Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015335.1 Kokia drynarioides strain JFW-HI SEQ_130382, 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: 733037
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 878 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:464345 original size:20 final size:20
Alignment explanation
Indices: 464320--464357 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
464310 ACTACGTTGT
464320 CTATTAGATTATTATTTTGC
1 CTATTAGATTATTATTTTGC
464340 CTATTAGATTATTATTTT
1 CTATTAGATTATTATTTT
464358 TGACACTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.58
Consensus pattern (20 bp):
CTATTAGATTATTATTTTGC
Found at i:464367 original size:20 final size:20
Alignment explanation
Indices: 464324--464367 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
464314 CGTTGTCTAT
* *
464324 TAGATTATTATTTTGCCTAT
1 TAGATTATTATTTTGACTAC
464344 TAGATTATTATTTTTGAC-AC
1 TAGATTATTA-TTTTGACTAC
464364 TAGA
1 TAGA
464368 GACTCATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (20 bp):
TAGATTATTATTTTGACTAC
Found at i:479621 original size:58 final size:58
Alignment explanation
Indices: 479544--479670 Score: 141
Period size: 58 Copynumber: 2.2 Consensus size: 58
479534 TTGAATCTTA
* * * * *
479544 AAAAAAACTTAGGTGTCAAATTAGGAAAAAA-TACCAAGTTCAGGTA-TCAGATTGGGTC
1 AAAAAAATTTAGGTATCAAAATA-AAAAAAAGTACCAAGTTCAGGTACT-AAATTGGGTC
* ***
479602 AAAAAAGTTTAGGTATCAAAATAAAAAAAAGTGTTAAGTTCAGGTACTAAATTGGGTC
1 AAAAAAATTTAGGTATCAAAATAAAAAAAAGTACCAAGTTCAGGTACTAAATTGGGTC
479660 AAAAAAATTTA
1 AAAAAAATTTA
479671 AATACTAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
57 6 0.11
58 50 0.88
59 1 0.02
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (58 bp):
AAAAAAATTTAGGTATCAAAATAAAAAAAAGTACCAAGTTCAGGTACTAAATTGGGTC
Found at i:487874 original size:30 final size:30
Alignment explanation
Indices: 487840--487904 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
487830 TTAGTAAAAG
* *
487840 TAAAATTGT-ATTTTAGCTTCTTAAAAATAA
1 TAAAATTGTGATTTAAACTT-TTAAAAATAA
* *
487870 TAAAATTTTGATTTAAACTTTTAAAAATTA
1 TAAAATTGTGATTTAAACTTTTAAAAATAA
487900 TAAAA
1 TAAAA
487905 ATATAAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (30 bp):
TAAAATTGTGATTTAAACTTTTAAAAATAA
Found at i:501547 original size:39 final size:40
Alignment explanation
Indices: 501468--501547 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 40
501458 AACCATAAAC
* *
501468 AGTCTAAGCTTCAATTGCAATATTCTCCATACACATTATG
1 AGTCTAAGCTTCAAGTGCAATATTCTCCATACACAATATG
* *
501508 AGTCTGAA-CTTCAAGTGCAA-ATTCTCTATACAGAATATG
1 AGTCT-AAGCTTCAAGTGCAATATTCTCCATACACAATATG
501547 A
1 A
501548 AAGCATATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 17 0.49
40 16 0.46
41 2 0.06
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (40 bp):
AGTCTAAGCTTCAAGTGCAATATTCTCCATACACAATATG
Found at i:520893 original size:15 final size:14
Alignment explanation
Indices: 520870--520912 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
520860 GGGTTTATTA
520870 TTTTTAATATATAT
1 TTTTTAATATATAT
520884 TTTTTGAATAT-TATT
1 TTTTT-AATATATA-T
520899 GTTTTTAATATATA
1 -TTTTTAATATATA
520913 ATTATTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.28
15 11 0.44
16 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (14 bp):
TTTTTAATATATAT
Found at i:524117 original size:151 final size:153
Alignment explanation
Indices: 523833--524136 Score: 531
Period size: 151 Copynumber: 2.0 Consensus size: 153
523823 ATGGTTTGTA
* *
523833 GAATCGTATTGATTTTGAAAATTTAAAGCTTGAAAATATTGAATATTTTTTAATTTGAAACAAAA
1 GAATCGTATTGAATTTGAAAATTTAAAGCTTGAAAATATCGAATATTTTTTAATTTGAAACAAAA
523898 AAAATTACGTTATTTTAGATTTTTATTTTTTTAATAATTAAGGTTTTTTAAGGGCATATAGATAA
66 AAAATTACGTTATTTTAGATTTTTATTTTTTTAATAATTAAGGTTTTTTAAGGGCATATAGATAA
523963 TTTTAGCTTTTAATGTTTATAGT
131 TTTTAGCTTTTAATGTTTATAGT
* *
523986 GAATCGTATTGAATTTGAAATTTTAAAGCTTGAAAATGTCGAATATTTTTTAATTTGAAAC-AAA
1 GAATCGTATTGAATTTGAAAATTTAAAGCTTGAAAATATCGAATATTTTTTAATTTGAAACAAAA
** *
524050 AAGGTT-CGTTATTTTAGATTTTTATTTTTTTAATAATTAAGGTTTTTTAAGGGCATATAGGTAA
66 AAAATTACGTTATTTTAGATTTTTATTTTTTTAATAATTAAGGTTTTTTAAGGGCATATAGATAA
524114 TTTTAGCTTTTAATGTTTATAGT
131 TTTTAGCTTTTAATGTTTATAGT
524137 TTTTATCAAT
Statistics
Matches: 144, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
151 80 0.56
152 7 0.05
153 57 0.40
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (153 bp):
GAATCGTATTGAATTTGAAAATTTAAAGCTTGAAAATATCGAATATTTTTTAATTTGAAACAAAA
AAAATTACGTTATTTTAGATTTTTATTTTTTTAATAATTAAGGTTTTTTAAGGGCATATAGATAA
TTTTAGCTTTTAATGTTTATAGT
Found at i:525902 original size:19 final size:20
Alignment explanation
Indices: 525855--525907 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
525845 ATTATGTTAG
* *
525855 AAATTAAAATATAATGATTA
1 AAATTAAAATTTAATGATAA
*
525875 AATTTAAAATTTAA-GATAA
1 AAATTAAAATTTAATGATAA
*
525894 AAATTAAAAATTAA
1 AAATTAAAATTTAA
525908 CCACTTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AAATTAAAATTTAATGATAA
Found at i:532823 original size:20 final size:20
Alignment explanation
Indices: 532798--532835 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
532788 CAGTCTGTGA
532798 TTTTATTA-ATTTTCTACTAC
1 TTTTATTATATTTT-TACTAC
532818 TTTTATTATATTTTTACT
1 TTTTATTATATTTTTACT
532836 TATAACTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATTATATTTTTACTAC
Found at i:547446 original size:15 final size:16
Alignment explanation
Indices: 547426--547455 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
547416 TAATAATTAA
547426 TTAAAAATA-ATATTT
1 TTAAAAATATATATTT
547441 TTAAAAATATATATT
1 TTAAAAATATATATT
547456 AAAAATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAAATATATATTT
Found at i:547465 original size:14 final size:15
Alignment explanation
Indices: 547425--547465 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
547415 TTAATAATTA
*
547425 ATTAAAAATAATATT
1 ATTAAAAATTATATT
*
547440 TTTAAAAA-TATA-T
1 ATTAAAAATTATATT
547453 ATTAAAAATTATA
1 ATTAAAAATTATA
547466 AACCGGTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 8 0.36
14 7 0.32
15 7 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAAAATTATATT
Found at i:553519 original size:31 final size:30
Alignment explanation
Indices: 553475--553613 Score: 110
Period size: 31 Copynumber: 4.6 Consensus size: 30
553465 CACTTAATTT
*
553475 TTTTTGTCC-AATTTAGTACTTAAACTTTAC
1 TTTTT-TCCTAATTTGGTACTTAAACTTTAC
553505 ATTTTTTCCTAATTTGGTACTTAAACTTGATAC
1 -TTTTTTCCTAATTTGGTACTTAAACTT--TAC
* *
553538 TTTTTT-TTAAGTTGGTACTTAAACTTT--
1 TTTTTTCCTAATTTGGTACTTAAACTTTAC
*** *
553565 TTGGGTCC-AATTTGGTA-TCTAAACTTGAC
1 TTTTTTCCTAATTTGGTACT-TAAACTTTAC
*
553594 TCTTTTTCTTAATTTGGTAC
1 T-TTTTTCCTAATTTGGTAC
553614 CTTATGTTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
26 1 0.01
27 18 0.21
29 2 0.02
30 6 0.07
31 49 0.58
32 6 0.07
33 3 0.04
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (30 bp):
TTTTTTCCTAATTTGGTACTTAAACTTTAC
Found at i:553607 original size:89 final size:88
Alignment explanation
Indices: 553428--553613 Score: 223
Period size: 89 Copynumber: 2.1 Consensus size: 88
553418 TTAATATAAT
* * * **
553428 ATTTGGTACATGAACTTGATACTTTTTCTTAATTTGACACTTAATTTTTTTTGTCCAATTTAGTA
1 ATTTGGTACATAAACTTGATACTTTTTCTTAAGTTGACACTTAACTTTTTGGGTCCAATTTAGTA
*
553493 CTTAAACTTTACATTTTTTCCTA
66 CTTAAACTTGACATTTTTTCCTA
* * ** *
553516 ATTTGGTACTTAAACTTGATACTTTTTTTTAAGTTGGTACTTAAACTTTTTGGGTCCAATTTGGT
1 ATTTGGTACATAAACTTGATACTTTTTCTTAAGTTGACACTT-AACTTTTTGGGTCCAATTTAGT
*
553581 A-TCTAAACTTGAC-TCTTTTTCTTA
65 ACT-TAAACTTGACAT-TTTTTCCTA
553605 ATTTGGTAC
1 ATTTGGTAC
553614 CTTATGTTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
88 38 0.46
89 45 0.54
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (88 bp):
ATTTGGTACATAAACTTGATACTTTTTCTTAAGTTGACACTTAACTTTTTGGGTCCAATTTAGTA
CTTAAACTTGACATTTTTTCCTA
Found at i:554526 original size:28 final size:26
Alignment explanation
Indices: 554491--554544 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
554481 AGATTAAAAG
*
554491 GGATCAAAATTTTTTTTAATTTTTAAA
1 GGATCAAAATATTTTTT-ATTTTTAAA
554518 GGATCCAAAATATTTTTTATTTTTAAA
1 GGAT-CAAAATATTTTTTATTTTTAAA
554545 AGCTAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (26 bp):
GGATCAAAATATTTTTTATTTTTAAA
Found at i:554546 original size:28 final size:28
Alignment explanation
Indices: 554484--554546 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
554474 GGGCATAAGA
*
554484 TTAAAAGGGATCAAAATTTTTTTTAATTT
1 TTAAAA-GGATCAAAATATTTTTTAATTT
554513 TT-AAAGGATCCAAAATATTTTTT-ATTT
1 TTAAAAGGAT-CAAAATATTTTTTAATTT
554540 TTAAAAG
1 TTAAAAG
554547 CTAAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 10 0.32
28 19 0.61
29 2 0.06
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.46
Consensus pattern (28 bp):
TTAAAAGGATCAAAATATTTTTTAATTT
Found at i:574197 original size:12 final size:12
Alignment explanation
Indices: 574177--574218 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
574167 TTTTTAAGAT
574177 TTTTAAAAAATA
1 TTTTAAAAAATA
*
574189 TTTTGAAAAAGTGA
1 TTTT-AAAAAAT-A
574203 TTTTAAAAAATA
1 TTTTAAAAAATA
574215 TTTT
1 TTTT
574219 TGAGAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 9 0.35
13 12 0.46
14 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (12 bp):
TTTTAAAAAATA
Found at i:591935 original size:31 final size:31
Alignment explanation
Indices: 591876--591938 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
591866 ATTTCTTTAA
* **
591876 ATGTATACATTTGATTCAAAATTAAAGTTTC
1 ATGTATACATATGAACCAAAATTAAAGTTTC
* *
591907 ATGTATACATATGAACCACAATTCAAGTTTC
1 ATGTATACATATGAACCAAAATTAAAGTTTC
591938 A
1 A
591939 AGTGCATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (31 bp):
ATGTATACATATGAACCAAAATTAAAGTTTC
Found at i:604922 original size:23 final size:22
Alignment explanation
Indices: 604890--605016 Score: 96
Period size: 23 Copynumber: 5.6 Consensus size: 22
604880 GAAACAATAA
*
604890 GCACATACAGTGCAATCCAGTAG
1 GCACACACAGTGCAAT-CAGTAG
604913 GCACACACAGTGCAATCAGTAG
1 GCACACACAGTGCAATCAGTAG
* * *
604935 GCGCACATAGCGCAAATCAGTAG
1 GCACACACAGTGC-AATCAGTAG
* * * *
604958 GCACACGA-GGTGTGAAACAGTAA
1 GCACAC-ACAGTG-CAATCAGTAG
* *
604981 GCACACGA-AGTGCGAAACAGTAA
1 GCACAC-ACAGTGC-AATCAGTAG
605004 GCACACACAGTGC
1 GCACACACAGTGC
605017 TGAACAGTAA
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
22 17 0.20
23 69 0.79
24 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.25, T:0.13
Consensus pattern (22 bp):
GCACACACAGTGCAATCAGTAG
Found at i:605022 original size:23 final size:23
Alignment explanation
Indices: 604952--605027 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
604942 TAGCGCAAAT
* * *
604952 CAGTAGGCACACGAGGTGTGAAA
1 CAGTAAGCACACGAAGTGCGAAA
604975 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
604998 CAGTAAGCACAC-ACAGTGCTG-AA
1 CAGTAAGCACACGA-AGTGC-GAAA
605021 CAGTAAG
1 CAGTAAG
605028 TGCGCTAGCG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
22 1 0.02
23 46 0.96
24 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.28, T:0.12
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:605129 original size:24 final size:26
Alignment explanation
Indices: 605091--605138 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
605081 TCTACATGGG
605091 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
605117 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
605139 AATTTCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:607145 original size:15 final size:16
Alignment explanation
Indices: 607125--607154 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
607115 CAAACTAGTC
607125 TTTTTTTTT-CTTTTT
1 TTTTTTTTTACTTTTT
607140 TTTTTTTTTACTTTT
1 TTTTTTTTTACTTTT
607155 AAGCTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTTTTTACTTTTT
Found at i:614119 original size:2 final size:2
Alignment explanation
Indices: 614069--614100 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
614059 TTGTACTACA
*
614069 AT AT AA 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 AT AT AT
614101 CATCTCCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:617204 original size:6 final size:6
Alignment explanation
Indices: 617193--617219 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
617183 ACCACGCTCT
617193 TTCATC TTCATC TTCATC TTCATC TTC
1 TTCATC TTCATC TTCATC TTCATC TTC
617220 CAGTTTAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCATC
Found at i:635967 original size:21 final size:20
Alignment explanation
Indices: 635941--635982 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
635931 TTATAGATAC
635941 AAAATAAT-ATTTGTTATTATA
1 AAAATAATAATTT-TT-TTATA
635962 AAAATAATAATTTTTTTATA
1 AAAATAATAATTTTTTTATA
635982 A
1 A
635983 TTTATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATAATAATTTTTTTATA
Found at i:642015 original size:11 final size:11
Alignment explanation
Indices: 641994--642024 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
641984 GTACGTTATT
641994 AAATAATTAAAA
1 AAAT-ATTAAAA
642006 AAATATTAAAA
1 AAATATTAAAA
642017 AAATATTA
1 AAATATTA
642025 CTATACAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATATTAAAA
Found at i:645926 original size:14 final size:14
Alignment explanation
Indices: 645903--645950 Score: 69
Period size: 14 Copynumber: 3.3 Consensus size: 14
645893 TAAAATATAA
645903 TTTTATATATTTAT
1 TTTTATATATTTAT
*
645917 TTTTACATATTTAATT
1 TTTTATATATTT-A-T
645933 TTTTATATATTTAT
1 TTTTATATATTTAT
645947 TTTT
1 TTTT
645951 TTTAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 16 0.53
15 2 0.07
16 12 0.40
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATATATTTAT
Found at i:645952 original size:16 final size:15
Alignment explanation
Indices: 645903--645951 Score: 73
Period size: 16 Copynumber: 3.3 Consensus size: 15
645893 TAAAATATAA
645903 TTTTATATATTTA-T
1 TTTTATATATTTATT
*
645917 TTTTACATATTTAATT
1 TTTTATATATTT-ATT
645933 TTTTATATATTTATT
1 TTTTATATATTTATT
645948 TTTT
1 TTTT
645952 TTAAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
14 11 0.35
15 8 0.26
16 12 0.39
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTATATATTTATT
Found at i:646378 original size:18 final size:17
Alignment explanation
Indices: 646355--646388 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
646345 TTCATCTCAA
*
646355 AATATTTTTGTATTTAAT
1 AATATTTATGT-TTTAAT
646373 AATATTTATGTTTTAA
1 AATATTTATGTTTTAA
646389 AAATTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
AATATTTATGTTTTAAT
Found at i:656800 original size:31 final size:30
Alignment explanation
Indices: 656765--656834 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
656755 ATTATAAAAT
* *
656765 AGTCATTAATTTTTTAAAAAAATTTTATTTA
1 AGTCATTAACTATTT-AAAAAATTTTATTTA
* **
656796 AGTCACTGAACTATTTAAAATTTTTTATTTA
1 AGTCA-TTAACTATTTAAAAAATTTTATTTA
656827 AGTCATTA
1 AGTCATTA
656835 GGCTATTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 2 0.06
31 23 0.72
32 7 0.22
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.49
Consensus pattern (30 bp):
AGTCATTAACTATTTAAAAAATTTTATTTA
Found at i:667885 original size:2 final size:2
Alignment explanation
Indices: 667878--667903 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
667868 CTGGTTTTGG
667878 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
667904 GGTGTTTGGA
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):
TA
Found at i:679240 original size:4 final size:4
Alignment explanation
Indices: 679233--679271 Score: 60
Period size: 4 Copynumber: 9.2 Consensus size: 4
679223 GGAAGGAAGG
679233 GTTT GTTT GTTT GTTT GTTT GTTT GTTT GGTTT GGTTT G
1 GTTT GTTT GTTT GTTT GTTT GTTT GTTT -GTTT -GTTT G
679272 GGGTCTCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.74
5 9 0.26
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (4 bp):
GTTT
Found at i:697212 original size:96 final size:96
Alignment explanation
Indices: 697033--697214 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
697023 AATGATGTTT
* *
697033 GATTATCTCGATTCGAAAAAAGGTTGCACCTAGTAAATTAAGGCGCAAATTTTCAGAATCGAAGA
1 GATTATCTCGATTCGAAAAAAGATTGCACCTAGTAAATTAAGGCGCAAATTTTCAAAATCGAAGA
* *
697098 TAAGGAAACATTGTCTCGATTAAGGGTATTC
66 TAAAGAAACATTGCCTCGATTAAGGGTATTC
* * * *
697129 GATTATTTCGATTTGAAGAAAA-ATTGCACCTAGTAAGTTAAGGCGCGAATTTTCAAAACTCGAA
1 GATTATCTCGATTCGAA-AAAAGATTGCACCTAGTAAATTAAGGCGCAAATTTTCAAAA-TCGAA
*
697193 -ATAAA-AGAATATTGCCTCGATT
64 GATAAAGA-AACATTGCCTCGATT
697215 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 1 0.01
96 64 0.86
97 9 0.12
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (96 bp):
GATTATCTCGATTCGAAAAAAGATTGCACCTAGTAAATTAAGGCGCAAATTTTCAAAATCGAAGA
TAAAGAAACATTGCCTCGATTAAGGGTATTC
Found at i:697475 original size:28 final size:28
Alignment explanation
Indices: 697426--697487 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
697416 AAATGAGATT
* *
697426 TTTTGGATACTCAGTGGCAAAATTGTAA
1 TTTTGGATACTCAGGGGCAAAATGGTAA
* * *
697454 TTTTGGATTCTCTGGGGTAAAATGGTAA
1 TTTTGGATACTCAGGGGCAAAATGGTAA
697482 TTTTGG
1 TTTTGG
697488 GAAAATTTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (28 bp):
TTTTGGATACTCAGGGGCAAAATGGTAA
Found at i:697594 original size:29 final size:29
Alignment explanation
Indices: 697560--697759 Score: 177
Period size: 29 Copynumber: 6.8 Consensus size: 29
697550 TTTCGGGATC
* *
697560 AAAAATAGAATTTTTGGAGGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* * * * *
697589 AAAAATGGAATTTTAGAAAGCTTCGAGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
*
697618 CAAAAATGGAATTTTTGGAAGTTTGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGGGGGT
* *
697648 AAAAATGTAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
* ***
697677 CAAAAATGGAATTTTTTGAAGTTCAAGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGGGGGT
** * * * *
697707 AAAAATATAATTTTCGAAAGTTTCGGGAT
1 AAAAATGGAATTTTTGGAAGTTTGGGGGT
697736 CAAAAATGGAA-TTTTGGATAGTTT
1 -AAAAATGGAATTTTTGGA-AGTTT
697760 AAGGACCTCC
Statistics
Matches: 133, Mismatches: 34, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
29 73 0.55
30 60 0.45
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGGGGGT
Found at i:697601 original size:59 final size:59
Alignment explanation
Indices: 697527--697759 Score: 290
Period size: 59 Copynumber: 3.9 Consensus size: 59
697517 GACATCCGAA
** * * *
697527 GGTAAAACGGTAATTTTAGAAAGTTTCGGGATCAAAAATAGAATTTTTGGAGGTTTGGG
1 GGTAAAAATGTAATTTTAGAAAGTTTCGGGATCAAAAATGGAATTTTTGGAAGTTTGAG
* *
697586 GGTAAAAATGGAATTTTAGAAAGCTTCGAGG-TCAAAAATGGAATTTTTGGAAGTTTGAG
1 GGTAAAAATGTAATTTTAGAAAGTTTCG-GGATCAAAAATGGAATTTTTGGAAGTTTGAG
* * * * * **
697645 GGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTTGAAGTTCAAG
1 GGTAAAAATGTAATTTTAGAAAGTTTCGGGATCAAAAATGGAATTTTTGGAAGTTTGAG
* *
697704 GGTAAAAATATAATTTTCGAAAGTTTCGGGATCAAAAATGGAA-TTTTGGATAGTTT
1 GGTAAAAATGTAATTTTAGAAAGTTTCGGGATCAAAAATGGAATTTTTGGA-AGTTT
697760 AAGGACCTCC
Statistics
Matches: 149, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
58 8 0.05
59 139 0.93
60 2 0.01
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.34
Consensus pattern (59 bp):
GGTAAAAATGTAATTTTAGAAAGTTTCGGGATCAAAAATGGAATTTTTGGAAGTTTGAG
Found at i:697625 original size:30 final size:30
Alignment explanation
Indices: 697538--697759 Score: 172
Period size: 30 Copynumber: 7.5 Consensus size: 30
697528 GTAAAACGGT
* *
697538 AATTTTAGAAAGTTTCG-GGATCAAAAATAG
1 AATTTTTGAAAGTTTCGAGG-TCAAAAATGG
* * * *
697568 AATTTTTGGAGGTTTGGGGGT-AAAAATGG
1 AATTTTTGAAAGTTTCGAGGTCAAAAATGG
* *
697597 AATTTTAGAAAGCTTCGAGGTCAAAAATGG
1 AATTTTTGAAAGTTTCGAGGTCAAAAATGG
* *
697627 AATTTTTGGAAGTTT-GAGGGT-AAAAATGT
1 AATTTTTGAAAGTTTCGA-GGTCAAAAATGG
* * *
697656 AATTTTTGGAAGTTTTGGGGTCAAAAATGG
1 AATTTTTGAAAGTTTCGAGGTCAAAAATGG
* **
697686 AATTTTTTG-AAG-TTCAAGGGT-AAAAATAT
1 AA-TTTTTGAAAGTTTCGA-GGTCAAAAATGG
*
697715 AATTTTCGAAAGTTTCG-GGATCAAAAATGG
1 AATTTTTGAAAGTTTCGAGG-TCAAAAATGG
* *
697745 AATTTTGGATAGTTT
1 AATTTTTGAAAGTTT
697760 AAGGACCTCC
Statistics
Matches: 153, Mismatches: 28, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
28 7 0.05
29 63 0.41
30 75 0.49
31 8 0.05
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
AATTTTTGAAAGTTTCGAGGTCAAAAATGG
Found at i:704774 original size:1 final size:1
Alignment explanation
Indices: 704768--704796 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
704758 NNNNNNNNNN
704768 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
704797 GTATCTTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:705135 original size:79 final size:78
Alignment explanation
Indices: 704982--705133 Score: 227
Period size: 77 Copynumber: 1.9 Consensus size: 78
704972 ATAATATATG
** * *
704982 TATTTTTTATATATAGTATGTATATATATATATATTTGCCATATACCTGCTGTTTCTTTAAATTG
1 TATTTTTTATATATAGTATG-ATATATATATATATTTGCCATATACCCACAGTTTCCTTAAATTG
705047 TATATATATAGTTT
65 TATATATATAGTTT
705061 TATTCTTTT-TATATAGTATG-TATATATATATATTTGCCATATACCCACAGTTTCCTTAAATTG
1 TATT-TTTTATATATAGTATGATATATATATATATTTGCCATATACCCACAGTTTCCTTAAATTG
*
705124 TATGTATATA
65 TATATATATA
705134 TACAACTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
77 48 0.72
79 15 0.22
80 4 0.06
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.51
Consensus pattern (78 bp):
TATTTTTTATATATAGTATGATATATATATATATTTGCCATATACCCACAGTTTCCTTAAATTGT
ATATATATAGTTT
Found at i:728092 original size:21 final size:21
Alignment explanation
Indices: 728068--728108 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
728058 AATATTTTAG
*
728068 TATTTATTTATAATTAAATAT
1 TATTTAGTTATAATTAAATAT
**
728089 TATTTAGTTATGTTTAAATA
1 TATTTAGTTATAATTAAATA
728109 AAATCAATAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
TATTTAGTTATAATTAAATAT
Found at i:728408 original size:25 final size:25
Alignment explanation
Indices: 728326--728414 Score: 72
Period size: 25 Copynumber: 3.4 Consensus size: 25
728316 AAAATATTAC
*
728326 TATAGTTATATTAGAATTGATTTAT
1 TATAATTATATTAGAATTGATTTAT
* * * *
728351 GT-TAATTTGTATATAAAATAAGAATATTTT
1 -TATAA-TTATAT-TAGAAT-TG-AT-TTAT
728381 TATAATTATATTAGAATTGATTTAT
1 TATAATTATATTAGAATTGATTTAT
728406 TATAATTAT
1 TATAATTAT
728415 TATAATATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 13
0.69 0.13 0.19
Matches are distributed among these distances:
25 14 0.29
26 8 0.17
27 6 0.12
28 6 0.12
29 8 0.17
30 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (25 bp):
TATAATTATATTAGAATTGATTTAT
Done.