Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015066.1 Kokia drynarioides strain JFW-HI SEQ_130110, 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: 364676
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 574 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:271489 original size:57 final size:56
Alignment explanation
Indices: 271392--271530 Score: 190
Period size: 57 Copynumber: 2.4 Consensus size: 56
271382 GATTATTGTT
* *
271392 ATTAAATTTTAATAAAATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTA
1 ATTAAATTTTAATATAATTATTA-TAAATACAATTTAAT-AAAATAATAAATAATTTA
* * *
271450 ATTATATTTTAACATAATTATTATAAATACAATTTAATAAAATAATATATAATTTA
1 ATTAAATTTTAATATAATTATTATAAATACAATTTAATAAAATAATAAATAATTTA
271506 A-TAACATTTTTAATATAATTATTAT
1 ATTAA-A-TTTTAATATAATTATTAT
271531 TAAAATATGA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
55 2 0.03
56 19 0.26
57 31 0.43
58 20 0.28
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (56 bp):
ATTAAATTTTAATATAATTATTATAAATACAATTTAATAAAATAATAAATAATTTA
Found at i:271554 original size:25 final size:24
Alignment explanation
Indices: 271526--271576 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
271516 TAATATAATT
*
271526 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
271551 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
271575 AT
1 AT
271577 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:276186 original size:14 final size:14
Alignment explanation
Indices: 276169--276261 Score: 60
Period size: 14 Copynumber: 6.6 Consensus size: 14
276159 CTAATATTTG
*
276169 AACCTTAAACCCTC
1 AACCTTAAACCCTA
* * *
276183 AACCTTAAATCATG
1 AACCTTAAACCCTA
* *
276197 AACTTTAAACCCTT
1 AACCTTAAACCCTA
* * **
276211 AATCTTGAACTATA
1 AACCTTAAACCCTA
276225 AACCTTAAACCCTA
1 AACCTTAAACCCTA
** *
276239 AATTTTAAACACTA
1 AACCTTAAACCCTA
*
276253 AACCCTAAA
1 AACCTTAAA
276262 TTTTAAACCA
Statistics
Matches: 56, Mismatches: 23, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
14 56 1.00
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.28
Consensus pattern (14 bp):
AACCTTAAACCCTA
Found at i:276186 original size:28 final size:27
Alignment explanation
Indices: 276126--276209 Score: 69
Period size: 28 Copynumber: 3.0 Consensus size: 27
276116 AAAAGTCTAA
* * * *
276126 AAACCCCAAACTTTGAACCCTGAATCCT
1 AAACCCTAAA-TTTGAACCTTAAACCCT
276154 AAACCCTAATATTTGAACCTTAAACCCT
1 AAACCCTAA-ATTTGAACCTTAAACCCT
* * * *
276182 CAACCTTAAATCATGAACTTTAAACCCT
1 AAACCCTAAAT-TTGAACCTTAAACCCT
276210 TAATCTTGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 2 0.04
28 43 0.93
29 1 0.02
ACGTcount: A:0.38, C:0.31, G:0.05, T:0.26
Consensus pattern (27 bp):
AAACCCTAAATTTGAACCTTAAACCCT
Found at i:276214 original size:21 final size:20
Alignment explanation
Indices: 276183--276232 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
276173 TTAAACCCTC
*
276183 AACCTTAAATCATGAACTTTA
1 AACCTT-AATCATGAACTATA
*
276204 AACCCTTAATCTTGAACTATA
1 AA-CCTTAATCATGAACTATA
276225 AACCTTAA
1 AACCTTAA
276233 ACCCTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 16 0.62
22 4 0.15
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.32
Consensus pattern (20 bp):
AACCTTAATCATGAACTATA
Found at i:276247 original size:21 final size:20
Alignment explanation
Indices: 276223--276270 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 20
276213 TCTTGAACTA
276223 TAAACCTTAAACCCTAAATTT
1 TAAACC-TAAACCCTAAATTT
276244 TAAACACTAAACCCTAAATTT
1 TAAAC-CTAAACCCTAAATTT
276265 TAAACC
1 TAAACC
276271 AAAAATCCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.04
21 24 0.92
22 1 0.04
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAACCTAAACCCTAAATTT
Found at i:276254 original size:28 final size:27
Alignment explanation
Indices: 276169--276261 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 27
276159 CTAATATTTG
* * *
276169 AACCTTAAACCCTCAACCTTAAATCATG
1 AACCTTAAACCCTAAATCTTAAA-CATA
* * *
276197 AACTTTAAACCCTTAATCTTGAACTATA
1 AACCTTAAACCCTAAATCTTAAAC-ATA
*
276225 AACCTTAAACCCTAAATTTTAAACACTA
1 AACCTTAAACCCTAAATCTTAAACA-TA
*
276253 AACCCTAAA
1 AACCTTAAA
276262 TTTTAAACCA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 2 0.04
28 51 0.96
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.28
Consensus pattern (27 bp):
AACCTTAAACCCTAAATCTTAAACATA
Found at i:277920 original size:29 final size:29
Alignment explanation
Indices: 277876--277945 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
277866 TAAAAAAGTA
* *
277876 TTTTTTAATATTTTAATATTC-AATATTATTG
1 TTTTTT-AT-TTTTAAAATTCAAAT-TTAATG
*
277907 TTTTTTATTTTTAAAATTTAAATTTAATG
1 TTTTTTATTTTTAAAATTCAAATTTAATG
277936 -TTTTTATTTT
1 TTTTTTATTTT
277946 AATTGTCACA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 10 0.29
29 14 0.40
30 5 0.14
31 6 0.17
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (29 bp):
TTTTTTATTTTTAAAATTCAAATTTAATG
Found at i:279571 original size:14 final size:15
Alignment explanation
Indices: 279552--279584 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
279542 CTACAATTAT
279552 AATAAA-ATATTAAA
1 AATAAATATATTAAA
*
279566 AATAAATATTTTAAA
1 AATAAATATATTAAA
279581 AATA
1 AATA
279585 CATAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAATATATTAAA
Found at i:287248 original size:24 final size:24
Alignment explanation
Indices: 287216--287261 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
287206 TAATTTAGCT
287216 TAATCGAACATGTTCACGAACATA
1 TAATCGAACATGTTCACGAACATA
* *
287240 TAATTGAACATGTTTACGAACA
1 TAATCGAACATGTTCACGAACA
287262 ATGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (24 bp):
TAATCGAACATGTTCACGAACATA
Found at i:287741 original size:19 final size:19
Alignment explanation
Indices: 287717--287756 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
287707 ACTATATATC
287717 ATTAAATTGTAGGTAAATT
1 ATTAAATTGTAGGTAAATT
287736 ATTAAATTGTAGGTAAATT
1 ATTAAATTGTAGGTAAATT
287755 AT
1 AT
287757 ATTCAAGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (19 bp):
ATTAAATTGTAGGTAAATT
Found at i:289425 original size:21 final size:21
Alignment explanation
Indices: 289390--289440 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
289380 TGCAGACTTT
**
289390 TACCGATACCTGTGACAG-TTC
1 TACCGATACAAGTGA-AGCTTC
289411 TACCGATACAAGTGAAGCTTC
1 TACCGATACAAGTGAAGCTTC
*
289432 TAGCGATAC
1 TACCGATAC
289441 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TACCGATACAAGTGAAGCTTC
Found at i:291296 original size:20 final size:20
Alignment explanation
Indices: 291273--291322 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
291263 TCATTAAGAT
291273 TTAATTAACCCT-TTTAAATC
1 TTAATTAACCCTATTTAAA-C
* *
291293 TTAATTAAACCTATTTATAC
1 TTAATTAACCCTATTTAAAC
291313 TTAATATAAC
1 TTAAT-TAAC
291323 TCATTCTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAACCCTATTTAAAC
Found at i:292909 original size:18 final size:18
Alignment explanation
Indices: 292888--292922 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
292878 CTTTATAACA
292888 CATTATATTATTATTATC
1 CATTATATTATTATTATC
292906 CATTATATTATTATTAT
1 CATTATATTATTATTAT
292923 TATTTGATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
CATTATATTATTATTATC
Found at i:295435 original size:3 final size:3
Alignment explanation
Indices: 295427--295471 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
295417 TAAAATAAAA
* *
295427 TAT TAT TAT TAT CA- CAT TA- TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
295472 GAATTACAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:295504 original size:20 final size:21
Alignment explanation
Indices: 295479--295517 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
295469 TATGAATTAC
295479 AATAATAAAAG-AAATATCTG
1 AATAATAAAAGTAAATATCTG
295499 AATAATAAAAGTAAATATC
1 AATAATAAAAGTAAATATC
295518 GCATGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (21 bp):
AATAATAAAAGTAAATATCTG
Found at i:301270 original size:21 final size:20
Alignment explanation
Indices: 301246--301302 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
301236 TATTAATAAC
* *
301246 TCTTGAATTTAATGTTTAGTG
1 TCTTG-ATTTAAGGTTTAGGG
*
301267 TCTTGAGTTAAGGTTTAGGG
1 TCTTGATTTAAGGTTTAGGG
301287 TCTTGGATTT-AGGTTT
1 TCTT-GATTTAAGGTTT
301303 CAATTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 22 0.71
21 9 0.29
ACGTcount: A:0.19, C:0.05, G:0.26, T:0.49
Consensus pattern (20 bp):
TCTTGATTTAAGGTTTAGGG
Found at i:302202 original size:22 final size:20
Alignment explanation
Indices: 302176--302221 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
302166 TTCATTTCTA
*
302176 ATTTATTGAAAGCATTTTTTTT
1 ATTTA-TGAAA-CATATTTTTT
*
302198 ATTTATGGAACATATTTTTT
1 ATTTATGAAACATATTTTTT
302218 ATTT
1 ATTT
302222 TCTAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 4 0.18
22 5 0.23
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (20 bp):
ATTTATGAAACATATTTTTT
Found at i:303209 original size:34 final size:35
Alignment explanation
Indices: 303171--303237 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
303161 CTTGAATTGC
* *
303171 TATTTAAATATTAAA-A-GTCTATTAATTATATTTA
1 TATTTAAATAATAAATATGACTATT-ATTATATTTA
303205 TATTTAAATAATAAATATGACTATTATTATATT
1 TATTTAAATAATAAATATGACTATTATTATATT
303238 ATTTACAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 14 0.48
35 9 0.31
36 6 0.21
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (35 bp):
TATTTAAATAATAAATATGACTATTATTATATTTA
Found at i:308692 original size:52 final size:51
Alignment explanation
Indices: 308583--308706 Score: 158
Period size: 52 Copynumber: 2.4 Consensus size: 51
308573 TGACCAATTG
* * *
308583 AAACTCAAGGGTCCTCCGACCAACTCAAATCAAGGGTCCTTAGACCCACTC
1 AAACTCAAGGGACCTTCGACCAACTCAAATCAAGGGTCCTCAGACCCACTC
* * * * * *
308634 AAACTCAAGGAACCTTCGACTAACTCAAACTTAAGGGTCCTCGGAGCCATTC
1 AAACTCAAGGGACCTTCGACCAACTCAAA-TCAAGGGTCCTCAGACCCACTC
308686 AAACTCAAGGGACCTTCGACC
1 AAACTCAAGGGACCTTCGACC
308707 CATCTCGGCT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 25 0.41
52 36 0.59
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.19
Consensus pattern (51 bp):
AAACTCAAGGGACCTTCGACCAACTCAAATCAAGGGTCCTCAGACCCACTC
Found at i:308709 original size:26 final size:26
Alignment explanation
Indices: 308569--308706 Score: 129
Period size: 26 Copynumber: 5.3 Consensus size: 26
308559 TGCTCATGGT
* *
308569 CTTCTGACCAATTGAAACTCAAGGGTC
1 CTTC-GACCAACTCAAACTCAAGGGTC
*
308596 CTCCGACCAACTCAAA-TCAAGGGTC
1 CTTCGACCAACTCAAACTCAAGGGTC
* * **
308621 CTTAGACCCACTCAAACTCAAGGAAC
1 CTTCGACCAACTCAAACTCAAGGGTC
* *
308647 CTTCGACTAACTCAAACTTAAGGGTC
1 CTTCGACCAACTCAAACTCAAGGGTC
* *
308673 C-TCGGAGCC-ATTCAAACTCAAGGGAC
1 CTTC-GA-CCAACTCAAACTCAAGGGTC
308699 CTTCGACC
1 CTTCGACC
308707 CATCTCGGCT
Statistics
Matches: 89, Mismatches: 18, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
25 26 0.29
26 57 0.64
27 6 0.07
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.20
Consensus pattern (26 bp):
CTTCGACCAACTCAAACTCAAGGGTC
Found at i:311921 original size:2 final size:2
Alignment explanation
Indices: 311916--311941 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
311906 ACTATATAAC
311916 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
311942 CATCAAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:315367 original size:17 final size:17
Alignment explanation
Indices: 315345--315379 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
315335 TTAAAAAGAA
315345 AGTTTTGTTTTCTTCGT
1 AGTTTTGTTTTCTTCGT
315362 AGTTTTGTTTTCTTCGT
1 AGTTTTGTTTTCTTCGT
315379 A
1 A
315380 ATTTGGTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.09, C:0.11, G:0.17, T:0.63
Consensus pattern (17 bp):
AGTTTTGTTTTCTTCGT
Found at i:316292 original size:25 final size:25
Alignment explanation
Indices: 316264--316312 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
316254 AGGTTTAACC
*
316264 GTTGATCGACCATTGACCGTTGACT
1 GTTGATCGAACATTGACCGTTGACT
* *
316289 GTTGTTCGAACGTTGACCGTTGAC
1 GTTGATCGAACATTGACCGTTGAC
316313 CATTGACCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (25 bp):
GTTGATCGAACATTGACCGTTGACT
Found at i:318053 original size:13 final size:13
Alignment explanation
Indices: 318019--318059 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
318009 CTATTGATGG
* *
318019 TTGACCATTAACT
1 TTGACCGTTGACT
318032 TTGACCGTTGACT
1 TTGACCGTTGACT
*
318045 TTGATCGTTGACT
1 TTGACCGTTGACT
318058 TT
1 TT
318060 TTTCGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:322353 original size:18 final size:18
Alignment explanation
Indices: 322330--322368 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
322320 CAACTGTTGC
*
322330 CCGACCGTTGACCATTGA
1 CCGACCATTGACCATTGA
322348 CCGACCATTGACCATTGA
1 CCGACCATTGACCATTGA
322366 CCG
1 CCG
322369 TTGACTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.36, G:0.21, T:0.21
Consensus pattern (18 bp):
CCGACCATTGACCATTGA
Found at i:326639 original size:25 final size:25
Alignment explanation
Indices: 326605--326679 Score: 132
Period size: 25 Copynumber: 3.0 Consensus size: 25
326595 TAAAGAAGAA
326605 AGATGGGTCACTTCGGTTGTGCATT
1 AGATGGGTCACTTCGGTTGTGCATT
* *
326630 AGATGGGTCACTTCGGTTATGTATT
1 AGATGGGTCACTTCGGTTGTGCATT
326655 AGATGGGTCACTTCGGTTGTGCATT
1 AGATGGGTCACTTCGGTTGTGCATT
326680 GACTATCTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.37
Consensus pattern (25 bp):
AGATGGGTCACTTCGGTTGTGCATT
Found at i:334605 original size:17 final size:17
Alignment explanation
Indices: 334572--334604 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
334562 ATTTCATATT
334572 TTTTAAAAATTATAAAA
1 TTTTAAAAATTATAAAA
334589 TTTTAAAAA-TATAAAA
1 TTTTAAAAATTATAAAA
334605 AAGTTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTTAAAAATTATAAAA
Found at i:335296 original size:15 final size:18
Alignment explanation
Indices: 335255--335292 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
335245 TAACCGTTAT
*
335255 ATATATATATATTATAAA
1 ATATAAATATATTATAAA
335273 ATATAAATATATT-TAAA
1 ATATAAATATATTATAAA
335290 ATA
1 ATA
335293 AATAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAAATATATTATAAA
Found at i:342710 original size:21 final size:21
Alignment explanation
Indices: 342684--342723 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
342674 ATAGATGTCT
*
342684 CAGTTTTCTTTCGAAAATCCA
1 CAGTTTGCTTTCGAAAATCCA
*
342705 CAGTTTGCTTTTGAAAATC
1 CAGTTTGCTTTCGAAAATC
342724 TATAAATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (21 bp):
CAGTTTGCTTTCGAAAATCCA
Found at i:344298 original size:21 final size:21
Alignment explanation
Indices: 344274--344313 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
344264 CGATCTAAGG
344274 AAAAATAAAAGAAACAGAATT
1 AAAAATAAAAGAAACAGAATT
* *
344295 AAAAATAAAATAAATAGAA
1 AAAAATAAAAGAAACAGAA
344314 AATAGAGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (21 bp):
AAAAATAAAAGAAACAGAATT
Found at i:349997 original size:20 final size:18
Alignment explanation
Indices: 349973--350020 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
349963 ATCTTTTTGT
349973 ATATTTTTTACAATTTCTTA
1 ATATTTTTTACAA-TTC-TA
* *
349993 TTATTTTGTAACAATTCTA
1 ATATTTT-TTACAATTCTA
350012 ATATTTTTT
1 ATATTTTTT
350021 TTAATTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.04
19 8 0.35
20 9 0.39
21 5 0.22
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.60
Consensus pattern (18 bp):
ATATTTTTTACAATTCTA
Found at i:350055 original size:8 final size:8
Alignment explanation
Indices: 350017--350152 Score: 62
Period size: 10 Copynumber: 15.5 Consensus size: 8
350007 TTCTAATATT
*
350017 TTTTTTAA
1 TTTTATAA
350025 TTTTAAATAA
1 TTTT--ATAA
350035 GTTTTATTAA
1 -TTTTA-TAA
350045 TTTTATAA
1 TTTTATAA
*
350053 TTTATTAGAA
1 -TT-TTATAA
*
350063 GTTTTATAT
1 -TTTTATAA
350072 TTTTATAA
1 TTTTATAA
*
350080 TATTTAGAAA
1 T-TTTA-TAA
350090 TTTTTATAA
1 -TTTTATAA
350099 TTTTTTATAA
1 --TTTTATAA
350109 TTTTTTATAA
1 --TTTTATAA
350119 TTTTA-ATA
1 TTTTATA-A
*
350127 TTTAAT-A
1 TTTTATAA
*
350134 TTTAAT-A
1 TTTTATAA
350141 TTTTATAA
1 TTTTATAA
350149 TTTT
1 TTTT
350153 TTTCTGCTGT
Statistics
Matches: 105, Mismatches: 10, Indels: 26
0.74 0.07 0.18
Matches are distributed among these distances:
7 14 0.13
8 30 0.29
9 18 0.17
10 38 0.36
11 5 0.05
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (8 bp):
TTTTATAA
Found at i:350056 original size:27 final size:27
Alignment explanation
Indices: 350033--350111 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 27
350023 AATTTTAAAT
*
350033 AAGTTTTATTAATTTTATAATTTATTAG
1 AAGTTTTA-TAATTTTATAATTTATAAG
*
350061 AAGTTTTATATTTTTATAATATT-T-AG
1 AAGTTTTATAATTTTATAAT-TTATAAG
*
350087 AAATTTTTATAATTTTTTATAATTT
1 -AAGTTTTATAA--TTTTATAATTT
350112 TTTATAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.05
27 21 0.48
28 12 0.27
29 9 0.20
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (27 bp):
AAGTTTTATAATTTTATAATTTATAAG
Found at i:350094 original size:20 final size:17
Alignment explanation
Indices: 350016--350129 Score: 68
Period size: 19 Copynumber: 6.2 Consensus size: 17
350006 ATTCTAATAT
*
350016 TTTTTTTAATTTTAAATAA
1 TTTTTATAATTTT-AA-AA
* *
350035 GTTTTATTAATTTTATAA
1 TTTTTA-TAATTTTAAAA
* *
350053 TTTATTAGAAGTTTT-ATA
1 TTT-TTATAA-TTTTAAAA
350071 TTTTTATAATATTTAGAAA
1 TTTTTATAAT-TTTA-AAA
*
350090 TTTTTATAATTTTTTATAAT
1 TTTTTATAA--TTTTA-AAA
*
350110 TTTTTATAATTTTAATA
1 TTTTTATAATTTTAAAA
350127 TTT
1 TTT
350130 AATATTTAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
16 1 0.01
17 12 0.16
18 15 0.20
19 23 0.31
20 22 0.30
21 1 0.01
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTTTATAATTTTAAAA
Found at i:350154 original size:10 final size:10
Alignment explanation
Indices: 350045--350122 Score: 74
Period size: 10 Copynumber: 8.2 Consensus size: 10
350035 GTTTTATTAA
350045 TTTTATAATT
1 TTTTATAATT
* * *
350055 TATTAGAA-G
1 TTTTATAATT
350064 TTTTAT-A-T
1 TTTTATAATT
350072 TTTTATAA-T
1 TTTTATAATT
* * *
350081 ATTTAGAAAT
1 TTTTATAATT
350091 TTTTATAATT
1 TTTTATAATT
350101 TTTTATAATT
1 TTTTATAATT
350111 TTTTATAATT
1 TTTTATAATT
350121 TT
1 TT
350123 AATATTTAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
8 7 0.13
9 12 0.22
10 36 0.65
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:350760 original size:2 final size:2
Alignment explanation
Indices: 350755--350789 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
350745 ACTCTAGATA
350755 AT AT AT AT 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 AT AT AT AT A
350790 GTCTGTCACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:354589 original size:16 final size:17
Alignment explanation
Indices: 354561--354593 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
354551 ATTGATTGAA
354561 TTAATTCTTTTTTATTT
1 TTAATTCTTTTTTATTT
354578 TTAATT-TTTTTTATTT
1 TTAATTCTTTTTTATTT
354594 AAAAGTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (17 bp):
TTAATTCTTTTTTATTT
Found at i:354904 original size:10 final size:10
Alignment explanation
Indices: 354891--355083 Score: 53
Period size: 10 Copynumber: 19.4 Consensus size: 10
354881 GTTATAATAA
354891 TTTTCTATAT
1 TTTTCTATAT
354901 TTTT-TAATAT
1 TTTTCT-ATAT
354911 TTTATACTA-AT
1 TTT-T-CTATAT
**
354922 TTTAATATAT
1 TTTTCTATAT
* *
354932 GTTT-AATAT
1 TTTTCTATAT
354941 TTTTCTATA-
1 TTTTCTATAT
354950 TTTTCTAT-T
1 TTTTCTATAT
* *
354959 CTTTT-AATAC
1 -TTTTCTATAT
*
354969 TTTTATATAT
1 TTTTCTATAT
* * *
354979 GTTATACTGTTT
1 -TT-TTCTATAT
*
354991 TTTTCTAAAT
1 TTTTCTATAT
*
355001 TTTT-AATAT
1 TTTTCTATAT
* *
355010 TTTTCAATGT
1 TTTTCTATAT
*
355020 TTTTATATAT
1 TTTTCTATAT
* **
355030 TTGTAAATAT
1 TTTTCTATAT
* *
355040 TTTTATAAAT
1 TTTTCTATAT
* *
355050 TTTT-AATAA
1 TTTTCTATAT
355059 TTTT-TATACCT
1 TTTTCTATA--T
355070 TTTTCTATAT
1 TTTTCTATAT
355080 TTTT
1 TTTT
355084 ATAATTTTAT
Statistics
Matches: 132, Mismatches: 35, Indels: 32
0.66 0.18 0.16
Matches are distributed among these distances:
9 40 0.30
10 68 0.52
11 14 0.11
12 9 0.07
13 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTTCTATAT
Found at i:354912 original size:19 final size:19
Alignment explanation
Indices: 354885--354978 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 19
354875 TTATAAGTTA
*
354885 TAATAATTTTCTATATTTTT
1 TAAT-ATTTTATATATTTTT
*
354905 TAATATTTTATACTAATTTT
1 TAATATTTTATA-TATTTTT
*
354925 AATATATGTTTA-ATATTTTT
1 TA-ATAT-TTTATATATTTTT
* *
354945 CT-ATATTTTCTAT-TCTTT
1 -TAATATTTTATATATTTTT
354963 TAATACTTTTATATAT
1 TAATA-TTTTATATAT
354979 GTTATACTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
17 1 0.02
18 10 0.17
19 20 0.34
20 18 0.31
21 5 0.09
22 4 0.07
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (19 bp):
TAATATTTTATATATTTTT
Found at i:354946 original size:50 final size:48
Alignment explanation
Indices: 354871--355062 Score: 140
Period size: 50 Copynumber: 3.9 Consensus size: 48
354861 ACAATGCAAC
* * *
354871 TTTTTTATAAGTTATAATAATTTTCTATATTTTTTAATATTTTATACTAA
1 TTTTATATATGTTATAATATTTTTCTATATTTTTTAATATTTTA-A-TAA
* * * *
354921 TTTTAATATATGTT-TAATATTTTTCTATATTTTCTATTCTTTTAATAC
1 TTTT-ATATATGTTATAATATTTTTCTATATTTTTTAATATTTTAATAA
* * * **
354969 TTTTATATATGTTATACTGTTTTTTTCTA-AATTTTTAATATTTTTCAATGT
1 TTTTATATATGTTATA--ATATTTTTCTATATTTTTTAATA-TTTT-AATAA
* * *
355020 TTTTATATAT-TTGTAAATATTTTTATA-AATTTTTAATAATTTT
1 TTTTATATATGTTAT-AATATTTTTCTATATTTTTTAAT-ATTTT
355063 TATACCTTTT
Statistics
Matches: 115, Mismatches: 19, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
47 9 0.08
48 8 0.07
49 30 0.26
50 47 0.41
51 21 0.18
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (48 bp):
TTTTATATATGTTATAATATTTTTCTATATTTTTTAATATTTTAATAA
Found at i:354991 original size:28 final size:28
Alignment explanation
Indices: 354933--354991 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
354923 TTAATATATG
* * * * *
354933 TTTAATATTTTTCTATATTTTCTATTCT
1 TTTAATACTTTTATATATGTTATACTCT
*
354961 TTTAATACTTTTATATATGTTATACTGT
1 TTTAATACTTTTATATATGTTATACTCT
354989 TTT
1 TTT
354992 TTTCTAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.64
Consensus pattern (28 bp):
TTTAATACTTTTATATATGTTATACTCT
Found at i:355065 original size:20 final size:20
Alignment explanation
Indices: 354998--355066 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
354988 TTTTTTTCTA
354998 AATTTTTA-ATATTTTTCAAT
1 AATTTTTATATATTTTT-AAT
* *
355018 -GTTTTTATATATTTGTAA-
1 AATTTTTATATATTTTTAAT
*
355036 ATATTTTTATAAATTTTTAAT
1 A-ATTTTTATATATTTTTAAT
355057 AATTTTTATA
1 AATTTTTATA
355067 CCTTTTTCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
19 8 0.20
20 31 0.77
21 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTTTATATATTTTTAAT
Found at i:355072 original size:20 final size:20
Alignment explanation
Indices: 355019--355091 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
355009 TTTTTCAATG
* * *
355019 TTTTTATATATTTGTAAATA
1 TTTTTATAAATTTTTATATA
355039 TTTTTATAAATTTTTA-ATAA
1 TTTTTATAAATTTTTATAT-A
** *
355059 TTTTTATACCTTTTTCTATA
1 TTTTTATAAATTTTTATATA
355079 TTTTTAT-AATTTT
1 TTTTTATAAATTTT
355092 ATTGCTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.14
20 36 0.82
21 2 0.05
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (20 bp):
TTTTTATAAATTTTTATATA
Found at i:355082 original size:9 final size:9
Alignment explanation
Indices: 355019--355091 Score: 56
Period size: 10 Copynumber: 7.4 Consensus size: 9
355009 TTTTTCAATG
355019 TTTTTATATA
1 TTTTTATA-A
* *
355029 TTTGTAAATA
1 TTTTTATA-A
355039 TTTTTATAAA
1 TTTTTAT-AA
355049 TTTTTAATAA
1 TTTTT-ATAA
*
355059 TTTTTATACC
1 TTTTTATA-A
*
355069 TTTTTCTATA
1 TTTTTATA-A
355079 TTTTTATAA
1 TTTTTATAA
355088 TTTT
1 TTTT
355092 ATTGCTTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
9 8 0.16
10 40 0.78
11 3 0.06
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:355210 original size:30 final size:30
Alignment explanation
Indices: 355167--355251 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
355157 AACTTAAAAT
*
355167 TTTATAATTTTTTCATATTTTTTAAATAAA
1 TTTATATTTTTTTCATATTTTTTAAATAAA
* ** *
355197 TTTCTATTTTTTTC-TATTTTATTATGTAAT
1 TTTATATTTTTTTCATATTTT-TTAAATAAA
*
355227 TTTATATTTTTTTAATATATTTTTA
1 TTTATATTTTTTTCATAT-TTTTTA
355252 TATTGTTTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
29 6 0.13
30 30 0.67
31 6 0.13
32 3 0.07
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67
Consensus pattern (30 bp):
TTTATATTTTTTTCATATTTTTTAAATAAA
Found at i:355237 original size:21 final size:21
Alignment explanation
Indices: 355206--355260 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
355196 ATTTCTATTT
* * *
355206 TTTTCTATTTTATT-ATGTAA
1 TTTTATATTTTTTTAATATAA
*
355226 TTTTATATTTTTTTAATATAT
1 TTTTATATTTTTTTAATATAA
*
355247 TTTTATATTGTTTT
1 TTTTATATTTTTTT
355261 CACGCAACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.71
Consensus pattern (21 bp):
TTTTATATTTTTTTAATATAA
Found at i:355598 original size:21 final size:21
Alignment explanation
Indices: 355552--355612 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
355542 CGATTTGAGG
*
355552 AAAAATAGAAGAAACA-AAATT
1 AAAAATAAAAGAAA-ATAAATT
355573 AAAAATAAAAGAAAATATAATT
1 AAAAATAAAAGAAAATA-AATT
*
355595 AAAAGA-AATAGAAAATAA
1 AAAA-ATAAAAGAAAATAA
355613 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 1 0.03
21 15 0.43
22 18 0.51
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAGAAAATAAATT
Found at i:356433 original size:19 final size:19
Alignment explanation
Indices: 356409--356451 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
356399 AAACATAAAT
356409 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
356428 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
356447 TAAAT
1 TAAAT
356452 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:364644 original size:25 final size:24
Alignment explanation
Indices: 364610--364663 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
364600 ATTTTATATT
*
364610 AATATTTATATTAACATTAAATAA
1 AATAATTATATTAACATTAAATAA
*
364634 ATATAATTATATTAATATTAAATAA
1 A-ATAATTATATTAACATTAAATAA
364659 AATAA
1 AATAA
364664 AAATCTCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
AATAATTATATTAACATTAAATAA
Done.