Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010970.1 Kokia drynarioides strain JFW-HI SEQ_125939, 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: 184175
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:168 original size:19 final size:20
Alignment explanation
Indices: 142--185 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
132 AAAATTTAAA
142 TTTA-AATATATATT-AATT
1 TTTATAATATATATTAAATT
* *
160 TTTATAATATTTTTTAAATT
1 TTTATAATATATATTAAATT
180 TTTATA
1 TTTATA
186 TATTATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 8 0.36
20 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATAATATATATTAAATT
Found at i:188 original size:19 final size:21
Alignment explanation
Indices: 156--203 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
146 AATATATATT
156 AATTTTTATAATATT-TTTTA
1 AATTTTTATAATATTATTTTA
*
176 AATTTTTAT-ATATTATTTTG
1 AATTTTTATAATATTATTTTA
*
196 ATTTTTTA
1 AATTTTTA
204 AAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
AATTTTTATAATATTATTTTA
Found at i:217 original size:29 final size:29
Alignment explanation
Indices: 168--224 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
158 TTTTTATAAT
** *
168 ATTTTTTAAATTTTTATATAT-TATTTTG
1 ATTTTTTAAATTTAAAAATATATATTTTG
196 ATTTTTTAAAATTTAAAAATATATATTTT
1 ATTTTTT-AAATTTAAAAATATATATTTT
225 ATAATTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.29
29 11 0.46
30 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTAAATTTAAAAATATATATTTTG
Found at i:660 original size:16 final size:17
Alignment explanation
Indices: 625--672 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
615 AACTTAAAAA
*
625 AATATTTTTTATAATTTT
1 AATAATTTTTAT-ATTTT
*
643 AATACTTTTTAT-TTTT
1 AATAATTTTTATATTTT
659 AATAATTTTTATAT
1 AATAATTTTTATAT
673 ATTTTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 15 0.56
17 1 0.04
18 11 0.41
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
AATAATTTTTATATTTT
Found at i:663 original size:25 final size:27
Alignment explanation
Indices: 627--686 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
617 CTTAAAAAAA
*
627 TATTTTTTATAA-TTTTA-ATACTTTT
1 TATTTTTAATAATTTTTATATACTTTT
*
652 TATTTTTAATAATTTTTATATATTTTT
1 TATTTTTAATAATTTTTATATACTTTT
*
679 TAATTTTA
1 TATTTTTA
687 TTTAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 11 0.37
26 5 0.17
27 14 0.47
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (27 bp):
TATTTTTAATAATTTTTATATACTTTT
Found at i:2350 original size:23 final size:22
Alignment explanation
Indices: 2297--2348 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
2287 CATCAAACAT
2297 ACAAAAAATTGTAGGTTTTTTA
1 ACAAAAAATTGTAGGTTTTTTA
2319 ACAAAAAATTGTAGGTTTTTTA
1 ACAAAAAATTGTAGGTTTTTTA
2341 ACAAAAAA
1 ACAAAAAA
2349 ATCAGTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (22 bp):
ACAAAAAATTGTAGGTTTTTTA
Found at i:6611 original size:4 final size:4
Alignment explanation
Indices: 6602--6626 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6592 CCAATATACA
6602 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
6627 CCTTAGGGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:13239 original size:15 final size:14
Alignment explanation
Indices: 13221--13264 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
13211 TATTGTTTGG
13221 TTAATTAAAGTTTAA
1 TTAATT-AAGTTTAA
* *
13236 TTAAATTAATTTTGA
1 TT-AATTAAGTTTAA
13251 TTAATTAAGTTTAA
1 TTAATTAAGTTTAA
13265 ACAAAGTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 10 0.42
15 10 0.42
16 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TTAATTAAGTTTAA
Found at i:15508 original size:38 final size:35
Alignment explanation
Indices: 15464--15535 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
15454 AAATTTCGAA
15464 TTTCGAATTTCGATTTATTCGAATCGAGTTGAATTTTT
1 TTTCGAATTTCGA---ATTCGAATCGAGTTGAATTTTT
* * *
15502 TTTCGAATTTTGAGTTCGAATCGAGTTTAATTTT
1 TTTCGAATTTCGAATTCGAATCGAGTTGAATTTT
15536 AAATTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 19 0.61
38 12 0.39
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.50
Consensus pattern (35 bp):
TTTCGAATTTCGAATTCGAATCGAGTTGAATTTTT
Found at i:15716 original size:58 final size:58
Alignment explanation
Indices: 15651--15770 Score: 197
Period size: 58 Copynumber: 2.1 Consensus size: 58
15641 ACCCATCAAC
*
15651 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAA-AACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCT-AAATAACACTCAT
* *
15709 AAACTAAACCCAAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
15767 AAAC
1 AAAC
15771 AACATTTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
57 3 0.05
58 55 0.95
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
Found at i:18615 original size:27 final size:29
Alignment explanation
Indices: 18557--18615 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 29
18547 AACTGCACCC
* **
18557 ATATTATTTTTAATTTTTTGAATTTTTTAA
1 ATATTATTTTTAA-TTTTTAAATTTTCAAA
18587 ATATTA-TTTTAA-TTTTAAATTTTCAAA
1 ATATTATTTTTAATTTTTAAATTTTCAAA
18614 AT
1 AT
18616 TTTAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 14 0.54
29 6 0.23
30 6 0.23
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
ATATTATTTTTAATTTTTAAATTTTCAAA
Found at i:18731 original size:26 final size:24
Alignment explanation
Indices: 18696--18751 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 24
18686 TACACTTACA
*
18696 AAATAAATTTAAAATACACATAAGAT
1 AAATAAATTTAAAAAACACA-AA-AT
*
18722 AAATAAATTTAAAAAATACAAAAT
1 AAATAAATTTAAAAAACACAAAAT
18746 AAATAA
1 AAATAA
18752 TTAATATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 8 0.29
25 2 0.07
26 18 0.64
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (24 bp):
AAATAAATTTAAAAAACACAAAAT
Found at i:18912 original size:42 final size:42
Alignment explanation
Indices: 18849--18976 Score: 193
Period size: 42 Copynumber: 3.0 Consensus size: 42
18839 CTAATTTAAT
* * * *
18849 TTAAATTATGATCTATCAAATTTGACAGGCCTAACCTGGAAA
1 TTAAATTATTATCTATCAAATTTGACAGGCCAAAACTAGAAA
* * *
18891 TTATATTATTATCTACCAAATTTGACTGGCCAAAACTAGAAA
1 TTAAATTATTATCTATCAAATTTGACAGGCCAAAACTAGAAA
18933 TTAAATTATTATCTATCAAATTTGACAGGCCAAAACTAGAAA
1 TTAAATTATTATCTATCAAATTTGACAGGCCAAAACTAGAAA
18975 TT
1 TT
18977 TACATCTTGG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.33
Consensus pattern (42 bp):
TTAAATTATTATCTATCAAATTTGACAGGCCAAAACTAGAAA
Found at i:19329 original size:18 final size:18
Alignment explanation
Indices: 19270--19329 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
19260 AACTCAACTT
19270 TTTTTACTTATTATAATA
1 TTTTTACTTATTATAATA
* *
19288 TTTATA-TTAATGCACTACATA
1 TTTTTACTT-AT-TA-TA-ATA
19309 TTTTTACTTATTATAATA
1 TTTTTACTTATTATAATA
19327 TTT
1 TTT
19330 ATTCAATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 2 0.06
18 13 0.39
19 3 0.09
20 3 0.09
21 10 0.30
22 2 0.06
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTTACTTATTATAATA
Found at i:21397 original size:39 final size:39
Alignment explanation
Indices: 21353--21471 Score: 220
Period size: 39 Copynumber: 3.1 Consensus size: 39
21343 TATAAATTAT
* *
21353 ATAATATATAAAAATAACTTATTACAAAATTAAGAAATA
1 ATAATATATAAAAATAACATGTTACAAAATTAAGAAATA
21392 ATAATATATAAAAATAACATGTTACAAAATTAAGAAATA
1 ATAATATATAAAAATAACATGTTACAAAATTAAGAAATA
21431 ATAATATATAAAAATAACATGTTACAAAATTAAGAAATA
1 ATAATATATAAAAATAACATGTTACAAAATTAAGAAATA
21470 AT
1 AT
21472 TGAGTTAAAC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.29
Consensus pattern (39 bp):
ATAATATATAAAAATAACATGTTACAAAATTAAGAAATA
Found at i:22771 original size:28 final size:28
Alignment explanation
Indices: 22739--22820 Score: 155
Period size: 28 Copynumber: 2.9 Consensus size: 28
22729 TAGTAAATGC
*
22739 TGATCTATATTTGTTGGATAACTTGTAT
1 TGATCTATATTTGCTGGATAACTTGTAT
22767 TGATCTATATTTGCTGGATAACTTGTAT
1 TGATCTATATTTGCTGGATAACTTGTAT
22795 TGATCTATATTTGCTGGATAACTTGT
1 TGATCTATATTTGCTGGATAACTTGT
22821 GTCGTTTGGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (28 bp):
TGATCTATATTTGCTGGATAACTTGTAT
Found at i:29122 original size:31 final size:31
Alignment explanation
Indices: 29057--29128 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
29047 CTAAAAAATC
* * *
29057 AATTTGACTATTTTTGAAAGGTTGATGGTTA
1 AATTTGACTATTTTTAAAAGCTTGATGGTCA
29088 AATTTGACTATTTTTAAAAGCTTGA-GGATCA
1 AATTTGACTATTTTTAAAAGCTTGATGG-TCA
*
29119 AATTTAACTA
1 AATTTGACTA
29129 AAAGAAGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 2 0.06
31 34 0.94
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
AATTTGACTATTTTTAAAAGCTTGATGGTCA
Found at i:34615 original size:21 final size:20
Alignment explanation
Indices: 34589--34640 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
34579 TATAACATAG
*
34589 TAAAAATTGTCTAGAAAATCT
1 TAAAAATTGTCTA-AAAATAT
* *
34610 TAAAAATTATTTAAAAATAT
1 TAAAAATTGTCTAAAAATAT
34630 TAAAAAGTTGT
1 TAAAAA-TTGT
34641 AAAATTTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.37
Consensus pattern (20 bp):
TAAAAATTGTCTAAAAATAT
Found at i:34626 original size:20 final size:21
Alignment explanation
Indices: 34589--34635 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
34579 TATAACATAG
* *
34589 TAAAAATTGTCTAGAAAATCT
1 TAAAAATTATCTAGAAAATAT
*
34610 TAAAAATTATTTA-AAAATAT
1 TAAAAATTATCTAGAAAATAT
34630 TAAAAA
1 TAAAAA
34636 GTTGTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.34
Consensus pattern (21 bp):
TAAAAATTATCTAGAAAATAT
Found at i:34653 original size:20 final size:19
Alignment explanation
Indices: 34630--34686 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
34620 TTAAAAATAT
34630 TAAAAAGTTGTAAAATTTCC
1 TAAAAA-TTGTAAAATTTCC
*
34650 TAAAAATTTGTTTAAAA-TTCT
1 TAAAAA-TTG--TAAAATTTCC
*
34671 TTAAAATTGTAAAATT
1 TAAAAATTGTAAAATT
34687 AATTATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 5 0.16
19 1 0.03
20 12 0.39
21 8 0.26
22 5 0.16
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (19 bp):
TAAAAATTGTAAAATTTCC
Found at i:34655 original size:40 final size:40
Alignment explanation
Indices: 34610--34686 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
34600 TAGAAAATCT
34610 TAAAAA-TTATTTAAAAATATTAAAAAGTTGTAAAATTTCC
1 TAAAAATTTATTTAAAAATATTAAAAA-TTGTAAAATTTCC
* * * *
34650 TAAAAATTTGTTTAAAATTCTTTAAAATTGTAAAATT
1 TAAAAATTTATTTAAAAATATTAAAAATTGTAAAATT
34687 AATTATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 16 0.50
41 16 0.50
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (40 bp):
TAAAAATTTATTTAAAAATATTAAAAATTGTAAAATTTCC
Found at i:34860 original size:19 final size:21
Alignment explanation
Indices: 34828--34866 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
34818 AAAGTTTTGG
*
34828 TAAATAAACTAAACTTTGAAC
1 TAAATAAACTAAACATTGAAC
34849 TAAA-AAAC-AAACATTGAA
1 TAAATAAACTAAACATTGAA
34867 TTCATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (21 bp):
TAAATAAACTAAACATTGAAC
Found at i:35244 original size:28 final size:28
Alignment explanation
Indices: 35186--35283 Score: 74
Period size: 28 Copynumber: 3.3 Consensus size: 28
35176 TATTTTCAAA
* *
35186 ATAATTTTTTAAAT-ATTTTTTACTGATTTT
1 ATAA-TTTTTAAATAATTTTTCA-AG-TTTT
*
35216 ATAATTTATT-TATAATTTTTCAAGTTTT
1 ATAATTT-TTAAATAATTTTTCAAGTTTT
* *
35244 ATAGTTTTTAAATAATTTTTCATAATTTT
1 ATAATTTTTAAATAATTTTTCA-AGTTTT
35273 AAATAATTTTT
1 --ATAATTTTT
35284 TGATTGATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
27 2 0.04
28 21 0.38
29 11 0.20
30 13 0.24
31 8 0.15
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (28 bp):
ATAATTTTTAAATAATTTTTCAAGTTTT
Found at i:43723 original size:48 final size:48
Alignment explanation
Indices: 43652--43748 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
43642 TTGTTGTTAA
*
43652 GAGAATGATTAAAAAAAATTCATTGGTTTAGAAGTACCATTTTGTAAT
1 GAGAATGATTAAAAAAAATTCATTGGTTTAGAAGTACCATATTGTAAT
*
43700 GAGAATGATTAAAAAAAGTTCATTGGTTTAGAAGTACCATATTGTAAT
1 GAGAATGATTAAAAAAAATTCATTGGTTTAGAAGTACCATATTGTAAT
43748 G
1 G
43749 CTATGAAAGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (48 bp):
GAGAATGATTAAAAAAAATTCATTGGTTTAGAAGTACCATATTGTAAT
Found at i:43821 original size:42 final size:42
Alignment explanation
Indices: 43762--43841 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
43752 TGAAAGGGTT
43762 GCAAGGATGATATATATTAAAGAAGATTGATTAAAATACATG
1 GCAAGGATGATATATATTAAAGAAGATTGATTAAAATACATG
43804 GCAAGGATGATATATATTAAAGAAGATTGATTAAAATA
1 GCAAGGATGATATATATTAAAGAAGATTGATTAAAATA
43842 TATTTTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.29
Consensus pattern (42 bp):
GCAAGGATGATATATATTAAAGAAGATTGATTAAAATACATG
Found at i:43842 original size:22 final size:22
Alignment explanation
Indices: 43775--43842 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
43765 AGGATGATAT
43775 ATATTAAAGAAGATTGATTAAA
1 ATATTAAAGAAGATTGATTAAA
* ** *
43797 ATA-CATGGCAAGGA-TGA-T-AT
1 ATATTAAAG-AA-GATTGATTAAA
43817 ATATTAAAGAAGATTGATTAAA
1 ATATTAAAGAAGATTGATTAAA
43839 ATAT
1 ATAT
43843 ATTTTTTCAA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 2 0.06
20 9 0.28
21 6 0.19
22 13 0.41
23 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.31
Consensus pattern (22 bp):
ATATTAAAGAAGATTGATTAAA
Found at i:43943 original size:15 final size:16
Alignment explanation
Indices: 43925--43960 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
43915 GAAAAGCTAG
43925 TATTTAAAAT-TGAAA
1 TATTTAAAATATGAAA
*
43940 TATTTAGAATATGAAA
1 TATTTAAAATATGAAA
43956 TATTT
1 TATTT
43961 TGTGATATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (16 bp):
TATTTAAAATATGAAA
Found at i:48014 original size:19 final size:18
Alignment explanation
Indices: 47990--48031 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
47980 TATTATTAAT
*
47990 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAAT-A
*
48009 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
48027 ATATT
1 ATATT
48032 AAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTTATAATTAAAATA
Found at i:48090 original size:16 final size:16
Alignment explanation
Indices: 48059--48095 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
48049 ATGTGAAGAA
48059 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
48075 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
48091 TATTA
1 TATTA
48096 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:55369 original size:31 final size:31
Alignment explanation
Indices: 55304--55369 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
55294 GAAAAATTTG
* *
55304 ATTAAAAATATTAAATTCGATAAATATTTTA
1 ATTAAAAATATTAAATTCGATAAATATATAA
55335 ATTAAAAATATTAAATTC-ATTTAAA-ATATAA
1 ATTAAAAATATTAAATTCGA--TAAATATATAA
55366 ATTA
1 ATTA
55370 GGTTTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 1 0.03
31 26 0.84
32 4 0.13
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (31 bp):
ATTAAAAATATTAAATTCGATAAATATATAA
Found at i:56074 original size:18 final size:18
Alignment explanation
Indices: 56036--56075 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
56026 TAAGGTTTAG
56036 AAAATTTAGAAATACTGGT
1 AAAATTTAGAAATA-TGGT
56055 AAAATATTAGAAAT-TGGT
1 AAAAT-TTAGAAATATGGT
56073 AAA
1 AAA
56076 GTCTCGTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 8 0.40
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.30
Consensus pattern (18 bp):
AAAATTTAGAAATATGGT
Found at i:56175 original size:20 final size:20
Alignment explanation
Indices: 56108--56221 Score: 51
Period size: 20 Copynumber: 5.9 Consensus size: 20
56098 GATCGAAATT
* **
56108 TTGGTAAATCGTTACATATT
1 TTGGTAAATCGTTAGATAAA
**
56128 TTGGTAAATTTTTAG--AAA
1 TTGGTAAATCGTTAGATAAA
*
56146 TGCTGATAAATCGTTAGATAAA
1 T--TGGTAAATCGTTAGATAAA
* * *
56168 TTGGTAAAGCGATAGA-AAC
1 TTGGTAAATCGTTAGATAAA
* ***
56187 TT--T-GATCGTTAGATTTT
1 TTGGTAAATCGTTAGATAAA
56204 TTGGTAAATCGTTAGATA
1 TTGGTAAATCGTTAGATA
56222 TATTTTTGAT
Statistics
Matches: 66, Mismatches: 20, Indels: 16
0.65 0.20 0.16
Matches are distributed among these distances:
16 7 0.11
17 3 0.05
18 2 0.03
19 5 0.08
20 45 0.68
22 4 0.06
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGGTAAATCGTTAGATAAA
Found at i:56283 original size:20 final size:20
Alignment explanation
Indices: 56239--56276 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56229 GATAAGACCA
* *
56239 TTAAATATTTTGATAAATGC
1 TTAAAAATTTTAATAAATGC
56259 TTAAAAATTTTAATAAAT
1 TTAAAAATTTTAATAAAT
56277 CGTTAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAAAAATTTTAATAAATGC
Found at i:63277 original size:3 final size:3
Alignment explanation
Indices: 63265--63298 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
63255 TGCCATTTCG
63265 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
63299 TTGTTGTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:70045 original size:4 final size:4
Alignment explanation
Indices: 70036--70065 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
70026 CTTTTTACAC
70036 TATT TATT TATT TATT TATT TATAT TATT T
1 TATT TATT TATT TATT TATT TAT-T TATT T
70066 TTTTTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:70053 original size:12 final size:13
Alignment explanation
Indices: 70036--70080 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
70026 CTTTTTACAC
70036 TATTTATTTAT-T
1 TATTTATTTATAT
70048 TATTTATTTATAT
1 TATTTATTTATAT
* *
70061 TATTTTTTTTATAA
1 TA-TTTATTTATAT
70075 TATTTA
1 TATTTA
70081 AATGTATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.39
13 6 0.21
14 11 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTATTTATAT
Found at i:70071 original size:14 final size:14
Alignment explanation
Indices: 70038--70079 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
70028 TTTTACACTA
70038 TTTATTTAT-TTA-
1 TTTATTTATATTAT
70050 TTTATTTATATTAT
1 TTTATTTATATTAT
* *
70064 TTTTTTTATAATAT
1 TTTATTTATATTAT
70078 TT
1 TT
70080 AAATGTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 9 0.35
13 3 0.12
14 14 0.54
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTATATTAT
Found at i:76386 original size:209 final size:210
Alignment explanation
Indices: 75996--76415 Score: 736
Period size: 209 Copynumber: 2.0 Consensus size: 210
75986 GATTGTTTAC
* *
75996 CTCTTTAATATCCAAGAAACTTATTTCTGTATCTTCTCAATCACGATATAAAATAGATTTTACTA
1 CTCTTTAATATCCAAGAAACTTATTTCTATATCTTCTCAATCACGATATAAAATAGATTTTAATA
*
76061 ATAAATCATGATTTCTTGTTCTTTAATTGTTTTTTCAACTAAAAATTGTGAGAGCTTAATAGGAG
66 ATAAATCATGATTTCTTGTTCTTTAATTGTTTTTTCAACTAAAAATTGTGAGAGCTTAATAAGAG
76126 TCCTTCTAAAATTTGCTCTCTGGTCAGTAATATGAGTTTTTCATATTTCATTAATAAAATTATAT
131 TCCTTCTAAAATTTGCTCTCTGGTCAGTAATATGAGTTTTTCATATTTCATTAATAAAATTATAT
76191 AACTTTAGTGGTAAA
196 AACTTTAGTGGTAAA
*
76206 CTCTTTAATATCCAAGAAACTTATTTTTATATCTTCTCAATCACGATATAAAATAGATTTTAATA
1 CTCTTTAATATCCAAGAAACTTATTTCTATATCTTCTCAATCACGATATAAAATAGATTTTAATA
* *
76271 ATAAATCATGATTTTCTTGTTCTTTAGTTG-TTTTT-AATTAAAAATTGTGAGAGCTTAATAAGA
66 ATAAATCATGA-TTTCTTGTTCTTTAATTGTTTTTTCAACTAAAAATTGTGAGAGCTTAATAAGA
* *
76334 GTCCTTCTAAATTTTGCTCTCTGGTCAGTAATATGGGTTTTTCATATTTCATTAATAAAATTATA
130 GTCCTTCTAAAATTTGCTCTCTGGTCAGTAATATGAGTTTTTCATATTTCATTAATAAAATTATA
*
76399 TAATTTTAGTGGTAAA
195 TAACTTTAGTGGTAAA
76415 C
1 C
76416 CTGGATTATA
Statistics
Matches: 200, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
209 105 0.52
210 78 0.39
211 17 0.09
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.43
Consensus pattern (210 bp):
CTCTTTAATATCCAAGAAACTTATTTCTATATCTTCTCAATCACGATATAAAATAGATTTTAATA
ATAAATCATGATTTCTTGTTCTTTAATTGTTTTTTCAACTAAAAATTGTGAGAGCTTAATAAGAG
TCCTTCTAAAATTTGCTCTCTGGTCAGTAATATGAGTTTTTCATATTTCATTAATAAAATTATAT
AACTTTAGTGGTAAA
Found at i:77002 original size:16 final size:16
Alignment explanation
Indices: 76981--77012 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
76971 AAATTTTTTT
76981 ATTCCTTTCTTTATAG
1 ATTCCTTTCTTTATAG
76997 ATTCCTTTCTTTATAG
1 ATTCCTTTCTTTATAG
77013 CTAGCAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (16 bp):
ATTCCTTTCTTTATAG
Found at i:81810 original size:133 final size:131
Alignment explanation
Indices: 81574--81828 Score: 377
Period size: 133 Copynumber: 1.9 Consensus size: 131
81564 CACGATCGTA
** ** *
81574 TCGTAGGTCGTGTGCCAAACCATGTATGTGTTCAAGTTGTGTCGTCGGTCGTGTCGCAGGCCGTG
1 TCGTAGGTCGTGTGCCAAACCATGTATGTGTTCAAGTTGTGTCCACAATCGTGTCGCAGGCCGTA
* * *
81639 TTCCAGACTGTGTAACCTGAATCAAAATATAAATGACACATGGTCGTGTGAAGTGACATGGCCAT
66 TTCCAAACTGTGTAACCTAAATCAAAATATAAATGACACATAGTCGTGTGAAGTGACATGGCCAT
81704 G
131 G
* * *
81705 TCGTAGGTCGTGTGTCAAACCGTGTATGTGTTCCAAGTTAG-GTCACACAATCTTGTCGCAGGCC
1 TCGTAGGTCGTGTGCCAAACCATGTATGTGTT-CAAGTT-GTGTC-CACAATCGTGTCGCAGGCC
81769 GTATTCCAAACTGTGTAACCTAAATCAAAATATAAATGACACATAGTCGTGTGAAGTGAC
63 GTATTCCAAACTGTGTAACCTAAATCAAAATATAAATGACACATAGTCGTGTGAAGTGAC
81829 TGAATGTAGC
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
131 30 0.27
132 9 0.08
133 71 0.65
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (131 bp):
TCGTAGGTCGTGTGCCAAACCATGTATGTGTTCAAGTTGTGTCCACAATCGTGTCGCAGGCCGTA
TTCCAAACTGTGTAACCTAAATCAAAATATAAATGACACATAGTCGTGTGAAGTGACATGGCCAT
G
Found at i:85852 original size:34 final size:34
Alignment explanation
Indices: 85809--85878 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
85799 CAAGCATTGT
85809 TAGAATGAGAATAATTAAATGTCTAGTAAACCCA
1 TAGAATGAGAATAATTAAATGTCTAGTAAACCCA
85843 TAGAATGAGAATAATTAAATGTCTAGTAAACCCA
1 TAGAATGAGAATAATTAAATGTCTAGTAAACCCA
85877 TA
1 TA
85879 TGACTGGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.27
Consensus pattern (34 bp):
TAGAATGAGAATAATTAAATGTCTAGTAAACCCA
Found at i:110199 original size:53 final size:53
Alignment explanation
Indices: 110099--110204 Score: 126
Period size: 53 Copynumber: 2.0 Consensus size: 53
110089 AAAATCATAA
* * *
110099 TTCATATAATCTCTTTCTAAAAAAAATAATACCAATCAAATATAATTGAGAAC
1 TTCATACAATCCCTTTCTAAAAAAAATAATACCAATCAAATAAAATTGAGAAC
* * *
110152 TTCATACAATCCCTTTCTCAAAAAAA-AATACTAA-GATAATCAAAATTGAGAAC
1 TTCATACAATCCCTTTCTAAAAAAAATAATACCAATCA-AAT-AAAATTGAGAAC
110205 CTGATCCACC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 1 0.02
52 10 0.22
53 34 0.76
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (53 bp):
TTCATACAATCCCTTTCTAAAAAAAATAATACCAATCAAATAAAATTGAGAAC
Found at i:113352 original size:36 final size:36
Alignment explanation
Indices: 113312--113402 Score: 89
Period size: 37 Copynumber: 2.5 Consensus size: 36
113302 TAAGTAGAGT
113312 TGAAATTCTTTTAACACTATTTGATATAAAGCATAG
1 TGAAATTCTTTTAACACTATTTGATATAAAGCATAG
**
113348 TGAAATTCGATACTTT---TTTATTTGATATAAAGCATAG
1 TGAAATTC--T--TTTAACACTATTTGATATAAAGCATAG
* *
113385 TAAAATTCTTGTAACACT
1 TGAAATTCTTTTAACACT
113403 TTTTTTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
33 2 0.05
35 1 0.02
36 9 0.21
37 26 0.62
38 1 0.02
40 3 0.07
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (36 bp):
TGAAATTCTTTTAACACTATTTGATATAAAGCATAG
Found at i:114361 original size:17 final size:17
Alignment explanation
Indices: 114335--114371 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
114325 TTTAATTTTT
114335 TAAA-AATAAAAAAATA
1 TAAATAATAAAAAAATA
*
114351 TAAATAATAAAATAATA
1 TAAATAATAAAAAAATA
114368 -AAAT
1 TAAAT
114372 TATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATAATAAAAAAATA
Found at i:114386 original size:17 final size:17
Alignment explanation
Indices: 114366--114401 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
114356 AATAAAATAA
*
114366 TAAAATTATATTTTTAG
1 TAAAATTATATTTCTAG
114383 TAAAATTATATTTCTAG
1 TAAAATTATATTTCTAG
114400 TA
1 TA
114402 TCATAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
TAAAATTATATTTCTAG
Found at i:117210 original size:23 final size:22
Alignment explanation
Indices: 117180--117255 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 22
117170 CATTAGCGCA
*
117180 CTTACTGTTCAGCACTGTGTGTT
1 CTTACTGTTCTGCACTGTGTG-T
*
117203 CTTACTGTTCTGCACTGCGTGT
1 CTTACTGTTCTGCACTGTGTGT
*
117225 GCCTACTGATT-TGCACTGTGTG-
1 -CTTACTG-TTCTGCACTGTGTGT
117247 CTTACTGTT
1 CTTACTGTT
117256 TCCCCAGCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 2 0.04
21 6 0.13
22 1 0.02
23 35 0.76
24 2 0.04
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (22 bp):
CTTACTGTTCTGCACTGTGTGT
Found at i:120242 original size:23 final size:23
Alignment explanation
Indices: 120178--120279 Score: 105
Period size: 23 Copynumber: 4.4 Consensus size: 23
120168 AGTGCTGGGG
*
120178 AACAGTAAGCACACACAATGCAA
1 AACAGTAAGCACACACAGTGCAA
* * * **
120201 ATCAGTAGGTACATGCAGTGCAA
1 AACAGTAAGCACACACAGTGCAA
* *
120224 AACAATAAGCACACACAGTGCGA
1 AACAGTAAGCACACACAGTGCAA
* **
120247 ATCAGTAAGCACACACAGTGCTG
1 AACAGTAAGCACACACAGTGCAA
120270 AACAGTAAGC
1 AACAGTAAGC
120280 GCGCTAATGT
Statistics
Matches: 61, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (23 bp):
AACAGTAAGCACACACAGTGCAA
Found at i:120279 original size:46 final size:46
Alignment explanation
Indices: 120177--120279 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
120167 AAGTGCTGGG
* * **
120177 GAACAGTAAGCACACACAATGCAAATCAGTAGGTACATGCAGTGCA
1 GAACAGTAAGCACACACAATGCAAATCAGTAAGCACACACAGTGCA
* * * * *
120223 AAACAATAAGCACACACAGTGCGAATCAGTAAGCACACACAGTGCT
1 GAACAGTAAGCACACACAATGCAAATCAGTAAGCACACACAGTGCA
120269 GAACAGTAAGC
1 GAACAGTAAGC
120280 GCGCTAATGT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (46 bp):
GAACAGTAAGCACACACAATGCAAATCAGTAAGCACACACAGTGCA
Found at i:122252 original size:24 final size:24
Alignment explanation
Indices: 122220--122272 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
122210 TGGAAAGTGC
*
122220 CTAATGCTAACGCCAATGCCAACG
1 CTAAGGCTAACGCCAATGCCAACG
* * * *
122244 CTAAGGCTAAGGCTAATGCTAATG
1 CTAAGGCTAACGCCAATGCCAACG
122268 CTAAG
1 CTAAG
122273 CCCTTGCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (24 bp):
CTAAGGCTAACGCCAATGCCAACG
Found at i:126014 original size:37 final size:37
Alignment explanation
Indices: 125962--126044 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 37
125952 TGTTATTTTT
*
125962 AAATTTTAAAGTAAAATAT-AA-AAT-AAATTCATTGAA
1 AAATTTTAAAGTAAAAT-TGAATAATAAAATTCAAT-AA
*
125998 AATATTTTAAATTAAAATTGAATAATAAAATTCAATAA
1 AA-ATTTTAAAGTAAAATTGAATAATAAAATTCAATAA
126036 AAATTTTAA
1 AAATTTTAA
126045 CTTTAGTAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 3 0.07
37 23 0.56
38 7 0.17
39 8 0.20
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (37 bp):
AAATTTTAAAGTAAAATTGAATAATAAAATTCAATAA
Found at i:127944 original size:23 final size:23
Alignment explanation
Indices: 127880--127946 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
127870 GTGTTTTTTT
*
127880 TACTGTTTTGATTGCTATTTTGG
1 TACTGTTTTTATTGCTATTTTGG
* * *
127903 TGCTACTTTTT-TTACTATTTTGG
1 TACT-GTTTTTATTGCTATTTTGG
*
127926 TACTGTTTTTATTGTTATTTT
1 TACTGTTTTTATTGCTATTTT
127947 TGTTGCTATT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 5 0.15
23 25 0.74
24 4 0.12
ACGTcount: A:0.13, C:0.09, G:0.15, T:0.63
Consensus pattern (23 bp):
TACTGTTTTTATTGCTATTTTGG
Found at i:127982 original size:46 final size:47
Alignment explanation
Indices: 127873--127993 Score: 131
Period size: 47 Copynumber: 2.6 Consensus size: 47
127863 TATTTTGGTG
* * *
127873 TTTTTTTTACTGTTTTGATTGCTA-TTTTGGTGCTACTTTTTTTACTA
1 TTTTTGTTACTGTTTT-ATTGTTATTTTTGGTGCTACTTTTTCTACTA
* * *
127920 -TTTTGGTACTGTTTTTATTGTTATTTTTGTTGCTA-TTTTTCTATTA
1 TTTTTGTTACTG-TTTTATTGTTATTTTTGGTGCTACTTTTTCTACTA
*
127966 TTTTTGTTGCTGTTTTAGTTGTTATTTT
1 TTTTTGTTACTGTTTTA-TTGTTATTTT
127994 GATTGTTTGG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
46 29 0.47
47 33 0.53
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (47 bp):
TTTTTGTTACTGTTTTATTGTTATTTTTGGTGCTACTTTTTCTACTA
Found at i:127994 original size:23 final size:23
Alignment explanation
Indices: 127932--127993 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
127922 TTGGTACTGT
*
127932 TTTTATTGTTATTTTTGTTGCTA
1 TTTTATTGTTATTTTTGTTGCTG
*
127955 TTTT-TCTATTATTTTTGTTGCTG
1 TTTTAT-TGTTATTTTTGTTGCTG
127978 TTTTAGTTGTTATTTT
1 TTTTA-TTGTTATTTT
127994 GATTGTTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 1 0.03
23 23 0.70
24 8 0.24
25 1 0.03
ACGTcount: A:0.11, C:0.05, G:0.13, T:0.71
Consensus pattern (23 bp):
TTTTATTGTTATTTTTGTTGCTG
Found at i:127994 original size:46 final size:47
Alignment explanation
Indices: 127873--127994 Score: 126
Period size: 46 Copynumber: 2.6 Consensus size: 47
127863 TATTTTGGTG
* * *
127873 TTTTTTTTACTGTTTT-GATTGCTATTTTGGTGCTACTTTTTTTACTA
1 TTTTTGTTACTGTTTTAG-TTGTTATTTTGGTGCTACTTTTTCTACTA
* * *
127920 -TTTTGGTACTGTTTTTA-TTGTTATTTTTGTTGCTA-TTTTTCTATTA
1 TTTTTGTTACTG-TTTTAGTTGTTA-TTTTGGTGCTACTTTTTCTACTA
*
127966 TTTTTGTTGCTGTTTTAGTTGTTATTTTG
1 TTTTTGTTACTGTTTTAGTTGTTATTTTG
127995 ATTGTTTGGA
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
46 33 0.53
47 29 0.47
ACGTcount: A:0.11, C:0.07, G:0.15, T:0.66
Consensus pattern (47 bp):
TTTTTGTTACTGTTTTAGTTGTTATTTTGGTGCTACTTTTTCTACTA
Found at i:132908 original size:15 final size:16
Alignment explanation
Indices: 132888--132918 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
132878 CAAACATTAA
132888 AAAATAAA-TAAATTT
1 AAAATAAATTAAATTT
132903 AAAATAAATTAAATTT
1 AAAATAAATTAAATTT
132919 TTTTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAAATTAAATTT
Found at i:132959 original size:24 final size:24
Alignment explanation
Indices: 132932--132980 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
132922 TAATATTAAG
132932 ATAGTTGCAAATAAATTAGTAAAA
1 ATAGTTGCAAATAAATTAGTAAAA
132956 ATAGTTGCAAATAAATTAGTAAAA
1 ATAGTTGCAAATAAATTAGTAAAA
132980 A
1 A
132981 AATTAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (24 bp):
ATAGTTGCAAATAAATTAGTAAAA
Found at i:132991 original size:23 final size:24
Alignment explanation
Indices: 132939--132993 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
132929 AAGATAGTTG
* *
132939 CAAATAAATTAGTAAAAATAGTTG
1 CAAATAAATTAGTAAAAATAATTA
132963 CAAATAAATTAGTAAAAA-AATTA
1 CAAATAAATTAGTAAAAATAATTA
132986 -ACAATAAA
1 CA-AATAAA
132994 ACGTAAGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 1 0.04
23 9 0.32
24 18 0.64
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (24 bp):
CAAATAAATTAGTAAAAATAATTA
Found at i:133164 original size:21 final size:21
Alignment explanation
Indices: 133100--133176 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
133090 AAAACAGTAG
* *
133100 CAAAAATAACAGCAAACAACAT
1 CAAAAATAACAGCAGA-AACAA
* ** * *
133122 TAAAAATAACAAAAGTAGCAA
1 CAAAAATAACAGCAGAAACAA
133143 CAAAAATAACAGCAGAAACAA
1 CAAAAATAACAGCAGAAACAA
133164 CACGAAAATAACA
1 CA--AAAATAACA
133177 ACCAAAACAG
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
21 21 0.51
22 11 0.27
23 9 0.22
ACGTcount: A:0.65, C:0.18, G:0.08, T:0.09
Consensus pattern (21 bp):
CAAAAATAACAGCAGAAACAA
Found at i:133201 original size:19 final size:19
Alignment explanation
Indices: 133177--133245 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 19
133167 GAAAATAACA
133177 ACCAAAACAGTAAAAAAGC
1 ACCAAAACAGTAAAAAAGC
133196 ACCAAAACAGTAAAAAAACAGC
1 ACCAAAACAGT--AAAAA-AGC
*
133218 AACCAAAACAAT-AAAAAGC
1 -ACCAAAACAGTAAAAAAGC
133237 ACCAAAACA
1 ACCAAAACA
133246 ACAATATAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
18 9 0.20
19 14 0.31
20 4 0.09
21 5 0.11
22 3 0.07
23 10 0.22
ACGTcount: A:0.65, C:0.23, G:0.07, T:0.04
Consensus pattern (19 bp):
ACCAAAACAGTAAAAAAGC
Found at i:133226 original size:23 final size:22
Alignment explanation
Indices: 133175--133234 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
133165 ACGAAAATAA
133175 CAACCAAAACAGT--AAAAAAG
1 CAACCAAAACAGTAAAAAAAAG
133195 C-ACCAAAACAGTAAAAAAACAG
1 CAACCAAAACAGTAAAAAAA-AG
*
133217 CAACCAAAACAATAAAAA
1 CAACCAAAACAGTAAAAA
133235 GCACCAAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
19 11 0.31
20 1 0.03
21 5 0.14
22 3 0.09
23 15 0.43
ACGTcount: A:0.67, C:0.22, G:0.07, T:0.05
Consensus pattern (22 bp):
CAACCAAAACAGTAAAAAAAAG
Found at i:133546 original size:14 final size:14
Alignment explanation
Indices: 133527--133555 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
133517 CATATTGTGA
133527 TGTATTTGAGACAT
1 TGTATTTGAGACAT
133541 TGTATTTGAGACAT
1 TGTATTTGAGACAT
133555 T
1 T
133556 TATGATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TGTATTTGAGACAT
Found at i:135108 original size:12 final size:12
Alignment explanation
Indices: 135091--135116 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
135081 TTGCTCTGTT
135091 TTATTTTTTGTC
1 TTATTTTTTGTC
135103 TTATTTTTTGTC
1 TTATTTTTTGTC
135115 TT
1 TT
135117 CCTTTCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (12 bp):
TTATTTTTTGTC
Found at i:143061 original size:18 final size:19
Alignment explanation
Indices: 143030--143073 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
143020 ACTCCACCAA
143030 AAATAT-AA-TATATATTT
1 AAATATAAACTATATATTT
143047 AAAT-TAAACTATATATTT
1 AAATATAAACTATATATTT
143065 AAATATAAA
1 AAATATAAA
143074 TAATAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.04
17 6 0.25
18 13 0.54
19 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATATAAACTATATATTT
Found at i:143420 original size:63 final size:60
Alignment explanation
Indices: 143353--143493 Score: 142
Period size: 63 Copynumber: 2.2 Consensus size: 60
143343 TTTTAAATTT
* * * *
143353 AAAAAAAAAATAAATCATTTGAGATTTAAGGAAAGTGGTGGCGTCATTTAATATGACCCCACA
1 AAAAAAAAAATAAATAAATT--GATTT-AGGAAAGTGGTGACGTCATTTAATATGACACCACA
*
143416 AAAAAATCATTTAAA-AAA-AAATTGATTTAGGAAAGTGGTGACGTCATTTAATATGACACTACA
1 AAAAAA--A---AAATAAATAAATTGATTTAGGAAAGTGGTGACGTCATTTAATATGACACCACA
*
143479 AAAAAAAAATTAAAT
1 AAAAAAAAAATAAAT
143494 TTTAAAAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
58 2 0.03
59 3 0.05
61 1 0.02
63 44 0.68
64 5 0.08
65 1 0.02
66 3 0.05
67 3 0.05
68 3 0.05
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (60 bp):
AAAAAAAAAATAAATAAATTGATTTAGGAAAGTGGTGACGTCATTTAATATGACACCACA
Found at i:144165 original size:27 final size:25
Alignment explanation
Indices: 144135--144194 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 25
144125 TGATAATTAA
*
144135 GTTTATTTTGATATTTATATATTTTTT
1 GTTTATTTTGATATTTA-A-ATTTATT
*
144162 GTTTAATTTGATATTTAAATTTATT
1 GTTTATTTTGATATTTAAATTTATT
144187 -TTTATTTT
1 GTTTATTTT
144195 TTAAATTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.23
25 6 0.20
26 1 0.03
27 16 0.53
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (25 bp):
GTTTATTTTGATATTTAAATTTATT
Found at i:146394 original size:2 final size:2
Alignment explanation
Indices: 146387--146414 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
146377 GATATGTCAG
146387 AT 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
146415 TGAAGCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:161216 original size:33 final size:31
Alignment explanation
Indices: 161168--161237 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
161158 ATTTTTCATA
161168 TTTTAAATTTTAAGTTTAACTATTAAAATTATT
1 TTTTAAATTTTAAG-TTAACTA-TAAAATTATT
* *
161201 TTATTAAA-TTTAAGTTCATTATAAAATTATT
1 TT-TTAAATTTTAAGTTAACTATAAAATTATT
161232 TTTTAA
1 TTTTAA
161238 TTATATTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 4 0.12
31 12 0.35
32 5 0.15
33 8 0.24
34 5 0.15
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTTAAATTTTAAGTTAACTATAAAATTATT
Found at i:161580 original size:19 final size:21
Alignment explanation
Indices: 161551--161591 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
161541 AATTCAATTT
*
161551 TTTTAATTTTTA-ATATATTC
1 TTTTAATTTTTATAAATATTC
161571 TTTT-ATTTTTATAAATATTC
1 TTTTAATTTTTATAAATATTC
161591 T
1 T
161592 AATAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTAATTTTTATAAATATTC
Found at i:162184 original size:23 final size:23
Alignment explanation
Indices: 162158--162203 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
162148 TATAAATTGG
162158 TTGATG-AAATCACTGAAAATATA
1 TTGATGTAAAT-ACTGAAAATATA
*
162181 TTGATGTCAATACTGAAAATATA
1 TTGATGTAAATACTGAAAATATA
162204 CCGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.33
Consensus pattern (23 bp):
TTGATGTAAATACTGAAAATATA
Found at i:165459 original size:18 final size:17
Alignment explanation
Indices: 165432--165468 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
165422 ACACCAATTT
*
165432 TTATTTGAGTTATTCGAA
1 TTATTCGAGTTATT-GAA
165450 TTATTCGAGTTATTGAA
1 TTATTCGAGTTATTGAA
165467 TT
1 TT
165469 TGAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.51
Consensus pattern (17 bp):
TTATTCGAGTTATTGAA
Found at i:165853 original size:19 final size:19
Alignment explanation
Indices: 165829--165870 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
165819 TATTCAAATT
165829 TTTAATTTCAAAATTAAAG
1 TTTAATTTCAAAATTAAAG
165848 TTTAATTTCAAAATTAAAG
1 TTTAATTTCAAAATTAAAG
165867 TTTA
1 TTTA
165871 GTAGACACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
TTTAATTTCAAAATTAAAG
Found at i:169539 original size:29 final size:29
Alignment explanation
Indices: 169470--169782 Score: 280
Period size: 29 Copynumber: 10.7 Consensus size: 29
169460 TGGACATTCG
169470 GGGTCAAAAATGGTAATTTTTGAAAGTTTTG-
1 GGGT-AAAAATGG-AATTTTTGAAAG-TTTGA
*
169501 GGGTCAAAAATGGAATTTTTGAAAGTTCGA
1 GGGT-AAAAATGGAATTTTTGAAAGTTTGA
* *
169531 GGGTAAAAATGTAATTTTTGGAAGTTTTG-
1 GGGTAAAAATGGAATTTTTGAAAG-TTTGA
* * *
169560 GGGTCAAAAATGGAATTTTTGGATGTTCGA
1 GGGT-AAAAATGGAATTTTTGAAAGTTTGA
** * *
169590 GGGTAAAAATATAATTTTCGAAAGTTT-T
1 GGGTAAAAATGGAATTTTTGAAAGTTTGA
* * *
169618 GGGTCAAAAATGGAATTTTTGGAAGTTAGG
1 GGGT-AAAAATGGAATTTTTGAAAGTTTGA
* * *
169648 GGGTAAAAATGTAATTTTAG-AAGTTTTA
1 GGGTAAAAATGGAATTTTTGAAAGTTTGA
169676 GGGTTAAAAATGGAATTTTTTG-AAGTTT-A
1 GGG-TAAAAATGGAA-TTTTTGAAAGTTTGA
* * *
169705 GGGGT-AAAATGTAATTTTTGGAAGTTTTA
1 -GGGTAAAAATGGAATTTTTGAAAGTTTGA
*
169734 GGGTCAAAAATGGAATTTTTGGAAGTTTGA
1 GGGT-AAAAATGGAATTTTTGAAAGTTTGA
* *
169764 GTGTAAAAATGTAATTTTT
1 GGGTAAAAATGGAATTTTT
169783 TGGACAATTT
Statistics
Matches: 237, Mismatches: 32, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
27 6 0.03
28 30 0.13
29 104 0.44
30 84 0.35
31 13 0.05
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGAAAGTTTGA
Found at i:169556 original size:59 final size:59
Alignment explanation
Indices: 169454--169782 Score: 436
Period size: 58 Copynumber: 5.6 Consensus size: 59
169444 GGTAAAAGGT
* *
169454 AATTTTTGGACA-TTCG-GGGTCAAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGG
1 AATTTTTGGA-AGTTCGAGGGT-AAAAAT-GTAATTTTTGGAAGTTTTAGGGTCAAAAATGG
* *
169514 AATTTTTGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGG
* * * *
169573 AATTTTTGGATGTTCGAGGGTAAAAATATAATTTTCGAAAGTTTT-GGGTCAAAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGG
* * * *
169631 AATTTTTGGAAGTTAGGGGGTAAAAATGTAA-TTTTAGAAGTTTTAGGGTTAAAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGG
* *
169689 AATTTTTTGAAGTT-TAGGGGT-AAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGG
1 AATTTTTGGAAGTTCGA-GGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGG
* *
169747 AATTTTTGGAAGTTTGAGTGTAAAAATGTAATTTTT
1 AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTT
169783 TGGACAATTT
Statistics
Matches: 239, Mismatches: 23, Indels: 15
0.86 0.08 0.05
Matches are distributed among these distances:
57 19 0.08
58 110 0.46
59 87 0.36
60 19 0.08
61 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.38
Consensus pattern (59 bp):
AATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAATGG
Done.