Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000819.1 Hibiscus syriacus cultivar Beakdansim tig00001586_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: 70338
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4553 original size:18 final size:19
Alignment explanation
Indices: 4527--4566 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
4517 ATAAAAAAGG
* *
4527 ACATGAAAAGCATTTTGTT
1 ACATGAAAAACAGTTTGTT
4546 ACAT-AAAAACAGTTTGTT
1 ACATGAAAAACAGTTTGTT
4564 ACA
1 ACA
4567 CCCTAATCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (19 bp):
ACATGAAAAACAGTTTGTT
Found at i:15601 original size:60 final size:60
Alignment explanation
Indices: 15533--15705 Score: 249
Period size: 60 Copynumber: 2.9 Consensus size: 60
15523 CTGATCTTTT
*
15533 ATATTGGACTCCTAGATCTTAGTGGTTTAGGGTAAGTCCTTATAGATGCATGTATCTTCC
1 ATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATAGATGCATGTATCTTCC
* ** *
15593 ATATTGGACTCCTAGATATTAGTGGTCTAGGGTAAGTCCTTATAGATGTTTGTATCTTCT
1 ATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATAGATGCATGTATCTTCC
* * * *
15653 ATGTTGGATTCTTATATCTTAGTGGTCTAGGGTAAGTCCTTAT-GTATGCATGT
1 ATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATAG-ATGCATGT
15706 TCTGGGAAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
59 1 0.01
60 99 0.99
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.41
Consensus pattern (60 bp):
ATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATAGATGCATGTATCTTCC
Found at i:20822 original size:17 final size:18
Alignment explanation
Indices: 20787--20852 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
20777 AATATATGTT
20787 TGATAATTGTAAAACATC
1 TGATAATTGTAAAACATC
*
20805 TGATAATTGT-AGACATC
1 TGATAATTGTAAAACATC
*
20822 TGATAACTG-AAAATCATC
1 TGATAATTGTAAAA-CATC
* *
20840 TAAAAATTGTAAA
1 TGATAATTGTAAA
20853 TATCTAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 16 0.41
18 20 0.51
19 3 0.08
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (18 bp):
TGATAATTGTAAAACATC
Found at i:20853 original size:18 final size:18
Alignment explanation
Indices: 20791--20863 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 18
20781 TATGTTTGAT
* * *
20791 AATTGTAAAACATCTGAT
1 AATTGTAAATCATCTAAA
* * *
20809 AATTGTAGA-CATCTGAT
1 AATTGTAAATCATCTAAA
* *
20826 AACTGAAAATCATCTAAA
1 AATTGTAAATCATCTAAA
20844 AATTGTAAAT-ATCTAAA
1 AATTGTAAATCATCTAAA
20861 AAT
1 AAT
20864 CATCTGATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
17 24 0.52
18 22 0.48
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.32
Consensus pattern (18 bp):
AATTGTAAATCATCTAAA
Found at i:24934 original size:60 final size:60
Alignment explanation
Indices: 24841--25072 Score: 340
Period size: 60 Copynumber: 3.9 Consensus size: 60
24831 TGTTCTCATT
* *
24841 TTCCATATTGGACCCCTAGATCTTAGTGGTATAGGGTAAGTCTTTATGGATGCATGTAAC
1 TTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATGCATGTAAC
*
24901 TTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCTTTATGGATGCATGTAAC
1 TTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATGCATGTAAC
* * ** *
24961 TTCCATATTGGACTCCTAGATATTATTGGTATAGGGTAAGTCCTTATGGATATATGTATC
1 TTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATGCATGTAAC
** * * *
25021 TTTTATATTGAACTCCTAGTTCTTAGTGGTCTA-GGTAAGTCCTTATGGATGC
1 TTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATGC
25073 CTATTCTGGG
Statistics
Matches: 156, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 17 0.11
60 139 0.89
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (60 bp):
TTCCATATTGGACTCCTAGATCTTAGTGGTATAGGGTAAGTCCTTATGGATGCATGTAAC
Found at i:30525 original size:17 final size:17
Alignment explanation
Indices: 30493--30524 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
30483 ACCTTTACAT
30493 TTTTTACTTGCTTTTTC
1 TTTTTACTTGCTTTTTC
30510 TTTTTACTTG-TTTTT
1 TTTTTACTTGCTTTTT
30525 TTTCCTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTTACTTGCTTTTTC
Found at i:31208 original size:111 final size:111
Alignment explanation
Indices: 30933--31431 Score: 594
Period size: 111 Copynumber: 4.5 Consensus size: 111
30923 GAGGCAGACT
* * * * *
30933 TGTTCCGCTTCTTCTAAAGGGAATATCATATATGGGGGAGCTGATCCATTGAATCGGGGAAGACT
1 TGTTCCGCTTCTTCT-AAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAGGCAGACT
* * *
30998 TGTTCCGCTGTCACT-AGGGGAATATCAAATCTTGGAAGAGAGGGATA
65 TGTTCCGTTGTCACTCA-GAGAATATCAAATCTTGGAAGAGAGGGATC
* * * * * *
31045 TGTTCCG-TTTTTCTATGGCAATATCAGATCTAGGGGAGTTTATCCATTGAATCGAGGCAGATTT
1 TGTTCCGCTTCTTCTAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAGGCAGACTT
* * *
31109 GATT-TGTTGTCACTCAGAGAATATCAAATCTTGGAAAAGAGGGATT
66 G-TTCCGTTGTCACTCAGAGAATATCAAATCTTGGAAGAGAGGGATC
* ** * * * * * *
31155 TATTATGCTTCTTCTATGGGAATATCAGATATGGGGGAGTTAATACATTGAATCGGGGTAGACTT
1 TGTTCCGCTTCTTCTAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAGGCAGACTT
* *
31220 GTTCCGTTATCACTCAGAGAATATCAAATCTTGGAAGAGAGTGATC
66 GTTCCGTTGTCACTCAGAGAATATCAAATCTTGGAAGAGAGGGATC
* * * *
31266 TGTTTCGCTTCTTCTAAGGGAATATCAGATCTGGAGGAGTTGATTCATTGAATC-AGTACAGACT
1 TGTTCCGCTTCTTCTAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAG-GCAGACT
* *
31330 TGTTCCGCTT-TCACTCAGGGAATATCAAGTCTTGGAAGAGAGGGATC
65 TGTTCCG-TTGTCACTCAGAGAATATCAAATCTTGGAAGAGAGGGATC
* *
31377 TGTTCCGCTTCTTCTAAGGGAATATCAGATCTGGGAGAGTTGATCTATTGAATCG
1 TGTTCCGCTTCTTCTAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCG
31432 GTATTGAACC
Statistics
Matches: 328, Mismatches: 52, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
110 83 0.25
111 236 0.72
112 9 0.03
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (111 bp):
TGTTCCGCTTCTTCTAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAGGCAGACTT
GTTCCGTTGTCACTCAGAGAATATCAAATCTTGGAAGAGAGGGATC
Found at i:43488 original size:2 final size:2
Alignment explanation
Indices: 43483--43509 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43473 GAAAAAATTA
43483 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
43510 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:43514 original size:2 final size:2
Alignment explanation
Indices: 43509--43538 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43499 ACACACACAC
43509 AT 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 AT
43539 TATCCATGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43861 original size:2 final size:2
Alignment explanation
Indices: 43850--43888 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
43840 TTTTATATGC
43850 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43889 ATACACTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:44821 original size:15 final size:16
Alignment explanation
Indices: 44801--44835 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
44791 AACCTTTACA
44801 TTTC-TTTACTTGTTT
1 TTTCTTTTACTTGTTT
44816 TTTCTTTTTACTTGTTT
1 TTTC-TTTTACTTGTTT
44833 TTT
1 TTT
44836 TCCTTAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
17 14 0.78
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTCTTTTACTTGTTT
Found at i:46270 original size:29 final size:29
Alignment explanation
Indices: 46226--46283 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
46216 GTATGTCCCC
* *
46226 CTTTTTTCTTCATCAACTTTTGTCCTCTT
1 CTTTTCTCTTCATCAACTTTTCTCCTCTT
* *
46255 CTTTTCTCTTCTTCAATTTTTCTCCTCTT
1 CTTTTCTCTTCATCAACTTTTCTCCTCTT
46284 TAGAAAGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.09, C:0.29, G:0.02, T:0.60
Consensus pattern (29 bp):
CTTTTCTCTTCATCAACTTTTCTCCTCTT
Found at i:49717 original size:18 final size:18
Alignment explanation
Indices: 49694--49729 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
49684 AAGGTCTCGA
*
49694 TAATCTACGTACATACAG
1 TAATCTACGCACATACAG
49712 TAATCTACGCACATACAG
1 TAATCTACGCACATACAG
49730 ACCTTCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (18 bp):
TAATCTACGCACATACAG
Found at i:54129 original size:35 final size:35
Alignment explanation
Indices: 54083--54152 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
54073 TTTTCGTTCC
54083 AAAACAATTAAAGTTGGCTCATCGCAAGCCGTCCT
1 AAAACAATTAAAGTTGGCTCATCGCAAGCCGTCCT
54118 AAAACAATTAAAGTTGGCTCATCGCAAGCCGTCCT
1 AAAACAATTAAAGTTGGCTCATCGCAAGCCGTCCT
54153 CATATCATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (35 bp):
AAAACAATTAAAGTTGGCTCATCGCAAGCCGTCCT
Found at i:58337 original size:2 final size:2
Alignment explanation
Indices: 58327--58565 Score: 67
Period size: 2 Copynumber: 122.0 Consensus size: 2
58317 AATTGAAAAA
58327 AT AT A- AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A- AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * * *
58367 TT AT AT AT AA AT -T AT AC AT AT AA ACT AT AT TT AT AT -T AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
58408 ACT AT AT A- AT -T AT -T AT A- AG CT AT AT AT AT AA AT -T AT GT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
58446 TT AT AT GA- ACT AA AT AT AT AA ACT AT AA AT GT AA ACT AT AT AT
1 AT AT AT -AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
* * * * * * * *
58489 GT AT AA ACT AT A- AA AG GT AT AT ACT TT AT AA ACT AT A- AT TT
1 AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT
58530 AT AT -T A- AT 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 AT AT AT AT AT
58566 TATTCAAAGT
Statistics
Matches: 168, Mismatches: 44, Indels: 50
0.64 0.17 0.19
Matches are distributed among these distances:
1 15 0.09
2 144 0.86
3 9 0.05
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:58688 original size:17 final size:18
Alignment explanation
Indices: 58666--58719 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
58656 TTGAGAAATT
*
58666 TTGAGAA-TATAGGGAAA
1 TTGAGAATTAGAGGGAAA
58683 TTGAGAATTTAGAGGGAAA
1 TTGAGAA-TTAGAGGGAAA
*
58702 TTGGGAAATTTAGAGGGA
1 TTGAG-AA-TTAGAGGGA
58720 TTAGAACAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 7 0.22
19 13 0.41
20 12 0.38
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.26
Consensus pattern (18 bp):
TTGAGAATTAGAGGGAAA
Found at i:58698 original size:19 final size:20
Alignment explanation
Indices: 58676--58719 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
58666 TTGAGAATAT
58676 AGGGAAATTGAG-AATTTAG
1 AGGGAAATTGAGAAATTTAG
*
58695 AGGGAAATTGGGAAATTTAG
1 AGGGAAATTGAGAAATTTAG
58715 AGGGA
1 AGGGA
58720 TTAGAACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.36, T:0.23
Consensus pattern (20 bp):
AGGGAAATTGAGAAATTTAG
Found at i:58979 original size:24 final size:25
Alignment explanation
Indices: 58943--58995 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
58933 TATATGTATG
* *
58943 TATATAAACTATATA-TGTATAAAC
1 TATATAAAATATATAGTGTATAAAA
*
58967 TATATAAAATATATAGTTTATAAAA
1 TATATAAAATATATAGTGTATAAAA
58992 TATA
1 TATA
58996 ATTTATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
TATATAAAATATATAGTGTATAAAA
Found at i:59524 original size:25 final size:22
Alignment explanation
Indices: 59486--59542 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
59476 ATTAATCATG
59486 TTTTATATAATTTACATTTAAATAA
1 TTTTATATAATTT--A-TTAAATAA
59511 TTTTAT-TAATTTTATTAAATAA
1 TTTTATATAA-TTTATTAAATAA
59533 -TTTATATAAT
1 TTTTATATAAT
59543 ATGTATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 6 0.20
22 11 0.37
23 1 0.03
24 3 0.10
25 9 0.30
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTATATAATTTATTAAATAA
Found at i:59551 original size:2 final size:2
Alignment explanation
Indices: 59535--59651 Score: 191
Period size: 2 Copynumber: 58.0 Consensus size: 2
59525 TTAAATAATT
* *
59535 TA TA TA -A TA TG TA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
59577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
59652 GTAAATTACT
Statistics
Matches: 108, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.01
2 104 0.96
3 3 0.03
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:59595 original size:526 final size:527
Alignment explanation
Indices: 59053--60102 Score: 1562
Period size: 526 Copynumber: 2.0 Consensus size: 527
59043 ATCTATAGAT
*
59053 TATATATATATATATATAT-TATAGA-A-ACACTATGCATAAACTATATAAAGTA-ATAAAGTAT
1 TATATATATATATATATATATATAGATATACA-TATACATAAA-TATATAAA-TATATAAA-TAT
* ** * *
59114 ATAGTTTA-T-TA-AAAAAAACCCTAAACACTAAACTTTAAACGATACACACTAAACACTAAACC
62 ATA-TATACTATAGAAAAAAA-CCTAAACACTAAA-TAGAAACCATAAACACTAAACACTAAACC
* * *
59176 TTAAA-CCCTGAACCCTAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAAAGT
124 CTAAATCAC-AAACCCTAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAAAGT
* * * *
59240 GGGCTTATGTATTCGGTCTATGTAATCTAATGTAAATGGACTAGCACTAATGCAAATGGATTTAT
188 GGGCTTATGTATTCGGCCTATGTAAACTAATGTAAATGGACAAGCACTAATGCAAATGGACTTAT
59305 TTTTGGGTTTTATTATTAATTATTCATAACAACAAAATAAATGGGCTATTAATGTGAATTAACCT
253 TTTTGGGTTTTATTATTAATTATTCATAACAACAAAATAAATGGG-TATTAATGTGAATTAACCT
59370 AACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGACATGTACTACTATTTATGAAC
317 AACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGACATGTACTACTATTTATGAAC
* *
59435 CATATAATATGCAATGTGACTTACTAATTATTTAACAACAAATTAATCATGTTTTATATAATTTA
382 CATATAATATGCAATGTGACATACTAATTATTTAACAACAAATTAATCATATTTTATATAATTTA
*
59500 CATTTAAATAATTTTATTAATTTTATTAAATAA-TTTATATAATATGTA-TATAAACTATATATA
447 CATTTAAATAATTTTATTAATTTTATTAAATAATTTTATATAATATGTAGTATAAACCATATATA
59563 TATATATATATATATA
512 TATATATATATATATA
* * * * * *
59579 TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
1 TATATATATATATATATATATATAGATATACATATACATAAATATATAAATATATAAATATATAT
* ** * * * * ** * * *
59644 ATACTATAGTAAATTACTTATATAGTTTATAGAAACCCTAAACCCTAAACCCTAAACCCTAAATC
66 ATACTATAGAAAAAAACCTAAACACTAAATAGAAACCATAAACACTAAACACTAAACCCTAAATC
* * *
59709 ACAAACCCTAATATAAATGGATTAGCACTAATGCATATATATTTGTAATAAAAGAGTGGGCTTAT
131 ACAAACCCTAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAAAGTGGGCTTAT
*
59774 GTATTGGGCCTATGTAAACTAATGTAAATGGACAAGCACTAATGCAAATGGACTTATTTTTGGGT
196 GTATTCGGCCTATGTAAACTAATGTAAATGGACAAGCACTAATGCAAATGGACTTATTTTTGGGT
*
59839 TTTATTATTACTTATTCATAACAACAAAATAAATGGGTATTAATGTGAATTAACCTAACATGCAA
261 TTTATTATTAATTATTCATAACAACAAAATAAATGGGTATTAATGTGAATTAACCTAACATGCAA
59904 CTAAAATACTAATTATGCAAATGAAATTAATATGACATGTACTACTATTTATGAACCATATAATA
326 CTAAAATACTAATTATGCAAATGAAATTAATATGACATGTACTACTATTTATGAACCATATAATA
* *
59969 TGCAATGTGACATACTAATTATTTAACACCTAATTAATCATATTTTATATAATTTACATTTAAAT
391 TGCAATGTGACATACTAATTATTTAACAACAAATTAATCATATTTTATATAATTTACATTTAAAT
*
60034 AATTTTATTAATTTTATTAAATAATTTTATATAATATGTATGTATAAACCATGTATATATATATA
456 AATTTTATTAATTTTATTAAATAATTTTATATAATATGTA-GTATAAACCATATATATATATATA
60099 TATA
520 TATA
60103 ACCAGCTAGA
Statistics
Matches: 471, Mismatches: 42, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
525 181 0.38
526 224 0.48
527 27 0.06
528 37 0.08
529 2 0.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (527 bp):
TATATATATATATATATATATATAGATATACATATACATAAATATATAAATATATAAATATATAT
ATACTATAGAAAAAAACCTAAACACTAAATAGAAACCATAAACACTAAACACTAAACCCTAAATC
ACAAACCCTAATATAAATAGACTAGCACTAATGCATATATATTTGTAATAAAAAAGTGGGCTTAT
GTATTCGGCCTATGTAAACTAATGTAAATGGACAAGCACTAATGCAAATGGACTTATTTTTGGGT
TTTATTATTAATTATTCATAACAACAAAATAAATGGGTATTAATGTGAATTAACCTAACATGCAA
CTAAAATACTAATTATGCAAATGAAATTAATATGACATGTACTACTATTTATGAACCATATAATA
TGCAATGTGACATACTAATTATTTAACAACAAATTAATCATATTTTATATAATTTACATTTAAAT
AATTTTATTAATTTTATTAAATAATTTTATATAATATGTAGTATAAACCATATATATATATATAT
ATATATA
Found at i:59686 original size:7 final size:7
Alignment explanation
Indices: 59676--59719 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
59666 TAGTTTATAG
59676 AAACCCT
1 AAACCCT
59683 AAACCCT
1 AAACCCT
59690 AAACCCT
1 AAACCCT
59697 AAACCCT
1 AAACCCT
*
59704 AAATCAC-
1 AAA-CCCT
59711 AAACCCT
1 AAACCCT
59718 AA
1 AA
59720 TATAAATGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 2 0.06
7 29 0.88
8 2 0.06
ACGTcount: A:0.48, C:0.39, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:60686 original size:22 final size:25
Alignment explanation
Indices: 60639--60694 Score: 82
Period size: 22 Copynumber: 2.4 Consensus size: 25
60629 ATTAATCATG
60639 TTTTATATAATTTACATTTAAATAA
1 TTTTATATAATTTACATTTAAATAA
*
60664 TTTTAT-TAATTT-CA-TTGAATAA
1 TTTTATATAATTTACATTTAAATAA
60686 TTTTATATA
1 TTTTATATA
60695 TGTATGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 13 0.45
23 4 0.14
24 6 0.21
25 6 0.21
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTATATAATTTACATTTAAATAA
Found at i:60751 original size:25 final size:24
Alignment explanation
Indices: 60712--60758 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
60702 ATAAACCATG
60712 TATATTATATATAAACTATATATA
1 TATATTATATATAAACTATATATA
60736 TATATATATATATAAACTATATA
1 TATAT-TATATATAAACTATATA
60759 AAGTAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (24 bp):
TATATTATATATAAACTATATATA
Found at i:60758 original size:2 final size:2
Alignment explanation
Indices: 60712--60749 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
60702 ATAAACCATG
*
60712 TA TA T- TA TA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
60750 AACTATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:60774 original size:25 final size:25
Alignment explanation
Indices: 60717--60766 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
60707 CCATGTATAT
* *
60717 TATATATAAACTATATATATATATA
1 TATATATAAACTATATAAATAAATA
60742 TATATATAAACTATATAAAGTAAAT
1 TATATATAAACTATATAAA-TAAAT
60767 TACTTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
TATATATAAACTATATAAATAAATA
Found at i:60862 original size:7 final size:7
Alignment explanation
Indices: 60852--60889 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
60842 ATCCTAATCA
60852 TAAACCC
1 TAAACCC
**
60859 TAAACTT
1 TAAACCC
60866 TAAACCC
1 TAAACCC
60873 TAAACCC
1 TAAACCC
60880 TAAACCC
1 TAAACCC
60887 TAA
1 TAA
60890 TGTAAATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:61078 original size:22 final size:23
Alignment explanation
Indices: 61052--61098 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
61042 ATTTTTTTCT
61052 TTATATAAATTAAACTATA-TAA
1 TTATATAAATTAAACTATATTAA
61074 TTATATAAATTAAACTATATTAA
1 TTATATAAATTAAACTATATTAA
61097 TT
1 TT
61099 TTCCTTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATATAAATTAAACTATATTAA
Found at i:61356 original size:16 final size:16
Alignment explanation
Indices: 61337--61386 Score: 100
Period size: 16 Copynumber: 3.1 Consensus size: 16
61327 AAATATCAGA
61337 TCAGGTTGAAAACAGG
1 TCAGGTTGAAAACAGG
61353 TCAGGTTGAAAACAGG
1 TCAGGTTGAAAACAGG
61369 TCAGGTTGAAAACAGG
1 TCAGGTTGAAAACAGG
61385 TC
1 TC
61387 GGGTAATACC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (16 bp):
TCAGGTTGAAAACAGG
Found at i:62053 original size:22 final size:23
Alignment explanation
Indices: 62020--62070 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
62010 TGAAACATAA
*
62020 ATTTTATATCATCCAATGGCTCT
1 ATTTTATATCATCAAATGGCTCT
**
62043 ATTTT-TATCATCAAATTTCTCT
1 ATTTTATATCATCAAATGGCTCT
62065 ATTTTA
1 ATTTTA
62071 ACAAATCCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTTTATATCATCAAATGGCTCT
Done.