Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012549.1 Kokia drynarioides strain JFW-HI SEQ_127558, 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: 31081
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:423 original size:28 final size:27
Alignment explanation
Indices: 391--462 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
381 GGACATAATT
391 TTAAAAAAATTTGAAAATAAATTTAAAC
1 TTAAAAAAATTT-AAAATAAATTTAAAC
* * * *
419 TTAAATGAAATTTAAATTTAATTTAAAT
1 TTAAA-AAAATTTAAAATAAATTTAAAC
*
447 TTAAAATAAATCTAAA
1 TTAAAA-AAATTTAAA
463 TTTAAAACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 30 0.83
29 6 0.17
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (27 bp):
TTAAAAAAATTTAAAATAAATTTAAAC
Found at i:441 original size:5 final size:6
Alignment explanation
Indices: 408--468 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
398 AATTTGAAAA
* * *
408 TAAATT TAAACT TAAA-T GAAATT TAAATT T-AATT TAAATT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
453 TAAATC TAAATT TAAA
1 TAAATT TAAATT TAAA
469 ACAAATTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
5 13 0.28
6 33 0.72
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:456 original size:11 final size:11
Alignment explanation
Indices: 385--462 Score: 52
Period size: 11 Copynumber: 7.0 Consensus size: 11
375 GTATTGGGAC
*
385 ATAATTTTAAA
1 ATAAATTTAAA
396 A-AAATTTGAAA
1 ATAAATTT-AAA
407 ATAAATTTAAA
1 ATAAATTTAAA
* *
418 CTTAAA-TGAAA
1 -ATAAATTTAAA
* *
429 TTTAAATTTAAT
1 -ATAAATTTAAA
*
441 TTAAATTTAAA
1 ATAAATTTAAA
*
452 ATAAATCTAAA
1 ATAAATTTAAA
463 TTTAAAACAA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
10 5 0.09
11 36 0.67
12 13 0.24
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (11 bp):
ATAAATTTAAA
Found at i:462 original size:17 final size:17
Alignment explanation
Indices: 408--479 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
398 AATTTGAAAA
*
408 TAAATTTAAACTTAAA-T
1 TAAATTTAAA-ATAAATT
* * *
425 GAAATTTAAATTTAATT
1 TAAATTTAAAATAAATT
*
442 TAAATTTAAAATAAATC
1 TAAATTTAAAATAAATT
*
459 TAAATTTAAAACAAATT
1 TAAATTTAAAATAAATT
476 TAAA
1 TAAA
480 ATAAACTTAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 4 0.09
17 42 0.91
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:463 original size:28 final size:28
Alignment explanation
Indices: 410--484 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
400 TTTGAAAATA
* *
410 AATTTAAACTT-AAATGAAATTTAAATTT
1 AATTTAAATTTAAAAT-AAATCTAAATTT
438 AATTTAAATTTAAAATAAATCTAAATTT
1 AATTTAAATTTAAAATAAATCTAAATTT
***
466 AAAACAAATTTAAAATAAA
1 AATTTAAATTTAAAATAAA
485 CTTAGAAGGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 37 0.90
29 4 0.10
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (28 bp):
AATTTAAATTTAAAATAAATCTAAATTT
Found at i:1279 original size:194 final size:194
Alignment explanation
Indices: 786--1955 Score: 1570
Period size: 194 Copynumber: 6.0 Consensus size: 194
776 GTGTCGTTAT
* * * * * * * ** *
786 TTGGTCTACTTCTTAGTATCTTATCAGGAAGACGACCGCATCGCTTGTTTCAATTTGCTTCTCTA
1 TTGGTATACTTCTTTGTATCTCATCAGGAAGATGATCGCCTCGTTTGTTTCAATCCGCTTCTCTG
* * * * * *
851 TACCTCATCAGGAAGACGAATTTGGTTTACTTCTCAGTATTTCATCAGGAAACTAACCATTTTAT
66 TACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATGTCTCATCAGGAAGCTAACCTTTTTAT
*
916 TGCTTCGACCTGTTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGC
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTG-T----TC--GC
**
981 CCTGAG
189 ATTGAG
* * *
987 TTGGTATACTTCTCTGTATCTCATCGGGAAGAT-AGTCGCCCCGTTTGTTTCAATCCGCTTCTCT
1 TTGGTATACTTCTTTGTATCTCATCAGGAAGATGA-TCGCCTCGTTTGTTTCAATCCGCTTCTCT
* * * * *
1051 GTACCTCATTAGAAAGATGAATTTGGTTCACTTCTCACTGTCTTATCAGGAAGCTAACCTTTTTA
65 GTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATGTCTCATCAGGAAGCTAACCTTTTTA
*
1116 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGATTCGAAGATTTGTTCGCATTGAG
130 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGTTCGCATTGAG
* * * **
1181 TTTGTATACTTCTTTGTATCTCATCAGGAAGATAATTGTCC-CGTTTGTTTCAATATGCTTCTCT
1 TTGGTATACTTCTTTGTATCTCATCAGGAAGATGATCG-CCTCGTTTGTTTCAATCCGCTTCTCT
* * *
1245 GTACCTCATTAGGAATATGAATTTGGTTCACTTCTCAATGTCTCATCAGGAAGCTAACCTTTTTA
65 GTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATGTCTCATCAGGAAGCTAACCTTTTTA
* *
1310 TTGCTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGAATCGAAGATTTGTTCGCATTGAG
130 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGTTCGCATTGAG
* * * *
1375 TTGGTAAACTTCTTTGTATCTCATCAGGAAGGTGACCGCCTCGTTTGTTTCAATTCGCTTCTCTG
1 TTGGTATACTTCTTTGTATCTCATCAGGAAGATGATCGCCTCGTTTGTTTCAATCCGCTTCTCTG
* * *
1440 TACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTGTCTCATCAAGAAGCTAACATTTTTAT
66 TACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATGTCTCATCAGGAAGCTAACCTTTTTAT
* * *
1505 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTCGTATTGAG
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGTTCGCATTGAG
* * ** * *
1569 TTGGTATACTTCTCTGTACCTCATCAGGAAGATGATCGCCTCACTTGTTTCAGTCCGCTTCTTTG
1 TTGGTATACTTCTTTGTATCTCATCAGGAAGATGATCGCCTCGTTTGTTTCAATCCGCTTCTCTG
* *
1634 TACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATGTCTCATCAGGAAGCTAACATTTTTAT
66 TACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATGTCTCATCAGGAAGCTAACCTTTTTAT
* * * * * *
1699 TGCTTCGACTTTCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGTCCGTATTGAG
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGTTCGCATTGAG
* * **
1763 TTGGTATACTTCTTTGTACCTCATCAGGAATATGATCGCCTCACTTGTTTCAATCCGCTTCTCTG
1 TTGGTATACTTCTTTGTATCTCATCAGGAAGATGATCGCCTCGTTTGTTTCAATCCGCTTCTCTG
* * * ** *
1828 TACCTCATCAGGAAGACAAATTTTGTCCACTTCTCAGCGTCTCATCAAGAAGCTAACCTTTTTAT
66 TACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATGTCTCATCAGGAAGCTAACCTTTTTAT
* * *
1893 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGTATTGA
131 TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGTTCGCATTGA
1956 ACCTTGAGTT
Statistics
Matches: 873, Mismatches: 92, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
193 2 0.00
194 708 0.81
195 3 0.00
196 2 0.00
200 2 0.00
201 156 0.18
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (194 bp):
TTGGTATACTTCTTTGTATCTCATCAGGAAGATGATCGCCTCGTTTGTTTCAATCCGCTTCTCTG
TACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAATGTCTCATCAGGAAGCTAACCTTTTTAT
TGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGTTCGCATTGAG
Found at i:5107 original size:58 final size:59
Alignment explanation
Indices: 5059--5430 Score: 472
Period size: 59 Copynumber: 6.3 Consensus size: 59
5049 TTAGACACTT
* **
5059 TAGGGCAAAATGGTAACTTTTT-GTGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTC
1 TAGGGTAAAATGGTAA-TTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
** * * * *
5118 GGGGGTAAAATTGTAATTTTTGGTAAAATTGGGGGTCAAAAATGGAATTTTGGAAAGTTC
1 TAGGGTAAAATGGTAATTTTTGGTGAAA-TCGGGGTTAAAAATGGAATTTTGGAAAGTTC
* * *
5178 GA-GGTAAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC
1 TAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
** **
5236 GGGGGTAAAAAT-GTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTC
1 TAGGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
*
5295 TA-GGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT-
1 TAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
*
5352 TAAGGGTAAAATGGTAATTTTTGGTGAAATCGGGG-TCAAAATGGAATTTTGGAAAGTT-
1 T-AGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
5410 TAAGGGTAAAAAT-GTAATTTT
1 T-AGGGT-AAAATGGTAATTTT
5431 CAAAAGTTTA
Statistics
Matches: 277, Mismatches: 28, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
57 6 0.02
58 117 0.42
59 121 0.44
60 33 0.12
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (59 bp):
TAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
Found at i:5313 original size:117 final size:116
Alignment explanation
Indices: 5065--5430 Score: 506
Period size: 117 Copynumber: 3.1 Consensus size: 116
5055 ACTTTAGGGC
* *
5065 AAAATGGTAACTTTTTGTGAAATCAAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATT
1 AAAATGGTAA-TTTTTGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAAAT
* * * *
5130 GTAATTTTTGGTAAAATTGGGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGT
65 GTAATTTTTGGTGAAATT-AGGGTTAAAAATGGAATTTTGGAAAGTTCTAGGT
5183 AAAATGGTAATTTTTGATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAAAT
1 AAAATGGTAATTTTTG-TGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAAAT
5248 GTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTCTAGGT
65 GTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTCTAGGT
* * ***
5300 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTTAAGGGT-AAAAT
1 AAAATGGTAATTTTT-GTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAAAT
* * *
5364 GGTAATTTTTGGTGAAA-TCGGGGTCAAAATGGAATTTTGGAAAGTT-TAAGGGT
65 -GTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTCT-A-GGT
5417 AAAAAT-GTAATTTT
1 -AAAATGGTAATTTT
5431 CAAAAGTTTA
Statistics
Matches: 228, Mismatches: 14, Indels: 13
0.89 0.05 0.05
Matches are distributed among these distances:
115 1 0.00
116 32 0.14
117 116 0.51
118 79 0.35
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (116 bp):
AAAATGGTAATTTTTGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAAATG
TAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTCTAGGT
Found at i:6522 original size:3 final size:3
Alignment explanation
Indices: 6510--6596 Score: 68
Period size: 3 Copynumber: 28.0 Consensus size: 3
6500 CTTTTTTTTG
*
6510 TTA TTAA TTA TTA TTAA ATA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TT-A TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
6558 TTA -AA TTCA TTA TTA CTG TTA TTA ATA ATA TTA TCA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6597 ATAATATTTA
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
2 1 0.01
3 56 0.84
4 10 0.15
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:6569 original size:21 final size:20
Alignment explanation
Indices: 6510--6596 Score: 76
Period size: 21 Copynumber: 4.5 Consensus size: 20
6500 CTTTTTTTTG
6510 TTATTAATTATTATTAAA-TA
1 TTATT-ATTATTATTAAATTA
6530 -T-TTATTATTATT--ATTA
1 TTATTATTATTATTAAATTA
6546 TTATTATTATTATTAAATTCA
1 TTATTATTATTATTAAATT-A
* * *
6567 TTATTACTGTTATTAATAATA
1 TTATTATTATTATTAA-ATTA
*
6588 TTATCATTA
1 TTATTATTA
6597 ATAATATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 10 0.19
18 13 0.24
19 1 0.02
20 3 0.06
21 22 0.41
22 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (20 bp):
TTATTATTATTATTAAATTA
Found at i:6598 original size:12 final size:12
Alignment explanation
Indices: 6516--6609 Score: 77
Period size: 12 Copynumber: 7.8 Consensus size: 12
6506 TTTGTTATTA
6516 ATTATTATTAA-
1 ATTATTATTAAT
*
6527 A-TATTTATTATT
1 ATTA-TTATTAAT
*
6539 ATTATTATTATT
1 ATTATTATTAAT
6551 ATTATTATTAA-
1 ATTATTATTAAT
*
6562 ATTCATTATTACT
1 ATT-ATTATTAAT
* *
6575 GTTATTAATAAT
1 ATTATTATTAAT
*
6587 ATTATCATTAAT
1 ATTATTATTAAT
*
6599 AATATTTATTA
1 ATTA-TTATTA
6610 GGTTATAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
10 2 0.03
11 10 0.15
12 45 0.68
13 9 0.14
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (12 bp):
ATTATTATTAAT
Found at i:11960 original size:14 final size:14
Alignment explanation
Indices: 11937--11966 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11927 AAATAATGGG
11937 ATTAAATAAAAAAA
1 ATTAAATAAAAAAA
*
11951 ATTAATTAAAAAAA
1 ATTAAATAAAAAAA
11965 AT
1 AT
11967 ATGAAAGGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATTAAATAAAAAAA
Found at i:13438 original size:14 final size:14
Alignment explanation
Indices: 13419--13445 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13409 AAATTCTTAT
13419 TTATTTTTTGGTTA
1 TTATTTTTTGGTTA
13433 TTATTTTTTGGTT
1 TTATTTTTTGGTT
13446 TGGTTTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.00, G:0.15, T:0.74
Consensus pattern (14 bp):
TTATTTTTTGGTTA
Found at i:13792 original size:47 final size:47
Alignment explanation
Indices: 13721--13813 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
13711 GAAATGACAG
*
13721 TTTATCTACAAAAGTGGTGACTTGTCCACAATATTATTAAGTGGCAA
1 TTTATCTACAAAAGTGGTGACTTGTCCACAACATTATTAAGTGGCAA
* *
13768 TTTATCTATAAAAGTGGTTG-CTTGTCCATAACATTATTAAGTGGCA
1 TTTATCTACAAAAGTGG-TGACTTGTCCACAACATTATTAAGTGGCA
13814 GCTTATCTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
47 40 0.95
48 2 0.05
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (47 bp):
TTTATCTACAAAAGTGGTGACTTGTCCACAACATTATTAAGTGGCAA
Found at i:14960 original size:14 final size:14
Alignment explanation
Indices: 14941--14971 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
14931 AAATATCCGG
*
14941 TTTACTAACCCGAT
1 TTTACTAACCCAAT
14955 TTTACTAACCCAAT
1 TTTACTAACCCAAT
14969 TTT
1 TTT
14972 GGGATGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.42
Consensus pattern (14 bp):
TTTACTAACCCAAT
Found at i:18629 original size:26 final size:25
Alignment explanation
Indices: 18598--18647 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
18588 TATAAAACAC
18598 TTAAATAAAACATCAAAATCCCAAAT
1 TTAAAT-AAACATCAAAATCCCAAAT
* *
18624 TTAAATTAACATCATAATCCCAAA
1 TTAAATAAACATCAAAATCCCAAA
18648 ATAATCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (25 bp):
TTAAATAAACATCAAAATCCCAAAT
Found at i:19054 original size:254 final size:254
Alignment explanation
Indices: 18605--19114 Score: 1020
Period size: 254 Copynumber: 2.0 Consensus size: 254
18595 CACTTAAATA
18605 AAACATCAAAATCCCAAATTTAAATTAACATCATAATCCCAAAATAATCTTGAAAAATCTAAAAT
1 AAACATCAAAATCCCAAATTTAAATTAACATCATAATCCCAAAATAATCTTGAAAAATCTAAAAT
18670 AACTCATATTGAATGATAAAAAAAACGATTAAAATTAAGAGATCCTCCGAGTACTAAGTTGTTTA
66 AACTCATATTGAATGATAAAAAAAACGATTAAAATTAAGAGATCCTCCGAGTACTAAGTTGTTTA
18735 TGTCCAATGTATCTATAAGAGAAACTAAAGCGGGATGAGCTAAAGCCCAATGTGTCTCTAAAGTG
131 TGTCCAATGTATCTATAAGAGAAACTAAAGCGGGATGAGCTAAAGCCCAATGTGTCTCTAAAGTG
18800 CATACATCCACAAACACAATATCACAGTAATTTTCACAAAATATTTAAACGAAGTATAC
196 CATACATCCACAAACACAATATCACAGTAATTTTCACAAAATATTTAAACGAAGTATAC
18859 AAACATCAAAATCCCAAATTTAAATTAACATCATAATCCCAAAATAATCTTGAAAAATCTAAAAT
1 AAACATCAAAATCCCAAATTTAAATTAACATCATAATCCCAAAATAATCTTGAAAAATCTAAAAT
18924 AACTCATATTGAATGATAAAAAAAACGATTAAAATTAAGAGATCCTCCGAGTACTAAGTTGTTTA
66 AACTCATATTGAATGATAAAAAAAACGATTAAAATTAAGAGATCCTCCGAGTACTAAGTTGTTTA
18989 TGTCCAATGTATCTATAAGAGAAACTAAAGCGGGATGAGCTAAAGCCCAATGTGTCTCTAAAGTG
131 TGTCCAATGTATCTATAAGAGAAACTAAAGCGGGATGAGCTAAAGCCCAATGTGTCTCTAAAGTG
19054 CATACATCCACAAACACAATATCACAGTAATTTTCACAAAATATTTAAACGAAGTATAC
196 CATACATCCACAAACACAATATCACAGTAATTTTCACAAAATATTTAAACGAAGTATAC
19113 AA
1 AA
19115 CATATCACAA
Statistics
Matches: 256, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
254 256 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.26
Consensus pattern (254 bp):
AAACATCAAAATCCCAAATTTAAATTAACATCATAATCCCAAAATAATCTTGAAAAATCTAAAAT
AACTCATATTGAATGATAAAAAAAACGATTAAAATTAAGAGATCCTCCGAGTACTAAGTTGTTTA
TGTCCAATGTATCTATAAGAGAAACTAAAGCGGGATGAGCTAAAGCCCAATGTGTCTCTAAAGTG
CATACATCCACAAACACAATATCACAGTAATTTTCACAAAATATTTAAACGAAGTATAC
Found at i:21405 original size:2 final size:2
Alignment explanation
Indices: 21398--21429 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21388 NNNNNNNNNN
21398 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
21430 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:21558 original size:26 final size:25
Alignment explanation
Indices: 21527--21576 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21517 TATCAAACAC
21527 TTAAATAAAACATAAAAATCCCAAAT
1 TTAAAT-AAACATAAAAATCCCAAAT
* * *
21553 TTAAATTAACATTATAATCCCAAA
1 TTAAATAAACATAAAAATCCCAAA
21577 ATAATATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (25 bp):
TTAAATAAACATAAAAATCCCAAAT
Found at i:23313 original size:49 final size:50
Alignment explanation
Indices: 23190--23368 Score: 279
Period size: 51 Copynumber: 3.6 Consensus size: 50
23180 ATAAGCGAAG
* *
23190 GGTCCGATGACTAAGTGTCATCTTGAGAAAATGAATCCTTTATGGACTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGA-TAAA
* * *
23241 GGTCCAATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGG-TAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATAAA
*
23290 GGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGA-TAAA
23341 GGTCCGATGACTAAGTGTCATCGTGAGT
1 GGTCCGATGACTAAGTGTCATCGTGAGT
23369 TTATGGATTC
Statistics
Matches: 116, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
49 45 0.39
51 71 0.61
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (50 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATAAA
Found at i:25212 original size:14 final size:15
Alignment explanation
Indices: 25180--25214 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
25170 GGTGACAGAC
*
25180 TTGGGTCTCACGAGT
1 TTGGGTCACACGAGT
25195 TTGGGTCACACG-GT
1 TTGGGTCACACGAGT
25209 TTGGGT
1 TTGGGT
25215 ATTGGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.11, C:0.17, G:0.37, T:0.34
Consensus pattern (15 bp):
TTGGGTCACACGAGT
Found at i:27406 original size:2 final size:2
Alignment explanation
Indices: 27393--27427 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
27383 TAAACCATAA
*
27393 AC AC AC AG AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
27428 TATAATTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.46, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:27548 original size:26 final size:25
Alignment explanation
Indices: 27517--27566 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
27507 TAGCAAACAC
27517 TTAAATAAAACATCAAAATCCCAAAT
1 TTAAAT-AAACATCAAAATCCCAAAT
* *
27543 TTAAATTAACATCATAATCCCAAA
1 TTAAATAAACATCAAAATCCCAAA
27567 ATAATATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (25 bp):
TTAAATAAACATCAAAATCCCAAAT
Done.