Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014694.1 Kokia drynarioides strain JFW-HI SEQ_129733, 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: 570195
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 173 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:328206 original size:20 final size:21
Alignment explanation
Indices: 328170--328208 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
328160 ATTTTTTTTA
*
328170 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
328191 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
328209 AATTCCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:335486 original size:19 final size:19
Alignment explanation
Indices: 335445--335495 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
335435 TATTAAATTG
*
335445 GCTTGTAAGAGCAATATCG
1 GCTTGTAAGAGCAATATCA
*
335464 GCTTGTAAGAGCCATA-CTA
1 GCTTGTAAGAGCAATATC-A
*
335483 GCTTGGAAGAGCA
1 GCTTGTAAGAGCA
335496 TTATACTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 1 0.04
19 26 0.96
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (19 bp):
GCTTGTAAGAGCAATATCA
Found at i:335537 original size:19 final size:19
Alignment explanation
Indices: 335503--335539 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
335493 GCATTATACT
*
335503 ATACTGGCTCGTAAGAGCG
1 ATACTGGCTCGCAAGAGCG
*
335522 ATACTGGCTTGCAAGAGC
1 ATACTGGCTCGCAAGAGC
335540 ATGTACTGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (19 bp):
ATACTGGCTCGCAAGAGCG
Found at i:335622 original size:35 final size:35
Alignment explanation
Indices: 335570--335651 Score: 130
Period size: 35 Copynumber: 2.3 Consensus size: 35
335560 TGAGCAAGAT
*
335570 ATTATT-AGGAATCTTGAAAAACTCGTATGAGTTAA
1 ATTATTGA-GAATATTGAAAAACTCGTATGAGTTAA
*
335605 ATTATTGAGAATATTGAAGAACTCGTATGAGTTAA
1 ATTATTGAGAATATTGAAAAACTCGTATGAGTTAA
335640 ATTATTGAGAAT
1 ATTATTGAGAAT
335652 CTTAAAGAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
35 43 0.98
36 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (35 bp):
ATTATTGAGAATATTGAAAAACTCGTATGAGTTAA
Found at i:335678 original size:35 final size:35
Alignment explanation
Indices: 335602--335678 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
335592 TCGTATGAGT
* * * *
335602 TAAATTATTGAGAATATTGAAGAACTCGTATGAGT
1 TAAATTATTGAGAATATTAAAGAACTCATATAAGC
* *
335637 TAAATTATTGAGAATCTTAAAGAGCTCATATAAGC
1 TAAATTATTGAGAATATTAAAGAACTCATATAAGC
*
335672 TGAATTA
1 TAAATTA
335679 CTAAGAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34
Consensus pattern (35 bp):
TAAATTATTGAGAATATTAAAGAACTCATATAAGC
Found at i:341133 original size:15 final size:15
Alignment explanation
Indices: 341113--341141 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
341103 ATAGATGTAG
341113 TTGAAACTGCTCTTA
1 TTGAAACTGCTCTTA
341128 TTGAAACTGCTCTT
1 TTGAAACTGCTCTT
341142 GTATCATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (15 bp):
TTGAAACTGCTCTTA
Found at i:343255 original size:116 final size:116
Alignment explanation
Indices: 343051--343287 Score: 465
Period size: 116 Copynumber: 2.0 Consensus size: 116
343041 GTTACTGATG
343051 TATTTACCAAGCCTCTCAAGTTGGCATCATTTGTCAAGTTTTGTAAAATACTTGGCCTTTTACAT
1 TATTTACCAAGCCTCTCAAGTTGGCATCATTTGTCAAGTTTTGTAAAATACTTGGCCTTTTACAT
343116 AAAATAGTAAGTATGTATTAAACTGAAATCGTAAGGGAGGGATTGTTGAGA
66 AAAATAGTAAGTATGTATTAAACTGAAATCGTAAGGGAGGGATTGTTGAGA
343167 TATTTACCAAGCCTCTCAAGTTGGCATCATTTGTCAAGTTTTGTAAAATACTTGGCCTTTTACAT
1 TATTTACCAAGCCTCTCAAGTTGGCATCATTTGTCAAGTTTTGTAAAATACTTGGCCTTTTACAT
*
343232 AAAATAGTAAGTATGTATTAAACTGAAATTGTAAGGGAGGGATTGTTGAGA
66 AAAATAGTAAGTATGTATTAAACTGAAATCGTAAGGGAGGGATTGTTGAGA
343283 TATTT
1 TATTT
343288 TTATATTTGG
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 120 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (116 bp):
TATTTACCAAGCCTCTCAAGTTGGCATCATTTGTCAAGTTTTGTAAAATACTTGGCCTTTTACAT
AAAATAGTAAGTATGTATTAAACTGAAATCGTAAGGGAGGGATTGTTGAGA
Found at i:343662 original size:21 final size:21
Alignment explanation
Indices: 343638--343684 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
343628 AAAATGCAAT
343638 TTTTAAAGGATTAAATCAAAA
1 TTTTAAAGGATTAAATCAAAA
**
343659 TTTTATCGGATTAAATCAAAA
1 TTTTAAAGGATTAAATCAAAA
343680 TTTTA
1 TTTTA
343685 TCATTTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTTAAAGGATTAAATCAAAA
Found at i:343685 original size:21 final size:21
Alignment explanation
Indices: 343645--343686 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
343635 AATTTTTAAA
343645 GGATTAAATCAAAATTTTATC
1 GGATTAAATCAAAATTTTATC
343666 GGATTAAATCAAAATTTTATC
1 GGATTAAATCAAAATTTTATC
343687 ATTTTTAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
GGATTAAATCAAAATTTTATC
Found at i:344873 original size:18 final size:18
Alignment explanation
Indices: 344847--344888 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
344837 ATTACCAATG
*
344847 AATTAAGAGAAATATTAA
1 AATTCAGAGAAATATTAA
344865 AATTCAGAGAAATATTAA
1 AATTCAGAGAAATATTAA
344883 AATTCA
1 AATTCA
344889 TCTACAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.29
Consensus pattern (18 bp):
AATTCAGAGAAATATTAA
Found at i:345674 original size:16 final size:16
Alignment explanation
Indices: 345655--345686 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
345645 AAACATAAAT
*
345655 ATAAATAGATATGAAA
1 ATAAATAAATATGAAA
345671 ATAAATAAATATGAAA
1 ATAAATAAATATGAAA
345687 TAAGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (16 bp):
ATAAATAAATATGAAA
Found at i:346406 original size:19 final size:19
Alignment explanation
Indices: 346384--346450 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
346374 CATATTTTAA
*
346384 TTTTTAAAAAT-CTAATTT
1 TTTTTAAAAATACTACTTT
*
346402 TTTTTTAAAATACTACTTT
1 TTTTTAAAAATACTACTTT
* * *
346421 TTTTTAAAAAAATTACTAT
1 TTTTTAAAAATACTACTTT
*
346440 TTCTTAAAAAT
1 TTTTTAAAAAT
346451 TAAAGTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
18 10 0.25
19 30 0.75
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTTAAAAATACTACTTT
Found at i:346550 original size:161 final size:163
Alignment explanation
Indices: 346253--346567 Score: 460
Period size: 161 Copynumber: 1.9 Consensus size: 163
346243 AAAAAATTTT
346253 CTTTTGTTTTAAAACAAAATCACTATTTTTCTTAAAAATTAAAGTTTTTATTTCGAAATGATTAA
1 CTTTTGTTTTAAAACAAAATCACTA-TTTTCTTAAAAATTAAAGTTTTTATTTCGAAATGATTAA
* * * *
346318 AAAAGTTAAACTTTGTTTAAAAATTTTAAACATTTTCCATTAAAATGACTAAAAAACATATTTTA
65 AAAAATAAAACTTTGTTTAAAAAATTTAAACATTTTCCATTAAAATGACTAAAAAACAAATTTTA
*
346383 ATTTTTAAAAATCTAATTTTTTTTTAAAATACTA
130 ATTTTTAAAAATCTAAATTTTTTTTAAAATACTA
*
346417 CTTTT-TTTT-AAA-AAAATTACTA-TTTCTTAAAAATTAAAGTTTTTATTTCGAAAT-AGTTAA
1 CTTTTGTTTTAAAACAAAATCACTATTTTCTTAAAAATTAAAGTTTTTATTTCGAAATGA-TTAA
* * **
346477 AAAAATCAAAATTTTGTTTAAAAAAATTTAAACTTTTTCTTTTAAAATGACTAAAAAACAAATTT
65 AAAAAT-AAAACTTTGTTT-AAAAAATTTAAACATTTTCCATTAAAATGACTAAAAAACAAATTT
*
346542 TTATTTTTAAAAATCTAAATTTTTTT
128 TAATTTTTAAAAATCTAAATTTTTTT
346568 AATAATTTAT
Statistics
Matches: 137, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
158 1 0.01
159 41 0.30
160 10 0.07
161 73 0.53
162 3 0.02
163 4 0.03
164 5 0.04
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (163 bp):
CTTTTGTTTTAAAACAAAATCACTATTTTCTTAAAAATTAAAGTTTTTATTTCGAAATGATTAAA
AAAATAAAACTTTGTTTAAAAAATTTAAACATTTTCCATTAAAATGACTAAAAAACAAATTTTAA
TTTTTAAAAATCTAAATTTTTTTTAAAATACTA
Found at i:346846 original size:146 final size:146
Alignment explanation
Indices: 346426--346866 Score: 594
Period size: 146 Copynumber: 3.0 Consensus size: 146
346416 ACTTTTTTTT
* *
346426 AAAAAA-ATTACTATTTCTTAAAAATTAAAGTTTTTATTTCGAAATAGTTAAAAAAATCAAAATT
1 AAAAAATATTACT-TTTCTTAAAAATTAAA-ATTTTATTTCGAAATAATTAAAAAAATCAAAATT
* * *
346490 TTGTTTAAAAAAATTTAAACTTTTTCT-TTTAAAATGACTAAAAAACAAATTTTTATTTTTAAAA
64 TTG--TATAAAAATTTAAACTTTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTAAAA
346554 ATCT-AA-A-TTTTTTT--A
127 ATCTAAACATTTTTTTTCAA
* ** * * * *
346569 ATAATTTATTACTTGTCTTAAAAATCAAAATTTTATTTCGAAATAATT-AAAAAATAAAAAATTT
1 AAAAAATATTACTTTTCTTAAAAATTAAAATTTTATTTCGAAATAATTAAAAAAATCAAAATTTT
* * * *
346633 GTTTAAAATTTTAAAC-TTTTTCCTTTAAAATGATTAAAAAACATATTTTTATTTTTAAAAATCT
66 GTATAAAAATTTAAACTTTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCT
346697 AAACATTTTTTTTCAA
131 AAACATTTTTTTTCAA
346713 AAAAAATATTACTTTTCTTAAAAATTAAAATTTTATTTCGAAATAATTAAAAAAATCAAAATTTT
1 AAAAAATATTACTTTTCTTAAAAATTAAAATTTTATTTCGAAATAATTAAAAAAATCAAAATTTT
* *
346778 GTATAAAAATTTAAACTTTTTTTCTTTAAAAGGACTAAAAAACATATTTTTATTTTTAGAAATCT
66 GTATAAAAATTTAAACTTTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCT
*
346843 AAACTTTTTTTTTCTAA
131 AAACATTTTTTTTC-AA
*
346860 AGAAAAT
1 AAAAAAT
346867 TCATTTTCCC
Statistics
Matches: 257, Mismatches: 31, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
138 4 0.02
139 51 0.20
140 2 0.01
141 16 0.06
142 24 0.09
143 17 0.07
144 50 0.19
145 28 0.11
146 57 0.22
147 8 0.03
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (146 bp):
AAAAAATATTACTTTTCTTAAAAATTAAAATTTTATTTCGAAATAATTAAAAAAATCAAAATTTT
GTATAAAAATTTAAACTTTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCT
AAACATTTTTTTTCAA
Found at i:347258 original size:10 final size:10
Alignment explanation
Indices: 347243--347274 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
347233 GACAGGCCAA
347243 AAAAATAAAT
1 AAAAATAAAT
347253 AAAAATAAAT
1 AAAAATAAAT
347263 --AAATAAAT
1 AAAAATAAAT
347271 AAAA
1 AAAA
347275 CAAACACTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.40
10 12 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:347264 original size:14 final size:13
Alignment explanation
Indices: 347241--347274 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
347231 TTGACAGGCC
347241 AAAAAAATAAATA
1 AAAAAAATAAATA
347254 AAAATAAATAAATA
1 AAAA-AAATAAATA
347268 AATAAAA
1 AA-AAAA
347275 CAAACACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 13 0.68
15 2 0.11
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAAAAATAAATA
Found at i:357699 original size:20 final size:20
Alignment explanation
Indices: 357674--357715 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
357664 CAGCTACATT
*
357674 AGGGAGCATCGAGCAGTACC
1 AGGGAGCATCGAGCAATACC
357694 AGGGAGCATCGAGCAATACC
1 AGGGAGCATCGAGCAATACC
357714 AG
1 AG
357716 ACATTGTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.33, T:0.10
Consensus pattern (20 bp):
AGGGAGCATCGAGCAATACC
Found at i:369348 original size:6 final size:6
Alignment explanation
Indices: 369339--369363 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
369329 GCTTCTTCCA
369339 CTTCTC CTTCTC CTTCTC CTTCTC C
1 CTTCTC CTTCTC CTTCTC CTTCTC C
369364 CCCTTCTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CTTCTC
Found at i:369384 original size:15 final size:15
Alignment explanation
Indices: 369366--369426 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
369356 CCTTCTCCCC
* *
369366 CTTCTTCATCTTCTT
1 CTTCTTCATCATCAT
369381 CTTCTTCATCATCAT
1 CTTCTTCATCATCAT
*
369396 CTTCTTCTTC-TACAT
1 CTTCTTCATCAT-CAT
* *
369411 CGTCGTCATCATCAT
1 CTTCTTCATCATCAT
369426 C
1 C
369427 GGACGGATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
14 1 0.03
15 36 0.95
16 1 0.03
ACGTcount: A:0.15, C:0.34, G:0.03, T:0.48
Consensus pattern (15 bp):
CTTCTTCATCATCAT
Found at i:369395 original size:21 final size:21
Alignment explanation
Indices: 369371--369411 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
369361 TCCCCCTTCT
*
369371 TCATCTTCTTCTTCTTCATCA
1 TCATCTTCTTCTTCTACATCA
369392 TCATCTTCTTCTTCTACATC
1 TCATCTTCTTCTTCTACATC
369412 GTCGTCATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.34, G:0.00, T:0.51
Consensus pattern (21 bp):
TCATCTTCTTCTTCTACATCA
Found at i:370020 original size:12 final size:13
Alignment explanation
Indices: 370003--370032 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
369993 CCACAACAAG
370003 AAGCTAAA-GCTA
1 AAGCTAAAGGCTA
370015 AAGCTAAAGGCTA
1 AAGCTAAAGGCTA
370028 AAGCT
1 AAGCT
370033 TTTACTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.17
Consensus pattern (13 bp):
AAGCTAAAGGCTA
Found at i:370029 original size:7 final size:6
Alignment explanation
Indices: 370003--370032 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
369993 CCACAACAAG
370003 AAGCTA AAGCTA AAGCTA AAGGCTA AAGCT
1 AAGCTA AAGCTA AAGCTA AA-GCTA AAGCT
370033 TTTACTTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.17
Consensus pattern (6 bp):
AAGCTA
Found at i:370193 original size:2 final size:2
Alignment explanation
Indices: 370186--370210 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
370176 AACGTTTTAG
370186 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
370211 TTTGAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:376113 original size:32 final size:32
Alignment explanation
Indices: 376070--376180 Score: 114
Period size: 32 Copynumber: 3.5 Consensus size: 32
376060 AATAAAAAAT
*
376070 TATAACTATTTAAAAAATATTACTTGAATAGC
1 TATATCTATTTAAAAAATATTACTTGAATAGC
* * * * *
376102 TATATTTATTTAACAGATATTACTTTAATAGT
1 TATATCTATTTAAAAAATATTACTTGAATAGC
* * * **
376134 TATATCTATTTGAAATATATTAGTTGAATAAT
1 TATATCTATTTAAAAAATATTACTTGAATAGC
*
376166 TATGTCTATTTAAAA
1 TATATCTATTTAAAA
376181 GATGTGATTA
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.45
Consensus pattern (32 bp):
TATATCTATTTAAAAAATATTACTTGAATAGC
Found at i:382735 original size:24 final size:24
Alignment explanation
Indices: 382706--382764 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
382696 ACTGATGGCA
382706 CGGTAGCAAGTAACACATGGCAAG
1 CGGTAGCAAGTAACACATGGCAAG
382730 CGGTAGCAAGTAACACATGGCAAG
1 CGGTAGCAAGTAACACATGGCAAG
* *
382754 CAGCAGCAAGT
1 CGGTAGCAAGT
382765 GGTGTAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.37, C:0.22, G:0.29, T:0.12
Consensus pattern (24 bp):
CGGTAGCAAGTAACACATGGCAAG
Found at i:383999 original size:30 final size:31
Alignment explanation
Indices: 383944--384002 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
383934 GAGACAAGAC
* *
383944 AACCACTTGGAAATGCGGGAGGGTGTCTTAG
1 AACCACTTGAAAATGCGGAAGGGTGTCTTAG
*
383975 AACCACTTGAAAATG-TGAAGGGTGTCTT
1 AACCACTTGAAAATGCGGAAGGGTGTCTT
384003 GTTAACGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (31 bp):
AACCACTTGAAAATGCGGAAGGGTGTCTTAG
Found at i:386637 original size:13 final size:13
Alignment explanation
Indices: 386611--386648 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
386601 TATAAACAAT
386611 ATCCT-AATAATA
1 ATCCTAAATAATA
*
386623 ATCCTAAATATTA
1 ATCCTAAATAATA
*
386636 ATCCTAAAAAATA
1 ATCCTAAATAATA
386649 GAGTTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
ATCCTAAATAATA
Found at i:386849 original size:2 final size:2
Alignment explanation
Indices: 386842--386869 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
386832 CATACTCACA
386842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
386870 TCAAGGAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:387561 original size:16 final size:16
Alignment explanation
Indices: 387540--387573 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
387530 ATGACTCAGT
387540 ACTAGTAACTATAGAA
1 ACTAGTAACTATAGAA
387556 ACTAGTAACTATAGAA
1 ACTAGTAACTATAGAA
387572 AC
1 AC
387574 AAATCTATGT
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:0.50, C:0.15, G:0.12, T:0.24
Consensus pattern (16 bp):
ACTAGTAACTATAGAA
Found at i:390326 original size:21 final size:23
Alignment explanation
Indices: 390291--390333 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
390281 TAATAAATCA
390291 TAAACAGAAACAAATATCTTTTT
1 TAAACAGAAACAAATATCTTTTT
*
390314 TAAA-AGAAA-AAATATGTTTT
1 TAAACAGAAACAAATATCTTTT
390334 AAAAAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 5 0.26
23 4 0.21
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (23 bp):
TAAACAGAAACAAATATCTTTTT
Found at i:390339 original size:21 final size:22
Alignment explanation
Indices: 390296--390339 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
390286 AATCATAAAC
**
390296 AGAAACAAATATCTTTTTTAAA
1 AGAAACAAATATCTTTTAAAAA
*
390318 AGAAA-AAATATGTTTTAAAAA
1 AGAAACAAATATCTTTTAAAAA
390339 A
1 A
390340 TTGATCGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (22 bp):
AGAAACAAATATCTTTTAAAAA
Found at i:403528 original size:13 final size:13
Alignment explanation
Indices: 403502--403539 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
403492 TATAAACAAT
403502 ATCCT-AATAATA
1 ATCCTAAATAATA
*
403514 ATCCTAAATATTA
1 ATCCTAAATAATA
*
403527 ATCCTAAAAAATA
1 ATCCTAAATAATA
403540 GAGTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
ATCCTAAATAATA
Found at i:404116 original size:18 final size:17
Alignment explanation
Indices: 404078--404119 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
404068 CAAAGTTTTG
404078 GAAAATAATTATTTTAT
1 GAAAATAATTATTTTAT
404095 -AAAA-AATTATTTAATAT
1 GAAAATAATTATTT--TAT
404112 GAAAATAA
1 GAAAATAA
404120 ATGAATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 8 0.38
16 4 0.19
17 3 0.14
18 4 0.19
19 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
GAAAATAATTATTTTAT
Found at i:404549 original size:22 final size:23
Alignment explanation
Indices: 404502--404550 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
404492 TTTAGGGATT
* *
404502 TTAGGGTTTTTAATGTTAATTTA
1 TTAGGGTTTTTAAGGTTAATTAA
*
404525 TTAGGG-TTTTAAGGTTTATTAA
1 TTAGGGTTTTTAAGGTTAATTAA
404547 TTAG
1 TTAG
404551 TATCTTAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (23 bp):
TTAGGGTTTTTAAGGTTAATTAA
Found at i:407091 original size:20 final size:21
Alignment explanation
Indices: 407041--407091 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
407031 TTAGTAAAAA
407041 ATTTAAGAGATAATTTGAGAG
1 ATTTAAGAGATAATTTGAGAG
* *
407062 -TTGATTGAGA-AATTTGAGAG
1 ATTTA-AGAGATAATTTGAGAG
407082 ATTTAAGAGA
1 ATTTAAGAGA
407092 GAAATGTGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.33
Consensus pattern (21 bp):
ATTTAAGAGATAATTTGAGAG
Found at i:407382 original size:28 final size:28
Alignment explanation
Indices: 407351--407404 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
407341 AAAATTACCC
* * *
407351 ATTTTCATTATTTTTAAAAAAATGGCCT
1 ATTTTCATAATATTGAAAAAAATGGCCT
*
407379 ATTTTCGTAATATTGAAAAAAATGGC
1 ATTTTCATAATATTGAAAAAAATGGC
407405 TTTATTTGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (28 bp):
ATTTTCATAATATTGAAAAAAATGGCCT
Found at i:411147 original size:39 final size:39
Alignment explanation
Indices: 411104--411307 Score: 212
Period size: 39 Copynumber: 5.2 Consensus size: 39
411094 ATATTGAAAA
* *
411104 TATACTAAACTGACAGTGACACTGTAAACACTGCAACGC
1 TATACTGAACTGACAGTGACACTGTAAACACTGCAATGC
* ** * *
411143 TATACTGAACAGGTAGTGACACTGTAAACACTACAATGT
1 TATACTGAACTGACAGTGACACTGTAAACACTGCAATGC
* * *
411182 TATACTGAACTGGCAGTTG-CACTGTAAACAATGCAATGA
1 TATACTGAACTGACAG-TGACACTGTAAACACTGCAATGC
* *** *
411221 TATACTGAACTGACAATGATGTTGTAAATACTGCAATGC
1 TATACTGAACTGACAGTGACACTGTAAACACTGCAATGC
* * * **
411260 TATACTAAACTGAAAGTGACACTGTAAACACAGCAACAC
1 TATACTGAACTGACAGTGACACTGTAAACACTGCAATGC
411299 TATACTGAA
1 TATACTGAA
411308 GTAGTAGCGA
Statistics
Matches: 132, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
38 2 0.02
39 128 0.97
40 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.25
Consensus pattern (39 bp):
TATACTGAACTGACAGTGACACTGTAAACACTGCAATGC
Found at i:411205 original size:78 final size:78
Alignment explanation
Indices: 411104--411331 Score: 235
Period size: 78 Copynumber: 2.9 Consensus size: 78
411094 ATATTGAAAA
411104 TATACTAAACTGACAGTGACACTGTAAACACTGCAACGCTATACTGAACAGGTAGTGACACTGTA
1 TATACTAAACTGACAGTGACACTGTAAACACTGCAACGCTATACTGAACAGGTAGTGACACTGTA
*
411169 AACACTACAATGT
66 AACACTACAATGC
* * * * * * ** * ***
411182 TATACTGAACTGGCAGTTG-CACTGTAAACAATGCAATGATATACTGAACTGACAATGATGTTGT
1 TATACTAAACTGACAG-TGACACTGTAAACACTGCAACGCTATACTGAACAGGTAGTGACACTGT
* *
411246 AAATACTGCAATGC
65 AAACACTACAATGC
* * * * * *
411260 TATACTAAACTGAAAGTGACACTGTAAACACAGCAACACTATACTGAAGTA-GTAGCGACCCTGT
1 TATACTAAACTGACAGTGACACTGTAAACACTGCAACGCTATACTGAA-CAGGTAGTGACACTGT
411324 AAACACTA
65 AAACACTA
411332 TCAGACTATT
Statistics
Matches: 113, Mismatches: 34, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
77 2 0.02
78 109 0.96
79 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (78 bp):
TATACTAAACTGACAGTGACACTGTAAACACTGCAACGCTATACTGAACAGGTAGTGACACTGTA
AACACTACAATGC
Found at i:413386 original size:14 final size:14
Alignment explanation
Indices: 413367--413394 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
413357 ATACATGCAT
413367 GGTTGGGAAGATAA
1 GGTTGGGAAGATAA
413381 GGTTGGGAAGATAA
1 GGTTGGGAAGATAA
413395 AACAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (14 bp):
GGTTGGGAAGATAA
Found at i:418027 original size:7 final size:7
Alignment explanation
Indices: 418017--418044 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
418007 TTTCATTTCA
418017 TCTTCTT
1 TCTTCTT
418024 TCTTCTT
1 TCTTCTT
418031 TCTTCTT
1 TCTTCTT
418038 TCTTCTT
1 TCTTCTT
418045 CACACGGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
TCTTCTT
Found at i:429191 original size:9 final size:10
Alignment explanation
Indices: 429166--429222 Score: 52
Period size: 8 Copynumber: 5.9 Consensus size: 10
429156 ATTTTTATTT
429166 TTATTAAAAA
1 TTATTAAAAA
429176 TTA-T-AAAA
1 TTATTAAAAA
429184 TTATTAAAAA
1 TTATTAAAAA
429194 TATATTTTAAAAA
1 T-TA--TTAAAAA
429207 TTA-T-AAAA
1 TTATTAAAAA
429215 -TATTAAAA
1 TTATTAAAA
429223 TTTTATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
7 2 0.05
8 12 0.30
9 6 0.15
10 8 0.20
11 2 0.05
12 2 0.05
13 8 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:429307 original size:19 final size:20
Alignment explanation
Indices: 429283--429335 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
429273 AAAAGTTCTC
429283 ATAAATTATAAAAAAATTAT
1 ATAAATTATAAAAAAATTAT
** *
429303 A-AAATTATTTACAAATTAT
1 ATAAATTATAAAAAAATTAT
429322 ATAAACTTATAAAA
1 ATAAA-TTATAAAA
429336 TATAAAACAT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 16 0.64
20 4 0.16
21 5 0.20
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAATTATAAAAAAATTAT
Found at i:429374 original size:21 final size:19
Alignment explanation
Indices: 429332--429375 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
429322 ATAAACTTAT
*
429332 AAAATATAAAACATTCAAA
1 AAAATATAAAACATTAAAA
*
429351 AAAATATAAAATTTATTAAAA
1 AAAATATAAAA--CATTAAAA
429372 AAAA
1 AAAA
429376 GTATTTGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAATATAAAACATTAAAA
Found at i:429585 original size:14 final size:14
Alignment explanation
Indices: 429566--429605 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
429556 TTATTGATAA
429566 TTTATTTTTTTATT
1 TTTATTTTTTTATT
*
429580 TTTATTTTTATATT
1 TTTATTTTTTTATT
*
429594 TCTAATTTTTTT
1 T-TTATTTTTTT
429606 TGAAGTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTATTTTTTTATT
Found at i:429989 original size:20 final size:20
Alignment explanation
Indices: 429964--430128 Score: 59
Period size: 20 Copynumber: 8.4 Consensus size: 20
429954 TTTATATTTA
429964 TATAATTTTTTAATATTTTT
1 TATAATTTTTTAATATTTTT
* *
429984 TATAATGTATTAGA-A---TT
1 TATAATTTTTTA-ATATTTTT
430001 TAT--TTTTTT-ATA-TTTT
1 TATAATTTTTTAATATTTTT
430017 TATAAGTTTATTTATATATTTTTTT
1 TATAA-TTT-TTTA-ATA--TTTTT
** *
430042 TATAATTTACTAGA-ATTTAT
1 TATAATTTTTTA-ATATTTTT
*
430062 TATAACTTTTATAAT-TTTTT
1 TATAA-TTTTTTAATATTTTT
* * * *
430082 TATAA-ATTCT-ATAAGTTTA
1 TATAATTTTTTAAT-ATTTTT
*
430101 TATAAATTTTTAATA-TTTT
1 TATAATTTTTTAATATTTTT
430120 TATAATTTT
1 TATAATTTT
430129 ATGATTTTAA
Statistics
Matches: 107, Mismatches: 19, Indels: 39
0.65 0.12 0.24
Matches are distributed among these distances:
13 1 0.01
14 1 0.01
15 4 0.04
16 5 0.05
17 7 0.07
18 3 0.03
19 22 0.21
20 37 0.35
21 8 0.07
22 4 0.04
23 3 0.03
24 3 0.03
25 9 0.08
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (20 bp):
TATAATTTTTTAATATTTTT
Found at i:430040 original size:24 final size:24
Alignment explanation
Indices: 429997--430050 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
429987 AATGTATTAG
* *
429997 AATTTATTTTTTTA-TATTTTTAT
1 AATTTATTTATATATTATTTTTAT
*
430020 AAGTTTATTTATATATTTTTTTTAT
1 AA-TTTATTTATATATTATTTTTAT
430045 AATTTA
1 AATTTA
430051 CTAGAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.08
24 14 0.54
25 10 0.38
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
AATTTATTTATATATTATTTTTAT
Found at i:430040 original size:33 final size:33
Alignment explanation
Indices: 429958--430045 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 33
429948 TTTTCTTTTA
* *
429958 TATTTATATAATTTTTTAATATTTTTTATAATG
1 TATTTATATATTTTTTTTATATTTTTTATAATG
* * *
429991 TA-TTAGA-ATTTATTTTTTTATATTTTTATAAGTT
1 TATTTATATATTT-TTTTTATAT-TTTTTATAA-TG
430025 TATTTATATATTTTTTTTATA
1 TATTTATATATTTTTTTTATA
430046 ATTTACTAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
31 3 0.07
32 11 0.26
33 11 0.26
34 3 0.07
35 11 0.26
36 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (33 bp):
TATTTATATATTTTTTTTATATTTTTTATAATG
Found at i:430056 original size:58 final size:53
Alignment explanation
Indices: 429953--430062 Score: 148
Period size: 58 Copynumber: 2.0 Consensus size: 53
429943 TTAGATTTTC
*
429953 TTTTATATTTATATAATTTTTTAATATTTTTTATAATGTATTAGAATTTATTT
1 TTTTATATTTATATAATTTTTTAATATTTTTTATAATGTACTAGAATTTATTT
* *
430006 TTTTATATTTTTATAAGTTTATTTATATATTTTTTTTATAATTTACTAGAATTTATT
1 TTTTATATTTATATAA-TTT-TTTA-ATA--TTTTTTATAATGTACTAGAATTTATT
430063 ATAACTTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
53 15 0.31
54 3 0.06
55 4 0.08
56 3 0.06
58 24 0.49
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.65
Consensus pattern (53 bp):
TTTTATATTTATATAATTTTTTAATATTTTTTATAATGTACTAGAATTTATTT
Found at i:430094 original size:29 final size:27
Alignment explanation
Indices: 430062--430136 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
430052 TAGAATTTAT
*
430062 TATAACTTTTATAATTTTTTTATAAATTC
1 TATAA-TTTTATAATTTTTTAAT-AATTC
* * *
430091 TATAAGTTTATATAAATTTTTAATATTTT
1 TATAA-TTT-TATAATTTTTTAATAATTC
*
430120 TATAATTTTATGATTTT
1 TATAATTTTATAATTTT
430137 AAAGATTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 7 0.18
28 3 0.08
29 16 0.42
30 12 0.32
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (27 bp):
TATAATTTTATAATTTTTTAATAATTC
Found at i:430101 original size:40 final size:39
Alignment explanation
Indices: 430026--430124 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 39
430016 TTATAAGTTT
* *
430026 ATTTATATATTTTTTTTATAATTTACTAGAATTTATTATAA
1 ATTT-TATAATTTTTTTATAAATTACTAGAATTTA-TATAA
* *
430067 CTTTTATAATTTTTTTATAAATT-CTATAAGTTTATATAA
1 ATTTTATAATTTTTTTATAAATTACTAGAA-TTTATATAA
*
430106 ATTTT-TAATATTTTTATAA
1 ATTTTATAATTTTTTTATAA
430125 TTTTATGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
38 13 0.25
39 14 0.27
40 21 0.41
41 3 0.06
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (39 bp):
ATTTTATAATTTTTTTATAAATTACTAGAATTTATATAA
Found at i:430123 original size:19 final size:19
Alignment explanation
Indices: 430056--430128 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
430046 ATTTACTAGA
*
430056 ATTTATTATAACTTTTATAAT
1 ATTT-TTATAAATTTT-TAAT
* *
430077 TTTTTTATAAATTCTATAA-
1 ATTTTTATAAATT-TTTAAT
* *
430096 GTTTATATAAATTTTTAAT
1 ATTTTTATAAATTTTTAAT
430115 ATTTTTAT-AATTTT
1 ATTTTTATAAATTTT
430129 ATGATTTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
18 10 0.24
19 17 0.40
20 11 0.26
21 4 0.10
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (19 bp):
ATTTTTATAAATTTTTAAT
Found at i:433106 original size:21 final size:20
Alignment explanation
Indices: 433069--433194 Score: 108
Period size: 21 Copynumber: 6.0 Consensus size: 20
433059 AGGAGCACCA
* * *
433069 AAGTGCATTACGGGGGCACC
1 AAGTGCAATACAGGGGCATC
* *
433089 GAAGTGCAATACAAGGGCATTA
1 -AAGTGCAATACAGGGGCA-TC
*
433111 AAGTGCGATACAGGGGCATC
1 AAGTGCAATACAGGGGCATC
* *
433131 ATAGTGCGATACATGGGCATC
1 A-AGTGCAATACAGGGGCATC
*
433152 ATAGTGCAATACAAGGGCATC
1 A-AGTGCAATACAGGGGCATC
* *
433173 GTAGTGCGATACAGGGGCATC
1 -AAGTGCAATACAGGGGCATC
433194 A
1 A
433195 TAATATGATA
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
20 2 0.02
21 85 0.98
ACGTcount: A:0.32, C:0.19, G:0.31, T:0.18
Consensus pattern (20 bp):
AAGTGCAATACAGGGGCATC
Found at i:433127 original size:42 final size:41
Alignment explanation
Indices: 433067--433194 Score: 132
Period size: 42 Copynumber: 3.0 Consensus size: 41
433057 ACAGGAGCAC
* * *
433067 CAAAGTGCATTACGGGGGCACCGAAGTGCAATACAAGGGCAT
1 CAAAGTGCA-TACAGGGGCATCGAAGTGCGATACAAGGGCAT
* *
433109 TAAAGTGCGATACAGGGGCATC-ATAGTGCGATACATGGGCAT
1 CAAAGTGC-ATACAGGGGCATCGA-AGTGCGATACAAGGGCAT
* * * *
433151 CATAGTGCAATACAAGGGCATCGTAGTGCGATACAGGGGCAT
1 CAAAGTGC-ATACAGGGGCATCGAAGTGCGATACAAGGGCAT
433193 CA
1 CA
433195 TAATATGATA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 70 0.97
43 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.18
Consensus pattern (41 bp):
CAAAGTGCATACAGGGGCATCGAAGTGCGATACAAGGGCAT
Found at i:433159 original size:63 final size:63
Alignment explanation
Indices: 433082--433311 Score: 221
Period size: 63 Copynumber: 3.7 Consensus size: 63
433072 TGCATTACGG
* * *
433082 GGGCACCGA-AGTGCAATACAAGGGCATTAAAGTGCGATACAGGGGCATCATAGTGCGATACAT
1 GGGCACC-ATAGTGCAATACAAGGGCATCATAGTGCGATACAGGGGCATCATAGTGCGATACAA
* * * **
433145 GGGCATCATAGTGCAATACAAGGGCATCGTAGTGCGATACAGGGGCATCATAATATGATACAA
1 GGGCACCATAGTGCAATACAAGGGCATCATAGTGCGATACAGGGGCATCATAGTGCGATACAA
* * * * * * * *
433208 GGGCACCATAATACGATAC-AGAGGCACCATAGTACGATACAGGGGCACCATAGTGCGAGATAA
1 GGGCACCATAGTGCAATACAAG-GGCATCATAGTGCGATACAGGGGCATCATAGTGCGATACAA
** * * * * *
433271 GGGTGCCATAGTGCAATGCAGGGGCACCGTAGTGCAATACA
1 GGGCACCATAGTGCAATACAAGGGCATCATAGTGCGATACA
433312 AGGTCAATTT
Statistics
Matches: 133, Mismatches: 31, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
62 3 0.02
63 129 0.97
64 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.17
Consensus pattern (63 bp):
GGGCACCATAGTGCAATACAAGGGCATCATAGTGCGATACAGGGGCATCATAGTGCGATACAA
Found at i:433195 original size:42 final size:42
Alignment explanation
Indices: 433081--433311 Score: 191
Period size: 42 Copynumber: 5.5 Consensus size: 42
433071 GTGCATTACG
* * * *
433081 GGGGCACCGA-AGTGCAATACAAGGGCATTAAAGTGCGATACA
1 GGGGCACC-ATAGTGCGATACAGGGGCATCATAGTGCGATACA
* * *
433123 GGGGCATCATAGTGCGATACATGGGCATCATAGTGCAATACA
1 GGGGCACCATAGTGCGATACAGGGGCATCATAGTGCGATACA
* * * * **
433165 AGGGCATCGTAGTGCGATACAGGGGCATCATAATATGATACA
1 GGGGCACCATAGTGCGATACAGGGGCATCATAGTGCGATACA
* * * * * *
433207 AGGGCACCATAATACGATACAGAGGCACCATAGTACGATACA
1 GGGGCACCATAGTGCGATACAGGGGCATCATAGTGCGATACA
* *
433249 GGGGCACCATAGTGCGAGATA-AGGGTGC--CATAGTGCAATGCA
1 GGGGCACCATAGTGC--GATACAGGG-GCATCATAGTGCGATACA
* *
433291 GGGGCACCGTAGTGCAATACA
1 GGGGCACCATAGTGCGATACA
433312 AGGTCAATTT
Statistics
Matches: 154, Mismatches: 30, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
40 3 0.02
41 2 0.01
42 140 0.91
43 3 0.02
44 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.17
Consensus pattern (42 bp):
GGGGCACCATAGTGCGATACAGGGGCATCATAGTGCGATACA
Found at i:433204 original size:21 final size:21
Alignment explanation
Indices: 433097--433261 Score: 159
Period size: 21 Copynumber: 7.9 Consensus size: 21
433087 CCGAAGTGCA
* * * *
433097 ATACAAGGGCATTAAAGTGCG
1 ATACAGGGGCATCATAGTACG
*
433118 ATACAGGGGCATCATAGTGCG
1 ATACAGGGGCATCATAGTACG
* * *
433139 ATACATGGGCATCATAGTGCA
1 ATACAGGGGCATCATAGTACG
* * *
433160 ATACAAGGGCATCGTAGTGCG
1 ATACAGGGGCATCATAGTACG
* *
433181 ATACAGGGGCATCATAATATG
1 ATACAGGGGCATCATAGTACG
* * *
433202 ATACAAGGGCACCATAATACG
1 ATACAGGGGCATCATAGTACG
* *
433223 ATACAGAGGCACCATAGTACG
1 ATACAGGGGCATCATAGTACG
*
433244 ATACAGGGGCACCATAGT
1 ATACAGGGGCATCATAGT
433262 GCGAGATAAG
Statistics
Matches: 124, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 124 1.00
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (21 bp):
ATACAGGGGCATCATAGTACG
Found at i:437618 original size:2 final size:2
Alignment explanation
Indices: 437606--437637 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
437596 TTTAATAGTA
*
437606 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
437638 TAAAAAGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:439131 original size:16 final size:16
Alignment explanation
Indices: 439110--439176 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
439100 GGTTCACTGG
439110 AATGGAATAGAATTGT
1 AATGGAATAGAATTGT
** *
439126 AATGGAATAGAGCTAT
1 AATGGAATAGAATTGT
*
439142 AATGAAATA-AAGTTGT
1 AATGGAATAGAA-TTGT
*
439158 AATAGAATAGAATTGT
1 AATGGAATAGAATTGT
439174 AAT
1 AAT
439177 TAGTAATTCA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 1 0.03
16 37 0.93
17 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.21, T:0.30
Consensus pattern (16 bp):
AATGGAATAGAATTGT
Found at i:439215 original size:46 final size:44
Alignment explanation
Indices: 439155--439244 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 44
439145 GAAATAAAGT
*
439155 TGTAATAGAATAGAATTGTAATTAGTAATTC-AATTATTTGATTGAA
1 TGTAATAGAATAGAACTGTAA-TAGT-ATTCTAATT-TTTGATTGAA
*
439201 TGTAATAGAATAGAACTGTAATAGTATTCTAATTTTTTATTGAA
1 TGTAATAGAATAGAACTGTAATAGTATTCTAATTTTTGATTGAA
439245 AGGAATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 13 0.32
45 8 0.20
46 20 0.49
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.42
Consensus pattern (44 bp):
TGTAATAGAATAGAACTGTAATAGTATTCTAATTTTTGATTGAA
Found at i:439932 original size:29 final size:31
Alignment explanation
Indices: 439899--439956 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
439889 CAAACTTTTT
439899 ATTTTCTCCC-AAAACTTTTACTC-CCTCCC
1 ATTTTCTCCCTAAAACTTTTACTCTCCTCCC
439928 ATTTTCTCCCTAAAACTTTTACTCTCCTC
1 ATTTTCTCCCTAAAACTTTTACTCTCCTC
439957 TCATCCCACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 10 0.37
30 13 0.48
31 4 0.15
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (31 bp):
ATTTTCTCCCTAAAACTTTTACTCTCCTCCC
Found at i:439969 original size:30 final size:30
Alignment explanation
Indices: 439909--439970 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
439899 ATTTTCTCCC
** *
439909 AAAACTTTTACTCCCTCCCATTTTCTCCCT
1 AAAACTTTTACTCCCTCCCATTCCCACCCT
*
439939 AAAACTTTTACTCTCCTCTCA-TCCCACCCT
1 AAAACTTTTACTC-CCTCCCATTCCCACCCT
439969 AA
1 AA
439971 TCTACCTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAACTTTTACTCCCTCCCATTCCCACCCT
Found at i:445762 original size:31 final size:30
Alignment explanation
Indices: 445724--445781 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
445714 AAATTTTTAA
445724 AATAAAATTAT-ACTTTAATTCTTTTAAAAAT
1 AATAAAATTATGA-TTTAATT-TTTTAAAAAT
*
445755 AATAAAATTTTGATTTAATTTTTTAAA
1 AATAAAATTATGATTTAATTTTTTAAA
445782 TATTATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 7 0.28
31 17 0.68
32 1 0.04
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (30 bp):
AATAAAATTATGATTTAATTTTTTAAAAAT
Found at i:445782 original size:28 final size:28
Alignment explanation
Indices: 445710--445783 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 28
445700 AATTTATGCT
*
445710 CTTTAAATTTTT-AA-AATAAAATTATA
1 CTTTAATTTTTTAAATAATAAAATTATA
*
445736 CTTTAATTCTTTTAAAAATAATAAAATTTTGA
1 CTTTAATT-TTTT--AAATAATAAAATTAT-A
445768 -TTTAATTTTTTAAATA
1 CTTTAATTTTTTAAATA
445784 TTATATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
26 7 0.17
27 4 0.10
28 5 0.12
30 6 0.15
31 17 0.43
32 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (28 bp):
CTTTAATTTTTTAAATAATAAAATTATA
Found at i:445861 original size:2 final size:2
Alignment explanation
Indices: 445854--445880 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
445844 ACTTCACCCA
445854 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
445881 AGGTACTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:446899 original size:23 final size:23
Alignment explanation
Indices: 446845--446912 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
446835 ATTAACATTA
*
446845 TTCGTGAACATGTTCAATTATATG
1 TTCGTGAACATGTTCGATTA-ATG
* * *
446869 TTCATGAACATATTCGTTTAATG
1 TTCGTGAACATGTTCGATTAATG
446892 TTCGTGAACATGTTCGATTAA
1 TTCGTGAACATGTTCGATTAA
446913 ATTAAATGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 21 0.57
24 16 0.43
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (23 bp):
TTCGTGAACATGTTCGATTAATG
Found at i:446939 original size:23 final size:23
Alignment explanation
Indices: 446896--446941 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
446886 TTAATGTTCG
*
446896 TGAACATGTTCGATTAAATTAAA
1 TGAACATGTTCGATAAAATTAAA
446919 TGAACATGTTCG-TAAACATTAAA
1 TGAACATGTTCGATAAA-ATTAAA
446942 CAAACGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATAAAATTAAA
Found at i:472669 original size:21 final size:21
Alignment explanation
Indices: 472622--472675 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
472612 CCCTTGAAAG
* * *
472622 TTCTATCGATACAAGTGAGGC
1 TTCTACCGATACAAGTCAGAC
**
472643 AACTACCGATACAAGTCAGAC
1 TTCTACCGATACAAGTCAGAC
*
472664 TTCTACTGATAC
1 TTCTACCGATAC
472676 TAAAAACTCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (21 bp):
TTCTACCGATACAAGTCAGAC
Found at i:483126 original size:16 final size:18
Alignment explanation
Indices: 483083--483130 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
483073 GAATGAATTG
483083 ATTTCTTCTCTCTCTCTT
1 ATTTCTTCTCTCTCTCTT
483101 A-TT-TTCTCTCT-TCTCT
1 ATTTCTTCTCTCTCTCT-T
483117 ATTTCTTCTC-CTCT
1 ATTTCTTCTCTCTCT
483131 TTCGAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 6 0.23
18 7 0.27
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTCTTCTCTCTCTCTT
Found at i:483130 original size:19 final size:18
Alignment explanation
Indices: 483083--483131 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
483073 GAATGAATTG
483083 ATTTCTTCTCTC-TCTCT
1 ATTTCTTCTCTCTTCTCT
483100 -TATT-TTCTCTCTTCTCT
1 AT-TTCTTCTCTCTTCTCT
483117 ATTTCTTCTCCTCTT
1 ATTTCTTCT-CTCTT
483132 TCGAATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 8 0.30
17 9 0.33
18 5 0.19
19 5 0.19
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTCTTCTCTCTTCTCT
Found at i:491349 original size:2 final size:2
Alignment explanation
Indices: 491342--491371 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
491332 GCGTGGTCCA
*
491342 CT CT CT CT CT CT CT CT CT CT CG CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
491372 TAGGGTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
CT
Found at i:492337 original size:18 final size:20
Alignment explanation
Indices: 492279--492352 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
492269 AGGGATCAAC
* *
492279 CAAAAAGAAGAAGAAGAAATAA
1 CAAAAA-AAGAAGGAGAGA-AA
* *
492301 AAAAAGAAAGAAAGAGAGAAA
1 CAAAA-AAAGAAGGAGAGAAA
492322 -AAATAAAAGAAGGAGAGAAA
1 CAAA-AAAAGAAGGAGAGAAA
492342 CAAAAAAAGAA
1 CAAAAAAAGAA
492353 AAAAAAAAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 24 0.55
21 6 0.14
22 13 0.30
23 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.03
Consensus pattern (20 bp):
CAAAAAAAGAAGGAGAGAAA
Found at i:492672 original size:12 final size:11
Alignment explanation
Indices: 492648--492681 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
492638 GTTTTGTTTA
492648 ATTTAATTTTT
1 ATTTAATTTTT
*
492659 ATTTGATTTATT
1 ATTTAATTT-TT
492671 ATTTAATTTTT
1 ATTTAATTTTT
492682 TTATTTAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:494229 original size:43 final size:43
Alignment explanation
Indices: 494143--494249 Score: 137
Period size: 43 Copynumber: 2.5 Consensus size: 43
494133 AGGTATGTTA
*
494143 ATCATTGACATGTTATTAAATTATATTACTTGACCCGTTTTAAT
1 ATCA-TGACATGTTATTAAATTATATTACTTCACCCGTTTTAAT
* * *
494187 ATCATGTCATGCTATTAAATTATATTACTTCACTC-TTGTTAAT
1 ATCATGACATGTTATTAAATTATATTACTTCACCCGTT-TTAAT
*
494230 ATCGTGACATGTTA-TAAATT
1 ATCATGACATGTTATTAAATT
494250 GTGCAGTTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 8 0.15
43 43 0.78
44 4 0.07
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (43 bp):
ATCATGACATGTTATTAAATTATATTACTTCACCCGTTTTAAT
Found at i:514639 original size:79 final size:79
Alignment explanation
Indices: 514487--514710 Score: 229
Period size: 79 Copynumber: 2.8 Consensus size: 79
514477 TTGATTTATG
* * *
514487 TTGTCAGTTTAATTGACTAGAGCTGGGCTCAC-TTTCGCAGTTTATCCGCTAGGCATTGGGTGCC
1 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTT-GCGGTTTATCCGCTA-GCACTGGGTGCC
*
514551 AAGACTTGACGGACA-
64 AAGACTTGACAGACAT
* * *
514566 TTGTCAGTTTAACTGACTAGAGTTAGGCTCACATTTGCGGTTTATCCGCTAGCTACTGGGTGCTA
1 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGC-ACTGGGTGCCA
* * *
514631 GGATTTGACAGATAT
65 AGACTTGACAGACAT
* * ** * * *
514646 TTGT-TGGTTAATCCAACCAGAGCTGGGCTCACATCTGCGGTTTATCCGCTAGGCACTAGGTGCC
1 TTGTCAGTTTAA-CTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTA-GCACTGGGTGCC
514710 A
64 A
514711 TGATTGTCGG
Statistics
Matches: 120, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
78 2 0.02
79 67 0.56
80 49 0.41
81 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (79 bp):
TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGCACTGGGTGCCAA
GACTTGACAGACAT
Found at i:518158 original size:42 final size:42
Alignment explanation
Indices: 518094--518328 Score: 278
Period size: 42 Copynumber: 5.6 Consensus size: 42
518084 GAATCACTTG
* * *
518094 ATGTATAAAGGAAAACTCATGTCTGGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATT
518136 ATGTTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATT
** **
518178 ATGTTTAAAGGAAGACTTGTGTCTTAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATT
** *
518220 ATGTTTAAAGGAAGACTTGTGACTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATT
* * *
518262 ATGTTTAAAGGAAGAC-CTATATCTC-GGCTAGAGCATAAGATT
1 ATGTTTAAAGGAAGACTC-ATGTCTCGGGAT-GAGCATGAGATT
* *
518304 GT-TTATAAATGGAAGACTTATGTCT
1 ATGTT-TAAA-GGAAGACTCATGTCT
518329 TGACTAGAGC
Statistics
Matches: 169, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
41 5 0.03
42 152 0.90
43 12 0.07
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATT
Found at i:518336 original size:43 final size:42
Alignment explanation
Indices: 518124--518387 Score: 200
Period size: 42 Copynumber: 6.2 Consensus size: 42
518114 GTCTGGGGAT
* * *
518124 GAGCATGAGATTATGTTTAAA-GGAAGACTCATGTCTCGG-GA
1 GAGCATAAGATTAT-TTTAAATGGAAGACTTATGTCTCGGCTA
* * * *
518165 TGAGCATGAGATTATGTTTAAA-GGAAGACTTGTGTCTTAGGAT-
1 -GAGCATAAGATTAT-TTTAAATGGAAGACTTATGTC-TCGGCTA
* * * *
518208 GAGCATGAGATTATGTTTAAA-GGAAGACTTGTGACTCGG-GA
1 GAGCATAAGATTAT-TTTAAATGGAAGACTTATGTCTCGGCTA
* * *
518249 TGAGCATGAGATTATGTTTAAA-GGAAGACCTATATCTCGGCTA
1 -GAGCATAAGATTAT-TTTAAATGGAAGACTTATGTCTCGGCTA
* * *
518292 GAGCATAAGATTGTTTATAAATGGAAGACTTATGTCTTGACTA
1 GAGCATAAGATTATTT-TAAATGGAAGACTTATGTCTCGGCTA
* * * *
518335 GAGCATAAGATCATTTGTCAATGGAAGAACTTATGACTCGGGTA
1 GAGCATAAGATTATTT-TAAATGGAAG-ACTTATGTCTCGGCTA
518379 GAGCATAAG
1 GAGCATAAG
518388 GTTAATTCAG
Statistics
Matches: 188, Mismatches: 26, Indels: 14
0.82 0.11 0.06
Matches are distributed among these distances:
41 5 0.03
42 118 0.63
43 44 0.23
44 21 0.11
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (42 bp):
GAGCATAAGATTATTTTAAATGGAAGACTTATGTCTCGGCTA
Found at i:521955 original size:20 final size:20
Alignment explanation
Indices: 521932--521987 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
521922 TTGAGGATGC
521932 ACCAAAAATTATAAGTG-AGT
1 ACCAAAAATTATAAG-GAAGT
* *
521952 ACCAAAAAATATGAGGAAGT
1 ACCAAAAATTATAAGGAAGT
521972 A-CAATAAATTATAAGG
1 ACCAA-AAATTATAAGG
521988 GATTGCCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.21
Consensus pattern (20 bp):
ACCAAAAATTATAAGGAAGT
Found at i:524602 original size:14 final size:14
Alignment explanation
Indices: 524583--524611 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
524573 TTAATGTTTG
524583 ATTAACTTTAGTTA
1 ATTAACTTTAGTTA
524597 ATTAACTTTAGTTA
1 ATTAACTTTAGTTA
524611 A
1 A
524612 CTATGCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (14 bp):
ATTAACTTTAGTTA
Found at i:528955 original size:16 final size:17
Alignment explanation
Indices: 528930--528970 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
528920 AAAATGACAG
528930 AAAT-TTGT-AAATTAT
1 AAATATTGTAAAATTAT
528945 AAATATTGTAAAAATTAT
1 AAATATTGT-AAAATTAT
528963 AAATATTG
1 AAATATTG
528971 ATAATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.17
16 4 0.17
18 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (17 bp):
AAATATTGTAAAATTAT
Found at i:529492 original size:21 final size:20
Alignment explanation
Indices: 529447--529491 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
529437 GAGTTAAATA
529447 TAAAATAGATTAAGAAATTT
1 TAAAATAGATTAAGAAATTT
*
529467 TAAAATCAGATT-ATAAATTT
1 TAAAAT-AGATTAAGAAATTT
529487 TAAAA
1 TAAAA
529492 AGTTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (20 bp):
TAAAATAGATTAAGAAATTT
Found at i:530734 original size:33 final size:31
Alignment explanation
Indices: 530689--530753 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 31
530679 TTATGAATTC
*
530689 TTTTATATATTTTTTAATTTTTAATTTTTAATA
1 TTTTATATATTTTTTAATTTAT-A-TTTTAATA
530722 TTTT-TATGATTTTTTAATTTATATTTTAATA
1 TTTTATAT-ATTTTTTAATTTATATTTTAATA
530753 T
1 T
530754 AACATATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 9 0.30
32 4 0.13
33 17 0.57
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (31 bp):
TTTTATATATTTTTTAATTTATATTTTAATA
Found at i:530735 original size:26 final size:25
Alignment explanation
Indices: 530689--530741 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
530679 TTATGAATTC
530689 TTTTATATATTTTTTAATTTTTAAT
1 TTTTATATATTTTTTAATTTTTAAT
*
530714 TTTTA-ATATTTTTATGATTTTTTAAT
1 TTTTATATATTTTT-T-AATTTTTAAT
530740 TT
1 TT
530742 ATATTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
25 6 0.24
26 11 0.44
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTTATATATTTTTTAATTTTTAAT
Found at i:538757 original size:21 final size:21
Alignment explanation
Indices: 538733--538774 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
538723 CCTTATAACA
538733 AAAATAAGTTGTAATTTAGAT
1 AAAATAAGTTGTAATTTAGAT
538754 AAAATAAGTTGTAATTTAGAT
1 AAAATAAGTTGTAATTTAGAT
538775 CTGTCCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (21 bp):
AAAATAAGTTGTAATTTAGAT
Found at i:543418 original size:18 final size:18
Alignment explanation
Indices: 543375--543410 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
543365 AATTGTACTA
*
543375 ACAAAT-AAAATGCAGTG
1 ACAAATAAAAATGCAATG
543392 ACAAATAAAAATGCAATG
1 ACAAATAAAAATGCAATG
543410 A
1 A
543411 TAATTAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (18 bp):
ACAAATAAAAATGCAATG
Found at i:543552 original size:21 final size:21
Alignment explanation
Indices: 543514--543567 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
543504 TCTTTGGGCA
* *
543514 CTTTTCATTGTGCTT-CTTTTT
1 CTTTTC-TTGTCCTTCCTCTTT
543535 C-TTT-TTGTCCTTCCTCTTT
1 CTTTTCTTGTCCTTCCTCTTT
543554 CTTTTCTTGTCCTT
1 CTTTTCTTGTCCTT
543568 AGAGTCAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 7 0.25
19 6 0.21
20 6 0.21
21 9 0.32
ACGTcount: A:0.02, C:0.26, G:0.07, T:0.65
Consensus pattern (21 bp):
CTTTTCTTGTCCTTCCTCTTT
Found at i:543878 original size:18 final size:19
Alignment explanation
Indices: 543844--543883 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
543834 TCTCCTGTTC
543844 TTCCTTCTCTCCTTCA-GT
1 TTCCTTCTCTCCTTCAGGT
543862 TTCCTTCTTCTCC-TCAGGT
1 TTCCTTC-TCTCCTTCAGGT
543881 TTC
1 TTC
543884 GCCTTCTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.05, C:0.38, G:0.07, T:0.50
Consensus pattern (19 bp):
TTCCTTCTCTCCTTCAGGT
Found at i:549790 original size:52 final size:52
Alignment explanation
Indices: 549712--549816 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
549702 TATATACTTG
*
549712 GTTGGAACTGCTGCATAGCTCGATAGTTTGCTTTTCACTTCTCAGCATGATA
1 GTTGGAACTGCTGCATAGCTCGATAGTTTGCTTTCCACTTCTCAGCATGATA
* *
549764 GTTGGAATTGCTGCTTAGCTCGATAGTTTGCTTTCCACTTCTCAGCATGATA
1 GTTGGAACTGCTGCATAGCTCGATAGTTTGCTTTCCACTTCTCAGCATGATA
549816 G
1 G
549817 CCTTACAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (52 bp):
GTTGGAACTGCTGCATAGCTCGATAGTTTGCTTTCCACTTCTCAGCATGATA
Found at i:551439 original size:13 final size:13
Alignment explanation
Indices: 551421--551446 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
551411 CTGCTATTAC
551421 TGGTTGTTGTTGT
1 TGGTTGTTGTTGT
551434 TGGTTGTTGTTGT
1 TGGTTGTTGTTGT
551447 ATCTCCCTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (13 bp):
TGGTTGTTGTTGT
Found at i:555435 original size:17 final size:17
Alignment explanation
Indices: 555397--555456 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
555387 ATTAAAATGG
*
555397 AAATGCAACT-ACAAATGC
1 AAATGC-ACTAACAAAT-A
*
555415 AAATGTACTAACAAATA
1 AAATGCACTAACAAATA
* *
555432 AAATGCACTGATAAATAA
1 AAATGCACTAACAAAT-A
555450 AAATGCA
1 AAATGCA
555457 ATGACAACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 16 0.46
18 19 0.54
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.20
Consensus pattern (17 bp):
AAATGCACTAACAAATA
Found at i:555468 original size:18 final size:18
Alignment explanation
Indices: 555425--555468 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
555415 AAATGTACTA
*
555425 ACAAAT-AAAATGCACTG
1 ACAAATAAAAATGCAATG
*
555442 ATAAATAAAAATGCAATG
1 ACAAATAAAAATGCAATG
*
555460 ACAACTAAA
1 ACAAATAAA
555469 TGCTATGCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.59, C:0.14, G:0.09, T:0.18
Consensus pattern (18 bp):
ACAAATAAAAATGCAATG
Done.