAA TAA TTA TAT TTT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
206530 ACCGAAAGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Done.