Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011892.1 Kokia drynarioides strain JFW-HI SEQ_126889, 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: 90219
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:610 original size:25 final size:28
Alignment explanation
Indices: 559--628 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 28
549 TAGTCATATG
*
559 ATTATTTTTATTTATTATAAATACTATT-
1 ATTATTATTATTTATTAT-AATACTATTA
*
587 ATTATTATTATTTATT-T-ATGCTATTA
1 ATTATTATTATTTATTATAATACTATTA
*
613 ATT-GTATTATTTATTA
1 ATTATTATTATTTATTA
629 GTGTTATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
25 18 0.49
26 3 0.08
27 1 0.03
28 15 0.41
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (28 bp):
ATTATTATTATTTATTATAATACTATTA
Found at i:636 original size:25 final size:25
Alignment explanation
Indices: 592--640 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
582 CTATTATTAT
592 TATTATTTATTTATGCTATTAATTG
1 TATTATTTATTTATGCTATTAATTG
*
617 TATTATTTA-TTAGTGTTATTAATT
1 TATTATTTATTTA-TGCTATTAATT
641 TCATTTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (25 bp):
TATTATTTATTTATGCTATTAATTG
Found at i:1753 original size:46 final size:46
Alignment explanation
Indices: 1686--1774 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
1676 ATATGTGTGA
1686 TTAAAGTGTTGGAATCAATAGGACCTTCAACAAACAAAGATAATGG
1 TTAAAGTGTTGGAATCAATAGGACCTTCAACAAACAAAGATAATGG
*
1732 TTAAAGTGTTGGAATCAATAGGACTTTCAACAAACAAAGATAA
1 TTAAAGTGTTGGAATCAATAGGACCTTCAACAAACAAAGATAA
1775 AGGCAAAGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (46 bp):
TTAAAGTGTTGGAATCAATAGGACCTTCAACAAACAAAGATAATGG
Found at i:1970 original size:23 final size:23
Alignment explanation
Indices: 1934--2288 Score: 494
Period size: 23 Copynumber: 15.4 Consensus size: 23
1924 TTCTTATATC
1934 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
1957 TGTGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
1980 TATGCTTAGATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
2003 TATGCTTAAATATTAATATAATT
1 TATGCTTAAATATTAATGTGATT
* *
2026 TTTGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
2049 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
2072 TGTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
2095 TATGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
2118 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
2141 TATGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
2164 TGTGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
2187 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
2210 TGTGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
2233 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
2256 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
2279 TGTTCTTAAA
1 TATGCTTAAA
2289 GAATTAAAAT
Statistics
Matches: 294, Mismatches: 38, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 294 1.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:2045 original size:69 final size:69
Alignment explanation
Indices: 1934--2288 Score: 548
Period size: 69 Copynumber: 5.1 Consensus size: 69
1924 TTCTTATATC
*
1934 TATGCTTAAATATTAATGTGATTTGTGCTTAAGTATTAATGTGATTTATGCTTAGATATTAATAT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAGTATTAATGTGATTTATGCTTAAATATTAATAT
1999 GATT
66 GATT
* * *
2003 TATGCTTAAATATTAATATAATTTTTGCTTAAGTATTAATGTGATTTATGCTTAAATATTAATAT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAGTATTAATGTGATTTATGCTTAAATATTAATAT
2068 GATT
66 GATT
* * * * *
2072 TGTGCTCAAATATTAATGTGATTTATGCTCAAATATTAATGTGATTTATGCTTAAATATTAATAT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAGTATTAATGTGATTTATGCTTAAATATTAATAT
2137 GATT
66 GATT
*
2141 TATGCTTAAGTATTAATGTGATTTGTGCTTAAGTATTAATGTGATTTATGCTTAAATATTAATAT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAGTATTAATGTGATTTATGCTTAAATATTAATAT
2206 GATT
66 GATT
* * * * * *
2210 TGTGCTTAAGTATTAATGTGATTTGTGCTTAAATATTAATATGATTTATGATTAAATATTAATGT
1 TATGCTTAAATATTAATGTGATTTGTGCTTAAGTATTAATGTGATTTATGCTTAAATATTAATAT
2275 GATT
66 GATT
* *
2279 TGTTCTTAAA
1 TATGCTTAAA
2289 GAATTAAAAT
Statistics
Matches: 262, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 262 1.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (69 bp):
TATGCTTAAATATTAATGTGATTTGTGCTTAAGTATTAATGTGATTTATGCTTAAATATTAATAT
GATT
Found at i:4730 original size:15 final size:15
Alignment explanation
Indices: 4710--4740 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4700 ATTACATAAT
4710 ATATAAAATAATATA
1 ATATAAAATAATATA
*
4725 ATATAAAATATTATA
1 ATATAAAATAATATA
4740 A
1 A
4741 ACTTAAAAAT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAAAATAATATA
Found at i:6537 original size:66 final size:66
Alignment explanation
Indices: 6426--6554 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 66
6416 AGTTGAACCA
*
6426 AAACTGCTAGAAGGAAATGCCGTTGCGCTCGGTTTTGAAGCATTCTGAAAATCCCCAAATGCACT
1 AAACCGCTAGAAGGAAATGCCGTTGCGCTCGGTTTTGAAGCATTCTGAAAATCCCCAAATGCACT
6491 G
66 G
*
6492 AAACCGCTAGAAGGAAATGCAC-TTGTGCTCGGTTTTGAAGCATTCTGAAAATCCCCAAATGCA
1 AAACCGCTAGAAGGAAATGC-CGTTGCGCTCGGTTTTGAAGCATTCTGAAAATCCCCAAATGCA
6555 TCATTTGCAG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 59 0.98
67 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (66 bp):
AAACCGCTAGAAGGAAATGCCGTTGCGCTCGGTTTTGAAGCATTCTGAAAATCCCCAAATGCACT
G
Found at i:7771 original size:40 final size:40
Alignment explanation
Indices: 7727--7814 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
7717 TTAAAGAATA
* * * *
7727 AATATATTATCGTTTTTTAGGTTAAAACAAGGTACACATG
1 AATATATTATCATCTCTTAAGTTAAAACAAGGTACACATG
**
7767 AATATATTATCATCTCTTAAGTTAAAATGAGGTACACATG
1 AATATATTATCATCTCTTAAGTTAAAACAAGGTACACATG
7807 -ATATATTA
1 AATATATTA
7815 CATGTAACTG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 8 0.19
40 34 0.81
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (40 bp):
AATATATTATCATCTCTTAAGTTAAAACAAGGTACACATG
Found at i:19002 original size:20 final size:22
Alignment explanation
Indices: 18967--19006 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
18957 CAACTAATTA
18967 TTTTAAAATTATTAAAATTATT
1 TTTTAAAATTATTAAAATTATT
18989 TTTTAAAA-TA-TAAAATTA
1 TTTTAAAATTATTAAAATTA
19007 ATATATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAAATTATTAAAATTATT
Found at i:28450 original size:13 final size:12
Alignment explanation
Indices: 28425--28463 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28415 AAATATATTT
28425 TATAATAATAAA
1 TATAATAATAAA
*
28437 TATCATATATAAA
1 TATAATA-ATAAA
*
28450 TTTAATAATAAA
1 TATAATAATAAA
28462 TA
1 TA
28464 AGGTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TATAATAATAAA
Found at i:33633 original size:22 final size:22
Alignment explanation
Indices: 33608--33670 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
33598 GGGTGTTACA
*
33608 AGACACCGAAGTGCAAATCAGT
1 AGACACCGAAGTGCAAATCAAT
* * * *
33630 AGACACTGAAGTGTAGAGCAAT
1 AGACACCGAAGTGCAAATCAAT
*
33652 AGGCACCGAAGTGCAAATC
1 AGACACCGAAGTGCAAATC
33671 CTATACAAGC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.25, T:0.14
Consensus pattern (22 bp):
AGACACCGAAGTGCAAATCAAT
Found at i:37792 original size:16 final size:16
Alignment explanation
Indices: 37749--37804 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
37739 ATTGAACCAT
37749 AAATTTATAAAATTTA
1 AAATTTATAAAATTTA
* *
37765 ACCA-TTACAAAATTTA
1 A-AATTTATAAAATTTA
*
37781 AAATTTATAAAATTAA
1 AAATTTATAAAATTTA
*
37797 AAAATTAT
1 AAATTTAT
37805 TAAGCAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTTATAAAATTTA
Found at i:39223 original size:12 final size:12
Alignment explanation
Indices: 39206--39246 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
39196 GGCCAAACTA
39206 AAACTAAAAAAT
1 AAACTAAAAAAT
**
39218 AAACT-AACTA-
1 AAACTAAAAAAT
39228 AAACTAAAAAAT
1 AAACTAAAAAAT
39240 AAACTAA
1 AAACTAA
39247 GTCCTAAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.22
11 6 0.26
12 12 0.52
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (12 bp):
AAACTAAAAAAT
Found at i:39229 original size:22 final size:22
Alignment explanation
Indices: 39201--39246 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
39191 GATTGGGCCA
39201 AACTAAAACTAAAAAATAAACT
1 AACTAAAACTAAAAAATAAACT
39223 AACTAAAACTAAAAAATAAACT
1 AACTAAAACTAAAAAATAAACT
39245 AA
1 AA
39247 GTCCTAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (22 bp):
AACTAAAACTAAAAAATAAACT
Found at i:40131 original size:18 final size:19
Alignment explanation
Indices: 40095--40133 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
40085 TGTAAAGAAA
40095 TATCGATACCATCAATAAAT
1 TATCGATACCA-CAATAAAT
40115 TATCGATACCA-AATAAAT
1 TATCGATACCACAATAAAT
40133 T
1 T
40134 CCTTAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.31
Consensus pattern (19 bp):
TATCGATACCACAATAAAT
Found at i:47771 original size:3 final size:3
Alignment explanation
Indices: 47733--47785 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
47723 TAGGTTATTT
* *
47733 TTC TTC TTTC TT- TTC TTTC TT- TCC TTC TTT TTC TTC TTC TTC TTC
1 TTC TTC -TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
47778 TTC TTC TT
1 TTC TTC TT
47786 GATCCTTGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 3 0.07
3 33 0.79
4 6 0.14
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:50902 original size:18 final size:18
Alignment explanation
Indices: 50876--50924 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
50866 ACTTGATCTT
50876 CTTGTATCTGAATATGTA
1 CTTGTATCTGAATATGTA
*
50894 CTTGCATCTGAATATGTA
1 CTTGTATCTGAATATGTA
50912 CTTGTATCTGAAT
1 CTTGTATCTGAAT
50925 TTGGTTCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (18 bp):
CTTGTATCTGAATATGTA
Found at i:52734 original size:2 final size:2
Alignment explanation
Indices: 52727--52757 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
52717 ATTTAATTTG
52727 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
52758 TTTAGATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62047 original size:29 final size:29
Alignment explanation
Indices: 61998--62067 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
61988 AACTAATTTT
*
61998 TTATTTTTAAAAATTCAAAAATTATAAAGA
1 TTATTTTTTAAAATTCAAAAATTATAAA-A
62028 TTATTTTTTAAAATT-AAAAATTATAAAA
1 TTATTTTTTAAAATTCAAAAATTATAAAA
62056 TTATATTTTTAA
1 TTAT-TTTTTAA
62068 TATTTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 5 0.13
29 19 0.50
30 14 0.37
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
TTATTTTTTAAAATTCAAAAATTATAAAA
Found at i:69402 original size:18 final size:18
Alignment explanation
Indices: 69375--69418 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
69365 CAGATATGAA
69375 GGAAAAGAAGAAAGAGAT
1 GGAAAAGAAGAAAGAGAT
* **
69393 GGAAAGGAAGCGAGAGAT
1 GGAAAAGAAGAAAGAGAT
69411 GAGAAAAG
1 G-GAAAAG
69419 CACGACTGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.39, T:0.05
Consensus pattern (18 bp):
GGAAAAGAAGAAAGAGAT
Found at i:74501 original size:147 final size:146
Alignment explanation
Indices: 74100--74547 Score: 522
Period size: 147 Copynumber: 3.1 Consensus size: 146
74090 CATGAAACAC
*
74100 GAAGGGAAAGATCTAAGCCGCAACAGCGGATCCAGTACCACAAAGACACAAAGGAAAAGGTTTAA
1 GAAGGGAAAGATCTAAGCCGCAACAGCGGATCCAGTACCACAAAGACACAAAGGGAAAGGTTTAA
* * * * * * * *
74165 GTCGTAATAGCGAACCTAGTACCTCAGAAGCATGAAGGGAAAGATTTAGGCCACGACGGTGAATC
66 GTCGCAAGA-CGAACCTAGTACCTCAGAAGCATGAAGGGAAAGATCTAAGCCGCAACGGCGGATC
* *
74230 CAATACCACAAAGACAT
130 CAGTACCGCAAAGACAT
** ** * *
74247 GAAGGGAAAGATCTAAGCCATAATGGCGGATCTAGTACCACAAAGACA-TAAGGGAAAGGTTTAA
1 GAAGGGAAAGATCTAAGCCGCAACAGCGGATCCAGTACCACAAAGACACAAAGGGAAAGGTTTAA
* *
74311 GTCGCAATGGCGAACCTAGTACCTTAGAAGCATGAAGGGAAAGATCTAAGCCGCAACGGCGGATC
66 GTCGCAA-GACGAACCTAGTACCTCAGAAGCATGAAGGGAAAGATCTAAGCCGCAACGGCGGATC
*
74376 CAGTATCGCAAAGACAT
130 CAGTACCGCAAAGACAT
* * *** ** * * *
74393 GAAGGGAAAGATTTAAGCTGCAACAGAAAATCCAGTACCATGAAGACACGAGGGGAAGGGTTTAA
1 GAAGGGAAAGATCTAAGCCGCAACAGCGGATCCAGTACCACAAAGACACAAAGGGAAAGGTTTAA
* * *
74458 GTCGCAACGACGAACCTTGTACCTCAG-AGACATGAAGGGAAAGATCTAAGTCGCAATGGCGGAT
66 GTCGCAA-GACGAACCTAGTACCTCAGAAG-CATGAAGGGAAAGATCTAAGCCGCAACGGCGGAT
* *
74522 CTAGTACCGCAAAGACAC
129 CCAGTACCGCAAAGACAT
*
74540 AAAGGGAA
1 GAAGGGAA
74548 GGGTTTAAGT
Statistics
Matches: 253, Mismatches: 45, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
146 120 0.47
147 133 0.53
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (146 bp):
GAAGGGAAAGATCTAAGCCGCAACAGCGGATCCAGTACCACAAAGACACAAAGGGAAAGGTTTAA
GTCGCAAGACGAACCTAGTACCTCAGAAGCATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCC
AGTACCGCAAAGACAT
Found at i:74557 original size:49 final size:49
Alignment explanation
Indices: 74100--74557 Score: 312
Period size: 49 Copynumber: 9.4 Consensus size: 49
74090 CATGAAACAC
* * * * * *
74100 GAAGGGAAAGATCTAAGCCGCAACAGCGGATCCAGTACCACAAAGACAC
1 GAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACAAAGACAT
* * * * ** * *
74149 AAAGGAAAAGGTTTAAGTCGTAATAGCGAACCTAGTACCTCAGAAG-CAT
1 GAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACA-AAGACAT
* * * * * * *
74198 GAAGGGAAAGATTTAGGCCACGACGGTGAATCCAATACCACAAAGACAT
1 GAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACAAAGACAT
* * ** * *
74247 GAAGGGAAAGATCTAAGCCATAATGGCGGATCTAGTACCACAAAGACAT
1 GAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACAAAGACAT
* * * **
74296 -AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTTAGAAG-CAT
1 GAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACA-AAGACAT
* * * * * *
74344 GAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTATCGCAAAGACAT
1 GAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACAAAGACAT
* ** * ** *
74393 GAAGGGAAAGATTTAAG-CTGCAACAGAAAATCCAGTACCATGAAGACAC
1 GAAGGGAAAGATTTAAGTC-GCAACGGCGAATCTAGTACCACAAAGACAT
* * * * * * * *
74442 GAGGGGAAGGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAGACAT
1 GAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACAAAGACAT
* * * * *
74491 GAAGGGAAAGATCTAAGTCGCAATGGCGGATCTAGTACCGCAAAGACAC
1 GAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACAAAGACAT
* * *
74540 AAAGGGAAGGGTTTAAGT
1 GAAGGGAAAGATTTAAGT
74558 TGCAGCAGCG
Statistics
Matches: 306, Mismatches: 96, Indels: 14
0.74 0.23 0.03
Matches are distributed among these distances:
48 42 0.14
49 260 0.85
50 4 0.01
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (49 bp):
GAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACAAAGACAT
Found at i:74578 original size:49 final size:48
Alignment explanation
Indices: 74435--74578 Score: 135
Period size: 49 Copynumber: 2.9 Consensus size: 48
74425 CAGTACCATG
* *
74435 AAGACACGAGGGGAAGGGTTTAAGTCGCAACGACGAACCTTGTACCTCA
1 AAGACACGAAGGGAAGGGTTTAAGTCGCAACG-CGAACCTTGTACCGCA
* * * * * * * * *
74484 GAGACATGAAGGGAAAGATCTAAGTCGCAATGGCGGATCTAGTACCGCA
1 AAGACACGAAGGGAAGGGTTTAAGTCGCAA-CGCGAACCTTGTACCGCA
* * *
74533 AAGACACAAAGGGAAGGGTTTAAGTTGCAGCAGCGAACCTTGTACC
1 AAGACACGAAGGGAAGGGTTTAAGTCGCAAC-GCGAACCTTGTACC
74579 TTAGAAACAT
Statistics
Matches: 70, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
49 69 0.99
50 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.29, T:0.17
Consensus pattern (48 bp):
AAGACACGAAGGGAAGGGTTTAAGTCGCAACGCGAACCTTGTACCGCA
Found at i:75290 original size:23 final size:24
Alignment explanation
Indices: 75249--75303 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
75239 TTTATTTTAA
75249 ATTTAAATTGGAAATTT-AAATAT
1 ATTTAAATTGGAAATTTAAAATAT
*
75272 ATTATAAATTTG-AATTTAAAATAT
1 ATT-TAAATTGGAAATTTAAAATAT
75296 ATTTAAAT
1 ATTTAAAT
75304 AATGTCCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (24 bp):
ATTTAAATTGGAAATTTAAAATAT
Found at i:75990 original size:3 final size:3
Alignment explanation
Indices: 75984--76099 Score: 67
Period size: 3 Copynumber: 38.7 Consensus size: 3
75974 AATATTATTA
* * * * * * *
75984 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT GAT GAT GAT GAT GAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * *
76032 GACG AAT -AT AAT AAT ATT AAT AAT AAC AAT AAT AAT GAAT -TT ATT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
76077 AAT AAT AAT AAAT AAT -AT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AA
76100 ATAAAAAAAT
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
2 5 0.05
3 82 0.88
4 6 0.06
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:77224 original size:29 final size:28
Alignment explanation
Indices: 77191--77449 Score: 114
Period size: 29 Copynumber: 8.8 Consensus size: 28
77181 GACCTCGATT
77191 TTTTCAAAAATTACATTTTTACCCCTTAA
1 TTTTCAAAAATTACATTTTTA-CCCTTAA
* * * **
77220 CTTTCTAAAATT-CAATTTTTTACCATGTTTT
1 TTTTCAAAAATTAC-A-TTTTTACC--CTTAA
**
77251 TTTTCAAAAATTACATTTTTATCCCCGAA
1 TTTTCAAAAATTACATTTTTA-CCCTTAA
* * * * *
77280 CTTTC-CAAATTTCTATTTTTAACCTTATT
1 TTTTCAAAAATTAC-ATTTTTACCCTTA-A
*
77309 TTTTCAAAAATTACATTTTTACTCTTAAA
1 TTTTCAAAAATTACATTTTTACCCTT-AA
* ** * *
77338 TTTTCCAAAATCCCAATTTTGA-CCTTGAT
1 TTTTCAAAAATTAC-ATTTTTACCCTT-AA
*
77367 TTTTCCAAAAATTACATTTTTAGCCCTGAA
1 TTTT-CAAAAATTACATTTTTA-CCCTTAA
* * * *
77397 CTTT-ACAAAATTCCATTTTTTATCCC-GAT
1 TTTTCA-AAAATTACA-TTTTTA-CCCTTAA
*
77426 TTTTCCAAAAATTATATTTTTACC
1 TTTT-CAAAAATTACATTTTTACC
77450 ATCAAACTTT
Statistics
Matches: 167, Mismatches: 45, Indels: 37
0.67 0.18 0.15
Matches are distributed among these distances:
28 13 0.08
29 82 0.49
30 52 0.31
31 19 0.11
32 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.47
Consensus pattern (28 bp):
TTTTCAAAAATTACATTTTTACCCTTAA
Found at i:77269 original size:31 final size:30
Alignment explanation
Indices: 77189--77270 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
77179 TTGACCTCGA
77189 TTTTTTCAAAAATTACA-TTTTTACCCCTT
1 TTTTTTCAAAAATTACATTTTTTACCCCTT
*** * **
77218 AACTTTCTAAAATT-CAATTTTTTACCATGTT
1 TTTTTTCAAAAATTAC-ATTTTTTACC-CCTT
77249 TTTTTTCAAAAATTACATTTTT
1 TTTTTTCAAAAATTACATTTTT
77271 ATCCCCGAAC
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
28 1 0.03
29 11 0.28
30 8 0.21
31 18 0.46
32 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.01, T:0.52
Consensus pattern (30 bp):
TTTTTTCAAAAATTACATTTTTTACCCCTT
Found at i:77311 original size:59 final size:57
Alignment explanation
Indices: 77140--77580 Score: 347
Period size: 59 Copynumber: 7.6 Consensus size: 57
77130 TAAACTGTCC
* *
77140 AAAATTACATTTTTAACCCCAAACTTTCCAAAATT--ATTTTTGACCTCGATTTTTTCA
1 AAAATTACATTTTT-ACCCCAAACTTTCCAAAATTCCATTTTTAACCT-TATTTTTTCA
* * * * *
77197 AAAATTACATTTTTACCCCTTAACTTTCTAAAATTCAATTTTTTACCATGTTTTTTTTCA
1 AAAATTACATTTTTACCCC-AAACTTTCCAAAATTCCATTTTTAACC-T-TATTTTTTCA
* * *
77257 AAAATTACATTTTTATCCCCGAACTTTCCAAATTTCTATTTTTAACCTTATTTTTTCA
1 AAAATTACATTTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCTTATTTTTTCA
** * * * * *
77315 AAAATTACATTTTTACTCTTAAATTTTCCAAAATCCCAATTTTGACCTTGATTTTTCCA
1 AAAATTACATTTTTAC-CCCAAACTTTCCAAAATTCCATTTTTAACCTT-ATTTTTTCA
** * * ** *
77374 AAAATTACATTTTTAGCCCTGAACTTTACAAAATTCCATTTTTTATCCCGATTTTTCCA
1 AAAATTACATTTTTA-CCCCAAACTTTCCAAAATTCCA-TTTTTAACCTTATTTTTTCA
* * * * ** * *
77433 AAAATTATATTTTTACCATCAAACTTTCCAAAATTCCAATTTTATCCCCGATTTCTCCA
1 AAAATTACATTTTTACC-CCAAACTTTCCAAAATTCCATTTTTA-ACCTTATTTTTTCA
* * * * *
77492 AAAACTACCATTTTT-CCCC-GACTTT-TAAAATTCCATTTTTAACCTCGATTTTTCCA
1 AAAATTA-CATTTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCT-TATTTTTTCA
**
77548 AAAATTACCA-TTTTACCCCCGA-TTTCCAAAATT
1 AAAATTA-CATTTTTACCCCAAACTTTCCAAAATT
77581 ATCATTTTGT
Statistics
Matches: 317, Mismatches: 51, Indels: 32
0.79 0.13 0.08
Matches are distributed among these distances:
55 6 0.02
56 44 0.14
57 41 0.13
58 55 0.17
59 108 0.34
60 59 0.19
61 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (57 bp):
AAAATTACATTTTTACCCCAAACTTTCCAAAATTCCATTTTTAACCTTATTTTTTCA
Found at i:77408 original size:118 final size:113
Alignment explanation
Indices: 77140--77561 Score: 417
Period size: 118 Copynumber: 3.6 Consensus size: 113
77130 TAAACTGTCC
* * *
77140 AAAATTACATTTTTAACCCCAAACTTTCCAAAATT--ATTTTTGACCTCGATTTTTTCAAAAATT
1 AAAATTACATTTTT-ACCCCGAACTTT-CAAAATTCCATTTTTAACCTCGATTTTTCCAAAAATT
* * * *
77203 ACATTTTTACCCCTT-AACTTTCTAAAATTCAATTTTTTACCATGTTTTTTTTCA
64 ACATTTTTA--CCTTAAACTTTCCAAAATCCAA--TTTTACCATG-ATTTTTCCA
* * * *
77257 AAAATTACATTTTTATCCCCGAACTTTCCAAATTTCTATTTTTAACCT-TATTTTTTCAAAAATT
1 AAAATTACATTTTTA-CCCCGAACTTT-CAAAATTCCATTTTTAACCTCGATTTTTCCAAAAATT
* *
77321 ACATTTTTACTCTTAAATTTTCCAAAATCCCAATTTTGACCTTGATTTTTCCA
64 ACATTTTTAC-CTTAAACTTTCCAAAAT-CCAATTTT-ACCATGATTTTTCCA
* *
77374 AAAATTACATTTTTAGCCCTGAACTTTACAAAATTCCATTTTTTATCC-CGATTTTTCCAAAAAT
1 AAAATTACATTTTTA-CCCCGAACTTT-CAAAATTCCA-TTTTTAACCTCGATTTTTCCAAAAAT
* * ** *
77438 TATATTTTTACCATCAAACTTTCCAAAATTCCAATTTTATCCCCGATTTCTCCA
63 TACATTTTTACC-TTAAACTTTCCAAAA-TCCAATTTTA-CCATGATTTTTCCA
* *
77492 AAAACTACCATTTTT-CCCCG-ACTTTTAAAATTCCATTTTTAACCTCGATTTTTCCAAAAATTA
1 AAAATTA-CATTTTTACCCCGAACTTTCAAAATTCCATTTTTAACCTCGATTTTTCCAAAAATTA
77555 CCATTTT
65 -CATTTT
77562 ACCCCCGATT
Statistics
Matches: 261, Mismatches: 29, Indels: 31
0.81 0.09 0.10
Matches are distributed among these distances:
114 8 0.03
115 27 0.10
116 12 0.05
117 84 0.32
118 109 0.42
119 21 0.08
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.44
Consensus pattern (113 bp):
AAAATTACATTTTTACCCCGAACTTTCAAAATTCCATTTTTAACCTCGATTTTTCCAAAAATTAC
ATTTTTACCTTAAACTTTCCAAAATCCAATTTTACCATGATTTTTCCA
Found at i:77562 original size:30 final size:29
Alignment explanation
Indices: 77338--77588 Score: 96
Period size: 30 Copynumber: 8.7 Consensus size: 29
77328 TACTCTTAAA
* * *
77338 TTTTCCAAAA-TCCCAATTTTGACCTTGAT
1 TTTTCCAAAATTACC-ATTTTAACCTCGAT
* *
77367 TTTTCCAAAAATTA-CATTTTTAGCC-CTGAA
1 TTTTCC-AAAATTACCA-TTTTAACCTC-GAT
* * *
77397 CTTTACAAAATT-CCATTTTTTATCC-CGAT
1 TTTTCCAAAATTACCA--TTTTAACCTCGAT
* * * *
77426 TTTTCCAAAAATTA-TATTTTTACCATCAAA
1 TTTTCC-AAAATTACCATTTTAACC-TCGAT
* * *
77456 CTTTCCAAAATT-CCAATTTTATCCCCGAT
1 TTTTCCAAAATTACC-ATTTTAACCTCGAT
* * * * *
77485 TTCTCCAAAAACTACCATTTT-TCCCCGAC
1 TTTTCC-AAAATTACCATTTTAACCTCGAT
77514 TTTT--AAAATT-CCATTTTTAACCTCGAT
1 TTTTCCAAAATTACCA-TTTTAACCTCGAT
* *
77541 TTTTCCAAAAATTACCATTTTACCCCCGA-
1 TTTTCC-AAAATTACCATTTTAACCTCGAT
*
77570 -TTTCCAAAATTATCATTTT
1 TTTTCCAAAATTACCATTTT
77589 GTCTCGGGTA
Statistics
Matches: 167, Mismatches: 35, Indels: 42
0.68 0.14 0.17
Matches are distributed among these distances:
25 3 0.02
26 9 0.05
27 22 0.13
28 11 0.07
29 43 0.26
30 73 0.44
31 6 0.04
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.41
Consensus pattern (29 bp):
TTTTCCAAAATTACCATTTTAACCTCGAT
Found at i:85985 original size:22 final size:22
Alignment explanation
Indices: 85949--85991 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
85939 CCGTACTTTC
*
85949 ATTTTTAAGAATTTAATATTTT
1 ATTTTTAAGAATTTAAAATTTT
85971 ATTTTTAA-AATTTTAAAATTT
1 ATTTTTAAGAA-TTTAAAATTT
85992 AGATCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTTTAAGAATTTAAAATTTT
Found at i:86411 original size:31 final size:31
Alignment explanation
Indices: 86373--86439 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
86363 CTACGTGGCA
86373 GTCCATATGGGTTTTAAATATCAACTTGGAT
1 GTCCATATGGGTTTTAAATATCAACTTGGAT
*
86404 GTCCATATGGGTTTTAAATGTCAACTTGGAT
1 GTCCATATGGGTTTTAAATATCAACTTGGAT
86435 GTCCA
1 GTCCA
86440 ACTAGGATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (31 bp):
GTCCATATGGGTTTTAAATATCAACTTGGAT
Found at i:88097 original size:17 final size:17
Alignment explanation
Indices: 88075--88108 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
88065 CTAAGAATTT
88075 AAAGAAAATAAATTTAA
1 AAAGAAAATAAATTTAA
* *
88092 AAAGAAACTCAATTTAA
1 AAAGAAAATAAATTTAA
88109 GTATTAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAGAAAATAAATTTAA
Found at i:88964 original size:23 final size:23
Alignment explanation
Indices: 88938--88985 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
88928 CGTCCATCCT
88938 TGCTGACTAAACCTTCTAGAAGC
1 TGCTGACTAAACCTTCTAGAAGC
* **
88961 TGCTGATTGGACCTTCTAGAAGC
1 TGCTGACTAAACCTTCTAGAAGC
88984 TG
1 TG
88986 TTGATTGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (23 bp):
TGCTGACTAAACCTTCTAGAAGC
Found at i:88990 original size:23 final size:23
Alignment explanation
Indices: 88948--88994 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
88938 TGCTGACTAA
88948 ACCTTCTAGAAGCTGCTGATTGG
1 ACCTTCTAGAAGCTGCTGATTGG
*
88971 ACCTTCTAGAAGCTGTTGATTGG
1 ACCTTCTAGAAGCTGCTGATTGG
88994 A
1 A
88995 TGTCACATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (23 bp):
ACCTTCTAGAAGCTGCTGATTGG
Done.