Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168137.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_38, 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: 382840
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Warning! 2000 characters in sequence are not A, C, G, or T
File 8 of 8
Found at i:371539 original size:21 final size:20
Alignment explanation
Indices: 371509--371562 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 20
371499 TTATTATTTA
371509 ATAA-AGATTAAAATATTAATT
1 ATAATAGATTAAAATA--AATT
*
371530 ATAAT-TATT-AAATAAATT
1 ATAATAGATTAAAATAAATT
371548 ATAATAGATTAAAAT
1 ATAATAGATTAAAAT
371563 TAGTATTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 9 0.32
19 3 0.11
20 9 0.32
21 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
ATAATAGATTAAAATAAATT
Found at i:371571 original size:40 final size:38
Alignment explanation
Indices: 371509--371588 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 38
371499 TTATTATTTA
* *
371509 ATAAAGATTAAAATATTAATTATAATTATTAAATAAATT
1 ATAAAGATTAAAATAGTAATTATAA-TAATAAATAAATT
* *
371548 ATAATAGATTAAAATTAGT-ATTATGATAATAATTAAATT
1 ATAA-AGATTAAAA-TAGTAATTATAATAATAAATAAATT
371587 AT
1 AT
371589 CCTAATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
39 17 0.49
40 15 0.43
41 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (38 bp):
ATAAAGATTAAAATAGTAATTATAATAATAAATAAATT
Found at i:371693 original size:14 final size:14
Alignment explanation
Indices: 371674--371703 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
371664 AATAATTAAG
371674 ATAATAATATAATT
1 ATAATAATATAATT
371688 ATAATAATATAATT
1 ATAATAATATAATT
371702 AT
1 AT
371704 TTAGCTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATAATATAATT
Found at i:373414 original size:18 final size:19
Alignment explanation
Indices: 373380--373415 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
373370 TAATAGTCAT
373380 ATATTAGTTAATATTTATA
1 ATATTAGTTAATATTTATA
*
373399 ATATTA-TTACTATTTAT
1 ATATTAGTTAATATTTAT
373416 TATAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
ATATTAGTTAATATTTATA
Found at i:373492 original size:14 final size:15
Alignment explanation
Indices: 373451--373567 Score: 59
Period size: 18 Copynumber: 7.5 Consensus size: 15
373441 ATGTAATAAT
373451 TTAATAA-ATTATTA
1 TTAATAATATTATTA
373465 -TAATTAA-A-TATTA
1 TTAA-TAATATTATTA
373478 TTAATAATATT-TTA
1 TTAATAATATTATTA
* *
373492 TGAATCATATTAATTA
1 TTAATAATATT-ATTA
373508 TT-ATAATATGTAATTA
1 TTAATAATAT-T-ATTA
*
373524 -TAATTGTATATTATATA
1 TTAA-T-AATATTAT-TA
373541 TTATATAATAATTATTTA
1 TTA-ATAAT-ATTA-TTA
373559 TTATATAAT
1 TTA-ATAAT
373568 TTAATTGGAC
Statistics
Matches: 82, Mismatches: 6, Indels: 26
0.72 0.05 0.23
Matches are distributed among these distances:
13 11 0.13
14 20 0.24
15 8 0.10
16 13 0.16
17 6 0.07
18 22 0.27
19 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAATAATATTATTA
Found at i:373525 original size:13 final size:13
Alignment explanation
Indices: 373506--373538 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
373496 TCATATTAAT
373506 TATTATAATATGTA
1 TATTATAAT-TGTA
373520 -ATTATAATTGTA
1 TATTATAATTGTA
373532 TATTATA
1 TATTATA
373539 TATTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (13 bp):
TATTATAATTGTA
Found at i:373551 original size:25 final size:25
Alignment explanation
Indices: 373506--373565 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
373496 TCATATTAAT
* *
373506 TATTATAATATGTAATTATAATTGTA
1 TATTAT-ATATGTAATAATAATTATA
*
373532 TATTATATAT-TATATAATAATTATT
1 TATTATATATGTA-ATAATAATTATA
373557 TATTATATA
1 TATTATATA
373566 ATTTAATTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.07
25 22 0.73
26 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (25 bp):
TATTATATATGTAATAATAATTATA
Found at i:373560 original size:18 final size:18
Alignment explanation
Indices: 373533--373567 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
373523 ATAATTGTAT
373533 ATTATATATTATATAATA
1 ATTATATATTATATAATA
*
373551 ATTATTTATTATATAAT
1 ATTATATATTATATAAT
373568 TTAATTGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATATATTATATAATA
Found at i:373666 original size:13 final size:12
Alignment explanation
Indices: 373620--373671 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
373610 ATTGTTTGAC
373620 AATAATAGTTAAT
1 AATAATA-TTAAT
373633 AA-AATATTAAT
1 AATAATATTAAT
373644 AATAACTATTAACT
1 AATAA-TATTAA-T
*
373658 ATTAATATT-AT
1 AATAATATTAAT
373669 AAT
1 AAT
373672 TAATTATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 10 0.29
12 7 0.21
13 12 0.35
14 5 0.15
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:376705 original size:180 final size:181
Alignment explanation
Indices: 376125--376941 Score: 741
Period size: 181 Copynumber: 4.5 Consensus size: 181
376115 TATTAAATCT
* * * * *
376125 CTTATTAATTTTTAAAATATTAATAAATTAATATTATTTTATTTCG-ATCAAACTTATATGAACA
1 CTTATTAATTTTTATAATATTAATAAATTAATATTATTTTATTTTGAAT-AAGCTTGTATGAAGA
* * * *
376189 AAAACATTTGTTTTACGACAAAACAAAAAGGTCATAACGATTTGAAATAGATAATTATTCATATA
65 AAAACAATTGTTTTATGACAAAACAAAAAGGTCATAACGATTTGAAATAGATAATTGTTCAAATA
* * * *
376254 GCCTTAACTATTTGAATTGGTTC-AGTAAACAAATTTATTTTTTAAATCTATCA
130 GCCATAACTATTTGAATTGATTCGA-TAAAC-AATTTATTTTTTAAATCTCTAA
* * * * * * *
376307 GTTATTAAATTTCATAATATTACTAGATTAATATTATTTTATTTTGAACAAGCTTGTATGAAGAT
1 CTTATTAATTTTTATAATATTAATAAATTAATATTATTTTATTTTGAATAAGCTTGTATGAAGAA
* * * * * *
376372 AAATAATTGTTTTATGACAAAACAAAAA-GTTATAACGATTGGAAACATATAATTCTTCAAATAG
66 AAACAATTGTTTTATGACAAAACAAAAAGGTCATAACGATTTGAAATAGATAATTGTTCAAATAG
* * * *
376436 TCATAACTATTTGAACTGATTCGATAAACATATTTATTTTTTACATCTCTTA
131 CCATAACTATTTGAATTGATTCGATAAACA-ATTTATTTTTTAAATCTCTAA
** * * *
376488 CTTATTAATTTTT-TAAATATTAATAAATTTGTATTATTTTATTCTGAATAGGCTTGTATGATGA
1 CTTATTAATTTTTAT-AATATTAATAAATTAATATTATTTTATTTTGAATAAGCTTGTATGAAGA
* * * * *
376552 AAAATAATTGTTTTATGAC-GAAC-AAAAGTTCATAATGATTTGAAATAGATAATTGTTTAAAT-
65 AAAACAATTGTTTTATGACAAAACAAAAAGGTCATAACGATTTGAAATAGATAATTGTTCAAATA
* *
376614 GACCATAATTATTTGAATTGATTCGATAAACTAATTTATGTTTTAAATCTCTAA
130 G-CCATAACTATTTGAATTGATTCGATAAAC-AATTTATTTTTTAAATCTCTAA
* * * * * **
376668 CTTATCAATTTTTATAATATTAGTAAAGTAATATTATTTT-TTTTTAGATAAGCTTTTATGAACT
1 CTTATTAATTTTTATAATATTAATAAATTAATATTATTTTATTTTGA-ATAAGCTTGTATGAAGA
* * * * * * *
376732 GAAACAATTGTTTTATAATAAAA-TATAAGGTCATAATGATTTTAAATAGATAATTGTTCAAATA
65 AAAACAATTGTTTTATGACAAAACAAAAAGGTCATAACGATTTGAAATAGATAATTGTTCAAATA
* * * * * * * *
376796 GTCAAAAATATTTGAACTTG-TTCGGTAAATAGTTTTTTTTTTCTAAT-T-T--
130 GCCATAACTATTTGAA-TTGATTCGATAAACAATTTATTTTTT-AAATCTCTAA
* * * * *
376845 CTTAATAATTTTT-TGAATGTTAATAAATTAGTATTATTTTATTTCGAATAAGCATGTATG-AGT
1 CTTATTAATTTTTAT-AATATTAATAAATTAATATTATTTTATTTTGAATAAGCTTGTATGAAG-
** * * *
376908 TGAAGCAATTATTTTATGACTAAAC-AAAAGGTCA
64 AAAAACAATTGTTTTATGACAAAACAAAAAGGTCA
376942 GAATGATTAT
Statistics
Matches: 515, Mismatches: 102, Indels: 41
0.78 0.16 0.06
Matches are distributed among these distances:
176 2 0.00
177 70 0.14
178 4 0.01
179 10 0.02
180 145 0.28
181 202 0.39
182 81 0.16
183 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (181 bp):
CTTATTAATTTTTATAATATTAATAAATTAATATTATTTTATTTTGAATAAGCTTGTATGAAGAA
AAACAATTGTTTTATGACAAAACAAAAAGGTCATAACGATTTGAAATAGATAATTGTTCAAATAG
CCATAACTATTTGAATTGATTCGATAAACAATTTATTTTTTAAATCTCTAA
Found at i:376743 original size:361 final size:359
Alignment explanation
Indices: 376125--376905 Score: 855
Period size: 361 Copynumber: 2.2 Consensus size: 359
376115 TATTAAATCT
* * * *
376125 CTTATTAATTTTTAAAATATTAATAAATTAATATTATTTTATTTCG-ATCAAACTTATATGAACA
1 CTTATTAATTTTTTAAATATTAATAAATTAGTATTATTTTATTTCGAAT-AAGCTTGTATGAACA
* *
376189 AAAACATTTGTTTTACGACAAAACAAAAAGGTCATAACGATTTGAAATAGATAATTATTCATATA
65 AAAACAATTGTTTTACGACAAAACAAAAAGGTCATAACGATTTGAAATAGATAATTATTCAAATA
* * * * * *
376254 GCCTTAACTATTTGAATTGGTTCAGTAAACAAATTTATTTTTTAAATCTATCAGTTATTAAATTT
130 GCCATAACTATTTGAATTGATTCAGTAAACAAATTTATGTTTTAAATCTATAACTTATCAAATTT
* * *
376319 CATAATATTACTAGATTAATATTATTTTATTTTGAACAAGCTTGTATGAAGATAAATAATTGTTT
195 CATAATATTACTAAAGTAATATTATTTTATTTTGAACAAGCTTGTATGAAGATAAACAATTGTTT
* * * * *
376384 TATGACAAAACAAAAAGTTATAACGATTGGAAACATATAATTCTTCAAATAGTCATAACTATTTG
260 TATAACAAAACAAAAAGTCATAACGATTGGAAACAGATAATTCTTCAAATAGTCAAAAATATTTG
*
376449 AAC-TGATTCGATAAACATA-TTTATTTTTTACATCT-CTTA
325 AACTTG-TTCGAT-AA-ATAGTTT-TTTTTT---TCTAATTA
* * **
376488 CTTATTAATTTTTTAAATATTAATAAATTTGTATTATTTTA-TTCTGAATAGGCTTGTATGATGA
1 CTTATTAATTTTTTAAATATTAATAAATTAGTATTATTTTATTTC-GAATAAGCTTGTATGAACA
* * * * * * *
376552 AAAATAATTGTTTTATGAC-GAAC-AAAAGTTCATAATGATTTGAAATAGATAATTGTTTAAAT-
65 AAAACAATTGTTTTACGACAAAACAAAAAGGTCATAACGATTTGAAATAGATAATTATTCAAATA
* * * *
376614 GACCATAATTATTTGAATTGATTC-GATAAACTAATTTATGTTTTAAATCTCTAACTTATCAATT
130 G-CCATAACTATTTGAATTGATTCAG-TAAACAAATTTATGTTTTAAATCTATAACTTATCAAAT
* * * * * *
376678 TTTATAATATTAGTAAAGTAATATTATTTT-TTTTTAGATAAGCTTTTATGAA-CTGAAACAATT
193 TTCATAATATTACTAAAGTAATATTATTTTATTTTGA-ACAAGCTTGTATGAAGAT-AAACAATT
* * * * * ** * *
376741 GTTTTATAATAAAATATAAGGTCATAATGATTTTAAATAGATAATTGTTCAAATAGTCAAAAATA
256 GTTTTATAACAAAACAAAAAGTCATAACGATTGGAAACAGATAATTCTTCAAATAGTCAAAAATA
* *
376806 TTTGAACTTGTTCGGTAAATAGTTTTTTTTTTCTAATTT
321 TTTGAACTTGTTCGATAAATAGTTTTTTTTTTCTAATTA
* * * *
376845 CTTAATAATTTTTTGAATGTTAATAAATTAGTATTATTTTATTTCGAATAAGCATGTATGA
1 CTTATTAATTTTTTAAATATTAATAAATTAGTATTATTTTATTTCGAATAAGCTTGTATGA
376906 GTTGAAGCAA
Statistics
Matches: 349, Mismatches: 59, Indels: 26
0.80 0.14 0.06
Matches are distributed among these distances:
356 3 0.01
357 53 0.15
358 3 0.01
359 9 0.03
360 13 0.04
361 193 0.55
362 8 0.02
363 65 0.19
364 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (359 bp):
CTTATTAATTTTTTAAATATTAATAAATTAGTATTATTTTATTTCGAATAAGCTTGTATGAACAA
AAACAATTGTTTTACGACAAAACAAAAAGGTCATAACGATTTGAAATAGATAATTATTCAAATAG
CCATAACTATTTGAATTGATTCAGTAAACAAATTTATGTTTTAAATCTATAACTTATCAAATTTC
ATAATATTACTAAAGTAATATTATTTTATTTTGAACAAGCTTGTATGAAGATAAACAATTGTTTT
ATAACAAAACAAAAAGTCATAACGATTGGAAACAGATAATTCTTCAAATAGTCAAAAATATTTGA
ACTTGTTCGATAAATAGTTTTTTTTTTCTAATTA
Found at i:379347 original size:180 final size:179
Alignment explanation
Indices: 379046--379429 Score: 479
Period size: 180 Copynumber: 2.1 Consensus size: 179
379036 TAATTTTTAA
* * * * *
379046 TTATTAA-AATTCAAAAAATTAATAAGCAAAAGGTATGAAAAAATAAATCTGTTTACCGATCAAG
1 TTATTAATATTTC-AAAAATTAATAAGCAAAAGGTATGAAAAAATAAATCTATTTACCAAACAAA
* *
379110 TTCAAATAATTATAACTATTTGAATTGTTCATTTAAAACCATTATGACCTTTTGTTTTGACAAAA
65 TTCAAATAACTACAACTATTTGAATTGTTCATTTAAAACCATTATGACCTTTTGTTTTGACAAAA
*
379175 AACAATTGTTTCAGTTCATAAAAACTTATCCAAAATAAAATAATACTAAT
130 AACAATTGTTTCAGTTCATAAAAACTTATCCAAAATAAAATAAAACTAAT
* * * *
379225 TTATTAATATTTCAAAAATTAATAAGCAAAA-GT-TTAAAAAATTAATTTATTTACTAAACAAAT
1 TTATTAATATTTCAAAAATTAATAAGCAAAAGGTATGAAAAAATAAATCTATTTACCAAACAAAT
* * * *
379288 TTAAATAGCTACAACTATTTGAACAATTG-TCTATTTAAAATCATTATGACCTTTTGTTTTGTCA
66 TCAAATAACTACAACTATTTG---AATTGTTC-ATTTAAAACCATTATGACCTTTTGTTTTGACA
* * * * * *
379352 TAAAACAATTGTTTTAGTTCCTACAAGCTTATTCAAAATAAAATAAAACTAAT
127 AAAAACAATTGTTTCAGTTCATAAAAACTTATCCAAAATAAAATAAAACTAAT
* *
379405 TTATTAATATTCCAAAAATAAATAA
1 TTATTAATATTTCAAAAATTAATAA
379430 CTAAGTGATT
Statistics
Matches: 176, Mismatches: 24, Indels: 9
0.84 0.11 0.04
Matches are distributed among these distances:
177 39 0.22
178 2 0.01
179 27 0.15
180 108 0.61
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (179 bp):
TTATTAATATTTCAAAAATTAATAAGCAAAAGGTATGAAAAAATAAATCTATTTACCAAACAAAT
TCAAATAACTACAACTATTTGAATTGTTCATTTAAAACCATTATGACCTTTTGTTTTGACAAAAA
ACAATTGTTTCAGTTCATAAAAACTTATCCAAAATAAAATAAAACTAAT
Found at i:379522 original size:15 final size:17
Alignment explanation
Indices: 379502--379533 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
379492 GTTTAAAGAA
379502 ATTTGA-TA-TAATAAT
1 ATTTGATTATTAATAAT
379517 ATTTGATTATTAATAAT
1 ATTTGATTATTAATAAT
379534 TTATTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTGATTATTAATAAT
Found at i:379535 original size:15 final size:15
Alignment explanation
Indices: 379501--379543 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
379491 TGTTTAAAGA
379501 AATTTGATATAATAAT
1 AATTTGAT-TAATAAT
*
379517 -ATTTGATTATTAAT
1 AATTTGATTAATAAT
379531 AATTT-ATTAATAA
1 AATTTGATTAATAA
379544 ATATAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
AATTTGATTAATAAT
Found at i:379562 original size:26 final size:27
Alignment explanation
Indices: 379533--379584 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
379523 TTATTAATAA
* *
379533 TTTATTAATAAATATAATA-TTATATT
1 TTTACTAAGAAATATAATAGTTATATT
*
379559 TTTACTGAGAAATATAATAGTTATAT
1 TTTACTAAGAAATATAATAGTTATAT
379585 AAATTATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (27 bp):
TTTACTAAGAAATATAATAGTTATATT
Found at i:380544 original size:8 final size:8
Alignment explanation
Indices: 380470--380544 Score: 53
Period size: 9 Copynumber: 9.0 Consensus size: 8
380460 ATTATGATAA
*
380470 ATAATTCT
1 ATAATTAT
380478 ATAATT-T
1 ATAATTAT
*
380485 AAAATTAT
1 ATAATTAT
380493 ATAATTAAT
1 ATAATT-AT
* *
380502 TTTATTATT
1 ATAATTA-T
*
380511 ATAATTGT
1 ATAATTAT
*
380519 ATATATTTT
1 ATA-ATTAT
380528 ATAATTTAT
1 ATAA-TTAT
380537 ATAATTAT
1 ATAATTAT
380545 TCAAATACTA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
7 6 0.11
8 22 0.42
9 25 0.47
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (8 bp):
ATAATTAT
Found at i:380617 original size:17 final size:18
Alignment explanation
Indices: 380585--380646 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 18
380575 TATTAATAGT
*
380585 TATAATATTAATTTATTA
1 TATAATATTAAATTATTA
380603 TATAAT-TTAAATTATTA
1 TATAATATTAAATTATTA
* *
380620 GT-TAATATAAAGATTATAA
1 -TATAATATTAA-ATTATTA
380639 TATTAATA
1 TA-TAATA
380647 ATTTATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 14 0.39
18 11 0.31
19 6 0.17
20 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (18 bp):
TATAATATTAAATTATTA
Found at i:381731 original size:180 final size:181
Alignment explanation
Indices: 381369--381814 Score: 506
Period size: 180 Copynumber: 2.5 Consensus size: 181
381359 TTTGTACTTG
* ** * *
381369 TTCGGTAAATAAATTTATTTTTTTAAATCTCATTTTTATTAATTTTTTTAATGTTACTAAATTAG
1 TTCGGTAAATAAATTTA-TTTTTTAAATCTC-TTGTTATTAATTTTTCAAATATTATTAAATTAG
* * * * * * *
381434 TATTAATTTATTCTAAAT-AGCCTTTTATGAACTAAAACAAATGTTTTATAACCAAATAAAATAT
64 TATTATTTTATTCCAAATAAGCCTTGTATGAACTAAAACAAATGTTTTACAACAAAAGAAAAGAT
* * *
381498 TAGAACGATTTGAAATAGATAATTATTCTAATAGTCTTAACCATTTGAACTAA
129 CAGAACGATTTGAAATAGATAATCATTCTAATAGTCTTAACCATTTCAACTAA
* *
381551 TTTGGTAAATAAATTTATTTTTTAAATCTCTTAGTTATTAATTTTTGAAATATTATTAAATTAGT
1 TTCGGTAAATAAATTTATTTTTTAAATCTCTT-GTTATTAATTTTTCAAATATTATTAAATTAGT
* * *
381616 ATTATTTTAATCCAAATAAG-CTTGTATGAAC-AAAACAATTGTTTTACAACAAAAGAAAAGGTC
65 ATTATTTTATTCCAAATAAGCCTTGTATGAACTAAAACAAATGTTTTACAACAAAAGAAAAGATC
* * *
381679 ATAACGATTTGAAATAGATAATCATTC-ATCTAGTCTTAACTATTTCAACTAA
130 AGAACGATTTGAAATAGATAATCATTCTA-ATAGTCTTAACCATTTCAACTAA
** * * * * * *
381731 TTCGACAATTAGATTTATTTTTTAATTTTCTTGGTTAATAA-GTTTCAGAATATTATTAAATTAG
1 TTCGGTAAATAAATTTATTTTTTAAATCTCTT-GTTATTAATTTTTCA-AATATTATTAAATTAG
* *
381795 TTTTATTTTATTTCAAATAA
64 TATTATTTTATTCCAAATAA
381815 AATAGTATAA
Statistics
Matches: 224, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
179 5 0.02
180 137 0.61
181 64 0.29
182 18 0.08
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (181 bp):
TTCGGTAAATAAATTTATTTTTTAAATCTCTTGTTATTAATTTTTCAAATATTATTAAATTAGTA
TTATTTTATTCCAAATAAGCCTTGTATGAACTAAAACAAATGTTTTACAACAAAAGAAAAGATCA
GAACGATTTGAAATAGATAATCATTCTAATAGTCTTAACCATTTCAACTAA
Found at i:382121 original size:20 final size:19
Alignment explanation
Indices: 382094--382192 Score: 79
Period size: 20 Copynumber: 5.5 Consensus size: 19
382084 ATATATTTAT
382094 TAATATTAATAAATTAATA
1 TAATATTAATAAATTAATA
382113 TAATCATTAATAAATTAA-A
1 TAAT-ATTAATAAATTAATA
382132 T-AT-TTAAT-AATTAATA
1 TAATATTAATAAATTAATA
* *
382148 -ATTATATATTAAA-TAAT-
1 TAATAT-TAATAAATTAATA
*
382165 T-ATATTAGTTAAATTAATA
1 TAATATTA-ATAAATTAATA
*
382184 TAAAATTAA
1 TAATATTAA
382193 ATAATACAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 22
0.70 0.05 0.24
Matches are distributed among these distances:
15 6 0.09
16 9 0.14
17 9 0.14
18 13 0.20
19 9 0.14
20 18 0.28
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (19 bp):
TAATATTAATAAATTAATA
Found at i:382140 original size:7 final size:7
Alignment explanation
Indices: 382092--382166 Score: 59
Period size: 7 Copynumber: 10.6 Consensus size: 7
382082 ATATATATTT
382092 ATTAAT-
1 ATTAATA
382098 ATTAATAA
1 ATTAAT-A
382106 ATTAAT-
1 ATTAATA
*
382112 A-TAATC
1 ATTAATA
382118 ATTAATAA
1 ATTAAT-A
382126 ATTAAATA
1 ATT-AATA
*
382134 TTTAATA
1 ATTAATA
382141 ATTAATA
1 ATTAATA
382148 ATT-ATA
1 ATTAATA
382154 TATTAAATA
1 -ATT-AATA
382163 ATTA
1 ATTA
382167 TATTAGTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
5 4 0.07
6 11 0.19
7 21 0.37
8 15 0.26
9 6 0.11
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTAATA
Found at i:382145 original size:15 final size:15
Alignment explanation
Indices: 382118--382197 Score: 67
Period size: 15 Copynumber: 5.1 Consensus size: 15
382108 TAATATAATC
382118 ATTAATAAATTAAATA
1 ATTAAT-AATTAAATA
*
382134 TTTAATAATT-AATA
1 ATTAATAATTAAATA
382148 ATT-ATATATTAAATA
1 ATTAATA-ATTAAATA
*
382163 ATTATATTAGTTAAATTA
1 ATTA-A-TAATTAAA-TA
382181 ATATAA-AATTAAATA
1 AT-TAATAATTAAATA
382196 AT
1 AT
382198 ACAGTTAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
13 3 0.06
14 9 0.17
15 15 0.28
16 11 0.21
17 6 0.11
18 7 0.13
19 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (15 bp):
ATTAATAATTAAATA
Found at i:382198 original size:15 final size:16
Alignment explanation
Indices: 382102--382198 Score: 60
Period size: 15 Copynumber: 5.9 Consensus size: 16
382092 ATTAATATTA
382102 ATAAATTAATATAATCATT
1 ATAAATTAA-ATAAT-A-T
*
382121 AATAAATTAAAT-ATTT
1 -ATAAATTAAATAATAT
382137 A-ATAATT-AATAAT-T
1 ATA-AATTAAATAATAT
*
382151 ATATATTAAATAATTAT
1 ATAAATTAAATAA-TAT
* *
382168 ATTAGTTAAATTAATAT
1 ATAAATTAAA-TAATAT
382185 A-AAATTAAATAATA
1 ATAAATTAAATAATA
382199 CAGTTAATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
14 9 0.14
15 18 0.29
16 8 0.13
17 12 0.19
18 5 0.08
19 2 0.03
20 9 0.14
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
ATAAATTAAATAATAT
Found at i:382345 original size:23 final size:23
Alignment explanation
Indices: 382308--382354 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
382298 AATTATTAAA
*
382308 TTAATTAAATAATAATTAAATAT
1 TTAATTAAATAATAAATAAATAT
* * *
382331 TTAATTAATTTATAAATAATTAT
1 TTAATTAAATAATAAATAAATAT
382354 T
1 T
382355 AAAATTACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATTAAATAATAAATAAATAT
Found at i:382797 original size:24 final size:26
Alignment explanation
Indices: 382738--382799 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
382728 TTTAATTATC
*
382738 TATTTTAATTGT-A-ATTATATAACTA
1 TATTTTAATT-TAATATTATATAACAA
*
382763 TATTTTTATTTAATATTATATAA-AA
1 TATTTTAATTTAATATTATATAACAA
382788 TA-TTTAATTTAA
1 TATTTTAATTTAA
382800 CAATTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 10 0.31
25 13 0.41
26 9 0.28
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
TATTTTAATTTAATATTATATAACAA
Done.