Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009024.1 Hibiscus syriacus cultivar Beakdansim tig00112420_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: 60207
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1424 original size:90 final size:89
Alignment explanation
Indices: 1271--1445 Score: 262
Period size: 90 Copynumber: 2.0 Consensus size: 89
1261 TAACATACCC
*
1271 TTTTATAGCCAAGTTACCCTAATCATATCTGGGTTTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATCTGGGATTTTATTATTTCAAATTAATTAAATCTATA-
* *
1336 TTAATTAATTAGAATTTAATAATCT
65 TTAATTAATTAAAATTAAATAATCT
* * * *
1361 TTTTATATCTAAGTTACCGTAATCATAT-TAGGGATTTTATTATTTTAAATTAATTAAATCTATA
1 TTTTATAGCCAAGTTACCCTAATCATATCT-GGGATTTTATTATTTCAAATTAATTAAATCTATA
1425 TTAATTAATTAAAATTAAATA
65 TTAATTAATTAAAATTAAATA
1446 TTCGGGATTA
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
89 20 0.26
90 57 0.74
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATCTGGGATTTTATTATTTCAAATTAATTAAATCTATAT
TAATTAATTAAAATTAAATAATCT
Found at i:7471 original size:90 final size:90
Alignment explanation
Indices: 7318--7495 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
7308 CCTAACACAC
* * *
7318 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATCAATTAAATCTAT
1 CCTTTTATAGCCAAGTTAACCTAACCATATTAGGGATTTTATTATTTCAAATCAATTAAATCTAT
*
7383 ATTTAATTAATTAAAATTCAATAAT
66 ATTTAATTAATTAAAATTAAATAAT
* * *
7408 CCTTTTATATCCAAGTTAACCTAACCATATTAGGGATTTTATTATTTCAATTTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTAACCTAACCATATTAGGGATTTTATTATTTCAAATCAATTAAATCTAT
*
7473 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTAAAATTAAATA
7496 TTCGGATTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTAACCTAACCATATTAGGGATTTTATTATTTCAAATCAATTAAATCTAT
ATTTAATTAATTAAAATTAAATAAT
Found at i:9190 original size:137 final size:137
Alignment explanation
Indices: 8949--9526 Score: 879
Period size: 137 Copynumber: 4.2 Consensus size: 137
8939 AACCAGACAC
*
8949 CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAATCAT
1 CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
* * * *
9014 CCTTAGATAGCCATAATTCCTCATCACAAAGGAATCGTGTTATCTCAATTATCTTTAAATATGGA
66 CCTTAGATAGCCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGA
*
9079 CAGACAT
131 CAGACGT
* * * *
9086 CCTCATCACGAAGAAACAATGTCATCCACCAACCAGAACTCCTTATCATGTAGGAGCCGAGTCAT
1 CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
* *
9151 CCTTAGATAGTCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGC
66 CCTTAGATAGCCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGA
9216 CAGACGT
131 CAGACGT
*
9223 CCTCATCACGAATGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
1 CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
* *
9288 CCTTAGATAGCCAGAATTCCTCATCATGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGC
66 CCTTAGATAGCCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGA
9353 CAGACGT
131 CAGACGT
* * * *
9360 CCTCATCACAAAGGAACAATGTCATCCATCGACCAGAACTTCTCATCACGTAGGAGTCGAGTCAT
1 CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
* * * * * ** *
9425 CCTTTGATAGCCAGAATTCCTCATCGCGTAGGAACTGTGTTATCTCAATCATCCCTAAACAT-GA
66 CCTTAGATAGCCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGA
9489 CCAGACGT
131 -CAGACGT
* *
9497 CCTCATCATGAAGGAACAATGTCATACACC
1 CCTCATCACGAAGGAACAATGTCATCCACC
9527 AATTTGATCT
Statistics
Matches: 402, Mismatches: 38, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
136 1 0.00
137 401 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (137 bp):
CCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGTAGGAGCCGAGTCAT
CCTTAGATAGCCAGAATTCCTCATCACGAAGGAACCGTGTTATCTCAATTATCTTTAAAGATGGA
CAGACGT
Found at i:9693 original size:3 final size:3
Alignment explanation
Indices: 9685--9722 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
9675 CATCCCGTTT
* *
9685 TTA TTA TTA TTA -TA ATA ATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9723 CAAATAATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:13339 original size:16 final size:16
Alignment explanation
Indices: 13290--13339 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
13280 TTTAAGGACT
*
13290 AAATTG-AATACATATA
1 AAATTGAAATAAAT-TA
* *
13306 AAAGTGAAAT-ACTTA
1 AAATTGAAATAAATTA
13321 AAATTGAAATAAATTA
1 AAATTGAAATAAATTA
13337 AAA
1 AAA
13340 AACAGAAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 11 0.41
16 13 0.48
17 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (16 bp):
AAATTGAAATAAATTA
Found at i:13443 original size:2 final size:2
Alignment explanation
Indices: 13436--13736 Score: 100
Period size: 2 Copynumber: 151.5 Consensus size: 2
13426 TAAAAATAAA
* *
13436 AT AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
* * *
13478 AT AT AA ACT AT AT TT AT AT -T AT AA ACT AT AT A- AT -T AT -T AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
13518 AT GCT AT AT AT AT AA AT -T AT GT TT AT AT GA- ACT AT AT AT AT
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT
* * * * * * *
13559 AA ACT AT GT AT AT AA ACT AT AT AT GT AT AA ACT AT AA AA AGT AT
1 AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT
* * *
13603 AT AGT TT AT A- AT AT AT AT AT AT AT AA ACT AT AT A- AA AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
13645 AGT TT AT AA AT -T AT A- AT TT AT AT -T A- AT AT AGT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* *
13685 AT AT AT AT A- ACT A- AT AT A- AGT A- AT CT AT AG AT -T AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
13724 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
13737 GTTTATAGAA
Statistics
Matches: 219, Mismatches: 44, Indels: 72
0.65 0.13 0.21
Matches are distributed among these distances:
1 19 0.09
2 183 0.84
3 17 0.08
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:13478 original size:11 final size:11
Alignment explanation
Indices: 13464--13509 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
13454 AATATAAGTT
13464 TATATATAAAC
1 TATATATAAAC
13475 TATATATAAAC
1 TATATATAAAC
*
13486 TATAT-T-TA-
1 TATATATAAAC
13494 TAT-TATAAAC
1 TATATATAAAC
13504 TATATA
1 TATATA
13510 ATTATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
7 1 0.03
8 4 0.14
9 2 0.07
10 4 0.14
11 18 0.62
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (11 bp):
TATATATAAAC
Found at i:13480 original size:13 final size:13
Alignment explanation
Indices: 13431--13594 Score: 85
Period size: 13 Copynumber: 12.8 Consensus size: 13
13421 TTGAATAAAA
*
13431 ATAAAATATATAT
1 ATAAACTATATAT
*
13444 ATATA-TATATA-
1 ATAAACTATATAT
* *
13455 ATATAAGTTTATAT
1 ATA-AACTATATAT
13469 ATAAAC--TATAT
1 ATAAACTATATAT
13480 ATAAACTATAT-T
1 ATAAACTATATAT
* * *
13492 -TATATTATAAACT
1 ATAAACTATATA-T
13505 ATATAA-T-TAT-T
1 ATA-AACTATATAT
**
13516 ATATGCTATATAT
1 ATAAACTATATAT
* *
13529 ATAAATTATGTTTAT
1 ATAAACTA--TATAT
*
13544 ATGAACTATATAT
1 ATAAACTATATAT
*
13557 ATAAACTATGTAT
1 ATAAACTATATAT
13570 ATAAACTATATATGT
1 ATAAACTATATA--T
13585 ATAAACTATA
1 ATAAACTATA
13595 AAAAGTATAT
Statistics
Matches: 114, Mismatches: 21, Indels: 30
0.69 0.13 0.18
Matches are distributed among these distances:
11 26 0.23
12 11 0.10
13 49 0.43
14 6 0.05
15 22 0.19
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (13 bp):
ATAAACTATATAT
Found at i:13685 original size:40 final size:40
Alignment explanation
Indices: 13576--13653 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 40
13566 GTATATAAAC
*
13576 TATATATGTATAAACTATA-AAAAGTATATAGTTTATAATA
1 TATATATATATAAACTATATAAAA-TATATAGTTTATAATA
13616 TATATATATATAAACTATATAAAATATATAGTTTATAA
1 TATATATATATAAACTATATAAAATATATAGTTTATAA
13654 ATTATAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (40 bp):
TATATATATATAAACTATATAAAATATATAGTTTATAATA
Found at i:14029 original size:2 final size:2
Alignment explanation
Indices: 14017--14139 Score: 189
Period size: 2 Copynumber: 62.0 Consensus size: 2
14007 GTATAACTTG
**
14017 TA TA GTA TA TA TA -A CTA TA TA TA TA -A CC 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
14059 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
14100 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
14140 AATAAAACCA
Statistics
Matches: 113, Mismatches: 3, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
1 3 0.03
2 107 0.95
3 3 0.03
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:14358 original size:20 final size:21
Alignment explanation
Indices: 14303--14427 Score: 79
Period size: 20 Copynumber: 6.1 Consensus size: 21
14293 ACATGTAAAC
*
14303 TATATATATAACTTATATTATATG
1 TATATATA-AAC-TAT-GTATATG
*
14327 TATGTATAAACTATGTATA-G
1 TATATATAAACTATGTATATG
* *
14347 TATATATGAACTA--TACA--
1 TATATATAAACTATGTATATG
*
14364 TATATATAACCTATAGTATATG
1 TATATATAAACTAT-GTATATG
*
14386 TATATA-ACAATCTATTTATATG
1 TATATATA-AA-CTATGTATATG
14408 T-TATATAAACTA--TATATG
1 TATATATAAACTATGTATATG
14426 TA
1 TA
14428 ACCTATAGCT
Statistics
Matches: 82, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
17 11 0.13
18 10 0.12
20 18 0.22
21 11 0.13
22 18 0.22
23 7 0.09
24 7 0.09
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.43
Consensus pattern (21 bp):
TATATATAAACTATGTATATG
Found at i:14532 original size:20 final size:21
Alignment explanation
Indices: 14507--14546 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
14497 TAATTTATAA
14507 ACTATAT-TTTATATTAATGT
1 ACTATATATTTATATTAATGT
14527 ACTATATAGTTTATATTAAT
1 ACTATATA-TTTATATTAAT
14547 TTTAATTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (21 bp):
ACTATATATTTATATTAATGT
Found at i:14750 original size:16 final size:16
Alignment explanation
Indices: 14729--14818 Score: 69
Period size: 16 Copynumber: 5.3 Consensus size: 16
14719 AAACTGTATT
*
14729 ATATTAATATAAGTTA
1 ATATTAATATAATTTA
14745 ATATTAATATTAATTATA
1 ATATTAATA-TAATT-TA
*
14763 ATATATAAT-TATTTTA
1 ATAT-TAATATAATTTA
14779 ATATTAATTATAAATAGTT-
1 ATATTAA-TAT-AAT--TTA
14798 -TATTAATATAATTTA
1 ATATTAATATAATTTA
14813 TATATT
1 -ATATT
14819 GATGAAATTG
Statistics
Matches: 60, Mismatches: 3, Indels: 21
0.71 0.04 0.25
Matches are distributed among these distances:
14 2 0.03
15 3 0.05
16 19 0.32
17 16 0.27
18 14 0.23
19 4 0.07
20 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATTAATATAATTTA
Found at i:14773 original size:13 final size:12
Alignment explanation
Indices: 14729--14791 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
14719 AAACTGTATT
14729 ATATTAA-TATA
1 ATATTAATTATA
*
14740 A-GTTAA-TATTA
1 ATATTAATTA-TA
14751 ATATTAATTATA
1 ATATTAATTATA
14763 ATATATAATTATTTTA
1 ATAT-TAATTA---TA
14779 ATATTAATTATA
1 ATATTAATTATA
14791 A
1 A
14792 ATAGTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
10 6 0.14
11 4 0.09
12 13 0.30
13 8 0.19
15 6 0.14
16 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
ATATTAATTATA
Found at i:14813 original size:24 final size:22
Alignment explanation
Indices: 14730--14814 Score: 59
Period size: 23 Copynumber: 3.8 Consensus size: 22
14720 AACTGTATTA
* * *
14730 TATTAATATAAGTTA-ATATTAA
1 TATTAATATAATTTATA-AATAT
* *
14752 TATTAATTATAATATATAATTAT
1 TATTAA-TATAATTTATAAATAT
14775 T-TTAATATTAA-TTATAAATAGTT
1 TATTAATA-TAATTTATAAATA--T
14798 TATTAATATAATTTATA
1 TATTAATATAATTTATA
14815 TATTGATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
21 9 0.18
22 13 0.25
23 17 0.33
24 12 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTAATATAATTTATAAATAT
Found at i:15334 original size:20 final size:21
Alignment explanation
Indices: 15296--15335 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
15286 CAAAATTTTC
*
15296 TCCCAAGTTCATCTATATTCA
1 TCCCAAGTTCATATATATTCA
*
15317 TCCCAA-TTCATATTTATTC
1 TCCCAAGTTCATATATATTC
15336 TTCACAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.42
Consensus pattern (21 bp):
TCCCAAGTTCATATATATTCA
Found at i:15593 original size:6 final size:6
Alignment explanation
Indices: 15578--15624 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
15568 ACTGAGCCTG
*
15578 AACCTCA AACCTA AACCCA AACCCA AACCCA AACCCA AACCCA AACC
1 AACC-CA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACC
15625 TGAACACGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 34 0.89
7 4 0.11
ACGTcount: A:0.49, C:0.47, G:0.00, T:0.04
Consensus pattern (6 bp):
AACCCA
Found at i:15606 original size:18 final size:18
Alignment explanation
Indices: 15578--15693 Score: 83
Period size: 18 Copynumber: 6.4 Consensus size: 18
15568 ACTGAGCCTG
15578 AACCTCAAACCTAAACCCA
1 AACC-CAAACCTAAACCCA
*
15597 AACCCAAACCCAAACCCA
1 AACCCAAACCTAAACCCA
* * *
15615 AACCCAAACCTGAACACG
1 AACCCAAACCTAAACCCA
* * *
15633 AACCCATACCTGAAA-TCG
1 AACCCAAACCT-AAACCCA
* * *
15651 TACCCGAACCTGAA-CCA
1 AACCCAAACCTAAACCCA
** *
15668 AACCCAAACCCGAATCCA
1 AACCCAAACCTAAACCCA
15686 AACCCAAA
1 AACCCAAA
15694 TTCAAACTCG
Statistics
Matches: 78, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
17 14 0.18
18 58 0.74
19 6 0.08
ACGTcount: A:0.45, C:0.41, G:0.06, T:0.08
Consensus pattern (18 bp):
AACCCAAACCTAAACCCA
Found at i:17776 original size:21 final size:21
Alignment explanation
Indices: 17752--17794 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
17742 TCTAGTTGAA
* *
17752 TTTTAACTTATTTATTTCTTG
1 TTTTAACTTAGTAATTTCTTG
* *
17773 TTTTCATTTAGTAATTTCTTG
1 TTTTAACTTAGTAATTTCTTG
17794 T
1 T
17795 CTTTTGTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.09, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTAACTTAGTAATTTCTTG
Found at i:18883 original size:12 final size:11
Alignment explanation
Indices: 18855--18894 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
18845 TTGAATTAAC
18855 TCAAATGTTAT
1 TCAAATGTTAT
*
18866 TCAAATTTTAT
1 TCAAATGTTAT
18877 ATCAAATGTTAT
1 -TCAAATGTTAT
*
18889 TTAAAT
1 TCAAAT
18895 TATCATTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (11 bp):
TCAAATGTTAT
Found at i:19176 original size:23 final size:24
Alignment explanation
Indices: 19145--19199 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
19135 ATATTTTTTC
*
19145 TTTACATAAATTAAACTGTA-TAA
1 TTTACATAAATTAAACTATATTAA
*
19168 TTTATATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
19192 TTTACATA
1 TTTACATA
19200 TAATCAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:19286 original size:13 final size:13
Alignment explanation
Indices: 19254--19280 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19244 TAATTTACAT
19254 TTAAATAATTTTA
1 TTAAATAATTTTA
19267 TTAAATAATTTTA
1 TTAAATAATTTTA
19280 T
1 T
19281 ATAATAGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:19537 original size:16 final size:16
Alignment explanation
Indices: 19484--19538 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
19474 CGAATCATTT
19484 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* * **
19500 ACATGTCAGGTTCATC
1 ACAGGTCAGGTTAAAA
* *
19516 ATAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
19532 ACAGGTC
1 ACAGGTC
19539 GGGTAATACC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:20234 original size:44 final size:44
Alignment explanation
Indices: 20185--20282 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 44
20175 TATTGAGATT
20185 TAGCGGCATTTTTTGGATACAAACACCACAAAAGGAT-TGGTATA
1 TAGCGGCATTTTTTGGATACAAACACCACAAAAGG-TCTGGTATA
* ** * *
20229 TAGCGGC-GTTTTTGGATACAAATGCCGCAAAAGGTCTTGTATA
1 TAGCGGCATTTTTTGGATACAAACACCACAAAAGGTCTGGTATA
20272 TAGCGGCATTT
1 TAGCGGCATTT
20283 GTCAGATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.02
43 36 0.78
44 9 0.20
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (44 bp):
TAGCGGCATTTTTTGGATACAAACACCACAAAAGGTCTGGTATA
Found at i:20313 original size:44 final size:44
Alignment explanation
Indices: 20258--20343 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
20248 AAATGCCGCA
20258 AAAGGTCTTGTATATAGCGGCATTTGTCAG-ATATAAACGCTGCT
1 AAAGGTCTTGTATATAGCGGCATTTGTC-GTATATAAACGCTGCT
*
20302 AAAGGTCTTGTATATAGCGGCGTTTGTCGTATATAAACGCTG
1 AAAGGTCTTGTATATAGCGGCATTTGTCGTATATAAACGCTG
20344 ATATTGTTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
43 1 0.03
44 39 0.98
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (44 bp):
AAAGGTCTTGTATATAGCGGCATTTGTCGTATATAAACGCTGCT
Found at i:20730 original size:21 final size:21
Alignment explanation
Indices: 20706--20755 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
20696 CTGCTGATAT
*
20706 GTTGCTTCTCTCTGTGCTTCC
1 GTTGCTTCTCTCTCTGCTTCC
*
20727 GTTGCTGCTCTCTCTGCTTCC
1 GTTGCTTCTCTCTCTGCTTCC
*
20748 TTTGCTTC
1 GTTGCTTC
20756 ATTTTCGGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.00, C:0.34, G:0.18, T:0.48
Consensus pattern (21 bp):
GTTGCTTCTCTCTCTGCTTCC
Found at i:25586 original size:9 final size:9
Alignment explanation
Indices: 25572--25597 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
25562 CATAAAGTTG
25572 TTCATTCAT
1 TTCATTCAT
25581 TTCATTCAT
1 TTCATTCAT
25590 TTCATTCA
1 TTCATTCA
25598 ACAACTTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (9 bp):
TTCATTCAT
Found at i:29683 original size:39 final size:39
Alignment explanation
Indices: 29638--29713 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
29628 CATGTGGTGT
*
29638 ACACAAAAACAAGCAGTAACACAGATTGAATAGATAATC
1 ACACAAAAACAAGCAGTAACACAAATTGAATAGATAATC
*
29677 ACACAAAGACAAGCAGTAACACAAATTGAATAGATAA
1 ACACAAAAACAAGCAGTAACACAAATTGAATAGATAA
29714 CCTTTGTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.55, C:0.17, G:0.13, T:0.14
Consensus pattern (39 bp):
ACACAAAAACAAGCAGTAACACAAATTGAATAGATAATC
Found at i:30701 original size:3 final size:3
Alignment explanation
Indices: 30693--30722 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30683 GAGGCTGTTT
30693 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
30723 ATGTACAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:38681 original size:39 final size:39
Alignment explanation
Indices: 38614--38690 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 39
38604 TTATTCCTAT
38614 AATATTTTTTAATATTTTTTAAGTTAAATAAATAAATATG
1 AATATTTTTTAATATTTTTTAAG-TAAATAAATAAATATG
*
38654 AATATTTTTTTATATTTTTTTAA-TAAATAAATAAATA
1 AATATTTTTTAATA-TTTTTTAAGTAAATAAATAAATA
38691 CAAATATATG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 14 0.40
40 13 0.37
41 8 0.23
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (39 bp):
AATATTTTTTAATATTTTTTAAGTAAATAAATAAATATG
Found at i:41775 original size:21 final size:22
Alignment explanation
Indices: 41749--41789 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41739 CCAGGACAAG
41749 GAGTATCAGTACT-CCTTTAAT
1 GAGTATCAGTACTACCTTTAAT
*
41770 GAGTATCGGTACTACCTTTA
1 GAGTATCAGTACTACCTTTA
41790 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (22 bp):
GAGTATCAGTACTACCTTTAAT
Found at i:52840 original size:18 final size:18
Alignment explanation
Indices: 52817--52851 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
52807 GTTTTTAAGG
52817 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
52835 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
52852 AGTTTAAGTG
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:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Done.