Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005967.1 Kokia drynarioides strain JFW-HI SEQ_120373, 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: 249594
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:196 original size:12 final size:12
Alignment explanation
Indices: 179--203 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
169 AAATTAAAAT
179 ATTTTAAAATTA
1 ATTTTAAAATTA
191 ATTTTAAAATTA
1 ATTTTAAAATTA
203 A
1 A
204 CCATTCTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:386 original size:4 final size:4
Alignment explanation
Indices: 379--449 Score: 53
Period size: 4 Copynumber: 18.5 Consensus size: 4
369 ACCTTTTTTT
* *
379 TTTC TTTC --TC TTTC TTTCC CTTC -TTC CTTC TTT- TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
424 TTTC TCTTT TTTC TTT- TTTT TTTC TT
1 TTTC T-TTC TTTC TTTC TTTC TTTC TT
450 CAATTTTCGT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
2 2 0.04
3 9 0.16
4 38 0.69
5 6 0.11
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:425 original size:31 final size:28
Alignment explanation
Indices: 372--449 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 28
362 ACACATTACC
372 TTTT-TTTTTTCTTTCTCTTTCTTTCCCTT
1 TTTTCTTTTTTC-TT-TCTTTCTTTCCCTT
*
401 CTTCCTTCTTTTTTCTTTCTTTCTTTCTCTT
1 -TT--TTCTTTTTTCTTTCTTTCTTTCCCTT
*
432 TTTTCTTTTTTTTTTCTT
1 TTTTCTTTTTTCTTTCTT
450 CAATTTTCGT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 15 0.35
30 4 0.09
31 13 0.30
32 4 0.09
33 7 0.16
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTCTTTTTTCTTTCTTTCTTTCCCTT
Found at i:491 original size:136 final size:139
Alignment explanation
Indices: 331--605 Score: 477
Period size: 136 Copynumber: 2.0 Consensus size: 139
321 ACTAACAAAT
*
331 TAAAATATTTTAAAATTAAATTTAAAAATAAACACATTACC-TTTTTTTTTTCTTTCTCTT-TCT
1 TAAAATATTTTAAAATTAAATTTAAAAATAAACACATTACCTTTTTTTTTTTCTTTCT-TTCCCT
*
394 T-TCCCTTCTTCCTTCTTTTTTCTTTCTTTCTTTCTCTTTTTTCTTT-TTTTTTTCTTCAATTTT
65 TCTCCCTTCTTCCTTCTTCTTTCTTTCTTTCTTTCTCTTTTTTCTTTCTTTTTTTCTTCAATTTT
457 CGTTGGTCCC
130 CGTTGGTCCC
467 TAAAATATTTTAAAATTAAATTTAAAAATAAACACATTACCTTTTTTTTTTTCTTTCTTTCCCTT
1 TAAAATATTTTAAAATTAAATTTAAAAATAAACACATTACCTTTTTTTTTTTCTTTCTTTCCCTT
* *
532 CTTCCTTCTTCCTTCTTCTTTCTTTCTTTCTTTCTTTTTTTTCTTTCTTTTTTTCTTCAATTTTC
66 CTCCCTTCTTCCTTCTTCTTTCTTTCTTTCTTTCTCTTTTTTCTTTCTTTTTTTCTTCAATTTTC
597 GTTGGTCCC
131 GTTGGTCCC
606 CCCTCCCCAC
Statistics
Matches: 131, Mismatches: 4, Indels: 5
0.94 0.03 0.04
Matches are distributed among these distances:
136 43 0.33
137 19 0.15
138 42 0.32
139 27 0.21
ACGTcount: A:0.18, C:0.20, G:0.02, T:0.59
Consensus pattern (139 bp):
TAAAATATTTTAAAATTAAATTTAAAAATAAACACATTACCTTTTTTTTTTTCTTTCTTTCCCTT
CTCCCTTCTTCCTTCTTCTTTCTTTCTTTCTTTCTCTTTTTTCTTTCTTTTTTTCTTCAATTTTC
GTTGGTCCC
Found at i:523 original size:4 final size:4
Alignment explanation
Indices: 516--588 Score: 62
Period size: 4 Copynumber: 18.5 Consensus size: 4
506 CCTTTTTTTT
* * *
516 TTTC TTTC TTTCC CTTC -TTC CTTC -TTC CTTC -TTC TTTC TTTC TTTC
1 TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
562 TTTC TTTTT TTTC TTTC TTTT TTTC TT
1 TTTC -TTTC TTTC TTTC TTTC TTTC TT
589 CAATTTTCGT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
3 9 0.15
4 44 0.75
5 6 0.10
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTC
Found at i:4901 original size:23 final size:23
Alignment explanation
Indices: 4871--4918 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
4861 AGTTCAAGTT
4871 GAGGTTTATGTTCTACATTGCTG
1 GAGGTTTATGTTCTACATTGCTG
4894 GAGGTTTATGTTCTACATTGCTG
1 GAGGTTTATGTTCTACATTGCTG
4917 GA
1 GA
4919 TAGACTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.27, T:0.42
Consensus pattern (23 bp):
GAGGTTTATGTTCTACATTGCTG
Found at i:5920 original size:15 final size:15
Alignment explanation
Indices: 5891--5937 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
5881 AATACAGATT
5891 AAAAAAATT-AA-AA
1 AAAAAAATTAAATAA
5904 AAAAAAATTAAATAA
1 AAAAAAATTAAATAA
5919 AAAAAAATTAAATAA
1 AAAAAAATTAAATAA
5934 AAAA
1 AAAA
5938 TTATATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.28
14 2 0.06
15 21 0.66
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAAAATTAAATAA
Found at i:10689 original size:6 final size:6
Alignment explanation
Indices: 10679--10708 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
10669 GAAGATTGTA
*
10679 AAAAAA AAAAAC AAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
10709 CGTGGGTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:11034 original size:17 final size:18
Alignment explanation
Indices: 10995--11037 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
10985 TATTTTTGAG
10995 TTTTTTTTTTACCATCAAC
1 TTTTTTTTTTA-CATCAAC
*
11014 TTTTTTTTTTA-ATCTA-
1 TTTTTTTTTTACATCAAC
11030 TTTTTTTT
1 TTTTTTTT
11038 AACAGATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 8 0.35
17 4 0.17
19 11 0.48
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTTTTTACATCAAC
Found at i:21955 original size:2 final size:2
Alignment explanation
Indices: 21907--21938 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21897 ATAAGAGCTC
21907 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21939 AGTTCAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22295 original size:26 final size:26
Alignment explanation
Indices: 22264--22322 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
22254 TCAATAATTA
22264 ATTAATTTTTAAAATTAAAAAATA-T
1 ATTAATTTTTAAAATTAAAAAATATT
* *
22289 ATATAATTTTTAAATTTTAAAAATATT
1 AT-TAATTTTTAAAATTAAAAAATATT
22316 ATTAATT
1 ATTAATT
22323 GCTGACATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 25 0.83
27 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTAATTTTTAAAATTAAAAAATATT
Found at i:22790 original size:3 final size:3
Alignment explanation
Indices: 22782--22820 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
22772 GTGAAATGTG
* * *
22782 ATT ATT ATT ATT ATT ATT GTT GTT GTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
22821 GAAATGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23796 original size:60 final size:62
Alignment explanation
Indices: 23678--23820 Score: 182
Period size: 60 Copynumber: 2.3 Consensus size: 62
23668 AAATATTTTA
* * * * *
23678 ATATAAAAATAATTATATTAAAAATGTTATTAAATTATATATTATTATTATTTATTAAATTAT
1 ATATAATAATAATCATATT-AAAATATAATTAAATTATATATTATCATTATTTATTAAATTAT
* * *
23741 ATTTAATAATAATCATATTAAAATATAATTAATTTATTTA-TATCATT-TTTATTAAATTAT
1 ATATAATAATAATCATATTAAAATATAATTAAATTATATATTATCATTATTTATTAAATTAT
*
23801 ATATAATAATAATCCTATTA
1 ATATAATAATAATCATATTA
23821 TATTTAATAA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 31 0.44
61 6 0.09
62 17 0.24
63 16 0.23
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.49
Consensus pattern (62 bp):
ATATAATAATAATCATATTAAAATATAATTAAATTATATATTATCATTATTTATTAAATTAT
Found at i:24024 original size:16 final size:16
Alignment explanation
Indices: 24005--24035 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23995 CGATTTTATT
*
24005 TCATTACAACTCTATC
1 TCATTACAACCCTATC
24021 TCATTACAACCCTAT
1 TCATTACAACCCTAT
24036 TCAACTCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (16 bp):
TCATTACAACCCTATC
Found at i:27745 original size:40 final size:40
Alignment explanation
Indices: 27699--27780 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
27689 AGAGGATAGG
27699 AACCCCCAATGAAGGAAGCAAGATGACACTCTAAAGGGAA
1 AACCCCCAATGAAGGAAGCAAGATGACACTCTAAAGGGAA
27739 AACCCCCAATGAAGGAAGCAAGATGACACTCTAAAGGGAA
1 AACCCCCAATGAAGGAAGCAAGATGACACTCTAAAGGGAA
27779 AA
1 AA
27781 GAGTATAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (40 bp):
AACCCCCAATGAAGGAAGCAAGATGACACTCTAAAGGGAA
Found at i:30498 original size:245 final size:244
Alignment explanation
Indices: 29881--30563 Score: 732
Period size: 245 Copynumber: 2.8 Consensus size: 244
29871 AATAAATAGC
* * * *
29881 AAATAAGTAATTCAGATTAATAAATTTGTTTGCTATGGAAACTGATTAGAAACAAACAATAATTA
1 AAATAA-TAATTCAGATTAATCAATTTGTTAGCTA-CGAAACT--TTA-TAA-AAACAATAATTA
* * *
29946 ACAAAAATGTTAGGCTGATTTAATTGAATATAAATTTCGATTCCACGATCCTATTTTTTCCCCCT
60 ACAAAAATGTTAGGCTGATTTAATTGAATATAAATTTAGATTCTACGATCCTATTTTTTTCCCCT
* * * *
30011 AAATTCAATCCAAAATGAAAAACCAAATTCCACAAACTGGCGCAGGGAAACTAATAATTGAGAAG
125 AAATACAAT-CAAAATGAAAAACCAAATTCCACGAACTAGCGCAGGGAAACTAACAATTGAGAAG
* * *
30076 AAAAAAAAAAGACAAAGAAAAAAACAACCTAATCTTTATCAATTTTTTGCAAAATAA
189 AAAAAAAAAAGACAAAGAAAAAAACAACATAATCTTTATCAATATTTCGCAAAAT-A
* * *
30133 ATAATAAATAAGTTATTCAGATTAATCAATTTGTTAGGTACGGAA----AT-GAAACAATAATTA
1 A-AAT-AAT-A---ATTCAGATTAATCAATTTGTTAGCTACGAAACTTTATAAAAACAATAATTA
* * *
30193 ACAAAAA-GTTAGGCTGATATAATTGACTATAAATTTAGATTCTACGAT-AT-TTTATTTTCCCC
60 ACAAAAATGTTAGGCTGATTTAATTGAATATAAATTTAGATTCTACGATCCTATTT-TTTTCCCC
* * * * *
30255 TATATACAACTCGAAATGAAAAACCTAATTCCACGAACTAGCGCATTGG-AATTAACAATTGAGA
124 TAAATACAA-TCAAAATGAAAAACCAAATTCCACGAACTAGCGCA-GGGAAACTAACAATTGAGA
** * *
30319 A-ACAAAAATGAAGACAAAG-AAAAAGCAACATAATTTTTTATCAA-ATTTCGCAAAAT-
187 AGA-AAAAAAAAAGACAAAGAAAAAAACAACATAA-TCTTTATCAATATTTCGCAAAATA
*
30375 AAATAATAATTCAGATTAATCAATTTGTTAGCTACGAAACTTTATTAAAAACAATTATTAACAAA
1 AAATAATAATTCAGATTAATCAATTTGTTAGCTACGAAACTTTA-TAAAAACAATAATTAACAAA
30440 AATGTTAGGCTGATTTAATTGAATATAAATTTAGAATTCTACGATCCTATTTTTTTCCCCCTAAA
65 AATGTTAGGCTGATTTAATTGAATATAAATTTAG-ATTCTACGATCCTATTTTTTT-CCCCTAAA
* * * *
30505 TACAGTCAAAAATGGAAAACCAAATTCCACGAAC-AGACG--GTGAAACAAACAATTGAGAA
128 TACAATC-AAAATGAAAAACCAAATTCCACGAACTAG-CGCAGGGAAACTAACAATTGAGAA
30564 ATAAAAATGA
Statistics
Matches: 361, Mismatches: 45, Indels: 58
0.78 0.10 0.12
Matches are distributed among these distances:
236 29 0.08
239 1 0.00
240 4 0.01
241 4 0.01
242 19 0.05
243 30 0.08
244 50 0.14
245 91 0.25
246 79 0.22
247 19 0.05
250 1 0.00
252 1 0.00
253 4 0.01
254 3 0.01
256 3 0.01
257 23 0.06
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.29
Consensus pattern (244 bp):
AAATAATAATTCAGATTAATCAATTTGTTAGCTACGAAACTTTATAAAAACAATAATTAACAAAA
ATGTTAGGCTGATTTAATTGAATATAAATTTAGATTCTACGATCCTATTTTTTTCCCCTAAATAC
AATCAAAATGAAAAACCAAATTCCACGAACTAGCGCAGGGAAACTAACAATTGAGAAGAAAAAAA
AAAGACAAAGAAAAAAACAACATAATCTTTATCAATATTTCGCAAAATA
Found at i:32393 original size:11 final size:12
Alignment explanation
Indices: 32370--32409 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
32360 TCTTAATTAG
32370 TTTTATATCAATT
1 TTTTATAT-AATT
32383 TTTTATA-AATT
1 TTTTATATAATT
*
32394 TATTATATAATT
1 TTTTATATAATT
32406 TTTT
1 TTTT
32410 TTTTACTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 7 0.29
13 7 0.29
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTTATATAATT
Found at i:34325 original size:39 final size:39
Alignment explanation
Indices: 34282--34369 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 39
34272 TATTATGGTG
34282 TTTATAGTGTCACCATCAGTTCAGTA-CGACATTACGATA
1 TTTATAGTGTCACCATCAGTTCAGTATCG-CATTACGATA
* * * *
34321 TTTATAGTGTTATCGTCAGTTCAGTATTGCATTACGATA
1 TTTATAGTGTCACCATCAGTTCAGTATCGCATTACGATA
*
34360 TTTACAGTGT
1 TTTATAGTGT
34370 TACTGTCAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 42 0.98
40 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (39 bp):
TTTATAGTGTCACCATCAGTTCAGTATCGCATTACGATA
Found at i:34370 original size:39 final size:39
Alignment explanation
Indices: 34297--34424 Score: 120
Period size: 39 Copynumber: 3.3 Consensus size: 39
34287 AGTGTCACCA
* *
34297 TCAGTTCAGTA-CGACATTACGATATTTATAGTGTTA-TCG
1 TCAGTTCAGTATTG-CATTACGATATTTACAGTGTTACT-G
34336 TCAGTTCAGTATTGCATTACGATATTTACAGTGTTACTG
1 TCAGTTCAGTATTGCATTACGATATTTACAGTGTTACTG
* * * *
34375 TCAACTT-AGTATTGCATTGC-AGTGTTTACAGTGTCACTG
1 TC-AGTTCAGTATTGCATTACGA-TATTTACAGTGTTACTG
* *
34414 CCAATTCAGTA
1 TCAGTTCAGTA
34425 GTTTGATAAC
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
38 4 0.05
39 67 0.88
40 5 0.07
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (39 bp):
TCAGTTCAGTATTGCATTACGATATTTACAGTGTTACTG
Found at i:40919 original size:18 final size:18
Alignment explanation
Indices: 40896--40940 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
40886 ACCAAGTCAA
40896 ACCGTTGATCGACCGTTG
1 ACCGTTGATCGACCGTTG
*
40914 ACCGTTGATCGATCGTTG
1 ACCGTTGATCGACCGTTG
*
40932 ACCTTTGAT
1 ACCGTTGAT
40941 AGTTTATCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.33
Consensus pattern (18 bp):
ACCGTTGATCGACCGTTG
Found at i:40982 original size:14 final size:14
Alignment explanation
Indices: 40949--40975 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40939 ATAGTTTATC
40949 GTTGACCATTGATT
1 GTTGACCATTGATT
40963 GTTGACCATTGAT
1 GTTGACCATTGAT
40976 ATTTGACTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (14 bp):
GTTGACCATTGATT
Found at i:42576 original size:6 final size:6
Alignment explanation
Indices: 42565--42594 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
42555 CCCACGACCA
*
42565 AGGTCG AGGTCG AGGTCG AGGTCG ATGTCG
1 AGGTCG AGGTCG AGGTCG AGGTCG AGGTCG
42595 TACTGCTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.47, T:0.20
Consensus pattern (6 bp):
AGGTCG
Found at i:59161 original size:17 final size:17
Alignment explanation
Indices: 59136--59169 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59126 TGGTTTTTTA
*
59136 ATTTTTTTTATAAATAT
1 ATTTGTTTTATAAATAT
*
59153 ATTTGTTTTATATATAT
1 ATTTGTTTTATAAATAT
59170 TACCTCACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTTGTTTTATAAATAT
Found at i:60275 original size:60 final size:59
Alignment explanation
Indices: 60211--60372 Score: 164
Period size: 60 Copynumber: 2.7 Consensus size: 59
60201 AATATTTTTT
* *
60211 AATTTTTAGAGTTAGGACTAAATTGATAGATTTTATAAATGTCGAGGGCCAAATTTATTG
1 AATTTTTATA-TTAGGACTAAATTGATAGATTTTATAAATATCGAGGGCCAAATTTATTG
* * * * * * * * *
60271 AATTTTTATAATTAGAACTAAAATGACAAATTTTGTAAACATTGAGGGCTAAATTTGTTG
1 AATTTTTAT-ATTAGGACTAAATTGATAGATTTTATAAATATCGAGGGCCAAATTTATTG
* *
60331 AATTTTTATATTAAGGA-TCAAATTGATAGAATGTATAAATAT
1 AATTTTTATATT-AGGACT-AAATTGATAGATTTTATAAATAT
60373 TAGAGGATTA
Statistics
Matches: 80, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
59 4 0.05
60 75 0.94
61 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.39
Consensus pattern (59 bp):
AATTTTTATATTAGGACTAAATTGATAGATTTTATAAATATCGAGGGCCAAATTTATTG
Found at i:61763 original size:22 final size:22
Alignment explanation
Indices: 61694--61766 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
61684 ATCATGACTT
61694 TAATTTTTCATTTTTT-T-TATA
1 TAATTTTT-ATTTTTTATATATA
* * *
61715 TAAATTTTATTTATTA-ATTTAA
1 TAATTTTTATTTTTTATATAT-A
* *
61737 AAATTTTTATTTTTTATATCTA
1 TAATTTTTATTTTTTATATATA
61759 TAATTTTT
1 TAATTTTT
61767 CTTAGATGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
20 6 0.15
21 9 0.22
22 22 0.55
23 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (22 bp):
TAATTTTTATTTTTTATATATA
Found at i:62177 original size:20 final size:23
Alignment explanation
Indices: 62152--62193 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 23
62142 GTTAGTTTTT
62152 TTTTTAT-TT-TAA-ATTTATTA
1 TTTTTATCTTGTAATATTTATTA
62172 TTTTTATCTTGTAATATTTATT
1 TTTTTATCTTGTAATATTTATT
62194 TATATAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 3 0.16
23 7 0.37
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTATCTTGTAATATTTATTA
Found at i:62448 original size:21 final size:21
Alignment explanation
Indices: 62424--62474 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
62414 GGATTATGTA
62424 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
*
62445 ATTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
62466 ATTTGGATT
1 ATTTGGATT
62475 ATGCTATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.53
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:63565 original size:30 final size:30
Alignment explanation
Indices: 63531--63605 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
63521 ACAAAGCTGG
*
63531 CTGCTAACTTACGCTACACAACGTCACTAC
1 CTGCTATCTTACGCTACACAACGTCACTAC
63561 CTGCTATCTTACGCTACACAACGTCACTAC
1 CTGCTATCTTACGCTACACAACGTCACTAC
63591 CTGCTATCTTACGCT
1 CTGCTATCTTACGCT
63606 TGTATATTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.25, C:0.36, G:0.11, T:0.28
Consensus pattern (30 bp):
CTGCTATCTTACGCTACACAACGTCACTAC
Found at i:75944 original size:17 final size:17
Alignment explanation
Indices: 75922--75957 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
75912 ATAGCATGGT
*
75922 TCTTAATAAGGTTGCCA
1 TCTTAAGAAGGTTGCCA
75939 TCTTAAGAAGGTTGCCA
1 TCTTAAGAAGGTTGCCA
75956 TC
1 TC
75958 GTAGCACCAC
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:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (17 bp):
TCTTAAGAAGGTTGCCA
Found at i:80717 original size:15 final size:15
Alignment explanation
Indices: 80697--80729 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
80687 ATTTGATGTT
*
80697 AATTAAATATGGGTA
1 AATTAAATAAGGGTA
80712 AATTAAATAAGGGTA
1 AATTAAATAAGGGTA
80727 AAT
1 AAT
80730 CAGTAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (15 bp):
AATTAAATAAGGGTA
Found at i:84707 original size:21 final size:21
Alignment explanation
Indices: 84681--84733 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
84671 GGCAATAGAA
84681 TTCTACCGATAGAA-T-TGGGAG
1 TTCTACCGATAGAACTCT-GG-G
*
84702 TTCTACTGATAGAACTCTGGG
1 TTCTACCGATAGAACTCTGGG
84723 TTCTACCGATA
1 TTCTACCGATA
84734 CAACCCAGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 24 0.86
22 3 0.11
23 1 0.04
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (21 bp):
TTCTACCGATAGAACTCTGGG
Found at i:87080 original size:21 final size:21
Alignment explanation
Indices: 87056--87109 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
87046 CTTGTGATAG
*
87056 TTCTACCGATACAAGT-GTAAC
1 TTCTACCGATACAAGTCAT-AC
* * *
87077 TTCTATCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
87098 TTCTACCGATAC
1 TTCTACCGATAC
87110 TAAAAACTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:94636 original size:39 final size:39
Alignment explanation
Indices: 94592--94738 Score: 143
Period size: 39 Copynumber: 3.8 Consensus size: 39
94582 ATAGCTACAT
*
94592 AGTGTTTACAGTGTCACTGCTAGCTCAGTATTATATTAC
1 AGTGTTTACAGTGTCACTGCCAGCTCAGTATTATATTAC
* * * * *
94631 GGTGTTTACAGTGTCACTGCCAGTTCAGTGTTGTATTGC
1 AGTGTTTACAGTGTCACTGCCAGCTCAGTATTATATTAC
* * ** * *
94670 AGTGTTTACAGTGTTACTACCAATTCAGTGTTGTATTGA-
1 AGTGTTTACAGTGTCACTGCCAGCTCAGTATTATATT-AC
* * *
94709 AGTGTTTACAATGTCACTGTCAGTTCAGTA
1 AGTGTTTACAGTGTCACTGCCAGCTCAGTA
94739 ATTTGATAAC
Statistics
Matches: 90, Mismatches: 17, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 90 1.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCCAGCTCAGTATTATATTAC
Found at i:94674 original size:78 final size:78
Alignment explanation
Indices: 94592--94737 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 78
94582 ATAGCTACAT
* * * * *
94592 AGTGTTTACAGTGTCACTGCTAGCTCAGTATTATATT-ACGGTGTTTACAGTGTCACTGCCAGTT
1 AGTGTTTACAGTGTCACTACCAACTCAGTATTATATTGA-AGTGTTTACAATGTCACTGCCAGTT
94656 CAGTGTTGTATTGC
65 CAGTGTTGTATTGC
* * * * *
94670 AGTGTTTACAGTGTTACTACCAATTCAGTGTTGTATTGAAGTGTTTACAATGTCACTGTCAGTTC
1 AGTGTTTACAGTGTCACTACCAACTCAGTATTATATTGAAGTGTTTACAATGTCACTGCCAGTTC
94735 AGT
66 AGT
94738 AATTTGATAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
78 56 0.98
79 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (78 bp):
AGTGTTTACAGTGTCACTACCAACTCAGTATTATATTGAAGTGTTTACAATGTCACTGCCAGTTC
AGTGTTGTATTGC
Found at i:94962 original size:73 final size:73
Alignment explanation
Indices: 94828--94963 Score: 182
Period size: 73 Copynumber: 1.9 Consensus size: 73
94818 CCGTGTGTGT
* * * * * * *
94828 CACACGGTCTGGCACACACCCGTGTGTCCAGGCCGTGTAACTCATTGTTTTTGTTTTCACAAAAT
1 CACACGGTCTGGCACACACCCATGTGTCCAGCCCGTGTAACTCACTATTTATGATTCCACAAAAT
94893 GGTATGGG
66 GGTATGGG
* * *
94901 CACACGGTTTGGCACACCCCCATGTGTCCAGCCCGTGTAACTTACTATTTATGATTCCACAAA
1 CACACGGTCTGGCACACACCCATGTGTCCAGCCCGTGTAACTCACTATTTATGATTCCACAAA
94964 TAGAATATCC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 53 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (73 bp):
CACACGGTCTGGCACACACCCATGTGTCCAGCCCGTGTAACTCACTATTTATGATTCCACAAAAT
GGTATGGG
Found at i:97382 original size:11 final size:11
Alignment explanation
Indices: 97366--97398 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
97356 TCTAAAAAGA
97366 TAAATATAAAT
1 TAAATATAAAT
*
97377 TAAATACAAAT
1 TAAATATAAAT
97388 TAAATATAAAT
1 TAAATATAAAT
97399 AATATCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:103534 original size:12 final size:12
Alignment explanation
Indices: 103517--103544 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
103507 GAATAAGAAG
103517 CAAAATTATCAT
1 CAAAATTATCAT
103529 CAAAATTATCAT
1 CAAAATTATCAT
103541 CAAA
1 CAAA
103545 CAGTGTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (12 bp):
CAAAATTATCAT
Found at i:106693 original size:11 final size:11
Alignment explanation
Indices: 106677--106709 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
106667 TCTAAAATGA
106677 TAAATATAAAT
1 TAAATATAAAT
*
106688 TAAATACAAAT
1 TAAATATAAAT
106699 TAAATATAAAT
1 TAAATATAAAT
106710 AATATCCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:106757 original size:5 final size:5
Alignment explanation
Indices: 106747--106775 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
106737 AATAAAGTTT
106747 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
106776 GTCTTTTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:111054 original size:16 final size:16
Alignment explanation
Indices: 111033--111066 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
111023 AACGGAGGTT
111033 CAAGGTACAGACCCAA
1 CAAGGTACAGACCCAA
111049 CAAGGTACAGACCCAA
1 CAAGGTACAGACCCAA
111065 CA
1 CA
111067 CGAGTCCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.32, G:0.18, T:0.06
Consensus pattern (16 bp):
CAAGGTACAGACCCAA
Found at i:112100 original size:39 final size:39
Alignment explanation
Indices: 112054--112163 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 39
112044 ATATAGCTAC
*
112054 ACAGTGTTTACAGTGTCACTGTCAGCTCAGTATAGTATT
1 ACAGTGTTTACAGTGTCACTGTCAGTTCAGTATAGTATT
** * * * * * *
112093 ATGGTGTTTACAATATCACTGTCAATTCAATGTTGTATT
1 ACAGTGTTTACAGTGTCACTGTCAGTTCAGTATAGTATT
* *
112132 ACAGTGTTTATAGTGTCACTGCCAGTTCAGTA
1 ACAGTGTTTACAGTGTCACTGTCAGTTCAGTA
112164 ATTTGATAAT
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (39 bp):
ACAGTGTTTACAGTGTCACTGTCAGTTCAGTATAGTATT
Found at i:122608 original size:19 final size:20
Alignment explanation
Indices: 122577--122614 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
122567 GAAAATTTAA
122577 AATTTTTATAAA-TATTTTG
1 AATTTTTATAAATTATTTTG
122596 AATTTTTGA-AAATTATTTT
1 AATTTTT-ATAAATTATTTT
122615 ACTTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
AATTTTTATAAATTATTTTG
Found at i:124299 original size:13 final size:12
Alignment explanation
Indices: 124276--124310 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
124266 GAAAAAAAGT
*
124276 TATTTTTAAAAA
1 TATTTTGAAAAA
124288 TATTTATGAAAAA
1 TATTT-TGAAAAA
124301 TATTTTGAAA
1 TATTTTGAAA
124311 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (12 bp):
TATTTTGAAAAA
Found at i:124533 original size:22 final size:24
Alignment explanation
Indices: 124490--124533 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
124480 TGATAATATG
124490 TTTTGATATAATAAATTAAAGTGT
1 TTTTGATATAATAAATTAAAGTGT
*
124514 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAATAAATTAAAGT
124534 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (24 bp):
TTTTGATATAATAAATTAAAGTGT
Found at i:124620 original size:20 final size:20
Alignment explanation
Indices: 124565--124621 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 20
124555 AATAAAATCA
*
124565 AGTTAAAAATGATTTCAATT
1 AGTTAAAAATGTTTTCAATT
*
124585 GAGTTAAACA--TTTTCAA-T
1 -AGTTAAAAATGTTTTCAATT
124603 ATGTTAAAAATGTTTTCAA
1 A-GTTAAAAATGTTTTCAA
124622 ACTTGTCAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 1 0.03
18 8 0.27
19 6 0.20
20 7 0.23
21 8 0.27
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (20 bp):
AGTTAAAAATGTTTTCAATT
Found at i:128270 original size:24 final size:23
Alignment explanation
Indices: 128232--128281 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
128222 AAATTTTGTT
*
128232 TGGGCTCGAATGAGCTAACTTATC
1 TGGGCTCGAATGAGCTAAATT-TC
128256 TGGGCTCGTAA-GAGCTAAATTTC
1 TGGGCTCG-AATGAGCTAAATTTC
128279 TGG
1 TGG
128282 AAGACTTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 17 0.71
25 2 0.08
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGGCTCGAATGAGCTAAATTTC
Found at i:131731 original size:117 final size:117
Alignment explanation
Indices: 131571--131805 Score: 346
Period size: 117 Copynumber: 2.0 Consensus size: 117
131561 TCACAAAAGG
* ** *
131571 GTTAAGAACCTTACCCACTTTTTGGTTTCTGTACTTTTCCAGCTTCATCTTTATGAAGAATGCTT
1 GTTAAGAACCTTACCCACTTGTTGGTTTCCCTACTTTTCCAGCTTCATCCTTATGAAGAATGCTT
*
131636 CATACAAAACCTTCCATGGGTACTCCTTCTTTGAGCTA-TCGAAAAAGATGAA
66 CATACAAAACCTTCCATGGGTACCCCTTCTTTGAGCTACT-GAAAAAGATGAA
*** *
131688 GTTAAGAACCTTACTTGCTTGTTGGTTTCCCTACTTTTCCAGCTTCATCCTTATGAAGTATGCTT
1 GTTAAGAACCTTACCCACTTGTTGGTTTCCCTACTTTTCCAGCTTCATCCTTATGAAGAATGCTT
* * *
131753 CATGCAAAACCTTCTATGGGTACCCCTTCTTTGAGCTACTGAAAAATATGAA
66 CATACAAAACCTTCCATGGGTACCCCTTCTTTGAGCTACTGAAAAAGATGAA
131805 G
1 G
131806 AACGAGAGAA
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
117 104 0.99
118 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (117 bp):
GTTAAGAACCTTACCCACTTGTTGGTTTCCCTACTTTTCCAGCTTCATCCTTATGAAGAATGCTT
CATACAAAACCTTCCATGGGTACCCCTTCTTTGAGCTACTGAAAAAGATGAA
Found at i:133964 original size:22 final size:21
Alignment explanation
Indices: 133939--134001 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
133929 ATAAACATAA
133939 AAAACTAAAAAATAATAATATT
1 AAAACTAAAAAAT-ATAATATT
* * *
133961 AAAACTTAATAATGATATTAATT
1 AAAACTAAAAAAT-ATAAT-ATT
133984 AAAA-TAAAAAATATAATA
1 AAAACTAAAAAATATAATA
134002 ATATTTTCTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 4 0.12
22 21 0.64
23 7 0.21
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAACTAAAAAATATAATATT
Found at i:134930 original size:29 final size:29
Alignment explanation
Indices: 134898--134956 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
134888 AATCAATTAC
134898 AAAATA-GATTAATTAATTAATAA-AAAATA
1 AAAATATGATT-ATTAATTAA-AATAAAATA
*
134927 AAAATATTATTATTAATTAAAATAAAATA
1 AAAATATGATTATTAATTAAAATAAAATA
134956 A
1 A
134957 TTAAGTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 2 0.07
29 22 0.81
30 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATATGATTATTAATTAAAATAAAATA
Found at i:137093 original size:129 final size:130
Alignment explanation
Indices: 136935--137193 Score: 475
Period size: 129 Copynumber: 2.0 Consensus size: 130
136925 ACCGTGTTGA
* *
136935 CGTGACAATTTTTTTCCGACTGAGCGCATCCACGTAAGCATCTGCTGACGTAGCACTATTTTGTT
1 CGTGACAATTTTTTTCCAACTGAGCGCATCCACGTAAGCATCTGCTGACGTAGCACTATTTTGTC
137000 TTATATGCCACGTCAACAAATGATTTTAAAATTATTAAAATTATTTTTTTT-AAATATAAAATTT
66 TTATATGCCACGTCAACAAATGATTTTAAAATTATTAAAATTATTTTTTTTAAAATATAAAATTT
* *
137064 CGTGGCAATTTTTTTCCAACTGAGCGCATCCACGTAAGCTTCTGCTGACGTAGCACTATTTTGTC
1 CGTGACAATTTTTTTCCAACTGAGCGCATCCACGTAAGCATCTGCTGACGTAGCACTATTTTGTC
137129 TTATATGCCACGTCAACAAATGATTTTAAAATTATTAAAATTATTTTTTTTAAAATATAAAATTT
66 TTATATGCCACGTCAACAAATGATTTTAAAATTATTAAAATTATTTTTTTTAAAATATAAAATTT
137194 TTTGAATTAT
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
129 112 0.90
130 13 0.10
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (130 bp):
CGTGACAATTTTTTTCCAACTGAGCGCATCCACGTAAGCATCTGCTGACGTAGCACTATTTTGTC
TTATATGCCACGTCAACAAATGATTTTAAAATTATTAAAATTATTTTTTTTAAAATATAAAATTT
Found at i:137216 original size:29 final size:29
Alignment explanation
Indices: 137155--137263 Score: 116
Period size: 29 Copynumber: 3.7 Consensus size: 29
137145 CAAATGATTT
137155 TAAAA-TTATTAAAATTATTTTTTTTAAAATA
1 TAAAATTTATT-AAATTA--TTTTTTAAAATA
* *
137186 TAAAATTTTTTGAATTATTTTTTAAAATA
1 TAAAATTTATTAAATTATTTTTTAAAATA
* *
137215 TAAAA-TTATTAAATTTTTTTTTGAAATAA
1 TAAAATTTATTAAATTATTTTTTAAAAT-A
*
137244 TAAAA-TTATTAAATAATTTT
1 TAAAATTTATTAAATTATTTT
137264 AATTTTTAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 18 0.26
29 36 0.53
31 10 0.15
32 4 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TAAAATTTATTAAATTATTTTTTAAAATA
Found at i:143856 original size:27 final size:27
Alignment explanation
Indices: 143825--143881 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
143815 TAAAGGCCAA
143825 AAGTTAGCATGTCTCCTTCAAAAGATT
1 AAGTTAGCATGTCTCCTTCAAAAGATT
*
143852 AAGTTAGCATGTCTCCTTTAAAAGATT
1 AAGTTAGCATGTCTCCTTCAAAAGATT
143879 AAG
1 AAG
143882 ACTCTGACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (27 bp):
AAGTTAGCATGTCTCCTTCAAAAGATT
Found at i:146309 original size:94 final size:94
Alignment explanation
Indices: 146148--146336 Score: 333
Period size: 94 Copynumber: 2.0 Consensus size: 94
146138 AAAAAGGAAG
*
146148 GATCGAAGAAAGATGTAAGTCTCCTCAAACGTAGTGGGAGATGCTATAACGAGACAGATGCAGAA
1 GATCGAAGAAAGATGTAAGTCTCCTCAAACATAGTGGGAGATGCTATAACGAGACAGATGCAGAA
* * *
146213 AGTGAAGCCAGCAAAGAAAAATCCTTAGT
66 AGTGAAGCCAACAAAGAAAAAGCCCTAGT
*
146242 GATCGAAGAAAGATGTAAGTCTCCTCACACATAGTGGGAGATGCTATAACGAGACAGATGCAGAA
1 GATCGAAGAAAGATGTAAGTCTCCTCAAACATAGTGGGAGATGCTATAACGAGACAGATGCAGAA
146307 AGTGAAGCCAACAAAGAAAAAGCCCTAGT
66 AGTGAAGCCAACAAAGAAAAAGCCCTAGT
146336 G
1 G
146337 GTTGGGCCTG
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (94 bp):
GATCGAAGAAAGATGTAAGTCTCCTCAAACATAGTGGGAGATGCTATAACGAGACAGATGCAGAA
AGTGAAGCCAACAAAGAAAAAGCCCTAGT
Found at i:159089 original size:13 final size:14
Alignment explanation
Indices: 159064--159097 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
159054 GAAAACAGCC
*
159064 AAGAGAAAGAAAAT
1 AAGAGAAAAAAAAT
159078 AA-AGAAAAAAAAT
1 AAGAGAAAAAAAAT
159091 AAGAGAA
1 AAGAGAA
159098 TGCAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (14 bp):
AAGAGAAAAAAAAT
Found at i:164345 original size:50 final size:50
Alignment explanation
Indices: 164204--164375 Score: 184
Period size: 50 Copynumber: 3.4 Consensus size: 50
164194 GTGACAAAAT
* * ** ** *
164204 GAATCTTATACCCCTAAAGCTGTAGAGGAACAGATTAAAATCGTAATGGA
1 GAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTAAAGCCGTAATGGC
* * * * *
164254 AAATCTCATACACCCAAAGCTGTAAAGGGGTAGATTGAAGCCGTAATGGC
1 GAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTAAAGCCGTAATGGC
* * *
164304 GAATCTCATACACCTAAAGCTGTAGAGGGGCAAATTAAAGCCGCAAAGGC
1 GAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTAAAGCCGTAATGGC
*
164354 GAATCTTATAC-CCTTAAAGCTG
1 GAATCTCATACACC-TAAAGCTG
164376 AAGAATGGTG
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
49 2 0.02
50 98 0.98
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (50 bp):
GAATCTCATACACCTAAAGCTGTAGAGGGGCAGATTAAAGCCGTAATGGC
Found at i:167485 original size:37 final size:37
Alignment explanation
Indices: 167438--167512 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
167428 TTATTGTCAT
167438 GATTGTTTCATTGTGCATTATTTATTAATTATTGATA
1 GATTGTTTCATTGTGCATTATTTATTAATTATTGATA
167475 GATTGTTTCATTGTGCATTATTTATTAATTATTGATA
1 GATTGTTTCATTGTGCATTATTTATTAATTATTGATA
167512 G
1 G
167513 TCATTTAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.53
Consensus pattern (37 bp):
GATTGTTTCATTGTGCATTATTTATTAATTATTGATA
Found at i:170196 original size:46 final size:46
Alignment explanation
Indices: 170121--170208 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
170111 TATTGCAATT
*
170121 AGAGTTTTAGATTTATTTAATTTGTTTATTATATCAGGTTTTATTA
1 AGAGTTTTAGATTTAGTTAATTTGTTTATTATATCAGGTTTTATTA
* *
170167 AGAGTTTTA-ATTTTAGTT-ATTTTTCTTATTATATTAGGTTTT
1 AGAGTTTTAGA-TTTAGTTAATTTGT-TTATTATATCAGGTTTT
170209 TATTTCCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 6 0.16
46 31 0.84
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.59
Consensus pattern (46 bp):
AGAGTTTTAGATTTAGTTAATTTGTTTATTATATCAGGTTTTATTA
Found at i:178833 original size:17 final size:17
Alignment explanation
Indices: 178811--178845 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
178801 TTGATTCATT
*
178811 TATCGATAAACTAATAA
1 TATCGATAAAATAATAA
178828 TATCGATAAAATAATAA
1 TATCGATAAAATAATAA
178845 T
1 T
178846 TTTTTGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (17 bp):
TATCGATAAAATAATAA
Found at i:180639 original size:28 final size:28
Alignment explanation
Indices: 180607--180681 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
180597 TTTAAAGGCC
180607 CTTAAAAGTTAATAAAAAAATTT-GACCT
1 CTTAAAAGTTAA-AAAAAAATTTAGACCT
* *
180635 GTT-AAAGTTAAAAAAAAAAATTTAGACGT
1 CTTAAAAGTT--AAAAAAAAATTTAGACCT
*
180664 CTTAAAAATTAAAAAAAA
1 CTTAAAAGTTAAAAAAAA
180682 TTCTCTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 6 0.15
28 20 0.51
29 8 0.21
30 5 0.13
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (28 bp):
CTTAAAAGTTAAAAAAAAATTTAGACCT
Found at i:180652 original size:29 final size:30
Alignment explanation
Indices: 180523--180681 Score: 114
Period size: 31 Copynumber: 5.2 Consensus size: 30
180513 ATAAAAGTTG
**
180523 AAAAAAAAATTTAGGTCTCTTAAAAATTGGCAA
1 AAAAAAAAATTTAGACCTCTTAAAAATT---AA
*
180556 AAAAAAAAATTTA-ACC-CTTAAAAACTAAAAA
1 AAAAAAAAATTTAGACCTCTTAAAAA-T--TAA
* *
180587 AAAAAAAAATTTTAAAGGCC-CTTAAAAGTT-A
1 AAAAAAAAA-TTT--AGACCTCTTAAAAATTAA
* * *
180618 ATAAAAAAATTT-GACCTGTT-AAAGTTAA
1 AAAAAAAAATTTAGACCTCTTAAAAATTAA
*
180646 AAAAAAAAATTTAGACGTCTTAAAAATTAA
1 AAAAAAAAATTTAGACCTCTTAAAAATTAA
180676 AAAAAA
1 AAAAAA
180682 TTCTCTTAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 25
0.73 0.09 0.18
Matches are distributed among these distances:
27 9 0.09
28 14 0.14
29 6 0.06
30 16 0.16
31 28 0.27
32 5 0.05
33 13 0.13
34 2 0.02
35 9 0.09
ACGTcount: A:0.58, C:0.09, G:0.08, T:0.25
Consensus pattern (30 bp):
AAAAAAAAATTTAGACCTCTTAAAAATTAA
Found at i:185655 original size:34 final size:34
Alignment explanation
Indices: 185612--185680 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
185602 TTGATCTACA
185612 TTCAGATGAACTGTGTGCAAAATAGCAACTTCTG
1 TTCAGATGAACTGTGTGCAAAATAGCAACTTCTG
185646 TTCAGATGAACTGTGTGCAAAATAGCAACTTCTG
1 TTCAGATGAACTGTGTGCAAAATAGCAACTTCTG
185680 T
1 T
185681 ATGGTTTGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (34 bp):
TTCAGATGAACTGTGTGCAAAATAGCAACTTCTG
Found at i:190878 original size:16 final size:16
Alignment explanation
Indices: 190841--190880 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
190831 ATTTTTTATT
*
190841 TAAAATTGATTAAATAA
1 TAAAATT-AATAAATAA
190858 T-AAATTAATAAATAA
1 TAAAATTAATAAATAA
190873 TAAAATTA
1 TAAAATTA
190881 TATTTTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 9 0.43
16 11 0.52
17 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TAAAATTAATAAATAA
Found at i:195169 original size:14 final size:13
Alignment explanation
Indices: 195146--195184 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
195136 AATAAATATA
195146 TTATTTTTAATTT
1 TTATTTTTAATTT
195159 TTATATTTTAATTT
1 TTAT-TTTTAATTT
* *
195173 ATCTTTTTAATT
1 TTATTTTTAATT
195185 AATAACTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTTTAATTT
Found at i:197170 original size:31 final size:29
Alignment explanation
Indices: 197132--197193 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
197122 ATAAAATTAA
197132 ATATATTGTCAATTAATAAATAAATATATAT
1 ATATATTGTCAATT-AT-AATAAATATATAT
*
197163 ATATATTGTCAATTATAATATATATATAT
1 ATATATTGTCAATTATAATAAATATATAT
197192 AT
1 AT
197194 TATAGAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 14 0.47
30 2 0.07
31 14 0.47
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (29 bp):
ATATATTGTCAATTATAATAAATATATAT
Found at i:201703 original size:45 final size:45
Alignment explanation
Indices: 201639--201731 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
201629 AATTCATGCA
201639 TATGAGGTGTGTTGCACACATTCTTAATCTCATTGTGCAATACGG
1 TATGAGGTGTGTTGCACACATTCTTAATCTCATTGTGCAATACGG
201684 TATGAGGTGTGTTGCACACATTCTTAATCTCATTGTGCAATACGG
1 TATGAGGTGTGTTGCACACATTCTTAATCTCATTGTGCAATACGG
201729 TAT
1 TAT
201732 TAAGGATGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.37
Consensus pattern (45 bp):
TATGAGGTGTGTTGCACACATTCTTAATCTCATTGTGCAATACGG
Found at i:203156 original size:148 final size:149
Alignment explanation
Indices: 202882--203180 Score: 564
Period size: 148 Copynumber: 2.0 Consensus size: 149
202872 ATTTATAAAA
*
202882 TAAGCTTTTGTGTTATTTATATTAGTAAACATTTCCATAATTTAACTGACACTTTTGTTTTTAAA
1 TAAGCTTTTGTGTTATTTATATTAGTAAACATTTCCATAATTTAACTGACACTTTTGTTTTAAAA
*
202947 TTTGCTAGACTTATTCAAAATATCTGAAGATCAAGAAGGTTATATACTTAGCATTATTTTATAAA
66 TTTGCTAGACTTATTCAAAATATCTGAAGATCAAGAAGGTTATATACTTAGCATTAGTTTATAAA
203012 GTTAAATGTTTATTTAATT
131 GTTAAATGTTTATTTAATT
*
203031 TAAGCTTTTGTGTTATTTATATTAGTAAACATTTCCATATTTTAACTGACACTTTT-TTTTAAAA
1 TAAGCTTTTGTGTTATTTATATTAGTAAACATTTCCATAATTTAACTGACACTTTTGTTTTAAAA
203095 TTTGCTAGACTTATTCAAAATATCTGAAGATCAAGAAGGTTATATACTTAGCATTAGTTTATAAA
66 TTTGCTAGACTTATTCAAAATATCTGAAGATCAAGAAGGTTATATACTTAGCATTAGTTTATAAA
203160 GTTAAATGTTTATTTAATT
131 GTTAAATGTTTATTTAATT
203179 TA
1 TA
203181 TTCTTGCTAA
Statistics
Matches: 147, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
148 92 0.63
149 55 0.37
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (149 bp):
TAAGCTTTTGTGTTATTTATATTAGTAAACATTTCCATAATTTAACTGACACTTTTGTTTTAAAA
TTTGCTAGACTTATTCAAAATATCTGAAGATCAAGAAGGTTATATACTTAGCATTAGTTTATAAA
GTTAAATGTTTATTTAATT
Found at i:203348 original size:22 final size:22
Alignment explanation
Indices: 203307--203352 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
203297 TTTGAACTGA
*
203307 TGTGTTATTGTTATTAGTTTAT
1 TGTGTTATTGTTACTAGTTTAT
* *
203329 TGTGTTATTGTTGCTGGTTTAT
1 TGTGTTATTGTTACTAGTTTAT
203351 TG
1 TG
203353 GACTTATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.13, C:0.02, G:0.24, T:0.61
Consensus pattern (22 bp):
TGTGTTATTGTTACTAGTTTAT
Found at i:210761 original size:23 final size:22
Alignment explanation
Indices: 210730--210772 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
210720 ACTTTCATGA
*
210730 TTAACTTAATTAATCATATTTT
1 TTAACTTAATCAATCATATTTT
*
210752 TTAACCTTAATCAATCCTATT
1 TTAA-CTTAATCAATCATATT
210773 ATTAATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAACTTAATCAATCATATTTT
Found at i:210777 original size:22 final size:22
Alignment explanation
Indices: 210729--210777 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
210719 GACTTTCATG
*
210729 ATTAACTTAATTAATCATATTT
1 ATTAACTTAATCAATCATATTT
* *
210751 TTTAACCTTAATCAATCCTA-TT
1 ATTAA-CTTAATCAATCATATTT
210773 ATTAA
1 ATTAA
210778 TCAATATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTAACTTAATCAATCATATTT
Found at i:216171 original size:21 final size:20
Alignment explanation
Indices: 216126--216178 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
216116 TTGTGCTAGC
*
216126 TCTACCGGTACAAGTATGATT
1 TCTACCGATACAAGTATGA-T
216147 TCTACCGATACAAGTCATGCA-
1 TCTACCGATACAAGT-ATG-AT
216168 TCTACCGATAC
1 TCTACCGATAC
216179 CAAAAACTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 25 0.86
22 3 0.10
23 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (20 bp):
TCTACCGATACAAGTATGAT
Found at i:218443 original size:23 final size:23
Alignment explanation
Indices: 218413--218459 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
218403 AAAAGTACCA
*
218413 TAAATACATAGCTATT-TCCTTCT
1 TAAATACATAACTATTGT-CTTCT
218436 TAAATACATAACTATTGTCTTCT
1 TAAATACATAACTATTGTCTTCT
218459 T
1 T
218460 TATACCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (23 bp):
TAAATACATAACTATTGTCTTCT
Found at i:221464 original size:52 final size:52
Alignment explanation
Indices: 221386--221619 Score: 301
Period size: 52 Copynumber: 4.7 Consensus size: 52
221376 AATGAAAAAG
* * *
221386 GGTCCGATGACTAAGTGTCATAGTGAGTATATGAATCCTTTACAGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
221438 GGTCCGATGACTATGTGTCATCGTGAGTATCTGAATCCTTTACGGATTATAA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
221490 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
221542 GGTCCG--G----TG-G-CTAT-GT--GTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTC-ATCGTGAGTATATGAATCCTTTACGGATTATGA
* * *
221584 GGTCCGGTGGCTATGTGTGATCGTGAGTATATGAAT
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAAT
221620 GAAATGAAAT
Statistics
Matches: 161, Mismatches: 9, Indels: 24
0.83 0.05 0.12
Matches are distributed among these distances:
42 32 0.20
44 4 0.02
45 3 0.02
46 2 0.01
48 2 0.01
49 3 0.02
50 3 0.02
52 112 0.70
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:221575 original size:42 final size:42
Alignment explanation
Indices: 221516--221601 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
221506 GTCATCGTGA
221516 GTATATGAATCCTTTACGGATTATGAGGTCCGGTGGCTATGT
1 GTATATGAATCCTTTACGGATTATGAGGTCCGGTGGCTATGT
221558 GTATATGAATCCTTTACGGATTATGAGGTCCGGTGGCTATGT
1 GTATATGAATCCTTTACGGATTATGAGGTCCGGTGGCTATGT
221600 GT
1 GT
221602 GATCGTGAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (42 bp):
GTATATGAATCCTTTACGGATTATGAGGTCCGGTGGCTATGT
Found at i:222855 original size:32 final size:32
Alignment explanation
Indices: 222782--222865 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
222772 AAATTATTTC
*
222782 GTTGGATTTTGAAATTATTATGTTTTAAAGTA
1 GTTGGATATTGAAATTATTATGTTTTAAAGTA
* * * *
222814 GTTGAATATTGAATTTATTATG-TTTCAAGCTT
1 GTTGGATATTGAAATTATTATGTTTTAAAG-TA
* *
222846 GTTGGATATTTAAATGATTA
1 GTTGGATATTGAAATTATTA
222866 ACAATGACTA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 6 0.14
32 36 0.86
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (32 bp):
GTTGGATATTGAAATTATTATGTTTTAAAGTA
Found at i:223884 original size:46 final size:50
Alignment explanation
Indices: 223803--223921 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 50
223793 AGTACTAATT
* * *
223803 ATATGGTGTAATACTAGTTATGCACTTCGGC-A-A-TATTT-TAGTTATA
1 ATATGGTGTACTACTAATTATGTACTTCGGCAATATTATTTGTAGTTATA
* * *
223849 ATGTGGTGTACTACTAATTATGTACTT-GGATAATATTATTTGTAGTTATC
1 ATATGGTGTACTACTAATTATGTACTTCGG-CAATATTATTTGTAGTTATA
223899 ATATGGTGTACTACTAATT-TGTA
1 ATATGGTGTACTACTAATTATGTA
223922 ATATTAATAG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
45 2 0.03
46 23 0.38
47 1 0.02
48 1 0.02
49 9 0.15
50 25 0.41
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (50 bp):
ATATGGTGTACTACTAATTATGTACTTCGGCAATATTATTTGTAGTTATA
Found at i:231648 original size:19 final size:19
Alignment explanation
Indices: 231620--231657 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
231610 TGGGTATAAC
231620 CCCACGTTTGTTGCCCATT
1 CCCACGTTTGTTGCCCATT
* *
231639 CCCACTTTTGTTGCTCATT
1 CCCACGTTTGTTGCCCATT
231658 ACTTTGTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.34, G:0.13, T:0.42
Consensus pattern (19 bp):
CCCACGTTTGTTGCCCATT
Found at i:232695 original size:15 final size:16
Alignment explanation
Indices: 232668--232710 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
232658 AGAAAAAAAT
*
232668 AAAAATTTAAAAT-AA
1 AAAAATTAAAAATCAA
232683 AAAAATTAAAAATCCAAA
1 AAAAATTAAAAAT-C-AA
232701 AAAAATTAAA
1 AAAAATTAAA
232711 GTTATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 12 0.50
18 12 0.50
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATTAAAAATCAA
Found at i:232701 original size:22 final size:20
Alignment explanation
Indices: 232655--232705 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
232645 ATACATGCTA
**
232655 AAAAGAAAAAAATAAAAATTT
1 AAAA-AAAAAAATAAAAATCC
232676 AAAATAAAAAAATTAAAAATCC
1 AAAA-AAAAAAA-TAAAAATCC
232698 AAAAAAAA
1 AAAAAAAA
232706 TTAAAGTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAAAAAAATAAAAATCC
Found at i:242881 original size:6 final size:6
Alignment explanation
Indices: 242870--242939 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 6
242860 GGGCCCAACA
* * * *
242870 AAATTT AAATTT -ATTTT AAGTTT AAAATT -CATTT GAAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
242917 --ATTAT AAATTT AAATTT AAATTT
1 AAATT-T AAATTT AAATTT AAATTT
242940 TTTTAAATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
4 3 0.06
5 8 0.16
6 33 0.65
7 7 0.14
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:242895 original size:17 final size:17
Alignment explanation
Indices: 242870--242934 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
242860 GGGCCCAACA
242870 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* * *
242887 AAGTTTAAAATTCATTTG
1 AAATTT-AAATTTATTTT
*
242905 AAATTTAAATTTATTAT
1 AAATTTAAATTTATTTT
242922 AAATTTAAATTTA
1 AAATTTAAATTTA
242935 AATTTTTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
17 26 0.65
18 14 0.35
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:243678 original size:26 final size:24
Alignment explanation
Indices: 243623--243670 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 24
243613 ATTTTAGATA
243623 TAATTAATAAGTATATTAAATAATAT
1 TAATTAATAA--ATATTAAATAATAT
243649 TAATTAATAAATATTAAATAAT
1 TAATTAATAAATATTAAATAAT
243671 GTTTTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 12 0.55
26 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
TAATTAATAAATATTAAATAATAT
Found at i:243680 original size:22 final size:23
Alignment explanation
Indices: 243620--243681 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
243610 TGTATTTTAG
*
243620 ATATAATTAATAAGTATATTAAATA
1 ATATTATTAATAA--ATATTAAATA
243645 ATATTAATTAATAAATATTAAATA
1 ATATT-ATTAATAAATATTAAATA
*
243669 ATGTT-TTAATAAA
1 ATATTATTAATAAA
243682 AATAAAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 8 0.24
24 14 0.41
25 4 0.12
26 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (23 bp):
ATATTATTAATAAATATTAAATA
Found at i:244827 original size:29 final size:30
Alignment explanation
Indices: 244794--245006 Score: 142
Period size: 30 Copynumber: 7.2 Consensus size: 30
244784 AAAAGGTCCC
*
244794 CAAACTTTTC-AAAAATCATATTTGACCCT
1 CAAACTTTTCTAAAAATTATATTTGACCCT
*
244823 CAAAC-TTTCTAAAAATTATGTTTTGACCCT
1 CAAACTTTTCTAAAAATTAT-ATTTGACCCT
* *
244853 TAAAC-TTTCCAAAAATTATATTTGACCC-
1 CAAACTTTTCTAAAAATTATATTTGACCCT
* *
244881 CTAAA-TTTTCTAAAAATTACATTTTAACCC-
1 C-AAACTTTTCTAAAAATTATA-TTTGACCCT
* * *
244911 C-TACATTTTCTAAAAATTACATTTTAACCCAT
1 CAAAC-TTTTCTAAAAATTATA-TTTGACCC-T
* *
244943 -AAAC-TTTCTAAAAATTACATTTCGACAC-
1 CAAACTTTTCTAAAAATTATATTT-GACCCT
* * * **
244971 CGAACTTCTC-AAAAATTACATTTTTCCCT
1 CAAACTTTTCTAAAAATTATATTTGACCCT
245000 CAAACTT
1 CAAACTT
245007 CCAAAAAATA
Statistics
Matches: 151, Mismatches: 19, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
28 7 0.05
29 62 0.41
30 80 0.53
32 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
CAAACTTTTCTAAAAATTATATTTGACCCT
Found at i:244850 original size:30 final size:30
Alignment explanation
Indices: 244794--245118 Score: 234
Period size: 29 Copynumber: 11.1 Consensus size: 30
244784 AAAAGGTCCC
244794 CAAACTTT-TCAAAAA-T-CATATTTGACCCT
1 CAAACTTTCT-AAAAATTACAT-TTTGACCCT
**
244823 CAAACTTTCTAAAAATTATGTTTTGACCCT
1 CAAACTTTCTAAAAATTACATTTTGACCCT
* * *
244853 TAAACTTTCCAAAAATTATA-TTTGACCC-
1 CAAACTTTCTAAAAATTACATTTTGACCCT
* *
244881 CTAAATTTTCTAAAAATTACATTTTAACCC-
1 C-AAACTTTCTAAAAATTACATTTTGACCCT
* * *
244911 CTACATTTTCTAAAAATTACATTTTAACCCAT
1 C-AAACTTTCTAAAAATTACATTTTGACCC-T
* *
244943 -AAACTTTCTAAAAATTACATTTCGACAC-
1 CAAACTTTCTAAAAATTACATTTTGACCCT
* *
244971 CGAAC-TTCTCAAAAATTACATTTT-TCCCT
1 CAAACTTTCT-AAAAATTACATTTTGACCCT
* * * *
245000 CAAACTTCCAAAAAATAACATTTTTACCCT
1 CAAACTTTCTAAAAATTACATTTTGACCCT
* *
245030 CATAC-TTCCAAAAATTACATTTTTG-CCCT
1 CAAACTTTCTAAAAATTACA-TTTTGACCCT
*
245059 CAAACTTTC-AAAAATCACCATTTT-ACCC-
1 CAAACTTTCTAAAAATTA-CATTTTGACCCT
* * *
245087 CAAGC-ATCCAAAAATTACCATTTT-ACCCT
1 CAAACTTTCTAAAAATTA-CATTTTGACCCT
245116 CAA
1 CAA
245119 TTTTCCAAAA
Statistics
Matches: 243, Mismatches: 35, Indels: 36
0.77 0.11 0.11
Matches are distributed among these distances:
27 2 0.01
28 28 0.12
29 106 0.44
30 106 0.44
31 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
CAAACTTTCTAAAAATTACATTTTGACCCT
Found at i:244891 original size:59 final size:59
Alignment explanation
Indices: 244791--244964 Score: 199
Period size: 59 Copynumber: 2.9 Consensus size: 59
244781 CCCAAAAGGT
* * ** *
244791 CCCC-AAACTTTTCAAAAATCATATTTGA-CCCTCAAACTTTCTAAAAATTATGTTTTGA
1 CCCCTAAACTTTCCAAAAATTATATTTGACCCCT-AAACTTTCTAAAAATTACATTTTAA
* *
244849 CCCTTAAACTTTCCAAAAATTATATTTGACCCCTAAATTTTCTAAAAATTACATTTTAA
1 CCCCTAAACTTTCCAAAAATTATATTTGACCCCTAAACTTTCTAAAAATTACATTTTAA
* * * * * *
244908 CCCCTACATTTTCTAAAAATTACATTTTAACCCATAAACTTTCTAAAAATTACATTT
1 CCCCTAAACTTTCCAAAAATTATA-TTTGACCCCTAAACTTTCTAAAAATTACATTT
244965 CGACACCGAA
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
58 3 0.03
59 62 0.63
60 33 0.34
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (59 bp):
CCCCTAAACTTTCCAAAAATTATATTTGACCCCTAAACTTTCTAAAAATTACATTTTAA
Found at i:244933 original size:16 final size:16
Alignment explanation
Indices: 244885--244935 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
244875 TGACCCCTAA
244885 ATTTTCTAAAAATTAC
1 ATTTTCTAAAAATTAC
****
244901 A-TTT-TAACCCCTAC
1 ATTTTCTAAAAATTAC
244915 ATTTTCTAAAAATTAC
1 ATTTTCTAAAAATTAC
244931 ATTTT
1 ATTTT
244936 AACCCATAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
16 12 0.48
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTCTAAAAATTAC
Found at i:245140 original size:57 final size:56
Alignment explanation
Indices: 244860--245129 Score: 162
Period size: 59 Copynumber: 4.6 Consensus size: 56
244850 CCTTAAACTT
* * * *
244860 TCCAAAAATTATATTTGACCC-CTAAATTTTCTAAAAATTACATTTTAACCC-C-TACA
1 TCCAAAAATTACATTTTACCCTC-AAA-TTTCCAAAAATAACATTTT-ACCCTCATACA
* * * * * *
244916 TTTTCTAAAAATTACATTTTAACCCAT-AAACTTTCTAAAAATTACATTTCGACACC-GA-ACT
1 ---TCCAAAAATTACATTTT-ACCC-TCAAA-TTTCCAAAAATAACATTT-TAC-CCTCATACA
* * *
244977 TCTCAAAAATTACATTTTTCCCTCAAACTTCCAAAAAATAACATTTTTACCCTCATACT
1 TC-CAAAAATTACATTTTACCCTCAAATTTCC-AAAAATAACA-TTTTACCCTCATACA
* *
245036 TCCAAAAATTACATTTTTGCCCTCAAACTTT-CAAAAATCACCATTTTACCC-CA-AGCA
1 TCCAAAAATTACA-TTTTACCCTCAAA-TTTCCAAAAAT-AACATTTTACCCTCATA-CA
*
245093 TCCAAAAATTACCATTTTACCCTCAATTTTCCAAAAA
1 TCCAAAAATTA-CATTTTACCCTCAAATTTCCAAAAA
245130 GTTCGATTTT
Statistics
Matches: 173, Mismatches: 20, Indels: 38
0.75 0.09 0.16
Matches are distributed among these distances:
56 4 0.02
57 37 0.21
58 47 0.27
59 52 0.30
60 29 0.17
61 4 0.02
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.34
Consensus pattern (56 bp):
TCCAAAAATTACATTTTACCCTCAAATTTCCAAAAATAACATTTTACCCTCATACA
Found at i:248661 original size:6 final size:6
Alignment explanation
Indices: 248647--248710 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
248637 TTTAATTTAT
* *
248647 TTTAAA TTTAGA TTT-AC TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
*
248693 TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA
248711 AGTCCAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
4 2 0.04
5 10 0.21
6 28 0.60
7 7 0.15
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:248667 original size:17 final size:16
Alignment explanation
Indices: 248637--248700 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 16
248627 GTGCCCTTTT
*
248637 TTTAATTTATTTTAAA
1 TTTAATTTAATTTAAA
*
248653 TTTAGATTTACTTTAAA
1 TTTA-ATTTAATTTAAA
*
248670 TTTAAATTAATCTTAAA
1 TTTAATTTAAT-TTAAA
248687 TTTAAATTTAATTT
1 TTT-AATTTAATTT
248701 CAAAATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 9 0.22
17 25 0.61
18 7 0.17
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTAATTTAATTTAAA
Found at i:248679 original size:11 final size:12
Alignment explanation
Indices: 248647--248710 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 12
248637 TTTAATTTAT
*
248647 TTTAAATTTAGA
1 TTTAAATTTAAA
*
248659 TTT-ACTTTAAA
1 TTTAAATTTAAA
248670 TTTAAA-TT-AA
1 TTTAAATTTAAA
248680 TCTTAAATTTAAA
1 T-TTAAATTTAAA
248693 TTT-AATTTCAAA
1 TTTAAATTT-AAA
*
248705 ATTAAA
1 TTTAAA
248711 AGTCCAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 21 0.50
12 13 0.31
13 5 0.12
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:249444 original size:3 final size:3
Alignment explanation
Indices: 249429--249484 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
249419 TTAATTTATT
* **
249429 TAA TAA CTAA TAA TAA TAA TAA CT-G TTT TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
*
249475 TAA TAT TAA T
1 TAA TAA TAA T
249485 TATTTTAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 39 0.89
4 4 0.09
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Done.