Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012907.1 Kokia drynarioides strain JFW-HI SEQ_127921, 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: 64603
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:115 original size:13 final size:16
Alignment explanation
Indices: 84--126 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 16
74 ATATATATAT
*
84 AAGAAATAAAAGAATA
1 AAGAAACAAAAGAATA
100 AAGAAA-AAAA-AA-A
1 AAGAAACAAAAGAATA
113 AAGAAACAAAAGAA
1 AAGAAACAAAAGAA
127 GGAATAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 6 0.24
16 6 0.24
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (16 bp):
AAGAAACAAAAGAATA
Found at i:585 original size:17 final size:17
Alignment explanation
Indices: 563--615 Score: 88
Period size: 17 Copynumber: 3.1 Consensus size: 17
553 TAAATGAGTT
563 AATTAGGATTAAATTGG
1 AATTAGGATTAAATTGG
580 AATTAGGATTAAATTGG
1 AATTAGGATTAAATTGG
*
597 AATTAGGGTATAAATTGG
1 AATTAGGAT-TAAATTGG
615 A
1 A
616 TAGAAATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 25 0.74
18 9 0.26
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.34
Consensus pattern (17 bp):
AATTAGGATTAAATTGG
Found at i:3243 original size:23 final size:23
Alignment explanation
Indices: 3190--3362 Score: 175
Period size: 23 Copynumber: 7.5 Consensus size: 23
3180 AAGTGCTGGG
*
3190 AAAACAATAAGCACACACAGTGC
1 AAAACAGTAAGCACACACAGTGC
* * * * *
3213 GAATCAGTAACCACACGCAATGC
1 AAAACAGTAAGCACACACAGTGC
3236 AAAACAGTAAGCACACACAGTGC
1 AAAACAGTAAGCACACACAGTGC
* * *
3259 AAATCAGTAAGCACATATAGTGC
1 AAAACAGTAAGCACACACAGTGC
* * *
3282 GAATCAATAAGCACACACAGTGC
1 AAAACAGTAAGCACACACAGTGC
**
3305 TGAACAGTAAGCACACACAGTGC
1 AAAACAGTAAGCACACACAGTGC
** *
3328 TGAACAATAAGCACACACAGTGC
1 AAAACAGTAAGCACACACAGTGC
**
3351 TGAACAGTAAGC
1 AAAACAGTAAGC
3363 GCACTAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 126 1.00
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (23 bp):
AAAACAGTAAGCACACACAGTGC
Found at i:3257 original size:46 final size:46
Alignment explanation
Indices: 3190--3362 Score: 215
Period size: 46 Copynumber: 3.8 Consensus size: 46
3180 AAGTGCTGGG
* * *
3190 AAAACAATAAGCACACACAGTGC-GAATCAGTAACCACACGCAATGC
1 AAAACAATAAGCACACACAGTGCTGAA-CAGTAAGCACACACAGTGC
* * * *
3236 AAAACAGTAAGCACACACAGTGC-AAATCAGTAAGCACATATAGTGC
1 AAAACAATAAGCACACACAGTGCTGAA-CAGTAAGCACACACAGTGC
* *
3282 GAATCAATAAGCACACACAGTGCTGAACAGTAAGCACACACAGTGC
1 AAAACAATAAGCACACACAGTGCTGAACAGTAAGCACACACAGTGC
**
3328 TGAACAATAAGCACACACAGTGCTGAACAGTAAGC
1 AAAACAATAAGCACACACAGTGCTGAACAGTAAGC
3363 GCACTAATAT
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
46 108 0.98
47 2 0.02
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (46 bp):
AAAACAATAAGCACACACAGTGCTGAACAGTAAGCACACACAGTGC
Found at i:3362 original size:69 final size:68
Alignment explanation
Indices: 3191--3362 Score: 220
Period size: 69 Copynumber: 2.5 Consensus size: 68
3181 AGTGCTGGGA
* *
3191 AAACAATAAGCACACACAGTGCGAATCAGTAACCACACGCAATGCAAAACAGTAAGCACACACAG
1 AAACAATAAGCACACACAGTGCGAATCAGTAAGCACACACAATGCAAAACAGTAAGCACACACAG
3256 TGC
66 TGC
* * * * * **
3259 AAATCAGTAAGCACATATAGTGCGAATCAATAAGCACACACAGTGCTGAACAGTAAGCACACACA
1 AAA-CAATAAGCACACACAGTGCGAATCAGTAAGCACACACAATGCAAAACAGTAAGCACACACA
3324 GTGC
65 GTGC
*
3328 TGAACAATAAGCACACACAGTGCTGAA-CAGTAAGC
1 -AAACAATAAGCACACACAGTGC-GAATCAGTAAGC
3363 GCACTAATAT
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
68 3 0.03
69 79 0.91
70 5 0.06
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (68 bp):
AAACAATAAGCACACACAGTGCGAATCAGTAAGCACACACAATGCAAAACAGTAAGCACACACAG
TGC
Found at i:4534 original size:6 final size:6
Alignment explanation
Indices: 4523--4597 Score: 98
Period size: 6 Copynumber: 12.7 Consensus size: 6
4513 TTGAATTTAT
** * *
4523 TTTAAA TTTAAA TTTATT TTTAAA TTTAAA TTT-AA TTTAAG TTTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
4570 TTTAAG TTTAAA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
4598 TTCTAAATTT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
5 5 0.08
6 57 0.92
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:4555 original size:35 final size:34
Alignment explanation
Indices: 4495--4597 Score: 118
Period size: 35 Copynumber: 2.9 Consensus size: 34
4485 CTAAACACAT
* *
4495 TTTAAATTTATTTTAAGA-TTGAATTTATTTTAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTTAAA
*
4529 TTTAAATTTATTTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTA-TTTTAAATTTAAATTTAATTTAAA
* *
4564 TTTAAGTTTAAGTTTAAATTTAAATTTAAATTTA
1 TTTAAATTT-ATTTTAAATTTAAATTT-AATTTA
4598 TTCTAAATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
34 11 0.18
35 42 0.70
36 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
Found at i:4607 original size:17 final size:17
Alignment explanation
Indices: 4495--4591 Score: 115
Period size: 17 Copynumber: 5.6 Consensus size: 17
4485 CTAAACACAT
4495 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
4513 -TTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
4529 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
4547 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
* *
4564 TTTAAGTTTAAGTTTAAA
1 TTTAAATTT-ATTTTAAA
4582 TTTAAATTTA
1 TTTAAATTTA
4592 AATTTATTCT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
16 1 0.01
17 36 0.53
18 31 0.46
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:6362 original size:29 final size:29
Alignment explanation
Indices: 6310--6480 Score: 113
Period size: 29 Copynumber: 5.9 Consensus size: 29
6300 AATTATCTTG
* *
6310 AAATCATATTTTGACCCCCGAACTTTCCAA
1 AAAT-ATATTTTAACCCCCAAACTTTCCAA
* *
6340 AAATATATTTTAACCTCCAAACTATCCAA
1 AAATATATTTTAACCCCCAAACTTTCCAA
*
6369 AAAT-TCCAGTTTT-TCCCCCAAACTTTCCAA
1 AAATAT--A-TTTTAACCCCCAAACTTTCCAA
* * *
6399 AAATTACATTTTAA-CCCTAAACTTTCTAA
1 AAA-TATATTTTAACCCCCAAACTTTCCAA
*
6428 AAAT-TCCA-TTT-ACCCCTAAAC-TTCCAA
1 AAATAT--ATTTTAACCCCCAAACTTTCCAA
* * *
6455 AAATTACATTTTAACCCTCGAACTTT
1 AAA-TATATTTTAACCCCCAAACTTT
6481 ATAAAAATTT
Statistics
Matches: 110, Mismatches: 17, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
27 10 0.09
28 17 0.15
29 53 0.48
30 25 0.23
31 5 0.05
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.33
Consensus pattern (29 bp):
AAATATATTTTAACCCCCAAACTTTCCAA
Found at i:6421 original size:59 final size:57
Alignment explanation
Indices: 6323--6472 Score: 196
Period size: 59 Copynumber: 2.6 Consensus size: 57
6313 TCATATTTTG
* * *
6323 ACCCCCGAACTTTCCAAAAA-TATATTTTAACCTCCAAACTATCCAAAAATTCCAGTTTT
1 ACCCCCAAACTTTCCAAAAATTACATTTTAACC-CTAAACTATCCAAAAATTCCA--TTT
* * *
6382 TCCCCCAAACTTTCCAAAAATTACATTTTAACCCTAAACTTTCTAAAAATTCCATTT
1 ACCCCCAAACTTTCCAAAAATTACATTTTAACCCTAAACTATCCAAAAATTCCATTT
*
6439 ACCCCTAAAC-TTCCAAAAATTACATTTTAACCCT
1 ACCCCCAAACTTTCCAAAAATTACATTTTAACCCT
6473 CGAACTTTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
56 24 0.29
57 11 0.13
59 36 0.44
60 11 0.13
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.32
Consensus pattern (57 bp):
ACCCCCAAACTTTCCAAAAATTACATTTTAACCCTAAACTATCCAAAAATTCCATTT
Found at i:6444 original size:28 final size:29
Alignment explanation
Indices: 6330--6472 Score: 157
Period size: 29 Copynumber: 5.0 Consensus size: 29
6320 TTGACCCCCG
* *
6330 AACTTTCCAAAAA-TATATTTTAACCTCCA
1 AACTTTCCAAAAATTACATTTTAACC-CTA
* * ** *
6359 AACTATCCAAAAATTCCAGTTTTTCCCCCA
1 AACTTTCCAAAAATTACA-TTTTAACCCTA
6389 AACTTTCCAAAAATTACATTTTAACCCTA
1 AACTTTCCAAAAATTACATTTTAACCCTA
* * *
6418 AACTTTCTAAAAATTCCA-TTTACCCCTA
1 AACTTTCCAAAAATTACATTTTAACCCTA
6446 AAC-TTCCAAAAATTACATTTTAACCCT
1 AACTTTCCAAAAATTACATTTTAACCCT
6473 CGAACTTTAT
Statistics
Matches: 95, Mismatches: 16, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
27 12 0.13
28 20 0.21
29 36 0.38
30 21 0.22
31 6 0.06
ACGTcount: A:0.38, C:0.27, G:0.01, T:0.34
Consensus pattern (29 bp):
AACTTTCCAAAAATTACATTTTAACCCTA
Found at i:6486 original size:29 final size:28
Alignment explanation
Indices: 6398--6486 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 28
6388 AAACTTTCCA
*
6398 AAAATTACATTTTAACCCTAAACTTTCT
1 AAAATTACATTTTAACCCTAAACTTTAT
* * *
6426 AAAAATTCCA-TTTACCCCTAAACTTCCA-
1 -AAAATTACATTTTAACCCTAAACTT-TAT
*
6454 AAAATTACATTTTAACCCTCGAACTTTAT
1 AAAATTACATTTTAACCCT-AAACTTTAT
6483 AAAA
1 AAAA
6487 ATTTTATTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
27 8 0.17
28 23 0.48
29 17 0.35
ACGTcount: A:0.42, C:0.24, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAATTACATTTTAACCCTAAACTTTAT
Found at i:6605 original size:29 final size:29
Alignment explanation
Indices: 6446--6627 Score: 120
Period size: 30 Copynumber: 6.2 Consensus size: 29
6436 TTTACCCCTA
* *
6446 AACTTCCAAAAATTACA-TTTTAACCCTCG
1 AACTTCCAAAAATTTCATTTTTGA-CCTCG
** * *
6475 AACTTTATAAAAATTTTATTTTTTGACCCCG
1 AAC-TTCCAAAAATTTCA-TTTTTGACCTCG
*
6506 AACTTCCAAATATTTCATTTTTGACCTC-
1 AACTTCCAAAAATTTCATTTTTGACCTCG
* *** *
6534 AATTTTTCCAAAAATTATCATTTTACCCCTTG
1 AA--CTTCCAAAAATT-TCATTTTTGACCTCG
* * *
6566 GA-TGTCAAAAAATTCCATTTTTGACCTCG
1 AACT-TCCAAAAATTTCATTTTTGACCTCG
* *
6595 AACTTCCAAAAATTACA-TTTTGACCTCA
1 AACTTCCAAAAATTTCATTTTTGACCTCG
6623 AACTT
1 AACTT
6628 TTTGAAAATT
Statistics
Matches: 116, Mismatches: 28, Indels: 19
0.71 0.17 0.12
Matches are distributed among these distances:
28 17 0.15
29 36 0.31
30 40 0.34
31 17 0.15
32 6 0.05
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (29 bp):
AACTTCCAAAAATTTCATTTTTGACCTCG
Found at i:10773 original size:24 final size:25
Alignment explanation
Indices: 10739--10814 Score: 86
Period size: 24 Copynumber: 3.1 Consensus size: 25
10729 GTGGATGTTC
10739 AACCTTTCACCTTTCATCTCTC-TT
1 AACCTTTCACCTTTCATCTCTCTTT
* * *
10763 GACCTTCCACCTTTCAT-TTTCTTT
1 AACCTTTCACCTTTCATCTCTCTTT
*
10787 AACCTTTAACCTTTCATCTC-CTTAT
1 AACCTTTCACCTTTCATCTCTCTT-T
10812 AAC
1 AAC
10815 ATCTTTTTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
23 3 0.07
24 34 0.81
25 5 0.12
ACGTcount: A:0.20, C:0.34, G:0.01, T:0.45
Consensus pattern (25 bp):
AACCTTTCACCTTTCATCTCTCTTT
Found at i:11446 original size:28 final size:28
Alignment explanation
Indices: 11414--11481 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
11404 ATTGTTTATG
* *
11414 TAGTTAAATAATATTGTGCTTCGTTTAC
1 TAGTTAAATAATATTATACTTCGTTTAC
* * *
11442 TAGTTAAATAATCTTATATTTTGTTTAC
1 TAGTTAAATAATATTATACTTCGTTTAC
11470 TAGTTAAATAAT
1 TAGTTAAATAAT
11482 CGGTCCATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (28 bp):
TAGTTAAATAATATTATACTTCGTTTAC
Found at i:11667 original size:15 final size:15
Alignment explanation
Indices: 11647--11677 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11637 TCGAAATTTT
*
11647 TTGACTTGATTCGAC
1 TTGACTTGACTCGAC
11662 TTGACTTGACTCGAC
1 TTGACTTGACTCGAC
11677 T
1 T
11678 CGATCGAATA
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:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (15 bp):
TTGACTTGACTCGAC
Found at i:27372 original size:12 final size:12
Alignment explanation
Indices: 27347--27398 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
27337 ATCTACAAAA
27347 TAAATATTAAAT
1 TAAATATTAAAT
27359 TAAAT-TTAATAT
1 TAAATATTAA-AT
* *
27371 TAAGATAATCAAT
1 TAA-ATATTAAAT
*
27384 TTAATATTAAAT
1 TAAATATTAAAT
27396 TAA
1 TAA
27399 TAAAATAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
11 4 0.13
12 19 0.61
13 6 0.19
14 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:27397 original size:25 final size:25
Alignment explanation
Indices: 27356--27424 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
27346 ATAAATATTA
* *
27356 AATTAAAT-TTAATATTAAGATAAT
1 AATTTAATATTAATATTAAGAAAAT
*
27380 CAATTTAATATTAA-ATTAATAAAAT
1 -AATTTAATATTAATATTAAGAAAAT
27405 AATATTAATA-TAATTATTAA
1 AAT-TTAATATTAA-TATTAA
27425 ATTATTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 6 0.16
25 22 0.59
26 9 0.24
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (25 bp):
AATTTAATATTAATATTAAGAAAAT
Found at i:27399 original size:20 final size:19
Alignment explanation
Indices: 27349--27412 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
27339 CTACAAAATA
27349 AATATTAAATT-A-AATTT
1 AATATTAAATTAATAATTT
27366 AATATTAAGA-TAATCAATTT
1 AATATTAA-ATTAAT-AATTT
**
27386 AATATTAAATTAATAAAAT
1 AATATTAAATTAATAATTT
27405 AATATTAA
1 AATATTAA
27413 TATAATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 9 0.22
18 2 0.05
19 12 0.30
20 17 0.43
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
AATATTAAATTAATAATTT
Found at i:35169 original size:17 final size:18
Alignment explanation
Indices: 35149--35185 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
35139 TATTCTTGTT
35149 ATAAAATTT-ATTTTTTA
1 ATAAAATTTAATTTTTTA
*
35166 AT-AAGTTTAATTTTTTA
1 ATAAAATTTAATTTTTTA
35183 ATA
1 ATA
35186 TTCTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 3
0.81 0.05 0.14
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
ATAAAATTTAATTTTTTA
Found at i:38083 original size:90 final size:90
Alignment explanation
Indices: 37930--38121 Score: 366
Period size: 90 Copynumber: 2.1 Consensus size: 90
37920 CAGCTGAAAC
*
37930 AAATACATATCAAATCAGCATTTAGAAAGAAATACAAATCAACTCAATATTCAGGGTTTTGAATA
1 AAATACAAATCAAATCAGCATTTAGAAAGAAATACAAATCAACTCAATATTCAGGGTTTTGAATA
37995 GCAACTGAATCTAATTAATCAAAAG
66 GCAACTGAATCTAATTAATCAAAAG
38020 AAATACAAATCAAATCAGCATTTAGAAAGAAATACAAATCAACTCAATATTCAGGGTTTTGAATA
1 AAATACAAATCAAATCAGCATTTAGAAAGAAATACAAATCAACTCAATATTCAGGGTTTTGAATA
*
38085 GCAGCTGAATCTAATTAATCAAAAG
66 GCAACTGAATCTAATTAATCAAAAG
38110 AAATACAAATCA
1 AAATACAAATCA
38122 GTATTCAGGA
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 100 1.00
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (90 bp):
AAATACAAATCAAATCAGCATTTAGAAAGAAATACAAATCAACTCAATATTCAGGGTTTTGAATA
GCAACTGAATCTAATTAATCAAAAG
Found at i:38144 original size:56 final size:57
Alignment explanation
Indices: 38067--38175 Score: 166
Period size: 56 Copynumber: 1.9 Consensus size: 57
38057 ATCAACTCAA
* ** * *
38067 TATTCAGGGTTTTGAATAGCAGCTGAATCTAATTAAT-CAAAAGAAATACAAATCAG
1 TATTCAGGATTTCAAATAGCAGCTGAATCTAATTAATAAAAAAGAAACACAAATCAG
38123 TATTCAGGATTTCAAATAGCAGCTGAATCTAATTAATAAAAAAGAAACACAAA
1 TATTCAGGATTTCAAATAGCAGCTGAATCTAATTAATAAAAAAGAAACACAAA
38176 CCAAAACAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 34 0.72
57 13 0.28
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (57 bp):
TATTCAGGATTTCAAATAGCAGCTGAATCTAATTAATAAAAAAGAAACACAAATCAG
Found at i:38206 original size:62 final size:57
Alignment explanation
Indices: 38084--38225 Score: 155
Period size: 62 Copynumber: 2.4 Consensus size: 57
38074 GGTTTTGAAT
* * * * *
38084 AGCAGCTGAATCTAATTAAT-CAAAAGAAATACAAATCAGTATTCAGGATTTCAAAT
1 AGCAGCTGAATCTAATTAATAAAAAAGAAAAACAAAACAGTAATCAGGATTTCAAAG
38140 AGCAGCTGAATCTAATTAATAAAAAAGAAACACAAACCAAAACAGTAATCA-GAGTTTCAAAG
1 AGCAGCTGAATCTAATTAATAAAAAAG--A-A-AAA-CAAAACAGTAATCAGGA-TTTCAAAG
*
38202 AGCAGCTGAAGCTAATTAA-AAAAA
1 AGCAGCTGAATCTAATTAATAAAAA
38226 TACAAAACAA
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
56 20 0.27
57 5 0.07
59 1 0.01
60 1 0.01
61 9 0.12
62 37 0.51
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (57 bp):
AGCAGCTGAATCTAATTAATAAAAAAGAAAAACAAAACAGTAATCAGGATTTCAAAG
Found at i:41664 original size:64 final size:62
Alignment explanation
Indices: 41583--41710 Score: 166
Period size: 62 Copynumber: 2.0 Consensus size: 62
41573 TTACCTATAA
* * *
41583 CAAAATTCGAATTAAGGTATTTAAGACTTAAAGACTTTCGACTTTACTAACTACAACAAGGCCT
1 CAAAATTCAAATTAAGGTATTCAAGACTT--AGACTTCCGACTTTACTAACTACAACAAGGCCT
* * * * *
41647 CAAAATTTAAATTAAGGTATTCAAGACTTAGACTTCCGATTTTATTAACTACGACACGGCCT
1 CAAAATTCAAATTAAGGTATTCAAGACTTAGACTTCCGACTTTACTAACTACAACAAGGCCT
41709 CA
1 CA
41711 TTTGCACTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 30 0.54
64 26 0.46
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (62 bp):
CAAAATTCAAATTAAGGTATTCAAGACTTAGACTTCCGACTTTACTAACTACAACAAGGCCT
Found at i:47852 original size:25 final size:25
Alignment explanation
Indices: 47824--47892 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
47814 GTGGTGTATG
*
47824 TATAAATATTTAATAAATAAAAA-AA
1 TATAAATATTT-TTAAATAAAAATAA
*
47849 TAT-AAT-TTTTTAAATTAAAAATAG
1 TATAAATATTTTTAAA-TAAAAATAA
47873 TATAAATATTTTTAAATAAA
1 TATAAATATTTTTAAATAAA
47893 TTTAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 4 0.11
23 9 0.24
24 7 0.18
25 10 0.26
26 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (25 bp):
TATAAATATTTTTAAATAAAAATAA
Found at i:48803 original size:21 final size:21
Alignment explanation
Indices: 48779--48819 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48769 TCACTTTGAA
48779 AATT-TTTAAGATTTGGGTCAT
1 AATTGTTTAA-ATTTGGGTCAT
*
48800 AATTGTTTAAATTTTGGTCA
1 AATTGTTTAAATTTGGGTCA
48820 AAATATTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.49
Consensus pattern (21 bp):
AATTGTTTAAATTTGGGTCAT
Found at i:49500 original size:133 final size:134
Alignment explanation
Indices: 49262--49533 Score: 528
Period size: 133 Copynumber: 2.0 Consensus size: 134
49252 AACATTTCCC
49262 ATTTTTTAGATTAAACAAATATTATATTGTTGCAACAAAGTGGTCCTATGATGCTTATGGTGGTT
1 ATTTTTTAGATTAAACAAATATTATATTGTTGCAACAAAGTGGTCCTATGATGCTTATGGTGGTT
49327 CATCTATGCATTTTTTTCTCACTTAACTCATAAGCTTG-TTTTTTTTTTTTGATGAATGTGAACT
66 CATCTATGCATTTTTTTCTCACTTAACTCATAAGCTTGTTTTTTTTTTTTTGATGAATGTGAACT
49391 GTAT
131 GTAT
49395 ATTTTTTAGATTAAACAAATATTATATTGTTGCAACAAAGTGGTCCTATGATGCTTATGGTGGTT
1 ATTTTTTAGATTAAACAAATATTATATTGTTGCAACAAAGTGGTCCTATGATGCTTATGGTGGTT
*
49460 CATCTATGCATTTTTTTCTCACTTAACTGATAAGCTTGTTTTTTTTTTTTTGATGAATGTGAACT
66 CATCTATGCATTTTTTTCTCACTTAACTCATAAGCTTGTTTTTTTTTTTTTGATGAATGTGAACT
49525 GTAT
131 GTAT
49529 ATTTT
1 ATTTT
49534 CTATTTTATT
Statistics
Matches: 137, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
133 102 0.74
134 35 0.26
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.47
Consensus pattern (134 bp):
ATTTTTTAGATTAAACAAATATTATATTGTTGCAACAAAGTGGTCCTATGATGCTTATGGTGGTT
CATCTATGCATTTTTTTCTCACTTAACTCATAAGCTTGTTTTTTTTTTTTTGATGAATGTGAACT
GTAT
Found at i:54464 original size:24 final size:24
Alignment explanation
Indices: 54437--54491 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
54427 CAACTTTTTT
*
54437 CTCTTCCT-CTTTGGTATCTCCTTC
1 CTCTTCCTACTCTGGTATC-CCTTC
54461 CTCTT-CTAGCTCTGGTATCCCTTC
1 CTCTTCCTA-CTCTGGTATCCCTTC
*
54485 CTGTTCC
1 CTCTTCC
54492 CTCACCGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 2 0.08
24 14 0.54
25 10 0.38
ACGTcount: A:0.05, C:0.38, G:0.11, T:0.45
Consensus pattern (24 bp):
CTCTTCCTACTCTGGTATCCCTTC
Found at i:56544 original size:17 final size:17
Alignment explanation
Indices: 56522--56554 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56512 CTGAAGGAAA
56522 AAAGAAAGAAAAAAGAG
1 AAAGAAAGAAAAAAGAG
*
56539 AAAGAAAGAAAGAAGA
1 AAAGAAAGAAAAAAGA
56555 AGGAAGAAGG
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAGAG
Found at i:56571 original size:9 final size:9
Alignment explanation
Indices: 56549--56585 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
56539 AAAGAAAGAA
56549 AGAAGAA-G
1 AGAAGAAGG
56557 -GAAGAAGG
1 AGAAGAAGG
56565 AGAAGAAGG
1 AGAAGAAGG
*
56574 GGAAGAAGG
1 AGAAGAAGG
56583 AGA
1 AGA
56586 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.24
8 1 0.04
9 18 0.72
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Found at i:56986 original size:20 final size:21
Alignment explanation
Indices: 56945--56987 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
56935 TAATTTACTT
56945 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
*
56966 TAATTTAATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
56986 TA
1 TA
56988 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:62121 original size:24 final size:24
Alignment explanation
Indices: 62094--62148 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
62084 CAACTTTTTT
*
62094 CTCTTCCT-CTTTGGTATCTCCTTC
1 CTCTTCCTACTCTGGTATC-CCTTC
62118 CTCTT-CTAGCTCTGGTATCCCTTC
1 CTCTTCCTA-CTCTGGTATCCCTTC
*
62142 CTGTTCC
1 CTCTTCC
62149 CTCACCGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 2 0.08
24 14 0.54
25 10 0.38
ACGTcount: A:0.05, C:0.38, G:0.11, T:0.45
Consensus pattern (24 bp):
CTCTTCCTACTCTGGTATCCCTTC
Found at i:64201 original size:17 final size:17
Alignment explanation
Indices: 64179--64211 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
64169 CTGAAGGAAA
64179 AAAGAAAGAAAAAAGAG
1 AAAGAAAGAAAAAAGAG
*
64196 AAAGAAAGAAAGAAGA
1 AAAGAAAGAAAAAAGA
64212 AGGAAGAAGG
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAAAGAG
Found at i:64228 original size:9 final size:9
Alignment explanation
Indices: 64206--64242 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
64196 AAAGAAAGAA
64206 AGAAGAA-G
1 AGAAGAAGG
64214 -GAAGAAGG
1 AGAAGAAGG
64222 AGAAGAAGG
1 AGAAGAAGG
*
64231 GGAAGAAGG
1 AGAAGAAGG
64240 AGA
1 AGA
64243 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.24
8 1 0.04
9 18 0.72
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Done.