Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014126.1 Kokia drynarioides strain JFW-HI SEQ_129159, 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: 89174
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 115 characters in sequence are not A, C, G, or T
Found at i:903 original size:23 final size:23
Alignment explanation
Indices: 871--997 Score: 103
Period size: 23 Copynumber: 5.4 Consensus size: 23
861 ACACTAGCGC
*
871 GCTCTTTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
*
894 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTCTGT
* * *
919 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
* * * * *
942 GTTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
* * *
965 ACTCTCTTTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
988 GCTCTCTGTT
1 GCTCTCTGTT
998 GCCCAGCATT
Statistics
Matches: 87, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
23 66 0.76
24 1 0.01
25 17 0.20
26 3 0.03
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTCTGT
Found at i:971 original size:46 final size:46
Alignment explanation
Indices: 892--995 Score: 127
Period size: 46 Copynumber: 2.2 Consensus size: 46
882 AGCACGTCTC
* *
892 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGT
* * * **
940 GTGTTCTCTGATTAGTACTTTGTGTACTCTCTTTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGT
986 GTGCTCTCTG
1 GTGCTCTCTG
996 TTGCCCAGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 39 0.81
48 9 0.19
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTGTGTGTACTCTCTGATTAGCACTGTGT
Found at i:1036 original size:69 final size:71
Alignment explanation
Indices: 895--1043 Score: 202
Period size: 69 Copynumber: 2.1 Consensus size: 71
885 ACGTCTCGTG
* *
895 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGTTCTCTGATTAGTACTT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTT
960 TGTGTA
66 TGTGTA
966 CTCTCT-TT-TTAGCACTGTGTGTGCTCTCTG-TT-GCCCAGCATTTATGTGCTCTCTG-TTAGT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAG--CA-C-TTTATGTGCTCTCTGATTAGT
1026 ACTTTG-GTA
62 ACTTTGTGTA
1035 CTCTCTGTT
1 CTCTCTGTT
1044 TGTTCCGTAT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
67 1 0.01
68 2 0.03
69 33 0.46
70 16 0.23
71 19 0.27
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.46
Consensus pattern (71 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTT
TGTGTA
Found at i:1997 original size:7 final size:8
Alignment explanation
Indices: 1978--2005 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1968 ATTATTGTTA
1978 AAAAAATT
1 AAAAAATT
1986 AAAAAATT
1 AAAAAATT
1994 AAAAAATT
1 AAAAAATT
2002 AAAA
1 AAAA
2006 TGATATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAATT
Found at i:8484 original size:29 final size:31
Alignment explanation
Indices: 8412--8484 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
8402 TACTTTGATA
* *
8412 CAATTATATACATGAAATTTTAATTACGGTT
1 CAATTATATACATAAAACTTTAATTACGGTT
**
8443 CAAATT-TATACATAAAACTTTAATT-TTG-T
1 C-AATTATATACATAAAACTTTAATTACGGTT
8472 CAATTATATACAT
1 CAATTATATACAT
8485 TTAAATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 4 0.11
29 9 0.25
30 1 0.03
31 18 0.50
32 4 0.11
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.42
Consensus pattern (31 bp):
CAATTATATACATAAAACTTTAATTACGGTT
Found at i:12263 original size:94 final size:94
Alignment explanation
Indices: 12102--12289 Score: 376
Period size: 94 Copynumber: 2.0 Consensus size: 94
12092 ACACAAATCA
12102 TTTGAGCAGAAAGAGCTCCCATCCTCTTAAGCTTTCTTGCTCTCTTGTTCTCTTGTTCACTTTGC
1 TTTGAGCAGAAAGAGCTCCCATCCTCTTAAGCTTTCTTGCTCTCTTGTTCTCTTGTTCACTTTGC
12167 CAAGTTTCTTAAGGATGATTCGTTTAAAT
66 CAAGTTTCTTAAGGATGATTCGTTTAAAT
12196 TTTGAGCAGAAAGAGCTCCCATCCTCTTAAGCTTTCTTGCTCTCTTGTTCTCTTGTTCACTTTGC
1 TTTGAGCAGAAAGAGCTCCCATCCTCTTAAGCTTTCTTGCTCTCTTGTTCTCTTGTTCACTTTGC
12261 CAAGTTTCTTAAGGATGATTCGTTTAAAT
66 CAAGTTTCTTAAGGATGATTCGTTTAAAT
12290 GAGCAAGGTG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (94 bp):
TTTGAGCAGAAAGAGCTCCCATCCTCTTAAGCTTTCTTGCTCTCTTGTTCTCTTGTTCACTTTGC
CAAGTTTCTTAAGGATGATTCGTTTAAAT
Found at i:12804 original size:20 final size:20
Alignment explanation
Indices: 12763--12805 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12753 TTTTAAAAAT
*
12763 ATTTATTTAATAATATATCG
1 ATTTATTTAATAATATACCG
* *
12783 ATTTTTTTAATAATATGCCG
1 ATTTATTTAATAATATACCG
12803 ATT
1 ATT
12806 GAATTTACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (20 bp):
ATTTATTTAATAATATACCG
Found at i:16481 original size:82 final size:84
Alignment explanation
Indices: 16329--16497 Score: 306
Period size: 82 Copynumber: 2.0 Consensus size: 84
16319 GATTAAAAGC
16329 ATGACTGGATCTTAATGGCCAATCGGGGAAGGTACGTAGTTACAAAGTCGTTCCCAAGGTCGTTA
1 ATGACTGGATCTTAATGGCCAATCGGGGAAGG-A-GTAGTTACAAAGTCGTTCCCAAGGTCGTTA
16394 CTAAAACTGTTATAACAACCA
64 CTAAAACTGTTATAACAACCA
16415 ATGACTGGATCTTAATGGCCAATCGGGGAA-G-GTAGTTACAAAGTCGTTCCCAAGGTCGTTACT
1 ATGACTGGATCTTAATGGCCAATCGGGGAAGGAGTAGTTACAAAGTCGTTCCCAAGGTCGTTACT
16478 AAAACTGTTATAACAACCA
66 AAAACTGTTATAACAACCA
16497 A
1 A
16498 CGTGATACAC
Statistics
Matches: 83, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
82 52 0.63
85 1 0.01
86 30 0.36
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (84 bp):
ATGACTGGATCTTAATGGCCAATCGGGGAAGGAGTAGTTACAAAGTCGTTCCCAAGGTCGTTACT
AAAACTGTTATAACAACCA
Found at i:38245 original size:17 final size:17
Alignment explanation
Indices: 38214--38248 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38204 TATTTTGATT
**
38214 TTTTAAATTTTTAAAAA
1 TTTTAAATTAATAAAAA
38231 TTTTAAATTAATAAAAA
1 TTTTAAATTAATAAAAA
38248 T
1 T
38249 AAAATTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAATTAATAAAAA
Found at i:41099 original size:19 final size:18
Alignment explanation
Indices: 41056--41109 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
41046 AATAGTTATG
*
41056 AATTTTATATTTCTTTAC
1 AATTTTATATTTTTTTAC
41074 AATTTTTATATTTTTCTTAC
1 AA-TTTTATATTTTT-TTAC
*
41094 GATTTTATAATTTTTT
1 AATTTTAT-ATTTTTT
41110 CTATATTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 2 0.06
19 18 0.58
20 11 0.35
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (18 bp):
AATTTTATATTTTTTTAC
Found at i:41118 original size:29 final size:29
Alignment explanation
Indices: 41076--41139 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
41066 TTCTTTACAA
*
41076 TTTTTATATTTTTCT-TACGATTTTATAAT
1 TTTTTATATATTTCTATA-GATTTTATAAT
* * *
41105 TTTTTCTATATTTCTATATATTTTATATT
1 TTTTTATATATTTCTATAGATTTTATAAT
41134 TTTTTA
1 TTTTTA
41140 CGATTTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 27 0.93
30 2 0.07
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.69
Consensus pattern (29 bp):
TTTTTATATATTTCTATAGATTTTATAAT
Found at i:41173 original size:9 final size:9
Alignment explanation
Indices: 41156--41291 Score: 55
Period size: 9 Copynumber: 14.3 Consensus size: 9
41146 TTATAAAAAA
*
41156 TTTACAATT
1 TTTATAATT
41165 TTTATAATT
1 TTTATAATT
41174 TTT-TACCATAT
1 TTTATA--AT-T
*
41185 TTAATAATT
1 TTTATAATT
*
41194 TTTCCTAATT
1 TTT-ATAATT
*
41204 TTTAATAAAT
1 TTT-ATAATT
*
41214 TTTAAATATCT
1 TTTATA-AT-T
41225 TTTAT-ATT
1 TTTATAATT
*
41233 TTTAATTAAAAT
1 TTT-A-T-AATT
*
41245 TTAATAATT
1 TTTATAATT
*
41254 TTTATAACT
1 TTTATAATT
*
41263 TTTATTGATT
1 TTTA-TAATT
41273 TTTAT--TT
1 TTTATAATT
*
41280 TTTATCATT
1 TTTATAATT
41289 TTT
1 TTT
41292 TATCACATGT
Statistics
Matches: 96, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
7 7 0.07
8 6 0.06
9 39 0.41
10 29 0.30
11 9 0.09
12 6 0.06
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTATAATT
Found at i:41178 original size:10 final size:10
Alignment explanation
Indices: 41161--41276 Score: 62
Period size: 10 Copynumber: 11.8 Consensus size: 10
41151 AAAAATTTAC
41161 AATTTTT-AT
1 AATTTTTAAT
* *
41170 AATTTTTTAC
1 AATTTTTAAT
* *
41180 CATATTTAAT
1 AATTTTTAAT
**
41190 AATTTTTCCT
1 AATTTTTAAT
41200 AATTTTTAAT
1 AATTTTTAAT
*
41210 AAATTTTAA-
1 AATTTTTAAT
41219 ATATCTTTT-AT
1 A-AT-TTTTAAT
41230 -ATTTTTAATT
1 AATTTTTAA-T
**
41240 AAAATTTAAT
1 AATTTTTAAT
41250 AATTTTT-AT
1 AATTTTTAAT
* *
41259 AACTTTTATT
1 AATTTTTAAT
*
41269 GATTTTTA
1 AATTTTTA
41277 TTTTTTATCA
Statistics
Matches: 78, Mismatches: 21, Indels: 15
0.68 0.18 0.13
Matches are distributed among these distances:
8 4 0.05
9 19 0.24
10 45 0.58
11 10 0.13
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:41178 original size:19 final size:19
Alignment explanation
Indices: 41125--41196 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 19
41115 TTTCTATATA
* *
41125 TTTTATATTTTTTTACGAT
1 TTTTATAATTTTTTACAAT
***
41144 TTTTATAAAAAATTTACAAT
1 TTTTAT-AATTTTTTACAAT
*
41164 TTTTATAATTTTTTACCAT
1 TTTTATAATTTTTTACAAT
*
41183 ATTTAATAATTTTT
1 -TTTTATAATTTTT
41197 CCTAATTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
19 15 0.37
20 26 0.63
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:41266 original size:30 final size:29
Alignment explanation
Indices: 41142--41266 Score: 103
Period size: 30 Copynumber: 4.2 Consensus size: 29
41132 TTTTTTTACG
* *
41142 ATTTTTATAAAAAATTT-ACAATTTTTATA
1 ATTTTTA-ATAAAATTTAATAATTTTTATA
* ** * *
41171 ATTTTTTACCATATTTAATAATTTTTCCTA
1 ATTTTTAATAAAATTTAATAATTTTT-ATA
*
41201 ATTTTTAATAAATTTTAA-ATATCTTTTAT-
1 ATTTTTAATAAAATTTAATA-AT-TTTTATA
41230 ATTTTTAATTAAAATTTAATAATTTTTATA
1 ATTTTTAA-TAAAATTTAATAATTTTTATA
*
41260 ACTTTTA
1 ATTTTTA
41267 TTGATTTTTA
Statistics
Matches: 75, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
28 6 0.08
29 29 0.39
30 35 0.47
31 5 0.07
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (29 bp):
ATTTTTAATAAAATTTAATAATTTTTATA
Found at i:46220 original size:50 final size:50
Alignment explanation
Indices: 46140--46240 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
46130 CAGGTGACTT
46140 ACGCTCTCACTATTACTATCATTGTCTCGAAGAGAAAACATAACTAAGTA
1 ACGCTCTCACTATTACTATCATTGTCTCGAAGAGAAAACATAACTAAGTA
*
46190 ACGCTCTCACTATTACTATCATTGTGTCGAAGAGAAAACATAACTAAGTA
1 ACGCTCTCACTATTACTATCATTGTCTCGAAGAGAAAACATAACTAAGTA
46240 A
1 A
46241 GAATGATACA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.28
Consensus pattern (50 bp):
ACGCTCTCACTATTACTATCATTGTCTCGAAGAGAAAACATAACTAAGTA
Found at i:50201 original size:145 final size:145
Alignment explanation
Indices: 49938--50228 Score: 501
Period size: 145 Copynumber: 2.0 Consensus size: 145
49928 TTGGGAATAT
* *
49938 AAAATAAGAATATTTACTGAGTTATTAGAAAAATATATTGAAGCTCGTTTAAGTAATTTAGCCGA
1 AAAATAAGAATATTTACGGAGTTATTAGAAAAATATATTGAAGCTCGGTTAAGTAATTTAGCCGA
* **
50003 AAAAGTAGTTAATTAAGGCTCATGGATTAAATTGTAAAAATTTAATCGTTATTGAGTTTTAATTA
66 AAAAGTAGTTAATTAAGGCTCATGGACTAAATTGTAAAAATTTAATCACTATTGAGTTTTAATTA
50068 AGAAAAGACTTGGGG
131 AGAAAAGACTTGGGG
* *
50083 AAAATAATAATATTTACGGAGTTATTAGAAAAATATATTGAAGTTCGGTTAAGTAATTTAGCCGA
1 AAAATAAGAATATTTACGGAGTTATTAGAAAAATATATTGAAGCTCGGTTAAGTAATTTAGCCGA
* *
50148 AAAAGTAGTTAATTAAGGCTCATTGACTAAATTGTAAATATTTAATCACTATTGAGTTTTAATTA
66 AAAAGTAGTTAATTAAGGCTCATGGACTAAATTGTAAAAATTTAATCACTATTGAGTTTTAATTA
50213 AGAAAAGACTTGGGG
131 AGAAAAGACTTGGGG
50228 A
1 A
50229 CTTATATAGG
Statistics
Matches: 137, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
145 137 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.34
Consensus pattern (145 bp):
AAAATAAGAATATTTACGGAGTTATTAGAAAAATATATTGAAGCTCGGTTAAGTAATTTAGCCGA
AAAAGTAGTTAATTAAGGCTCATGGACTAAATTGTAAAAATTTAATCACTATTGAGTTTTAATTA
AGAAAAGACTTGGGG
Found at i:50365 original size:19 final size:19
Alignment explanation
Indices: 50323--50365 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
50313 TTTAATTTGT
50323 GTAATTAAGATTAAAGAAA
1 GTAATTAAGATTAAAGAAA
* * **
50342 ATAATTTAGATTAATTAAA
1 GTAATTAAGATTAAAGAAA
50361 GTAAT
1 GTAAT
50366 AAATCACAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (19 bp):
GTAATTAAGATTAAAGAAA
Found at i:52773 original size:3 final size:3
Alignment explanation
Indices: 52765--52790 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52755 TTCCACACCA
52765 TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TC
52791 TACTTCTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (3 bp):
TCC
Found at i:59700 original size:25 final size:25
Alignment explanation
Indices: 59651--59700 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
59641 ATATAACTTT
**
59651 TTATATTAATATTAAATAATTATAA
1 TTATATTAATATTAAATAAAAATAA
59676 TTATAATT-ATATTAAATAAAAATAA
1 TTAT-ATTAATATTAAATAAAAATAA
59701 AAATCACTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TTATATTAATATTAAATAAAAATAA
Found at i:70123 original size:400 final size:401
Alignment explanation
Indices: 69382--70182 Score: 1478
Period size: 400 Copynumber: 2.0 Consensus size: 401
69372 GTGTGATAGT
*
69382 CTAATATGTAAGAAATAGGTAACTCATATTTGCTCACCTAAACTGCAAAAGCTAAAAGCATCCTA
1 CTAATATGTAAGAAATAGGTAACTCATATTTGCTCACCTAAACTACAAAAGCTAAAAGCATCCTA
*
69447 AAAAGCATTCCCCGAATATAGATAGGAATTTAAGAGGGTCAGATGTGTAAGTATAGTTCAAAAAC
66 AAAAGCATTCCCCGAATATAGATAGGAATTTAAGAGGGTCAGATGTGTAAGTATAGTCCAAAAAC
69512 GAGAATCCCTGAAGTTAAATGCTTAAAGCTGGCATACGAGGACTCAGAAGAGCAACAAATGGTAT
131 GAGAATCCCTGAAGTTAAATGCTTAAAGCTGGCATACGAGGACTCAGAAGAGCAACAAATGGTAT
69577 TGATCCTTTGCAAGTTGGACTTGGTGGGATCAATTGATGAATTGCATAAAAGCTTTTCGTCCATG
196 TGATCCTTTGCAAGTTGGACTTGGTGGGATCAATTGATGAATTGCATAAAAGCTTTTCGTCCATG
*
69642 GACCAGCTCATTCGATTGAAGTACATGTAAAACGAACCCAATTTCCTTGCTTAACAAGCCCTTGT
261 GACCAGCTCATTCGATTGAAGTACATGTAAAACGAACCCAATTTCCTTGCTTAACAAGCCCCTGT
* *
69707 CTGGGCAAAATCTTTTTCCTATTTCAGTTTTTGGAATCTAGGCGACTGGGCTTGGCCCAGAACAT
326 CTGGGCAAAATCTTTTTCCTATTTCAGTTTTTGGAATCTAAGCGACTGGGCTTGGCCCAGAACAC
69772 CTTCGAGATCC
391 CTTCGAGATCC
69783 CTAATATGTAAGAAATAGGTAACTCATATTTGCTCACCTAAACTACAAAAGCTAAAAGCATCCT-
1 CTAATATGTAAGAAATAGGTAACTCATATTTGCTCACCTAAACTACAAAAGCTAAAAGCATCCTA
*
69847 AAAAGCATTCCCCGAATATAGATAGGAATTTAAGAGGGTCAGATGTGTAAGTATAGTCCGAAAAC
66 AAAAGCATTCCCCGAATATAGATAGGAATTTAAGAGGGTCAGATGTGTAAGTATAGTCCAAAAAC
*
69912 GAGAATCCCTGAAGTTAGATGCTTAAAGCTGGCATACGAGGACTCAGAAGAGCAACAAATGGTAT
131 GAGAATCCCTGAAGTTAAATGCTTAAAGCTGGCATACGAGGACTCAGAAGAGCAACAAATGGTAT
*
69977 TGATCCTTTGCAAGTTGGACTTGGTGGGATCAATTGATGAATTGCGTAAAAGCTTTTCGTCCATG
196 TGATCCTTTGCAAGTTGGACTTGGTGGGATCAATTGATGAATTGCATAAAAGCTTTTCGTCCATG
* *
70042 GACCAGCTCATTCGATTGAAGTACATGTAAAACGAACCCAATTTCCTTGTTTAATAAGCCCCTGT
261 GACCAGCTCATTCGATTGAAGTACATGTAAAACGAACCCAATTTCCTTGCTTAACAAGCCCCTGT
* * *
70107 TTGGGCAAAATCTTTTTCTTGTTTCAGTTTTTGGAATCTAAGCGACTGGGCTTGGCCCAGAACAC
326 CTGGGCAAAATCTTTTTCCTATTTCAGTTTTTGGAATCTAAGCGACTGGGCTTGGCCCAGAACAC
70172 CTTCGAGATCC
391 CTTCGAGATCC
70183 TATTTCCCGA
Statistics
Matches: 387, Mismatches: 13, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
400 324 0.84
401 63 0.16
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (401 bp):
CTAATATGTAAGAAATAGGTAACTCATATTTGCTCACCTAAACTACAAAAGCTAAAAGCATCCTA
AAAAGCATTCCCCGAATATAGATAGGAATTTAAGAGGGTCAGATGTGTAAGTATAGTCCAAAAAC
GAGAATCCCTGAAGTTAAATGCTTAAAGCTGGCATACGAGGACTCAGAAGAGCAACAAATGGTAT
TGATCCTTTGCAAGTTGGACTTGGTGGGATCAATTGATGAATTGCATAAAAGCTTTTCGTCCATG
GACCAGCTCATTCGATTGAAGTACATGTAAAACGAACCCAATTTCCTTGCTTAACAAGCCCCTGT
CTGGGCAAAATCTTTTTCCTATTTCAGTTTTTGGAATCTAAGCGACTGGGCTTGGCCCAGAACAC
CTTCGAGATCC
Found at i:71303 original size:27 final size:25
Alignment explanation
Indices: 71236--71304 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 25
71226 AAATTATTTT
*
71236 TTATTTTTTAA-AATATTAATATAA
1 TTATTTTTTAATTATATTAATATAA
*
71260 TTA-TTTTTATTTAATATTAATATAAAA
1 TTATTTTTTAATT-ATATTAATAT--AA
71287 TTATTTTTTAATTATATT
1 TTATTTTTTAATTATATT
71305 TTAATGGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.16
24 3 0.08
25 10 0.27
27 10 0.27
28 8 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTTTTTAATTATATTAATATAA
Found at i:74889 original size:9 final size:9
Alignment explanation
Indices: 74872--74924 Score: 63
Period size: 9 Copynumber: 5.7 Consensus size: 9
74862 TTTATAGTTC
*
74872 TTTTGTAAT
1 TTTTATAAT
74881 TTTTATAAT
1 TTTTATAAT
74890 TTTTA-AAT
1 TTTTATAAT
74898 TTATTATAAT
1 TT-TTATAAT
74908 ATTTTAATAAT
1 -TTTT-ATAAT
74919 TTTTAT
1 TTTTAT
74925 TTTAAATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 5 0.13
9 18 0.46
10 9 0.23
11 7 0.18
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:78111 original size:23 final size:23
Alignment explanation
Indices: 78077--78138 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
78067 ACACTAGCGC
78077 GCCCTCTATTTAGCACGTTTCAT
1 GCCCTCTATTTAGCACGTTTCAT
* *
78100 GCCCTCTGTTTAGCACGTTTCGT
1 GCCCTCTATTTAGCACGTTTCAT
*
78123 GCCCTTTATTTAGCAC
1 GCCCTCTATTTAGCAC
78139 TGTGTGTGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.15, C:0.31, G:0.16, T:0.39
Consensus pattern (23 bp):
GCCCTCTATTTAGCACGTTTCAT
Found at i:78147 original size:23 final size:23
Alignment explanation
Indices: 78077--78198 Score: 65
Period size: 23 Copynumber: 5.2 Consensus size: 23
78067 ACACTAGCGC
* * *
78077 GCCCTCTATTTAGCAC-GTTTCAT
1 GCCCTTTATTTAGCACTGTGT-GT
* * *
78100 GCCCTCTGTTTAGCAC-GTTTCGT
1 GCCCTTTATTTAGCACTGTGT-GT
78123 GCCCTTTATTTAGCACTGTGTGT
1 GCCCTTTATTTAGCACTGTGTGT
*
78146 GCCCTCCATTA-TTAGTACT-TCGTGT
1 GCCCT---TTATTTAGCACTGT-GTGT
* *
78171 GCCCTCTGA-TTAGCACTTTGTGT
1 GCCCT-TTATTTAGCACTGTGTGT
78194 GCCCT
1 GCCCT
78199 CTGTTATCCA
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
23 60 0.71
24 5 0.06
25 16 0.19
26 3 0.04
ACGTcount: A:0.13, C:0.29, G:0.19, T:0.39
Consensus pattern (23 bp):
GCCCTTTATTTAGCACTGTGTGT
Found at i:78199 original size:23 final size:23
Alignment explanation
Indices: 78099--78201 Score: 93
Period size: 23 Copynumber: 4.4 Consensus size: 23
78089 GCACGTTTCA
* *
78099 TGCCCTCTGTTTAGCACGTTT-CG
1 TGCCCTCTGATTAGCAC-TTTGTG
* *
78122 TGCCCT-TTATTTAGCACTGTGTG
1 TGCCCTCTGA-TTAGCACTTTGTG
* * *
78145 TGCCCTCCATTATTAGTACTTCGTG
1 TGCCCT-C-TGATTAGCACTTTGTG
78170 TGCCCTCTGATTAGCACTTTGTG
1 TGCCCTCTGATTAGCACTTTGTG
78193 TGCCCTCTG
1 TGCCCTCTG
78202 TTATCCAGCA
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
22 3 0.05
23 42 0.65
24 1 0.02
25 16 0.25
26 3 0.05
ACGTcount: A:0.12, C:0.28, G:0.20, T:0.40
Consensus pattern (23 bp):
TGCCCTCTGATTAGCACTTTGTG
Found at i:79205 original size:67 final size:70
Alignment explanation
Indices: 79089--79241 Score: 242
Period size: 71 Copynumber: 2.2 Consensus size: 70
79079 TATATTCACA
79089 AAAT-AATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAT-A
1 AAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTA-A-TTATTTATTTATATTCATAA
*
79152 CAATAAT
64 AAATAAT
79159 AAATAAATAAATAAATAATAAAACAAAATTAATATTATTTT-A-TATTTATTTATATTCATAAAA
1 AAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTAATTATTTATTTATATTCATAAAA
79222 ATAAT
66 ATAAT
*
79227 AAATAAATGAATAAA
1 AAATAAATAAATAAA
79242 AAAATAGAAT
Statistics
Matches: 79, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
67 17 0.22
68 21 0.27
69 1 0.01
70 4 0.05
71 36 0.46
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (70 bp):
AAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTAATTATTTATTTATATTCATAAAA
ATAAT
Found at i:79626 original size:23 final size:23
Alignment explanation
Indices: 79600--79643 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
79590 TTATAAGAAT
* * *
79600 AATTATATATTTGAAAGTTATAA
1 AATTATAAAATTGAAAATTATAA
79623 AATTATAAAATTGAAAATTAT
1 AATTATAAAATTGAAAATTAT
79644 TATATTTGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (23 bp):
AATTATAAAATTGAAAATTATAA
Found at i:83475 original size:2 final size:2
Alignment explanation
Indices: 83468--83494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
83458 GCATTATTTA
83468 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
83495 AGATTTTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.