Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003083.1 Hibiscus syriacus cultivar Beakdansim tig00006437_pilon, 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: 54995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1507 original size:16 final size:16
Alignment explanation
Indices: 1486--1525 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
1476 TTAAGTAACT
1486 AAATTGAAATTTTAGA
1 AAATTGAAATTTTAGA
1502 AAATTGAAATTTTAGA
1 AAATTGAAATTTTAGA
1518 AAA-TGAAA
1 AAATTGAAA
1526 GGGGAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (16 bp):
AAATTGAAATTTTAGA
Found at i:2113 original size:799 final size:771
Alignment explanation
Indices: 204--2222 Score: 2083
Period size: 799 Copynumber: 2.6 Consensus size: 771
194 TTTTTTTTAT
*
204 TTTTGATCCATTTTATTAGGATTTTGGACTAAGTTGAGAAATAAAAAAATATTCCCCATTAAATT
1 TTTTGATCCATTTTATTAGGATTTTGGACTAAG-TGAGAAATAGAAAAATATTCCCCATTAAATT
* * * * * * *
269 ATCTTTCA-TTGATGTTAGTATTGCACCCATGAGAGTTTGAATCTCTCAAGAGACGGTAATTATT
65 CTCTTTCATTTGGTGTTAGTATTTCACCCATGAGAGTTTAAATCTCTCTAGTGA-GGTAAATATT
* * * *
333 TATCCAAAATTTTGACAAGTGACCAAAATGTAGATCTTGAAAATTTTATGACCAAAGTAGAACTT
129 T-TCCAAAATTTTGACAAGTGACCAAAATGTAAATTTTGAAAATTTTGTGACCAAAGTAAAACTT
** *
398 AAGAAAAGTTCAA-GACCAAAGTGGTAATTTTCCCGAAAAGAAATTTTATTTCATAAATGAATAG
193 GGGAAAAGTTCAAGGAACAAAGTGGTAATTTTCCC--AAA-AAA--TTATTTCA-AAATGAATAG
* * ** * *
462 TTCATTTTTAAGAATGTG-TTTTATGGAATTTTAGATTTTGATCTTGAATTTGTGT-AAAGGCTA
252 TTCATTTTTAAGAATGAGTTTTTATGGAA-TTTAGATTTCGATCCGGAATTTGTATAAAATGCTA
** * *
525 TT-A-AGATAAAG-TCGGTAAAATATTCATATAACCATATCGAAT---TTTTACAAAAATTTGAA
316 TTAAGAGATAAAGTTCGGTAAAATATTCGGATAACCAGATCGAATAAAGTTTACAAAAATTTGAA
* * * *
584 GGATGGTAGCA-ATGTTGGAAATATTATGTTAATATTTTTAATTAGTATAATTTAACATGGATCG
381 -GATGGTAGTAGA-GTTGAAAATATTATGTTAATATTTTTAATCAGTAGAATTTAACATGGATCG
* *
648 ATGGAATTAGATGAATTTTCCATGATAAAGTGGAATAGTAGAATTTAAGTGACTAAATTGAAATT
444 ATGGAATTAGATGAATTTTCCATGATAAAGTGGAATAATAGAATTTAAGTAACTAAATTGAAATT
*
713 TGGAAAATTGAAAGAGGGAAGATGGAAATCAATAAATGACTTTTATATTTATTTAATATTATTAA
509 TGGAAAATTGAAAGAGGGAAGATGGAAACCAATAAATGACTTTTATATTTATTTAATATTATTAA
*
778 AATGGTGATGAAAGGATGGGGTAATTATCAAGATTCATTAGGGCAAATTGGACTTCTAGTTAAAA
574 AATAGTGATGAAAGGATGGGGTAATTATCAAGATTCATTAGGGCAAATTGGACTTCTAGTTAAAA
*
843 ATGAATTTTAAATTCATTTTTAACTAGAATATATACAGGTGTCCTAGATATTTTTGGAGAAAATT
639 ATGAATTTT-AA-T-A---TT-A-TAGAATATATACAAGTGTCCTAGATATTTTTGGAGAAAATT
* * *
908 CAAGAAGAATTCTCTCATATTCCTTTTCATGTTGTGGGTCTCCATACCCAAGGTGAGTGAGCTTT
696 CAAGAAGAAATCTCTCATATTCCTCTTCATGTGGTGGGTCTCCATACCCAAGGTGAGTGAGCTTT
* *
973 ATTTTTTTTTCAT
761 A--TTTTCTTCAA
** * * *
986 TTTTGATATATTTTATTAGGA-TTT-GACTAAATTGAGAAATAG-AAAA-ATTCCCTATTAAATA
1 TTTTGATCCATTTTATTAGGATTTTGGACT-AAGTGAGAAATAGAAAAATATTCCCCATTAAATT
* * * * *
1047 CTCTTTCATTTGGTGTTAGTATTTCATCCGTGAGAGTTTTAATCTCT-TA-TG-CG-ACAACATT
65 CTCTTTCATTTGGTGTTAGTATTTCACCCATGAGAGTTTAAATCTCTCTAGTGAGGTA-AATATT
* * *
1108 ATTCCCAAAAATTTTGATAAGTAACCAAAATGTAAATTTTGAAAA-TTTGTGACCAAAGTAAGAC
129 -TT-CC-AAAATTTTGACAAGTGACCAAAATGTAAATTTTGAAAATTTTGTGACCAAAGTAA-AA
* ** * * ** *
1172 CTTGGGAAAAGTTTAAGG-ACCCAGTGGTAATTTTTCCAAAAAGAATTTTACTTCTTGAATAAAT
190 CTTGGGAAAAGTTCAAGGAACAAAGTGGTAA-TTTTCCCAAAA-AA--TTATTTC-AAAATGAAT
* * *
1236 AGTTTA-TTTTAAGAATTGAGTTTTTATGGAATTTAGA-TTCTGATTCGGAATTTGTTTAAAAAT
250 AGTTCATTTTTAAGAA-TGAGTTTTTATGGAATTTAGATTTC-GATCCGGAATTTGTAT-AAAAT
* * * * *
1299 -TTATAAAGCGATAAAGTTTGGTAAAATATTCGGATAACCGGATCGAATAAAAAGTTTAC-AAAA
312 GCTATTAAGAGATAAAGTTCGGTAAAATATTCGGATAACCAGATCGAAT--AAAGTTTACAAAAA
* * ** * *
1362 TTTGAACGATGGTATTATGAGTTGAAAATATTATTTTGGTATTTTT-ATCATTAGAATTTAATAT
375 TTTGAA-GATGGTAGTA-GAGTTGAAAATATTATGTTAATATTTTTAATCAGTAGAATTTAACAT
* *
1426 GGATC-AGTGGAATTAGATGAATTTTCCATGTTAAAGTGGAATAATGGAATTTAAGTAACTAAAT
438 GGATCGA-TGGAATTAGATGAATTTTCCATGATAAAGTGGAATAATAGAATTTAAGTAACTAAAT
*
1490 TGAAATTTTAGAAAATTGAAATTTTAGAAAATGAAAGGGGAAAGATGGAAACCAATAAATATGTT
502 TGAAA-TTT-G------GAAA-ATT-G-AAA-G--A-GGG-AAGATGGAAACCAAT-AA-ATG--
** * *
1555 TTTTTTTATATTTATTTAATGTTATTAAATTAGTGATGAAAGGATGGCATGAGGTAATTATCAAG
547 -ACTTTTATATTTATTTAATATTATTAAAATAGTGATGAAAGGAT-G---G-GGTAATTATCAAG
* * *
1620 ATTCATTAAGGGTAAATTGGACTTTTGGATT-AAAATGAATTTT-A-A-T-TAGAATATATACAA
606 ATTCATT-AGGGCAAATTGGACTTCTAG-TTAAAAATGAATTTTAATATTATAGAATATATACAA
*
1680 GTGTCCTAGATATTTTTGGAGAAAATTCAAGAAGAAATCTCTCATCTTCCTCTTCAT-TGG-GTG
669 GTGTCCTAGATATTTTTGGAGAAAATTCAAGAAGAAATCTCTCATATTCCTCTTCATGTGGTG-G
* *
1743 GTCTCCATAGCCAAGGTTAGTGAGCTTTA-TTTCTTCAA
733 GTCTCCATACCCAAGGTGAGTGAGCTTTATTTTCTTCAA
* *
1781 TTTTGATCCATTTAATTAGGATTTTTGGACTAAGTGTGAAATAGAAAAATATTCCCCATTAAATT
1 TTTTGATCCATTTTATTAGGA-TTTTGGACTAAGTGAGAAATAGAAAAATATTCCCCATTAAATT
** *
1846 CTCTTTCATTTGGTGTTAGTATTTCACCCACAAGAGTTCAAATCTCTCTAGTGATGGTAAATATT
65 CTCTTTCATTTGGTGTTAGTATTTCACCCATGAGAGTTTAAATCTCTCTAGTGA-GGTAAATATT
* * * *
1911 TTCCTAAATTTTGACAAGTGACCAAAACGTAAATTTTGAAAATTTTGTGACAAAAGTATAAACAT
129 TTCCAAAATTTTGACAAGTGACCAAAATGTAAATTTTGAAAATTTTGTGACCAAAGTA-AAACTT
* ** *
1976 GGGAAAAATTCAAGGAACAAAGTGACAATTTTCCCAAAAAATTGTTTCGAAAATGAATAGTTCAT
193 GGGAAAAGTTCAAGGAACAAAGTGGTAATTTTCCCAAAAAATTATTTC-AAAATGAATAGTTCAT
* *
2041 TTTTAAGAATGGAGTTTTTATGGAATTTAGATTTCCATCCGGAATTTATATAAAATGCTATTAAG
257 TTTTAAGAAT-GAGTTTTTATGGAATTTAGATTTCGATCCGGAATTTGTATAAAATGCTATTAAG
* * *
2106 AGATAAAGTTCAGTAAAATATTCGGATAACTAGATTGAATCAGAAGTTTACAAAAATTTGAAGTA
321 AGATAAAGTTCGGTAAAATATTCGGATAACCAGATCGAAT-A-AAGTTTACAAAAATTTGAAG-A
* ** * *
2171 TGGTAGTAGGAGGTGAGAAATATTATCCTGATATTTATAATCAGTAGAATTT
383 TGGTAGTA-GAGTTGA-AAATATTATGTTAATATTTTTAATCAGTAGAATTT
2223 TTAACACCCC
Statistics
Matches: 1016, Mismatches: 143, Indels: 136
0.78 0.11 0.11
Matches are distributed among these distances:
774 1 0.00
775 18 0.02
776 62 0.06
777 71 0.07
778 32 0.03
779 44 0.04
780 39 0.04
781 5 0.00
782 19 0.02
783 1 0.00
784 95 0.09
785 30 0.03
786 2 0.00
792 4 0.00
793 2 0.00
794 1 0.00
795 28 0.03
796 1 0.00
797 15 0.01
798 62 0.06
799 214 0.21
800 79 0.08
801 63 0.06
802 27 0.03
803 6 0.01
804 1 0.00
805 39 0.04
806 2 0.00
809 2 0.00
810 20 0.02
811 29 0.03
812 2 0.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (771 bp):
TTTTGATCCATTTTATTAGGATTTTGGACTAAGTGAGAAATAGAAAAATATTCCCCATTAAATTC
TCTTTCATTTGGTGTTAGTATTTCACCCATGAGAGTTTAAATCTCTCTAGTGAGGTAAATATTTT
CCAAAATTTTGACAAGTGACCAAAATGTAAATTTTGAAAATTTTGTGACCAAAGTAAAACTTGGG
AAAAGTTCAAGGAACAAAGTGGTAATTTTCCCAAAAAATTATTTCAAAATGAATAGTTCATTTTT
AAGAATGAGTTTTTATGGAATTTAGATTTCGATCCGGAATTTGTATAAAATGCTATTAAGAGATA
AAGTTCGGTAAAATATTCGGATAACCAGATCGAATAAAGTTTACAAAAATTTGAAGATGGTAGTA
GAGTTGAAAATATTATGTTAATATTTTTAATCAGTAGAATTTAACATGGATCGATGGAATTAGAT
GAATTTTCCATGATAAAGTGGAATAATAGAATTTAAGTAACTAAATTGAAATTTGGAAAATTGAA
AGAGGGAAGATGGAAACCAATAAATGACTTTTATATTTATTTAATATTATTAAAATAGTGATGAA
AGGATGGGGTAATTATCAAGATTCATTAGGGCAAATTGGACTTCTAGTTAAAAATGAATTTTAAT
ATTATAGAATATATACAAGTGTCCTAGATATTTTTGGAGAAAATTCAAGAAGAAATCTCTCATAT
TCCTCTTCATGTGGTGGGTCTCCATACCCAAGGTGAGTGAGCTTTATTTTCTTCAA
Found at i:3007 original size:28 final size:28
Alignment explanation
Indices: 2954--3007 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2944 TACTCGGTCC
*
2954 GAGTCAACCTATCTGAGTTAAACCGTCT
1 GAGTCAACCTATCTGAGTCAAACCGTCT
*
2982 GAGTCAA-CTCATCTGAGTCAACCCGT
1 GAGTCAACCT-ATCTGAGTCAAACCGT
3008 TGACTTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (28 bp):
GAGTCAACCTATCTGAGTCAAACCGTCT
Found at i:11439 original size:21 final size:21
Alignment explanation
Indices: 11415--11502 Score: 149
Period size: 21 Copynumber: 4.2 Consensus size: 21
11405 ATTTGCAACA
11415 CGAACTTCGACTATCGCAATG
1 CGAACTTCGACTATCGCAATG
* *
11436 CGAACTTGGACTATCGCAACG
1 CGAACTTCGACTATCGCAATG
11457 CGAACTTCGACTATCGCAATG
1 CGAACTTCGACTATCGCAATG
*
11478 CGAACTTGGACTATCGCAATG
1 CGAACTTCGACTATCGCAATG
11499 CGAA
1 CGAA
11503 TATGTAAATC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (21 bp):
CGAACTTCGACTATCGCAATG
Found at i:11461 original size:42 final size:42
Alignment explanation
Indices: 11409--11502 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
11399 TTCCAGATTT
*
11409 GCAACACGAACTTCGACTATCGCAATGCGAACTTGGACTATC
1 GCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATC
11451 GCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATC
1 GCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATC
*
11493 GCAATGCGAA
1 GCAACGCGAA
11503 TATGTAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (42 bp):
GCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATC
Found at i:11541 original size:21 final size:20
Alignment explanation
Indices: 11511--11666 Score: 117
Period size: 21 Copynumber: 7.6 Consensus size: 20
11501 AATATGTAAA
*
11511 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTC-AAGT
*
11532 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGT-CAAGT
*
11553 TCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGT-CA-AGT
*
11573 TCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGT-CA-AGT
*
11593 TCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGT-CA-AGT
11613 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGT-CAAGT
*
11634 TCACATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTC-AAGT
*
11655 TCGCGTTGCGAT
1 TCGCATTGCGAT
11667 TTATTCCAAA
Statistics
Matches: 120, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
20 58 0.48
21 61 0.51
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAAGT
Found at i:11577 original size:20 final size:20
Alignment explanation
Indices: 11552--11624 Score: 146
Period size: 20 Copynumber: 3.6 Consensus size: 20
11542 ATAGTCCAAG
11552 TTCGCATTGCGATTTACATA
1 TTCGCATTGCGATTTACATA
11572 TTCGCATTGCGATTTACATA
1 TTCGCATTGCGATTTACATA
11592 TTCGCATTGCGATTTACATA
1 TTCGCATTGCGATTTACATA
11612 TTCGCATTGCGAT
1 TTCGCATTGCGAT
11625 AGTCCAAGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (20 bp):
TTCGCATTGCGATTTACATA
Found at i:12445 original size:21 final size:21
Alignment explanation
Indices: 12419--12535 Score: 123
Period size: 21 Copynumber: 5.6 Consensus size: 21
12409 GCAATACCAC
*
12419 GTTCGCGTTGCGATAGTCCAA
1 GTTCGCATTGCGATAGTCCAA
*
12440 GTTCGCATTGCGATAGT-CGA
1 GTTCGCATTGCGATAGTCCAA
* * *
12460 CTATCGCATTGCGAT-TTACATA
1 GT-TCGCATTGCGATAGTCCA-A
12482 -TTCGCATTGCGATAGTCCAA
1 GTTCGCATTGCGATAGTCCAA
* *
12502 GTTTGCATTGCGATAGTCGAA
1 GTTCGCATTGCGATAGTCCAA
*
12523 GTTCGCGTTGCGA
1 GTTCGCATTGCGA
12536 ATCTGGAAAC
Statistics
Matches: 80, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
20 17 0.21
21 62 0.77
22 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (21 bp):
GTTCGCATTGCGATAGTCCAA
Found at i:15980 original size:23 final size:23
Alignment explanation
Indices: 15954--16003 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
15944 CATCAAAAGA
* * *
15954 TAATATCACATCATTATTTTTTT
1 TAATATCACATCAATATATCTTT
15977 TAATATCACATCAATATATCTTT
1 TAATATCACATCAATATATCTTT
16000 TAAT
1 TAAT
16004 TTTTAACAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (23 bp):
TAATATCACATCAATATATCTTT
Found at i:16308 original size:3 final size:3
Alignment explanation
Indices: 16294--16338 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
16284 TAATTTTTTC
* *
16294 TAT TAT TTT TAT TAT TAT TAT TAT TCT ATAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
16339 AATAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.95
4 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:16308 original size:9 final size:9
Alignment explanation
Indices: 16289--16337 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
16279 TACACTAATT
16289 TTTTCTATTA
1 TTTT-TATTA
16299 TTTTTATTA
1 TTTTTATTA
*
16308 TTATTATTA
1 TTTTTATTA
*
16317 TTCTATATTA
1 TT-TTTATTA
*
16327 TTATTATTA
1 TTTTTATTA
16336 TT
1 TT
16338 AAATAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
9 22 0.67
10 11 0.33
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTTATTA
Found at i:18789 original size:28 final size:28
Alignment explanation
Indices: 18730--18787 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
18720 TAATTCTTTC
18730 TTTTCATAATTTTTATATATACTTATTA
1 TTTTCATAATTTTTATATATACTTATTA
* *
18758 TTTTCATAATATTTATATGTA--TATTA
1 TTTTCATAATTTTTATATATACTTATTA
18784 TTTT
1 TTTT
18788 TTTATTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 9 0.32
28 19 0.68
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTCATAATTTTTATATATACTTATTA
Found at i:21319 original size:15 final size:14
Alignment explanation
Indices: 21277--21318 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
21267 AAATAATTTA
21277 CATTTACATTTTTG
1 CATTTACATTTTTG
21291 CATTTATGCA-TTTTG
1 CATTTA--CATTTTTG
21306 CATTTACATTTTT
1 CATTTACATTTTT
21319 TTATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
15 11 0.44
16 2 0.08
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
CATTTACATTTTTG
Found at i:27062 original size:75 final size:75
Alignment explanation
Indices: 26907--27076 Score: 196
Period size: 75 Copynumber: 2.3 Consensus size: 75
26897 GAAGCATATA
* * * * * *
26907 CTGGGGCATACTGAAAGCCCCTCTCAATCAGAATCATGAATGTTGATGTATTTTGAACATTTATA
1 CTGGGGCATGCTGAAAGCCCCTCTCAATCAGAATCAAGAATATTAATGCATTTTGAACACTTATA
26972 TCAGCAAATG
66 TCAGCAAATG
* * ** *
26982 CTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATGAAGAATATTAATGCATTTTGAATGCTTGTA
1 CTGGGGCATGCTGAAAGCCCCTCTCAATCAGAATCAAGAATATTAATGCATTTTGAACACTTATA
* *
27047 TTAGCCAATG
66 TCAGCAAATG
* * *
27057 TTGGGGCATGTTGAAGGCCC
1 CTGGGGCATGCTGAAAGCCC
27077 GTATCATCTT
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.30
Consensus pattern (75 bp):
CTGGGGCATGCTGAAAGCCCCTCTCAATCAGAATCAAGAATATTAATGCATTTTGAACACTTATA
TCAGCAAATG
Found at i:28344 original size:22 final size:23
Alignment explanation
Indices: 28319--28395 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 23
28309 ATCTACACTT
28319 TTCAAAGATGATAGACTCT-TTC
1 TTCAAAGATGATAGACTCTATTC
28341 TTCAAAGATGATA-AC-CTATCTC
1 TTCAAAGATGATAGACTCTAT-TC
* * *
28363 TTTAAAGATGATAGATTCTCTT-
1 TTCAAAGATGATAGACTCTATTC
28385 TTCAAAGATGA
1 TTCAAAGATGA
28396 AAGCTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
20 2 0.04
21 3 0.06
22 37 0.79
23 2 0.04
24 3 0.06
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (23 bp):
TTCAAAGATGATAGACTCTATTC
Found at i:29123 original size:45 final size:45
Alignment explanation
Indices: 29059--31471 Score: 3947
Period size: 45 Copynumber: 53.8 Consensus size: 45
29049 CTATTTCCCA
*
29059 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
29104 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
29149 CATCTGTAAGCCCTTCAGTGCATGATG------------TCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
29182 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
29227 CATCTGTAAGCCCTTTAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
* *
29273 CATCTGTAAGCCCTTCAATGCTTGATGTTTTTAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* * *
29318 CATCCGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTAGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
29363 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* *
29408 CATCTGTAAGTCCTTCAATGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
29453 CATTTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
29498 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
29544 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
29590 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
29635 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* *
29680 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCCTTTGAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAA-CCTTCGGGT
*
29726 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* * *
29771 CATCTGTAAGTCCTTCAGTGCATGATGTTTTGAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
29816 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* *
29861 CATTTGTAAGCCCTTTAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
29906 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
29951 TATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
29996 CATCTGTAAGCTCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
*
30042 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
30088 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
*
30134 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
30179 CATCTGTAAGCCCTTCAGTGCATGATG------------TCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
30212 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
30257 CATCTGTAAGCCCTTTAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
* *
30303 CATCTGTAAGCCCTTCAATGCTTGATGTTTTTAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* * *
30348 CATCCGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTAGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
30393 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* *
30438 CATCTGTAAGTCCTTCAATGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
30483 CATTTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
30528 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
30574 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
30620 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
30665 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* *
30710 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTTGAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
*
30756 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* * * *
30801 CATCTGTATGTCCTTCAGTGCATGATGTTTTGAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
30846 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* * *
30891 CATTTATAAGCCCTTTAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
30936 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
* *
30981 TATTTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
31026 CATCTGTAAGCTCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
*
31072 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
31118 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
31164 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
*
31210 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
*
31256 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
* *
31302 CATCTATAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
31348 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
31393 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
*
31438 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAA
31472 CATTTCAAGA
Statistics
Matches: 2228, Mismatches: 108, Indels: 64
0.93 0.05 0.03
Matches are distributed among these distances:
33 64 0.03
45 1370 0.61
46 794 0.36
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
Found at i:29185 original size:33 final size:33
Alignment explanation
Indices: 29143--29209 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
29133 TTAAAAACCT
29143 TCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
*
29176 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATG
1 TCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
29209 T
1 T
29210 TTTCAAAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (33 bp):
TCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
Found at i:29228 original size:78 final size:78
Alignment explanation
Indices: 29098--29254 Score: 278
Period size: 78 Copynumber: 2.0 Consensus size: 78
29088 TTCAAAACCT
*
29098 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTAAAAACCTTCGGGTCATCTGTAAGCCCT
1 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTAAAAACCTTCAGGTCATCTGTAAGCCCT
29163 TCAGTGCATGATG
66 TCAGTGCATGATG
*
29176 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCT
1 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTAAAAACCTTCAGGTCATCTGTAAGCCCT
* *
29241 TTAGTGCTTGATG
66 TCAGTGCATGATG
29254 T
1 T
29255 TTTCAAAAAC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (78 bp):
TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTAAAAACCTTCAGGTCATCTGTAAGCCCT
TCAGTGCATGATG
Found at i:29538 original size:26 final size:26
Alignment explanation
Indices: 29509--29585 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
29499 ATCTGTAAGC
29509 CCTTCAGTGCTTGATGTTTTCAAAAA
1 CCTTCAGTGCTTGATGTTTTCAAAAA
* * * **
29535 CCTTCAG-G--TCAT-CTGT--AAGC
1 CCTTCAGTGCTTGATGTTTTCAAAAA
29555 CCTTCAGTGCTTGATGTTTTCAAAAA
1 CCTTCAGTGCTTGATGTTTTCAAAAA
29581 CCTTC
1 CCTTC
29586 GGGTCATCTG
Statistics
Matches: 35, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
20 9 0.26
21 1 0.03
22 2 0.06
23 6 0.17
24 2 0.06
25 1 0.03
26 14 0.40
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (26 bp):
CCTTCAGTGCTTGATGTTTTCAAAAA
Found at i:30215 original size:33 final size:33
Alignment explanation
Indices: 30173--30239 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
30163 TTAAAAACCT
30173 TCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
*
30206 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATG
1 TCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
30239 T
1 T
30240 TTTCAAAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (33 bp):
TCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
Found at i:30258 original size:78 final size:78
Alignment explanation
Indices: 30128--30284 Score: 278
Period size: 78 Copynumber: 2.0 Consensus size: 78
30118 TCAAAAACCT
*
30128 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTAAAAACCTTCGGGTCATCTGTAAGCCCT
1 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTAAAAACCTTCAGGTCATCTGTAAGCCCT
30193 TCAGTGCATGATG
66 TCAGTGCATGATG
*
30206 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCT
1 TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTAAAAACCTTCAGGTCATCTGTAAGCCCT
* *
30271 TTAGTGCTTGATG
66 TCAGTGCATGATG
30284 T
1 T
30285 TTTCAAAAAC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (78 bp):
TCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTAAAAACCTTCAGGTCATCTGTAAGCCCT
TCAGTGCATGATG
Found at i:30568 original size:26 final size:26
Alignment explanation
Indices: 30539--30615 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
30529 ATCTGTAAGC
30539 CCTTCAGTGCTTGATGTTTTCAAAAA
1 CCTTCAGTGCTTGATGTTTTCAAAAA
* * * **
30565 CCTTCAG-G--TCAT-CTGT--AAGC
1 CCTTCAGTGCTTGATGTTTTCAAAAA
30585 CCTTCAGTGCTTGATGTTTTCAAAAA
1 CCTTCAGTGCTTGATGTTTTCAAAAA
30611 CCTTC
1 CCTTC
30616 GGGTCATCTG
Statistics
Matches: 35, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
20 9 0.26
21 1 0.03
22 2 0.06
23 6 0.17
24 2 0.06
25 1 0.03
26 14 0.40
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (26 bp):
CCTTCAGTGCTTGATGTTTTCAAAAA
Found at i:31586 original size:3 final size:3
Alignment explanation
Indices: 31578--31651 Score: 85
Period size: 3 Copynumber: 23.7 Consensus size: 3
31568 TAATTTTTTC
* * *
31578 TAT TAT TAT TAT TAT TAT TAT TAT TAAA TAA AAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT -TAT TAT TAT TAT
*
31625 TAT TCT ATAT TAT TAT TAT TAT TAT TA
1 TAT TAT -TAT TAT TAT TAT TAT TAT TA
31652 AATAAAAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
3 56 0.90
4 6 0.10
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:34698 original size:19 final size:17
Alignment explanation
Indices: 34675--34725 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
34665 ATTTAGGGTA
34675 ATTTAATATATTTTTATT
1 ATTTAATATATTTTT-TT
34693 ATTTTAATACTACTTTTTTT
1 A-TTTAATA-TA-TTTTTTT
*
34713 AATTAATATATTT
1 ATTTAATATATTT
34726 AGCATTAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 13 0.45
20 5 0.17
21 5 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTAATATATTTTTTT
Found at i:39165 original size:2 final size:2
Alignment explanation
Indices: 39158--39191 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
39148 TAATATTAAA
*
39158 AT AT AT AT AT CT 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 AT
39192 GATTAAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40597 original size:3 final size:3
Alignment explanation
Indices: 40591--40678 Score: 133
Period size: 3 Copynumber: 29.0 Consensus size: 3
40581 TATTATTATT
*
40591 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
40638 TAA TAA TAA TATA TAA TAA TAA TAA AAA TAA TAAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA
40679 AAAAGGGACA
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
2 2 0.03
3 70 0.90
4 6 0.08
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:41388 original size:42 final size:42
Alignment explanation
Indices: 41304--41405 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 42
41294 AAGGTTTTAT
** * * *
41304 AGATGACCCGAAGG-TCTT-ATTATCTTGCTCGAAAGGCTTAC
1 AGATGACCCGAAGGAT-TTAAACATCATGCTCAAAAGACTTAC
41345 AGATGACCCGAAGGATTTAAACATCATGCTCAAAAGACTTAC
1 AGATGACCCGAAGGATTTAAACATCATGCTCAAAAGACTTAC
*
41387 AGATGACCCGAAAGATTTA
1 AGATGACCCGAAGGATTTA
41406 CGAATCAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 16 0.30
42 37 0.70
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (42 bp):
AGATGACCCGAAGGATTTAAACATCATGCTCAAAAGACTTAC
Found at i:41406 original size:20 final size:20
Alignment explanation
Indices: 41341--41406 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
41331 CTCGAAAGGC
*
41341 TTACAGATGACCCGAAGGAT
1 TTACAGATGACCCGAAAGAT
* * * *
41361 TTAAACATCATG-CTCAAAAGAC
1 TT--ACA-GATGACCCGAAAGAT
41383 TTACAGATGACCCGAAAGAT
1 TTACAGATGACCCGAAAGAT
41403 TTAC
1 TTAC
41407 GAATCAAGAA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
19 3 0.09
20 16 0.48
22 11 0.33
23 3 0.09
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (20 bp):
TTACAGATGACCCGAAAGAT
Found at i:43876 original size:17 final size:17
Alignment explanation
Indices: 43854--43898 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
43844 TCTCTTTCTA
43854 TTCTTTCTTTTTCTTTT
1 TTCTTTCTTTTTCTTTT
*
43871 TTCTTTTTTTTTCTTTT
1 TTCTTTCTTTTTCTTTT
43888 TT-TTTCTTTTT
1 TTCTTTCTTTTT
43899 GCTATTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (17 bp):
TTCTTTCTTTTTCTTTT
Found at i:43897 original size:10 final size:10
Alignment explanation
Indices: 43867--43898 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
43857 TTTCTTTTTC
43867 TTTTTTCTTT
1 TTTTTTCTTT
43877 TTTTTTCTTT
1 TTTTTTCTTT
43887 TTTTTTCTTT
1 TTTTTTCTTT
43897 TT
1 TT
43899 GCTATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:48814 original size:3 final size:3
Alignment explanation
Indices: 48808--48854 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
48798 TTAATATATA
*
48808 AAT AAT AAT AAT AAT ATAT AAT AAT AAT AAA AAT AA- AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
48853 AA
1 AA
48855 CAAAAAAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:48824 original size:20 final size:20
Alignment explanation
Indices: 48799--48854 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 20
48789 AATTATTATT
48799 TAATATATAAATAATAATAA
1 TAATATATAAATAATAATAA
48819 TAATATAT-AATAATAATAA
1 TAATATATAAATAATAATAA
48838 -AA-ATA-AAATAATAATAA
1 TAATATATAAATAATAATAA
48855 CAAAAAAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.40
18 2 0.06
19 11 0.31
20 8 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATATATAAATAATAATAA
Found at i:48826 original size:22 final size:22
Alignment explanation
Indices: 48800--48860 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
48790 ATTATTATTT
*
48800 AATATATAAATAATAATAATAA
1 AATATATAAATAATAAAAATAA
*
48822 TATATA-ATAATAATAAAAATAA
1 AATATATA-AATAATAAAAATAA
*
48844 AATA-AT-AATAACAAAAA
1 AATATATAAATAATAAAAA
48861 AGGGACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 10 0.30
21 2 0.06
22 21 0.64
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AATATATAAATAATAAAAATAA
Done.