Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012032.1 Kokia drynarioides strain JFW-HI SEQ_127030, 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: 175145
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:4094 original size:59 final size:59
Alignment explanation
Indices: 3992--4181 Score: 233
Period size: 60 Copynumber: 3.2 Consensus size: 59
3982 TGAAATTTTG
* *
3992 GTACCAAATTGTA-TCTAAAAAAAATCTTATGTACCAAATTAGGAAAAAA-GTCAAGTTTAA
1 GTACCAAATTG-AGTCCAAAAAAAAT-TTA-GTACCAAATTAGGAAAAAATGTCAAGTTCAA
* *
4052 GTACCAAATTGGGTCCAAAAAAAATTTAGATACCAAATTAGGAAAAAATATCAAGTTCAA
1 GTACCAAATTGAGTCCAAAAAAAATTTAG-TACCAAATTAGGAAAAAATGTCAAGTTCAA
* * * *
4112 GTACCAAATTGAGT-CAAAAAAAGTTTAGGTACCGAATTAGAAAAAAATTGTCAAGTTCAG
1 GTACCAAATTGAGTCCAAAAAAAATTTA-GTACCAAATTAGGAAAAAA-TGTCAAGTTCAA
4172 GTACCAAATT
1 GTACCAAATT
4182 TTATACTAAA
Statistics
Matches: 115, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
58 1 0.01
59 49 0.43
60 65 0.57
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (59 bp):
GTACCAAATTGAGTCCAAAAAAAATTTAGTACCAAATTAGGAAAAAATGTCAAGTTCAA
Found at i:8431 original size:21 final size:21
Alignment explanation
Indices: 8398--8437 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
8388 ATTACGTAAC
* * *
8398 AATCGGTTTAAAAATATAAAT
1 AATCGATTGAAAAAAATAAAT
8419 AATCGATTGAAAAAAATAA
1 AATCGATTGAAAAAAATAA
8438 TATTTTAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (21 bp):
AATCGATTGAAAAAAATAAAT
Found at i:8518 original size:57 final size:56
Alignment explanation
Indices: 8394--8525 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 56
8384 ATGTATTACG
* * * * *
8394 TAACAATCGGTTTAAAAATAT-AA-ATAATCGATTGAAAAAAATAATATTTTAATA
1 TAACAATAGATTTAAACATATAAACACAATCGATTGAAAAAAATAATATTTCAATA
** * * *
8448 TAACAATCTATTTAAATATATAAACACAATCGATTTAAAATAAGTAATATTTCAATA
1 TAACAATAGATTTAAACATATAAACACAATCGATTGAAAA-AAATAATATTTCAATA
*
8505 TAATAATAGATTTAAACATAT
1 TAACAATAGATTTAAACATAT
8526 TATTTTCTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
54 18 0.28
55 2 0.03
56 13 0.20
57 31 0.48
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (56 bp):
TAACAATAGATTTAAACATATAAACACAATCGATTGAAAAAAATAATATTTCAATA
Found at i:9435 original size:25 final size:25
Alignment explanation
Indices: 9401--9455 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
9391 GTTCTCCAAA
*
9401 GGAATACAATGTACAAATGGATACG
1 GGAAGACAATGTACAAATGGATACG
9426 GGAAGACAATGTACAAATGGATACG
1 GGAAGACAATGTACAAATGGATACG
9451 GGAAG
1 GGAAG
9456 TGATCAGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.29, T:0.16
Consensus pattern (25 bp):
GGAAGACAATGTACAAATGGATACG
Found at i:13633 original size:20 final size:20
Alignment explanation
Indices: 13605--13645 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13595 TATAATACTA
* *
13605 TATATTTTATTTTATTATTT
1 TATAATTTATTTAATTATTT
13625 TATAATTTATTTAATTATTT
1 TATAATTTATTTAATTATTT
13645 T
1 T
13646 TGGACCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TATAATTTATTTAATTATTT
Found at i:15405 original size:30 final size:29
Alignment explanation
Indices: 15371--15479 Score: 87
Period size: 30 Copynumber: 3.7 Consensus size: 29
15361 AATGACATTC
*
15371 AAGGATTAAATTGTAATTTTAGTGAAACTT
1 AAGGACTAAATTGTAATTTTAGTGAAA-TT
* * * *
15401 AAGGACTAAATTCTAA-GTTCGATGAATTTT
1 AAGGACTAAATTGTAATTTTAG-TGAA-ATT
* * * *
15431 AAGGATTAAATTGGAATTTTAATGACATT
1 AAGGACTAAATTGTAATTTTAGTGAAATT
15460 CAAGGACTAAATTG-AATTTT
1 -AAGGACTAAATTGTAATTTT
15480 GATTAAAATT
Statistics
Matches: 61, Mismatches: 14, Indels: 9
0.73 0.17 0.11
Matches are distributed among these distances:
29 11 0.18
30 48 0.79
31 2 0.03
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (29 bp):
AAGGACTAAATTGTAATTTTAGTGAAATT
Found at i:16364 original size:19 final size:19
Alignment explanation
Indices: 16342--16425 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
16332 CCGTTAATCA
*
16342 TTGACCATTGACTTGAACG
1 TTGACCATTGACTTGACCG
*
16361 TTGA-TAGTTGACTTGACCG
1 TTGACCA-TTGACTTGACCG
*
16380 TTG-CGCTTTGATCATTGACCG
1 TTGAC-CATTGA-C-TTGACCG
* *
16401 TTGATCATTGACTTTGACCA
1 TTGACCATTGAC-TTGACCG
16421 TTGAC
1 TTGAC
16426 TTTTTTGACC
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
18 1 0.02
19 22 0.44
20 12 0.24
21 15 0.30
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (19 bp):
TTGACCATTGACTTGACCG
Found at i:16422 original size:13 final size:13
Alignment explanation
Indices: 16385--16428 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
16375 GACCGTTGCG
16385 CTTTGATCATTGA
1 CTTTGATCATTGA
*
16398 CCGTTGATCATTGA
1 -CTTTGATCATTGA
*
16412 CTTTGACCATTGA
1 CTTTGATCATTGA
16425 CTTT
1 CTTT
16429 TTTGACCAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.43
Consensus pattern (13 bp):
CTTTGATCATTGA
Found at i:30010 original size:21 final size:21
Alignment explanation
Indices: 29985--30029 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
29975 TACGAGCTAG
* *
29985 TTATATGTTATGCGAACTCTT
1 TTATATGTCATGCAAACTCTT
30006 TTATATGTCATGCAAACTCTT
1 TTATATGTCATGCAAACTCTT
30027 TTA
1 TTA
30030 CATGATGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (21 bp):
TTATATGTCATGCAAACTCTT
Found at i:41355 original size:46 final size:46
Alignment explanation
Indices: 41139--41351 Score: 219
Period size: 46 Copynumber: 4.6 Consensus size: 46
41129 TAATATTCCA
* * *
41139 TATTCTCCAGTCCGTAACATATGCAGGAATTGGGAACCTAAATTCG
1 TATTCTCCAGTCCGTAACATATACAGGAGTTGGGAACCTAAATCCG
* *** * * * *
41185 TATTCTCTAGTCTACAACGTATGCAGGAGTTGGGAACCTACATCTG
1 TATTCTCCAGTCCGTAACATATACAGGAGTTGGGAACCTAAATCCG
* * * ** *
41231 TATTCTCCAATCCGTAACACATACAAGAGTTAAGAACCTAAATCCC
1 TATTCTCCAGTCCGTAACATATACAGGAGTTGGGAACCTAAATCCG
* * *
41277 TATTCTTCAGTCTGTAACATATACAGGAGCTGGGAACCTAAATCCG
1 TATTCTCCAGTCCGTAACATATACAGGAGTTGGGAACCTAAATCCG
* * *
41323 TATTCTCCAGTCCATCACATATATAGGAG
1 TATTCTCCAGTCCGTAACATATACAGGAG
41352 CTGGTAACTT
Statistics
Matches: 130, Mismatches: 37, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
46 130 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (46 bp):
TATTCTCCAGTCCGTAACATATACAGGAGTTGGGAACCTAAATCCG
Found at i:47941 original size:158 final size:158
Alignment explanation
Indices: 47648--47964 Score: 436
Period size: 158 Copynumber: 2.0 Consensus size: 158
47638 GTAATATTCT
* * *
47648 TGTATCATGTATTGCTCACACGAGCTATAAAATGGGCCTGCTCACACGAGCTGTGGGTCAAGATG
1 TGTAACATGTAATGCTCACACGAGCTATAAAATGGGCCTGCTCACACGAGCTGTGAGTCAAGATG
* * * * * * *
47713 TGAGGCTATACAATACTGCTCACACGAGCTGTGGAGAATCCGCAACCAATGTCAGACCTTAGCCA
66 TGAGGCTACACAATACTGCTCACACAAGCTGTGGAGAATCCACAACAAATGCCAGACCTCAACCA
47778 TCGATAGGACATCCAAGACCAGCACCCA
131 TCGATAGGACATCCAAGACCAGCACCCA
* * *
47806 TGTAACATGTAATGCTCACATGAGCTGTAAAATGGGCCTGCTCACACGAGCTGTGAGTCGAGATG
1 TGTAACATGTAATGCTCACACGAGCTATAAAATGGGCCTGCTCACACGAGCTGTGAGTCAAGATG
* * * * * * *
47871 TGGGGCTACACGATGCTGCTCACACAAGCTGTGGAGAATCTATAACAAATGCCGGATCTCAACCA
66 TGAGGCTACACAATACTGCTCACACAAGCTGTGGAGAATCCACAACAAATGCCAGACCTCAACCA
* *
47936 TCGATAGGACATCTAAGACCATCACCCA
131 TCGATAGGACATCCAAGACCAGCACCCA
47964 T
1 T
47965 ATAGCTTAAA
Statistics
Matches: 137, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
158 137 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (158 bp):
TGTAACATGTAATGCTCACACGAGCTATAAAATGGGCCTGCTCACACGAGCTGTGAGTCAAGATG
TGAGGCTACACAATACTGCTCACACAAGCTGTGGAGAATCCACAACAAATGCCAGACCTCAACCA
TCGATAGGACATCCAAGACCAGCACCCA
Found at i:50744 original size:196 final size:193
Alignment explanation
Indices: 50391--50744 Score: 428
Period size: 196 Copynumber: 1.8 Consensus size: 193
50381 TAAACTATTG
*
50391 CCTAACGATGCTGCTCACACGAGCTGTAGAATATACATTCAAGCATAAATCCTAGCCATCGTCAG
1 CCTAACGATGCTGCTCACACGAGCTATAGAATATACATTCAAGCATAAATCCTAGCCATCGTCAG
** *
50456 GCCTATAAATCATTTAGGATTTCATATCTCTTTTTCGACTCACGATGCTTCTCACACGAGCTATC
66 GCCTATAAATCATTTAGGATTTCATATCTCTTTCCCGACTCACGATGCTGCTCACACGAGCTATC
* * *
50521 GAGAACTCGCAACATTTGCGGTACCTCAGCCATCGATACGGTATCTGTGCATATAACGGTTTC
131 GAGAACTCACAACATATGCGATACCTCAGCCATCGATACGGTATCTGTGCATATAACGGTTTC
* * * * *
50584 CCTAACGATGCTGCTCACACGAGTTATCGAGAATATGCACTT-ATGTATTAATCCTAGCCATCGT
1 CCTAACGATGCTGCTCACACGAGCTAT--AGAATATACA-TTCAAGCATAAATCCTAGCCATCGT
* * * * *
50648 -AGGGCT-TGTAATCCATTCTTGGA-TTCATTTCTCATTTCCCGACTCATGATGCTGCTCACACG
63 CAGGCCTAT-AAAT-CATT-TAGGATTTCATATCTC-TTTCCCGACTCACGATGCTGCTCACACG
* * * *
50710 AGTTGTCGAGGACTTACAACATATGCGATACCTCA
124 AGCTATCGAGAACTCACAACATATGCGATACCTCA
50745 ATCATTGCAT
Statistics
Matches: 133, Mismatches: 21, Indels: 11
0.81 0.13 0.07
Matches are distributed among these distances:
193 26 0.20
194 8 0.06
195 41 0.31
196 58 0.44
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (193 bp):
CCTAACGATGCTGCTCACACGAGCTATAGAATATACATTCAAGCATAAATCCTAGCCATCGTCAG
GCCTATAAATCATTTAGGATTTCATATCTCTTTCCCGACTCACGATGCTGCTCACACGAGCTATC
GAGAACTCACAACATATGCGATACCTCAGCCATCGATACGGTATCTGTGCATATAACGGTTTC
Found at i:56454 original size:24 final size:24
Alignment explanation
Indices: 56427--56535 Score: 191
Period size: 24 Copynumber: 4.5 Consensus size: 24
56417 CTTAGCCCAC
*
56427 ACGAGCCCAGAATGGTTAACTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
56451 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
56475 ACGAGTCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
*
56499 ACGAGTCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
56523 ACGAGCCCAGAAT
1 ACGAGCCCAGAAT
56536 CAGAATAACA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 82 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:56571 original size:27 final size:27
Alignment explanation
Indices: 56517--56620 Score: 145
Period size: 27 Copynumber: 3.8 Consensus size: 27
56507 AGAATGGTTA
* *
56517 GCTCTTACGAGCCCAGAATCAGAATAAC
1 GCTCTTTCGAG-CCAGAATCAAAATAAC
* *
56545 ACTCTTTCGAGCCATAATCAAAATAAC
1 GCTCTTTCGAGCCAGAATCAAAATAAC
*
56572 GCTCTTTCGAGCCAAAATCAAAATAAC
1 GCTCTTTCGAGCCAGAATCAAAATAAC
*
56599 GCTTTTTCGAGCCAGAATCAAA
1 GCTCTTTCGAGCCAGAATCAAA
56621 TTACTCCTCA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
27 59 0.87
28 9 0.13
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (27 bp):
GCTCTTTCGAGCCAGAATCAAAATAAC
Found at i:64329 original size:20 final size:21
Alignment explanation
Indices: 64291--64330 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
64281 TAAATCGAGT
*
64291 ATCACTGAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
64312 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
64331 TAAAAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:64345 original size:13 final size:13
Alignment explanation
Indices: 64327--64351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64317 TAAGTTAAAA
64327 ATGCTAAAAATGC
1 ATGCTAAAAATGC
64340 ATGCTAAAAATG
1 ATGCTAAAAATG
64352 ATAAGATGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:65135 original size:35 final size:35
Alignment explanation
Indices: 65089--65159 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
65079 TTAAATGACT
65089 TATCCAACACATCAATGTGGTGACATTCTTCCCTG
1 TATCCAACACATCAATGTGGTGACATTCTTCCCTG
65124 TATCCAACACATCAATGTGGTGACATTCTTCCCTG
1 TATCCAACACATCAATGTGGTGACATTCTTCCCTG
65159 T
1 T
65160 CGCGACAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (35 bp):
TATCCAACACATCAATGTGGTGACATTCTTCCCTG
Found at i:68521 original size:23 final size:23
Alignment explanation
Indices: 68495--68546 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
68485 GGAATGCTCT
68495 TCGTCAGGAGTAGATTTACCTTC
1 TCGTCAGGAGTAGATTTACCTTC
*
68518 TCGTCAGGAGTAGATTTGCCTTC
1 TCGTCAGGAGTAGATTTACCTTC
*
68541 TTGTCA
1 TCGTCA
68547 CAATCAGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (23 bp):
TCGTCAGGAGTAGATTTACCTTC
Found at i:74216 original size:43 final size:43
Alignment explanation
Indices: 74138--74285 Score: 113
Period size: 43 Copynumber: 3.5 Consensus size: 43
74128 AGACACTTGA
* * *
74138 TGTATAAATGGAAGACTCATGTCTCGGATTAAGCATGAGAATT
1 TGTATAAATGGAAGACTCATGACTCGAAATAAGCATGAGAATT
* * * * *
74181 TGTATGAATGGAAGACTCGTGACTCGAAATGAGCATGAGGATA
1 TGTATAAATGGAAGACTCATGACTCGAAATAAGCATGAGAATT
* * ** * * * *
74224 TAT-TAAA-GGAAAACTCATCTCTCGAGATGAGAATGAGAATA
1 TGTATAAATGGAAGACTCATGACTCGAAATAAGCATGAGAATT
* *
74265 TGTTTATA-GGAAGACTCATGA
1 TGTATAAATGGAAGACTCATGA
74286 TAGCATTAGA
Statistics
Matches: 82, Mismatches: 22, Indels: 3
0.77 0.21 0.03
Matches are distributed among these distances:
41 29 0.35
42 16 0.20
43 37 0.45
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (43 bp):
TGTATAAATGGAAGACTCATGACTCGAAATAAGCATGAGAATT
Found at i:74254 original size:41 final size:42
Alignment explanation
Indices: 74203--74283 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 42
74193 AGACTCGTGA
* *
74203 CTCGAAATGAGCATGAGGATAT-ATTAAAGGAAAACTCATCT
1 CTCGAAATGAGAATGAGAATATGATTAAAGGAAAACTCATCT
* * * *
74244 CTCGAGATGAGAATGAGAATATGTTTATAGGAAGACTCAT
1 CTCGAAATGAGAATGAGAATATGATTAAAGGAAAACTCAT
74284 GATAGCATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 19 0.58
42 14 0.42
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (42 bp):
CTCGAAATGAGAATGAGAATATGATTAAAGGAAAACTCATCT
Found at i:75676 original size:40 final size:41
Alignment explanation
Indices: 75601--75679 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
75591 TGTGAGATTA
* * *
75601 TGTTTAAAGAGGAAGACTTATGACTCGATAGAGCATAAGAT
1 TGTTTAAAGAGGAAGACTCATGAATCGATAAAGCATAAGAT
*
75642 TGTTTAAA-AGGAAGACTCGTGAATCTG-TAAAGCATAAG
1 TGTTTAAAGAGGAAGACTCATGAATC-GATAAAGCATAAG
75680 TTCATCTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 24 0.73
41 9 0.27
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (41 bp):
TGTTTAAAGAGGAAGACTCATGAATCGATAAAGCATAAGAT
Found at i:76267 original size:24 final size:24
Alignment explanation
Indices: 76234--76293 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
76224 TTAATAGTAG
* *
76234 GTATCAGTAGTTTTATGTATGCTT
1 GTATCGGTAGTTCTATGTATGCTT
*
76258 GTATCGGTAGTTCTGTGTATGCTT
1 GTATCGGTAGTTCTATGTATGCTT
76282 GTATCGGTAGTT
1 GTATCGGTAGTT
76294 AAGATGCTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.17, C:0.10, G:0.27, T:0.47
Consensus pattern (24 bp):
GTATCGGTAGTTCTATGTATGCTT
Found at i:76302 original size:21 final size:21
Alignment explanation
Indices: 76276--76333 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
76266 AGTTCTGTGT
*
76276 ATGCTTGTATCGGTAGTTAAG
1 ATGCTTGTATCAGTAGTTAAG
*
76297 ATGCTTGTATTAGTAGTTAAG
1 ATGCTTGTATCAGTAGTTAAG
* *
76318 ATACTTATATCAGTAG
1 ATGCTTGTATCAGTAG
76334 AAGTTACAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (21 bp):
ATGCTTGTATCAGTAGTTAAG
Found at i:84681 original size:24 final size:24
Alignment explanation
Indices: 84648--84705 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
84638 ATTCTAGTTA
84648 AACTCTATCTAGGCTCG-AATGAGCT
1 AACT-TATCTAGGCTCGTAA-GAGCT
84673 AACTTATCTAGGCTCGTAAGAGCT
1 AACTTATCTAGGCTCGTAAGAGCT
*
84697 AACCTATCT
1 AACTTATCT
84706 GGGATCTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 25 0.81
25 6 0.19
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (24 bp):
AACTTATCTAGGCTCGTAAGAGCT
Found at i:84719 original size:24 final size:24
Alignment explanation
Indices: 84652--84722 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 24
84642 TAGTTAAACT
* *
84652 CTATCTAGGCTCGAATGAGCTAAC
1 CTATCTAGGATCGTATGAGCTAAC
* * *
84676 TTATCTAGGCTCGTAAGAGCTAAC
1 CTATCTAGGATCGTATGAGCTAAC
* *
84700 CTATCTGGGATCTTATGAGCTAA
1 CTATCTAGGATCGTATGAGCTAA
84723 TTTTGTTTGG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (24 bp):
CTATCTAGGATCGTATGAGCTAAC
Found at i:94299 original size:3 final size:3
Alignment explanation
Indices: 94291--94346 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
94281 TGAGGCAGCG
* *
94291 GAA GAA GAAA GAA -AA GAA GAA GAA GAA GAT GAT GAA -AA GGAA GAA
1 GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA
*
94336 AAA GAA GAA GA
1 GAA GAA GAA GA
94347 TGTTACCCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 36 0.80
4 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:94333 original size:24 final size:23
Alignment explanation
Indices: 94292--94348 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
94282 GAGGCAGCGG
*
94292 AAGAAGAA-A-GAAAAGAAGAAG
1 AAGAAGAAGATGAAAAGAAGAAA
*
94313 AAGAAGATGATGAAAAGGAAGAAA
1 AAGAAGAAGATGAAAA-GAAGAAA
94337 AAGAAGAAGATG
1 AAGAAGAAGATG
94349 TTACCCCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.23
22 1 0.03
23 5 0.17
24 17 0.57
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.05
Consensus pattern (23 bp):
AAGAAGAAGATGAAAAGAAGAAA
Found at i:113624 original size:34 final size:34
Alignment explanation
Indices: 113586--113667 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
113576 TATCACAGTG
* *
113586 GCATGCTTAACATGCAAATTAGAAT-AAATGTATA
1 GCATGCTTAACATGCAAATCAGAATCAAA-ATATA
*
113620 GCATGCTTAACATGCAGATCAGAATCAAAATATA
1 GCATGCTTAACATGCAAATCAGAATCAAAATATA
113654 GCATGCTTAACATG
1 GCATGCTTAACATG
113668 TGAATCAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
34 41 0.93
35 3 0.07
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (34 bp):
GCATGCTTAACATGCAAATCAGAATCAAAATATA
Found at i:114207 original size:35 final size:36
Alignment explanation
Indices: 114136--114209 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
114126 AAATAATAAA
**
114136 TAAACAACCCTTGATTATAAATTTTTTTTGATTCAG
1 TAAACAACCCTTGATTATAAATTGATTTTGATTCAG
114172 TAAACAACCCTTGATTATAAA-TGATTTTGATTCAG
1 TAAACAACCCTTGATTATAAATTGATTTTGATTCAG
114207 TAA
1 TAA
114210 TACTTACCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 15 0.42
36 21 0.58
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (36 bp):
TAAACAACCCTTGATTATAAATTGATTTTGATTCAG
Found at i:117967 original size:17 final size:17
Alignment explanation
Indices: 117947--117989 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
117937 AAATGTTCTA
*
117947 ACAAATAAAATGCAGTG
1 ACAAATAAAATGCACTG
* *
117964 ACAAAAAAAATGTACTG
1 ACAAATAAAATGCACTG
*
117981 ACAACTAAA
1 ACAAATAAA
117990 TGCTATGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (17 bp):
ACAAATAAAATGCACTG
Found at i:126245 original size:37 final size:37
Alignment explanation
Indices: 126195--126278 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 37
126185 TTACTACTAA
* * **
126195 TGTCGCTGCATGAGAACTTCTAGATTGTGCCCAAAAC
1 TGTCGCCGCATGAGAACTTCCAGATTGCACCCAAAAC
*
126232 TGTCGCCGCATGAGCACTTCCAGATTGCACCCAAAAC
1 TGTCGCCGCATGAGAACTTCCAGATTGCACCCAAAAC
* *
126269 TATCGTCGCA
1 TGTCGCCGCA
126279 GAAATATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (37 bp):
TGTCGCCGCATGAGAACTTCCAGATTGCACCCAAAAC
Found at i:130313 original size:26 final size:26
Alignment explanation
Indices: 130277--130328 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
130267 ACAAAGGAAA
130277 GTCGCTGCATGAACATGTCAAGAATT
1 GTCGCTGCATGAACATGTCAAGAATT
* *
130303 GTCGCTGCATGAACGTGTCTAGAATT
1 GTCGCTGCATGAACATGTCAAGAATT
130329 ACATCCAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (26 bp):
GTCGCTGCATGAACATGTCAAGAATT
Found at i:132915 original size:21 final size:21
Alignment explanation
Indices: 132889--132931 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
132879 AATAATGTAT
*
132889 ATATATATATACTTAAGTTAATG
1 ATATATA-AGACTTAA-TTAATG
132912 ATATATAAGACTTAATTAAT
1 ATATATAAGACTTAATTAAT
132932 CATGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
ATATATAAGACTTAATTAATG
Found at i:136164 original size:2 final size:2
Alignment explanation
Indices: 136157--136201 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
136147 GAGGGCTTAA
* * *
136157 AT AT AT AT AT AC GT AT AT AT AT AT AT AT AT AT AG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
136199 AT A
1 AT A
136202 CACTTAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:137211 original size:54 final size:54
Alignment explanation
Indices: 137136--137260 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 54
137126 TCCCAGATCA
* * * * * * **
137136 TGTAGCTCATTGACTTAAGTAACACGCTCGTGTCACAGGTCGTGTGCCAAGTTG
1 TGTAACTCACTGACTTGAGTAACACGCCCGTGTCAAAGATCGTGTGCCAAGCAG
* * *
137190 TGTAACTCACTGACTTGAGTAACACGCCCGTGTTAAAGATTGTGTGCCAGGCAG
1 TGTAACTCACTGACTTGAGTAACACGCCCGTGTCAAAGATCGTGTGCCAAGCAG
137244 TGTAACTCACTGACTTG
1 TGTAACTCACTGACTTG
137261 GGCCTCACGG
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (54 bp):
TGTAACTCACTGACTTGAGTAACACGCCCGTGTCAAAGATCGTGTGCCAAGCAG
Found at i:138720 original size:20 final size:22
Alignment explanation
Indices: 138695--138747 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
138685 TTTCTAGGGA
*
138695 TATCGAATA-TT-TCAAAAAGG
1 TATCGAATACTTGCCAAAAAGG
138715 TATCG-ATACTTGGCCAAAAAGG
1 TATCGAATACTT-GCCAAAAAGG
138737 TATCG-ATACTT
1 TATCGAATACTT
138748 TTTGGCATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.10
20 7 0.24
22 19 0.66
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (22 bp):
TATCGAATACTTGCCAAAAAGG
Found at i:139372 original size:37 final size:37
Alignment explanation
Indices: 139331--139409 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
139321 ACAAAAAACA
* * *
139331 TCAATTGTATTTAAAAATACCAATAAAGCATTCAAGT
1 TCAATTGTATCTAAAAATACCAATAAAACAATCAAGT
*
139368 TCAATTGTATCTAAAAATATCAATAAAACAATCAAGT
1 TCAATTGTATCTAAAAATACCAATAAAACAATCAAGT
139405 TCAAT
1 TCAAT
139410 CAAAATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (37 bp):
TCAATTGTATCTAAAAATACCAATAAAACAATCAAGT
Found at i:143732 original size:24 final size:24
Alignment explanation
Indices: 143658--143942 Score: 187
Period size: 24 Copynumber: 11.9 Consensus size: 24
143648 ATTCATTTCA
* *
143658 TTTACGCTCGTTAGTTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
*** *
143682 TTTACGCTCGTCAAG-TTGCGTATG
1 TTTACGCTCGTC-AGCTTATATACG
* *
143706 TTTACACTCGTCATCTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
* * ** * *
143730 TTTACACTTGTCAGCTTGCACATG
1 TTTACGCTCGTCAGCTTATATACG
** *
143754 TTTACGCTTATCAGCTTATATATG
1 TTTACGCTCGTCAGCTTATATACG
* * *
143778 TTTACGCTCATCAACTT-TCACACG
1 TTTACGCTCGTCAGCTTAT-ATACG
*
143802 TTTATGCTCGTCAGCTTATATACG
1 TTTACGCTCGTCAGCTTATATACG
* * ** * *
143826 TTTATGTTCGTCAGCTTGCACACA
1 TTTACGCTCGTCAGCTTATATACG
* * *
143850 TTTATGCTCGTCAACTTATATACC
1 TTTACGCTCGTCAGCTTATATACG
* ** *
143874 TTTACGCTCGTCAACTTGCACACG
1 TTTACGCTCGTCAGCTTATATACG
* * *
143898 TTTACACTCATCAGCTTATATATG
1 TTTACGCTCGTCAGCTTATATACG
* *
143922 TTTACACTCCTCAGCTTATAT
1 TTTACGCTCGTCAGCTTATAT
143943 GTATACACAT
Statistics
Matches: 203, Mismatches: 54, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
23 2 0.01
24 198 0.98
25 3 0.01
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (24 bp):
TTTACGCTCGTCAGCTTATATACG
Found at i:143755 original size:48 final size:48
Alignment explanation
Indices: 143658--143938 Score: 285
Period size: 48 Copynumber: 5.9 Consensus size: 48
143648 ATTCATTTCA
* * ** *
143658 TTTACGCTCGTTAGTTTATATACGTTTACGCTCGTCAAG-TTGCGTATG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTC-AGCTTGCACACG
* * * * *
143706 TTTACACTCGTCATCTTATATACGTTTACACTTGTCAGCTTGCACATG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
** * * * *
143754 TTTACGCTTATCAGCTTATATATGTTTACGCTCATCAACTTTCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * * *
143802 TTTATGCTCGTCAGCTTATATACGTTTATGTTCGTCAGCTTGCACACA
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * * *
143850 TTTATGCTCGTCAACTTATATACCTTTACGCTCGTCAACTTGCACACG
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
* * * * *
143898 TTTACACTCATCAGCTTATATATGTTTACACTCCTCAGCTT
1 TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTT
143939 ATATGTATAC
Statistics
Matches: 188, Mismatches: 44, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
47 2 0.01
48 186 0.99
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (48 bp):
TTTACGCTCGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACACG
Found at i:143949 original size:22 final size:24
Alignment explanation
Indices: 143900--143950 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
143890 TGCACACGTT
*
143900 TACACTCATCAGCTTATATATGTT
1 TACACTCATCAGCTTATATATGTA
*
143924 TACACTCCTCAGC-T-TATATGTA
1 TACACTCATCAGCTTATATATGTA
143946 TACAC
1 TACAC
143951 ATTTCTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.48
23 1 0.04
24 12 0.48
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (24 bp):
TACACTCATCAGCTTATATATGTA
Found at i:149777 original size:21 final size:20
Alignment explanation
Indices: 149723--149778 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 20
149713 TTTCATGACG
*
149723 TTCAATTATA--ATTTC-AT
1 TTCAATTATATCATTTCAAA
149740 TTCAATTATATCATTTCAAA
1 TTCAATTATATCATTTCAAA
149760 TTCATATTCATAT-ATTTCA
1 TTCA-ATT-ATATCATTTCA
149779 TATTTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 10 0.30
19 5 0.15
20 5 0.15
21 9 0.27
22 4 0.12
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (20 bp):
TTCAATTATATCATTTCAAA
Found at i:154009 original size:24 final size:24
Alignment explanation
Indices: 153599--154049 Score: 409
Period size: 24 Copynumber: 18.8 Consensus size: 24
153589 AAATTCTTTT
* * *
153599 CGTTTACGTTCGTCAACTTGCACG
1 CGTTTACGCTCGTCAGCTTGCACA
* * ** *
153623 CATTTACGCTCGTCAACTTATATA
1 CGTTTACGCTCGTCAGCTTGCACA
* *
153647 CATTTACGCTCGTCAGCTTGCGCA
1 CGTTTACGCTCGTCAGCTTGCACA
* ** *
153671 CATTTACGCTCGTCAGCTTAAATA
1 CGTTTACGCTCGTCAGCTTGCACA
153695 CGTTTACGCTCGTCAGCTTGCACA
1 CGTTTACGCTCGTCAGCTTGCACA
153719 CGTTTACGCTCGTCAGCTTGCACA
1 CGTTTACGCTCGTCAGCTTGCACA
** *
153743 CGTTTACGCTCGTCAGCTTATATA
1 CGTTTACGCTCGTCAGCTTGCACA
153767 CGTTTACGCTCGTCAGCTTGCACA
1 CGTTTACGCTCGTCAGCTTGCACA
* * ** *
153791 CATTTACGCTTGTCAGCTTATATA
1 CGTTTACGCTCGTCAGCTTGCACA
* * *
153815 CGTTAACGCTCGTCAACTTGCAGA
1 CGTTTACGCTCGTCAGCTTGCACA
* * * ** *
153839 CATTTACGCTTGTTAGCTTATATA
1 CGTTTACGCTCGTCAGCTTGCACA
153863 CGTTTACGGC-CGTCAGCTTGCACA
1 CGTTTAC-GCTCGTCAGCTTGCACA
* * *
153887 CGTTTAAGCTCATCAGCTTGTACA
1 CGTTTACGCTCGTCAGCTTGCACA
*
153911 CGTTTACACTCGTCAGCTTGCACA
1 CGTTTACGCTCGTCAGCTTGCACA
* * * *
153935 TGTTTAAGCTCATCAGCTTGTACA
1 CGTTTACGCTCGTCAGCTTGCACA
** *
153959 CGTTTACGCTCGTCAGCTTATATA
1 CGTTTACGCTCGTCAGCTTGCACA
* *
153983 TGTTTACGCTCATCAGCTTGCACA
1 CGTTTACGCTCGTCAGCTTGCACA
* * * * ****
154007 TGTTTATGATTGTCAGCTTATGTA
1 CGTTTACGCTCGTCAGCTTGCACA
*
154031 CGTTTACACTCGTCAGCTT
1 CGTTTACGCTCGTCAGCTT
154050 ATATATATAC
Statistics
Matches: 339, Mismatches: 86, Indels: 4
0.79 0.20 0.01
Matches are distributed among these distances:
23 2 0.01
24 335 0.99
25 2 0.01
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (24 bp):
CGTTTACGCTCGTCAGCTTGCACA
Found at i:154721 original size:18 final size:18
Alignment explanation
Indices: 154695--154733 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
154685 TTGATCTAGA
* *
154695 TAATAATTCCCATGAATT
1 TAATAATTCCAATAAATT
*
154713 TAATCATTCCAATAAATT
1 TAATAATTCCAATAAATT
154731 TAA
1 TAA
154734 AATATCTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (18 bp):
TAATAATTCCAATAAATT
Found at i:159042 original size:11 final size:12
Alignment explanation
Indices: 159026--159058 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
159016 CAACACCAAT
159026 CTTTTTCTT-TC
1 CTTTTTCTTCTC
159037 CTTTTTCTTCTC
1 CTTTTTCTTCTC
159049 CTTTGTTCTT
1 CTTT-TTCTT
159059 GAGTCTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 6 0.30
13 5 0.25
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (12 bp):
CTTTTTCTTCTC
Found at i:163601 original size:14 final size:14
Alignment explanation
Indices: 163582--163612 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
163572 CATTTTCTAG
*
163582 TTTAGTTTACTGCA
1 TTTAGTTTACTACA
163596 TTTAGTTTACTACA
1 TTTAGTTTACTACA
163610 TTT
1 TTT
163613 TCTAACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.55
Consensus pattern (14 bp):
TTTAGTTTACTACA
Found at i:163757 original size:26 final size:26
Alignment explanation
Indices: 163728--163828 Score: 166
Period size: 26 Copynumber: 3.9 Consensus size: 26
163718 AAATTATCGC
** * *
163728 TGTATGAATATGTCTAGAGTTACCGT
1 TGTATGAGCATGTCTAGAATTGCCGT
163754 TGTATGAGCATGTCTAGAATTGCCGT
1 TGTATGAGCATGTCTAGAATTGCCGT
163780 TGTATGAGCATGTCTAGAATTGCCGT
1 TGTATGAGCATGTCTAGAATTGCCGT
163806 TGTATGAGCATGTCTAGAATTGC
1 TGTATGAGCATGTCTAGAATTGC
163829 ACCCACATCT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.36
Consensus pattern (26 bp):
TGTATGAGCATGTCTAGAATTGCCGT
Found at i:168266 original size:29 final size:29
Alignment explanation
Indices: 168234--168304 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
168224 TAGTACGAAA
168234 GTAAAATAAAAGGGTTGTGATTGTAAAAC
1 GTAAAATAAAAGGGTTGTGATTGTAAAAC
168263 GTAAAATAAAAGGGTTGTGATTGTAAAAC
1 GTAAAATAAAAGGGTTGTGATTGTAAAAC
* *
168292 ATAAAATTAAAGG
1 GTAAAATAAAAGG
168305 AAATAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.48, C:0.03, G:0.23, T:0.27
Consensus pattern (29 bp):
GTAAAATAAAAGGGTTGTGATTGTAAAAC
Found at i:170493 original size:36 final size:36
Alignment explanation
Indices: 170410--170576 Score: 160
Period size: 36 Copynumber: 4.6 Consensus size: 36
170400 GCGTTCAGTG
*
170410 CTAGTCGGATAAACCGACAATAGATGTGTCA--T-GCA
1 CTAGTCGGATAAACCGACAA-AGATTTG-CACCTAGCA
* * * * *
170445 CTAGTTGTATAAACCGACAAAGATTTGCACCCAACG
1 CTAGTCGGATAAACCGACAAAGATTTGCACCTAGCA
* * *
170481 CTAGTCCGATAAACCGACAACATCAATTGTGTACCTAGCA
1 CTAGTCGGATAAACCGACAA-A--GATT-TGCACCTAGCA
*
170521 CTAGTCGGATAAACCGACAAAGATTTACACCTAGCA
1 CTAGTCGGATAAACCGACAAAGATTTGCACCTAGCA
*
170557 CTAGTCGGGTAAACCGACAA
1 CTAGTCGGATAAACCGACAA
170577 CATCAAATGT
Statistics
Matches: 106, Mismatches: 19, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
33 2 0.02
34 6 0.06
35 18 0.17
36 46 0.43
37 4 0.04
39 4 0.04
40 26 0.25
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (36 bp):
CTAGTCGGATAAACCGACAAAGATTTGCACCTAGCA
Found at i:170533 original size:40 final size:40
Alignment explanation
Indices: 170481--170616 Score: 145
Period size: 40 Copynumber: 3.5 Consensus size: 40
170471 GCACCCAACG
* *
170481 CTAGTCCGATAAACCGACAACATCAATTGTGTACCTAGCA
1 CTAGTCGGATAAACCGACAACATCAATTGTATACCTAGCA
* *
170521 CTAGTCGGATAAACCGACAA-A--GATT-TACACCTAGCA
1 CTAGTCGGATAAACCGACAACATCAATTGTATACCTAGCA
* * * * *
170557 CTAGTCGGGTAAACCGACAACATCAAATGTATGCCCAACA
1 CTAGTCGGATAAACCGACAACATCAATTGTATACCTAGCA
* *
170597 CTAGTAGGATAAACTGACAA
1 CTAGTCGGATAAACCGACAA
170617 TTTACATACA
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
36 28 0.36
37 4 0.05
39 3 0.04
40 43 0.55
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (40 bp):
CTAGTCGGATAAACCGACAACATCAATTGTATACCTAGCA
Found at i:170543 original size:76 final size:76
Alignment explanation
Indices: 170442--170616 Score: 215
Period size: 76 Copynumber: 2.3 Consensus size: 76
170432 GATGTGTCAT
* * * *
170442 GCACTAGTTGTATAAACCGACAAAGATTTGCACCCAACGCTAGTCCGATAAACCGACAACATCAA
1 GCACTAGTAGGATAAACCGACAAAGATTTACACCCAACACTAGTCCGATAAACCGACAACATCAA
* * *
170507 TTGTGTACCTA
66 ATGTATACCCA
* * * * *
170518 GCACTAGTCGGATAAACCGACAAAGATTTACACCTAGCACTAGTCGGGTAAACCGACAACATCAA
1 GCACTAGTAGGATAAACCGACAAAGATTTACACCCAACACTAGTCCGATAAACCGACAACATCAA
*
170583 ATGTATGCCCA
66 ATGTATACCCA
* *
170594 ACACTAGTAGGATAAACTGACAA
1 GCACTAGTAGGATAAACCGACAA
170617 TTTACATACA
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 84 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (76 bp):
GCACTAGTAGGATAAACCGACAAAGATTTACACCCAACACTAGTCCGATAAACCGACAACATCAA
ATGTATACCCA
Found at i:172039 original size:29 final size:29
Alignment explanation
Indices: 171999--172066 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
171989 TACATTATAT
*
171999 TATATGTGTGAGTCTGTAGGTGAT-AAATA
1 TATATGCGTGAGTCTG-AGGTGATAAAATA
* * *
172028 TATATGCGTGAGTTTGGGGTTATAAAATA
1 TATATGCGTGAGTCTGAGGTGATAAAATA
172057 TATATGCGTG
1 TATATGCGTG
172067 CTATATATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.29, C:0.04, G:0.28, T:0.38
Consensus pattern (29 bp):
TATATGCGTGAGTCTGAGGTGATAAAATA
Found at i:172701 original size:17 final size:15
Alignment explanation
Indices: 172663--172708 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 15
172653 TATGATGGAG
172663 TATGAACTGTTATTT
1 TATGAACTGTTATTT
172678 TGCATGAACTGTTATGTGT
1 T--ATGAACTGTTAT-T-T
172697 TATGAACTGTTA
1 TATGAACTGTTA
172709 ATTGGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
17 23 0.85
18 1 0.04
19 2 0.07
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGAACTGTTATTT
Done.