Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004132.1 Kokia drynarioides strain JFW-HI SEQ_117325, 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: 119505
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 6 characters in sequence are not A, C, G, or T
Found at i:162 original size:60 final size:58
Alignment explanation
Indices: 69--253 Score: 236
Period size: 60 Copynumber: 3.2 Consensus size: 58
59 GTGGCAATTT
*
69 TGGTGGCGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTGTTTCGGTGGTTCTGACAC
1 TGGTGGTGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTGTTTCGGTGGTT-TG-CAC
129 TGGTGGTGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTG-TTCTGGTGGTTT----
1 TGGTGGTGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTGTTTC-GGTGGTTTGCAC
** * *
183 TTTTGGTGGAGATCGTTCCCTTATTACGGGTGATTCCTCTTGTTTCGGTGGTTTTTGCAC
1 TGGTGGTGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTGTTTCGGTGG--TTTGCAC
*
243 TGGTGTTGGAG
1 TGGTGGTGGAG
254 GCTTAACAAG
Statistics
Matches: 109, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
54 43 0.39
55 3 0.03
56 3 0.03
59 4 0.04
60 56 0.51
ACGTcount: A:0.10, C:0.18, G:0.31, T:0.41
Consensus pattern (58 bp):
TGGTGGTGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTGTTTCGGTGGTTTGCAC
Found at i:198 original size:54 final size:54
Alignment explanation
Indices: 66--239 Score: 224
Period size: 54 Copynumber: 3.1 Consensus size: 54
56 GAGGTGGCAA
* *
66 TTTTGGTGGCGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTGTTTCGGTGG
1 TTTTTGTGGTGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTGTTTCGGTGG
*
120 TTCTGACACTGGTGGTGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTG-TTCTGGTGG
1 TT-T-----TTGTGGTGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTGTTTC-GGTGG
* * *
180 TTTTTTTGGTGGAGATCGTTCCCTTATTACGGGTGATTCCTCTTGTTTCGGTGG
1 TTTTTGTGGTGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTGTTTCGGTGG
234 TTTTTG
1 TTTTTG
240 CACTGGTGTT
Statistics
Matches: 106, Mismatches: 6, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
54 50 0.47
55 4 0.04
59 4 0.04
60 48 0.45
ACGTcount: A:0.10, C:0.18, G:0.29, T:0.43
Consensus pattern (54 bp):
TTTTTGTGGTGGAGATCGTTCCCTTGTTACAGGTGATTCCTCTTGTTTCGGTGG
Found at i:2550 original size:3 final size:3
Alignment explanation
Indices: 2542--2568 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2532 GAAGTAAAAT
2542 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2569 GAATTATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6935 original size:5 final size:5
Alignment explanation
Indices: 6925--6986 Score: 62
Period size: 5 Copynumber: 13.0 Consensus size: 5
6915 TTTCTTGGAT
6925 ATAAA ATAAA A-ATAA AT-AA ATAAA ATAAA A-AATA A-AAA AT-AA ATAAA
1 ATAAA ATAAA ATA-AA ATAAA ATAAA ATAAA ATAA-A ATAAA ATAAA ATAAA
*
6972 ATCAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA
6987 TTGCCTCCCA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 13 0.27
5 36 0.73
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:6943 original size:4 final size:4
Alignment explanation
Indices: 6934--6987 Score: 58
Period size: 4 Copynumber: 13.0 Consensus size: 4
6924 TATAAAATAA
6934 AAAT AAAT AAAT AAAAT AAA- AAAT AAA- AAAT AAAT AAAAT CAAAT AAAAT
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT -AAAT
6984 AAAT
1 AAAT
6988 TGCCTCCCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 6 0.14
4 22 0.50
5 16 0.36
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:6949 original size:19 final size:19
Alignment explanation
Indices: 6925--6986 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
6915 TTTCTTGGAT
6925 ATAAAATAAAAATAAATAA
1 ATAAAATAAAAATAAATAA
6944 ATAAAATAAAAAATAAA-AA
1 ATAAAAT-AAAAATAAATAA
6963 AT-AAAT-AAAATCAAATAAA
1 ATAAAATAAAAAT-AAAT-AA
6982 ATAAA
1 ATAAA
6987 TTGCCTCCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.13
17 3 0.08
18 4 0.11
19 15 0.39
20 11 0.29
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (19 bp):
ATAAAATAAAAATAAATAA
Found at i:6958 original size:7 final size:7
Alignment explanation
Indices: 6927--6967 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
6917 TCTTGGATAT
6927 AAAAT-A
1 AAAATAA
6933 AAAATAA
1 AAAATAA
6940 ATAAAT--
1 A-AAATAA
6946 AAAATAA
1 AAAATAA
6953 AAAATAA
1 AAAATAA
6960 AAAATAA
1 AAAATAA
6967 A
1 A
6968 TAAAATCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
5 4 0.13
6 6 0.19
7 17 0.55
8 4 0.13
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAATAA
Found at i:6968 original size:23 final size:24
Alignment explanation
Indices: 6925--6987 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
6915 TTTCTTGGAT
6925 ATAAAATAAAAATAAATAAATAAA
1 ATAAAATAAAAATAAATAAATAAA
6949 ATAAAA-AATAAA-AAATAAATAAA
1 ATAAAATAA-AAATAAATAAATAAA
*
6972 ATCAAAT-AAAATAAAT
1 ATAAAATAAAAATAAAT
6988 TGCCTCCCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
22 3 0.09
23 23 0.66
24 9 0.26
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.21
Consensus pattern (24 bp):
ATAAAATAAAAATAAATAAATAAA
Found at i:6968 original size:27 final size:27
Alignment explanation
Indices: 6927--6982 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 27
6917 TCTTGGATAT
6927 AAAATAAAAATAAAT-AAATAAAATAA
1 AAAATAAAAATAAATAAAATAAAATAA
*
6953 AAAATAAAAAATAAATAAAATCAAATAA
1 AAAAT-AAAAATAAATAAAATAAAATAA
6981 AA
1 AA
6983 TAAATTGCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 5 0.19
27 10 0.37
28 12 0.44
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (27 bp):
AAAATAAAAATAAATAAAATAAAATAA
Found at i:10592 original size:17 final size:17
Alignment explanation
Indices: 10550--10593 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
10540 ATTTAAACTC
*
10550 TAAATAT-AATAAAACT
1 TAAATATAAATAAAAAT
*
10566 TAAAAGATAAATAAAAAT
1 T-AAATATAAATAAAAAT
10584 TAAATATAAA
1 TAAATATAAA
10594 CAATATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 13 0.57
18 9 0.39
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATATAAATAAAAAT
Found at i:12845 original size:17 final size:17
Alignment explanation
Indices: 12823--12878 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
12813 TATGGAAACC
12823 ATTAATTATAATTATTA
1 ATTAATTATAATTATTA
12840 ATTAA-T-TAATTAACTTA
1 ATTAATTATAATT-A-TTA
* *
12857 ATTAATAAAAAATTATTA
1 ATTAAT-TATAATTATTA
12875 ATTA
1 ATTA
12879 GTTTAATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 5 0.16
16 2 0.06
17 13 0.41
18 7 0.22
19 1 0.03
20 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTAATTATAATTATTA
Found at i:12857 original size:13 final size:12
Alignment explanation
Indices: 12823--12862 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
12813 TATGGAAACC
12823 ATTAATT-A-TA
1 ATTAATTAATTA
12833 ATT-ATTAATTA
1 ATTAATTAATTA
12844 ATTAATTAACTTA
1 ATTAATTAA-TTA
12857 ATTAAT
1 ATTAAT
12863 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.12
10 4 0.15
11 5 0.19
12 5 0.19
13 9 0.35
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTAATTAATTA
Found at i:12878 original size:4 final size:4
Alignment explanation
Indices: 12823--12862 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
12813 TATGGAAACC
12823 ATTA ATT- A-TA ATT- ATTA ATTA ATTA ATTA ACTTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A-TTA ATTA AT
12863 AAAAAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 1 0.03
3 5 0.16
4 22 0.69
5 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:15846 original size:21 final size:21
Alignment explanation
Indices: 15822--15883 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
15812 TGGGACTACA
15822 CAAAAAATTATGAAAGTGTAC
1 CAAAAAATTATGAAAGTGTAC
* * **
15843 CAAAAATTTA-AAAAGAAATAC
1 CAAAAAATTATGAAAG-TGTAC
*
15864 C-AAAAATTATGAAGGTGTAC
1 CAAAAAATTATGAAAGTGTAC
15884 TAAATTAGTT
Statistics
Matches: 30, Mismatches: 9, Indels: 5
0.68 0.20 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.23
Consensus pattern (21 bp):
CAAAAAATTATGAAAGTGTAC
Found at i:15847 original size:20 final size:20
Alignment explanation
Indices: 15824--15883 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
15814 GGACTACACA
15824 AAAAATTATGAAAGTGTACC
1 AAAAATTATGAAAGTGTACC
* **
15844 AAAAATT-TAAAAAGAAATACC
1 AAAAATTAT-GAAAG-TGTACC
*
15865 AAAAATTATGAAGGTGTAC
1 AAAAATTATGAAAGTGTAC
15884 TAAATTAGTT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.47
21 14 0.47
22 1 0.03
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.23
Consensus pattern (20 bp):
AAAAATTATGAAAGTGTACC
Found at i:16156 original size:20 final size:19
Alignment explanation
Indices: 16092--16163 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
16082 TTTTGAAACT
16092 ATACCAAAAATTTTAAGGTA
1 ATACCAAAAATTTTAAGG-A
*
16112 ATA-TAAAAATTTATAAGGA
1 ATACCAAAAATTT-TAAGGA
*
16131 AGTACCAAAAATTTTGAGAGA
1 A-TACCAAAAATTTTAAG-GA
*
16152 ATACCATAAATT
1 ATACCAAAAATT
16164 ATGAGAGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.23
20 23 0.52
21 11 0.25
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.29
Consensus pattern (19 bp):
ATACCAAAAATTTTAAGGA
Found at i:16168 original size:20 final size:20
Alignment explanation
Indices: 16133--16181 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
16123 TATAAGGAAG
*
16133 TACCAAAAATTTTGAGAGAA
1 TACCAAAAATTATGAGAGAA
*
16153 TACCATAAATTATGAGAGAA
1 TACCAAAAATTATGAGAGAA
*
16173 TGCCAAAAA
1 TACCAAAAA
16182 AATATAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.14, T:0.22
Consensus pattern (20 bp):
TACCAAAAATTATGAGAGAA
Found at i:16358 original size:14 final size:15
Alignment explanation
Indices: 16329--16377 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 15
16319 AAGTTAGGAG
16329 AGGATATACCAAAAAT
1 AGGATATA-CAAAAAT
*
16345 AGGATATAAAAAATAT
1 AGGATATACAAAA-AT
16361 GAGGATATATCAAAAAT
1 -AGGATATA-CAAAAAT
16378 TACGAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 10 0.36
17 10 0.36
18 4 0.14
ACGTcount: A:0.57, C:0.06, G:0.14, T:0.22
Consensus pattern (15 bp):
AGGATATACAAAAAT
Found at i:16476 original size:21 final size:21
Alignment explanation
Indices: 16452--16498 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
16442 AGAGCGTACT
*
16452 AAAAAT-ATAAGAAAGTATAA
1 AAAAATCATAAGAAAATATAA
*
16472 AAAAATCATGAGAAAATATAA
1 AAAAATCATAAGAAAATATAA
16493 AAAAAT
1 AAAAAT
16499 ACGAAAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (21 bp):
AAAAATCATAAGAAAATATAA
Found at i:16499 original size:10 final size:10
Alignment explanation
Indices: 16452--16499 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
16442 AGAGCGTACT
16452 AAAAATATAA
1 AAAAATATAA
* *
16462 GAAAGTATAA
1 AAAAATATAA
*
16472 AAAAATCATGA
1 AAAAAT-ATAA
*
16483 GAAAATATAA
1 AAAAATATAA
16493 AAAAATA
1 AAAAATA
16500 CGAAAATACA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (10 bp):
AAAAATATAA
Found at i:16504 original size:18 final size:18
Alignment explanation
Indices: 16451--16514 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
16441 GAGAGCGTAC
* *
16451 TAAAAATATAAGAAAGTA
1 TAAAAAAATAAGAAAATA
16469 TAAAAAAATCATGAGAAAATA
1 TAAAAAAAT-A--AGAAAATA
*
16490 TAAAAAAATACGAAAATA
1 TAAAAAAATAAGAAAATA
*
16508 CAAAAAA
1 TAAAAAA
16515 TTATACCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 21 0.54
19 1 0.03
20 1 0.03
21 16 0.41
ACGTcount: A:0.70, C:0.05, G:0.08, T:0.17
Consensus pattern (18 bp):
TAAAAAAATAAGAAAATA
Found at i:23892 original size:3 final size:3
Alignment explanation
Indices: 23884--23920 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
23874 AGTATTGATC
23884 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
23921 TGGTGGTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:42418 original size:62 final size:59
Alignment explanation
Indices: 42351--42470 Score: 168
Period size: 62 Copynumber: 2.0 Consensus size: 59
42341 TTAAAGTGAT
* * *
42351 TATTTAATATTAAATTAAATCTAATGTTTATTTTGTAGATAAATATTCTATTAATTTAATAA
1 TATTTAATATTAAATTAAATCTAATATTTA-TCT-T-GATAAATATTATATTAATTTAATAA
* *
42413 TATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 TATTTAATATTAAATTAAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
42471 TTAAAGTGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 22 0.42
60 1 0.02
61 2 0.04
62 28 0.53
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (59 bp):
TATTTAATATTAAATTAAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAA
Found at i:43235 original size:24 final size:24
Alignment explanation
Indices: 43203--43252 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
43193 TAGAACATAA
43203 ATACTAATGCATACACATGCACAC
1 ATACTAATGCATACACATGCACAC
43227 ATACTAATGCATACACATGCACAC
1 ATACTAATGCATACACATGCACAC
43251 AT
1 AT
43253 GACACAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.28, G:0.08, T:0.22
Consensus pattern (24 bp):
ATACTAATGCATACACATGCACAC
Found at i:66421 original size:58 final size:57
Alignment explanation
Indices: 66275--66423 Score: 138
Period size: 58 Copynumber: 2.6 Consensus size: 57
66265 TTGAATTTGC
* * * *
66275 CATTTTTTTTAATTTGATA-CTTAAATTTTTTTTATCCAATTTGGCACCTAAACTTTA
1 CATTTTTTTTAATTTGGTATC-AAAATTTTTTTTATCCAATTTGACACCTAAACTTGA
* * * ** *
66332 CATTTTTTTTAATTTGGTATCAAAACCTTTTTTAATCCAATTTGATATTTGAACTTGA
1 CATTTTTTTTAATTTGGTATCAAAA-TTTTTTTTATCCAATTTGACACCTAAACTTGA
* * * *
66390 TATTTTTTTCTATTTTGGTATCTAATTTTTTTTT
1 CATTTTTTT-TAATTTGGTATCAAAATTTTTTTT
66424 TAAAATTTAA
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
57 21 0.29
58 39 0.53
59 13 0.18
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (57 bp):
CATTTTTTTTAATTTGGTATCAAAATTTTTTTTATCCAATTTGACACCTAAACTTGA
Found at i:66567 original size:21 final size:21
Alignment explanation
Indices: 66526--66567 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
66516 ACGAATTAAT
*
66526 ATTAAAAAAATTAAATATCAA
1 ATTAAAAAAATCAAATATCAA
66547 ATTAAAAAAAGTCAAAT-TCAA
1 ATTAAAAAAA-TCAAATATCAA
66568 GTTCCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.26
Consensus pattern (21 bp):
ATTAAAAAAATCAAATATCAA
Found at i:68510 original size:61 final size:61
Alignment explanation
Indices: 68407--68528 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 61
68397 CATTAGCTAT
**
68407 TTGTCTTAAAGGAAGAAGTATGCTATTTCATAATCCTAAAAGAGGAAAAAGCAAGAGAAAG
1 TTGTCTTAAAGGAAGAAGTAAACTATTTCATAATCCTAAAAGAGGAAAAAGCAAGAGAAAG
* *
68468 TTGTCTTAAAGGAAGAAGTAAACTATTTCATAATTCTCAAAGAGGAAAAAGCAAGAGAAAG
1 TTGTCTTAAAGGAAGAAGTAAACTATTTCATAATCCTAAAAGAGGAAAAAGCAAGAGAAAG
68529 ATGAACACTG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (61 bp):
TTGTCTTAAAGGAAGAAGTAAACTATTTCATAATCCTAAAAGAGGAAAAAGCAAGAGAAAG
Found at i:69588 original size:7 final size:6
Alignment explanation
Indices: 69552--69600 Score: 71
Period size: 6 Copynumber: 7.7 Consensus size: 6
69542 TGAAAAGAGA
69552 AAAGGC AAAGGC AAAGGC AAAGGC AAAGGC GAAAGGC GAAAGGC GAAAG
1 AAAGGC AAAGGC AAAGGC AAAGGC AAAGGC -AAAGGC -AAAGGC -AAAG
69601 CCCCCTCTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 24 0.57
7 18 0.43
ACGTcount: A:0.49, C:0.14, G:0.37, T:0.00
Consensus pattern (6 bp):
AAAGGC
Found at i:69748 original size:2 final size:2
Alignment explanation
Indices: 69741--69769 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
69731 TCCCTCCTTC
69741 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
69770 CCCCCTTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:97220 original size:824 final size:813
Alignment explanation
Indices: 95891--97394 Score: 2153
Period size: 824 Copynumber: 1.8 Consensus size: 813
95881 ATCTCAACAC
* *
95891 AAATAATAAAATAAAATAATTATTTTATTTTAATAAAATAAATTTTCATTAAAAAACAACACAAA
1 AAATAATAAAATAAAATAATTATTTTAATTTAATAAAATAAATTTCCATTAAAAAACAACACAAA
* * *
95956 AGGCCTATGTATGTAATTACTAAAATTTAAAATAACGTTGGTTTTCATGGTTTTCCTTCACTAGA
66 AGGCCCATGTATGTAATTACTAAAATTTAAAATAACATTGATTTTCATGGTTTTCCTTCACTAGA
* * * *
96021 TCTTTTCCTTAATCCATTCGGTCCATGATTCCTTAGATATACCTTGTCCCTCAGGAGTTGGTGCA
131 TCTTTTCCTTAATCCAATCGGTCCATGATTCCTTAGATATACCATGTCCCTCAGGAGCTAGTGCA
* * *
96086 TAAGCTTTTTCAGGCTTTGATTCTGTTGATGATGTAGATGACGTTGCGATTGTGTCACCAATAAC
196 TAAGCTTTTTCAGGCTTTGATTCTGTTGATGATGTAGATGACGTTGCGATAGTCTCACCAACAAC
* * *
96151 GGAATGCATTGTAACAACAATGATCATTGAGATCAAAACAATGACCAAAGCAATCCTTGCCATTT
261 GGAATGCATTGAAACAACAACGATCATTGAGATCAAAACAATGACCAAAGCAATCCTTGCCATAT
96216 TTGTTTTTTGAGTTAATGTAAAAAAATTAAAGAGAAAGGAATGAATTTATTTATGCTTTATTTTT
326 TTGTTTTTTGAGTTAATGTAAAAAAATTAAAGAGAAAGGAATGAATTTATTTATGCTTTATTTTT
*
96281 TTTATGAATATGAAATTATTTAGTAAAATGTGATTGATGAATTTAAGATTGAAATCATGAAATAT
391 TTTACGAATATGAAATTATTTAGTAAAATGTGATTGATGAATTTAAGATTGAAATCATGAAATAT
** *
96346 TTATAGCGTTTAAGAGGAGACATCTTCGTCGAATCCATTGGTTTAGTGCCTAATGACCAAACACG
456 TTATAGCGTTTAAGAGGAGACATCTTCAACGAATCCATTGGTTTAGTGCCTAATGACCAAACACA
* * * * * *
96411 TATTTAACTGTGAGATAATTTTGCTTATAAAAATACCATAAAAGTCAATTCAAACCTATGTGTTT
521 TATTTAACTATGAGATAATTTCGCTTATAAAAATACCAAAAAAATCAATTCAAACCAATGTATTT
* *
96476 TCTTCCATTTATAACAATTTTTTTA-AAAATTAATATGGTTAACTTATGAA-TATCGTATAAATA
586 GCTTCCATTTATAACAATTTTTTTATAAAATTAATATGGTTAACTTA-AAATTATCGTAT-AA-A
96539 TCATCAAAATTAAATAACTCGATTTTATCAAAATGGCAATTGCACAGCCTTATATCACACATAAG
648 TCATCAAAATTAAATAACTCGATTTTATCAAAATGGCAATTGCACAGCCTTATATCACACATAAG
96604 TTTAAGTTATTTTTAATGTAAAATTATCAAAATCAAATTAAAAAAATTAGAAATTATGTATTTAA
713 TTTAAGTTATTTTTAATGTAAAATTATCAAAATCAAATTAAAAAAATTAGAAATTATGTATTTAA
96669 AATATAGATGTTTGTTTAAAAATAGCATACAATTAA
778 AATATAGATGTTTGTTTAAAAATAGCATACAATTAA
*
96705 AAATAATAAAATAAAATAATTATTTTAATTTAATAAAATAAATTTCCATT-AAAAACAACATAAA
1 AAATAATAAAATAAAATAATTATTTTAATTTAATAAAATAAATTTCCATTAAAAAACAACACAAA
* * **
96769 AGGCCCATGTATGTAATTACTAAATTTTAAAATAATATTGATTTTCATGGTTTTTTTTTCACTAG
66 AGGCCCATGTATGTAATTACTAAAATTTAAAATAACATTGATTTTCATGG-TTTTCCTTCACTAG
* * *
96834 ATTCTACATTTTTTTCCTTAATCCAATCGGTCCATGATTCTTTAGATTTATCATGTCCCTC-GAG
130 A---T-C----TTTTCCTTAATCCAATCGGTCCATGATTCCTTAGATATACCATGTCCCTCAG-G
* * * * * *
96898 AGCTAGTGCATCATCTTTTTCA-GCTTTTGATTCTGTTGATGATTTAGGTGTCGTTTC-AGTAGT
186 AGCTAGTGCATAAGCTTTTTCAGGC-TTTGATTCTGTTGATGATGTAGATGACGTTGCGA-TAGT
* * * ** * * *
96961 CTCACCAACGACGGAATGGATTGAAACAACCACGATTGTTGATATCAAAATAATGACCAATGCAA
249 CTCACCAACAACGGAATGCATTGAAACAACAACGATCATTGAGATCAAAACAATGACCAAAGCAA
* * *
97026 TCCTTGTCATATTTGTTTTTTGATTTTATGTAAAAAAAAATTAAAGAGAAAGGAAT-ATATTTAT
314 TCCTTGCCATATTTGTTTTTTGAGTTAATGT--AAAAAAATTAAAGAGAAAGGAATGA-ATTTAT
* *
97090 TTGTGTTTTATTTTTTTTACGAATATGAAATTATTTAGTAAAATGTGATTGATGAATTTAAGATT
376 TTATGCTTTATTTTTTTTACGAATATGAAATTATTTAGTAAAATGTGATTGATGAATTTAAGATT
* * *
97155 GAAATTATGAAATATTTATAGCGTTTAAGAGGAGATAT-TTGCAACGAATTCA-TGAGTTTAGTG
441 GAAATCATGAAATATTTATAGCGTTTAAGAGGAGACATCTT-CAACGAATCCATTG-GTTTAGTG
* * * *
97218 CCTAATGACTAAACACATGTTTAACTATTAGATAATTTCGCTTTTAAAAATACCAAAAAAATCAA
504 CCTAATGACCAAACACATATTTAACTATGAGATAATTTCGCTTATAAAAATACCAAAAAAATCAA
**
97283 TTCAAACCAATGTATTTGCTTCCATTTATCTCAATTTTTTTATTAAAATTAATATGGTTAACTTA
569 TTCAAACCAATGTATTTGCTTCCATTTATAACAATTTTTTTA-TAAAATTAATATGGTTAACTTA
* * * *
97348 AAATTTTCGTATAAATCGTCAAAATTAAATAACTTGTTTTTATCAAA
633 AAATTATCGTATAAATCATCAAAATTAAATAACTCGATTTTATCAAA
97395 TCATTTTATC
Statistics
Matches: 603, Mismatches: 67, Indels: 30
0.86 0.10 0.04
Matches are distributed among these distances:
813 58 0.10
814 61 0.10
817 1 0.00
818 1 0.00
821 4 0.01
822 175 0.29
823 5 0.01
824 266 0.44
825 4 0.01
826 28 0.05
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (813 bp):
AAATAATAAAATAAAATAATTATTTTAATTTAATAAAATAAATTTCCATTAAAAAACAACACAAA
AGGCCCATGTATGTAATTACTAAAATTTAAAATAACATTGATTTTCATGGTTTTCCTTCACTAGA
TCTTTTCCTTAATCCAATCGGTCCATGATTCCTTAGATATACCATGTCCCTCAGGAGCTAGTGCA
TAAGCTTTTTCAGGCTTTGATTCTGTTGATGATGTAGATGACGTTGCGATAGTCTCACCAACAAC
GGAATGCATTGAAACAACAACGATCATTGAGATCAAAACAATGACCAAAGCAATCCTTGCCATAT
TTGTTTTTTGAGTTAATGTAAAAAAATTAAAGAGAAAGGAATGAATTTATTTATGCTTTATTTTT
TTTACGAATATGAAATTATTTAGTAAAATGTGATTGATGAATTTAAGATTGAAATCATGAAATAT
TTATAGCGTTTAAGAGGAGACATCTTCAACGAATCCATTGGTTTAGTGCCTAATGACCAAACACA
TATTTAACTATGAGATAATTTCGCTTATAAAAATACCAAAAAAATCAATTCAAACCAATGTATTT
GCTTCCATTTATAACAATTTTTTTATAAAATTAATATGGTTAACTTAAAATTATCGTATAAATCA
TCAAAATTAAATAACTCGATTTTATCAAAATGGCAATTGCACAGCCTTATATCACACATAAGTTT
AAGTTATTTTTAATGTAAAATTATCAAAATCAAATTAAAAAAATTAGAAATTATGTATTTAAAAT
ATAGATGTTTGTTTAAAAATAGCATACAATTAA
Found at i:98928 original size:39 final size:40
Alignment explanation
Indices: 98766--98952 Score: 175
Period size: 40 Copynumber: 4.7 Consensus size: 40
98756 TAGTCTAGTT
* * * *
98766 GTGTTTACACTGTCAC-GACTAGTTCAGTAAAAAATATTTCA
1 GTGTTTACAGTGTCACTG-CCAGTTCAGT-AATAATATTGCA
* * * *
98807 GTGTTT-CAGCGTCACTACCAGTTCAGTAGTAATA-TCCA
1 GTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATTGCA
* * **
98845 TGTGTTTACAATGTCAGTGCCAGTTCAGTGGTAATATTGCA
1 -GTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATTGCA
* *
98886 GTGTTTACAGTGTCATTGCCAG-TCAGTAATAATATTGTA
1 GTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATTGCA
* *
98925 GTGTTTATAGTGTCACTGCCAATTCAGT
1 GTGTTTACAGTGTCACTGCCAGTTCAGT
98953 CACTTATTTT
Statistics
Matches: 120, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
38 3 0.03
39 44 0.37
40 64 0.53
41 9 0.08
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (40 bp):
GTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATTGCA
Found at i:98929 original size:79 final size:79
Alignment explanation
Indices: 98798--98952 Score: 179
Period size: 79 Copynumber: 2.0 Consensus size: 79
98788 TTCAGTAAAA
* * *
98798 AATATTTCAGTGTTTCAGCGTCACTACCAGTTCAGTAGTAATATCCATGTGTTTACAATGTCAGT
1 AATATTGCAGTGTTTCAGCGTCACTACCAGTTCAGTAATAATATCCATGTGTTTACAATGTCACT
*
98863 GCCAGTTCAGTGGT
66 GCCAATTCAGTGGT
* * * ** * *
98877 AATATTGCAGTGTTTACAGTGTCATTGCCAG-TCAGTAATAATAT-TGTAGTGTTTATAGTGTCA
1 AATATTGCAGTGTTT-CAGCGTCACTACCAGTTCAGTAATAATATCCAT-GTGTTTACAATGTCA
98940 CTGCCAATTCAGT
64 CTGCCAATTCAGT
98953 CACTTATTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
78 1 0.02
79 50 0.79
80 12 0.19
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (79 bp):
AATATTGCAGTGTTTCAGCGTCACTACCAGTTCAGTAATAATATCCATGTGTTTACAATGTCACT
GCCAATTCAGTGGT
Found at i:100843 original size:51 final size:51
Alignment explanation
Indices: 100767--100870 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
100757 TTCTAATGGT
100767 CTCCTGCACACTCACAAAGTGTGTTAGCTTACCCTTAGGCCTCATTCGGCC
1 CTCCTGCACACTCACAAAGTGTGTTAGCTTACCCTTAGGCCTCATTCGGCC
100818 CTCCTGCACACTCACAAAGTGTGTTAGCTTACCCTTAGGCCTCATTCGGCC
1 CTCCTGCACACTCACAAAGTGTGTTAGCTTACCCTTAGGCCTCATTCGGCC
100869 CT
1 CT
100871 TAAGGTCAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.19, C:0.36, G:0.17, T:0.28
Consensus pattern (51 bp):
CTCCTGCACACTCACAAAGTGTGTTAGCTTACCCTTAGGCCTCATTCGGCC
Found at i:102987 original size:21 final size:19
Alignment explanation
Indices: 102945--102988 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
102935 AAGCCTATTT
*
102945 AAATTATAAAAATTCATAA
1 AAATTATAAAAATTAATAA
102964 AAATTATAACTAAATTAATTAA
1 AAATTATAA--AAATTAA-TAA
102986 AAA
1 AAA
102989 AAAGTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
21 6 0.29
22 6 0.29
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATTATAAAAATTAATAA
Found at i:104671 original size:40 final size:40
Alignment explanation
Indices: 104626--104739 Score: 120
Period size: 40 Copynumber: 2.9 Consensus size: 40
104616 CATTTGGGTG
*
104626 TATTATCACTGAATTGGTAGTGACACTGTAAACACTACAA
1 TATTATTACTGAATTGGTAGTGACACTGTAAACACTACAA
* ** * *
104666 TATTATTACTAAATTGACAGTGAAACTGTAAACGCTACAA
1 TATTATTACTGAATTGGTAGTGACACTGTAAACACTACAA
** * * * *
104706 CGTTATTACTGTACTAGTTGTGACACTGTAAACA
1 TATTATTACTGAATTGGTAGTGACACTGTAAACA
104740 TTGCTAGACT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (40 bp):
TATTATTACTGAATTGGTAGTGACACTGTAAACACTACAA
Found at i:112525 original size:24 final size:24
Alignment explanation
Indices: 112498--112565 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
112488 TTAAACTCTG
*
112498 TCTGGGCTCGAATGAGCTAACTTA
1 TCTGGGCTCGAATGAGCTAACCTA
*
112522 TCTGGGCTCGTAA-CAGCTAACCTA
1 TCTGGGCTCG-AATGAGCTAACCTA
* *
112546 TCTAGGCTCGTATGAGCTAA
1 TCTGGGCTCGAATGAGCTAA
112566 TTTTGACTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.92
25 2 0.05
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (24 bp):
TCTGGGCTCGAATGAGCTAACCTA
Found at i:113302 original size:21 final size:21
Alignment explanation
Indices: 113268--113322 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
113258 TGTGTCACAT
* *
113268 GTATCAGTAAAACCATCTAGA
1 GTATCGGTAGAACCATCTAGA
*
113289 GTATCGGTAGAACCATCTCGA
1 GTATCGGTAGAACCATCTAGA
*
113310 GTATCGATAGAAC
1 GTATCGGTAGAAC
113323 TCCGCACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (21 bp):
GTATCGGTAGAACCATCTAGA
Found at i:117026 original size:40 final size:40
Alignment explanation
Indices: 116951--117030 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
116941 ATTATCATTG
*
116951 AACTGGCAGTGACACTGTAAACACTACAATATTATTACTA
1 AACTGGCAGTGAAACTGTAAACACTACAATATTATTACTA
* * * *
116991 AACTGGTAGTGAAATTGTAAACGCTGCAACT-TTATTACTA
1 AACTGGCAGTGAAACTGTAAACACTACAA-TATTATTACTA
117031 TATTAGCCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (40 bp):
AACTGGCAGTGAAACTGTAAACACTACAATATTATTACTA
Done.