Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001753.1 Hibiscus syriacus cultivar Beakdansim tig00003547_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: 39948
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:5681 original size:14 final size:14
Alignment explanation
Indices: 5626--5696 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 14
5616 ACTTATGTTA
5626 TATAGTTTAATA-TT
1 TATA-TTTAATACTT
*
5640 TATA-TTATATATTT
1 TATATTTA-ATACTT
*
5654 TAGTACTTATATACTT
1 TA-TATTTA-ATACTT
5670 TATATTTAATAC-T
1 TATATTTAATACTT
*
5683 TATATTTTATACTT
1 TATATTTAATACTT
5697 AGTACTTATA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
12 3 0.06
13 15 0.31
14 13 0.27
15 7 0.14
16 11 0.22
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.58
Consensus pattern (14 bp):
TATATTTAATACTT
Found at i:5686 original size:43 final size:43
Alignment explanation
Indices: 5626--5757 Score: 119
Period size: 43 Copynumber: 3.1 Consensus size: 43
5616 ACTTATGTTA
* *
5626 TATAGTTTAATATTTATATTATATATTTTAGTACTTATATACTT
1 TATACTTTAATACTTATATTATATA-TTTAGTACTTATATACTT
* * **
5670 TATA-TTTAATACTTATATTTTATACTTAGTACTTATAT-CCA
1 TATACTTTAATACTTATATTATATATTTAGTACTTATATACTT
* * * *
5711 AACACTTTATTACTTTATATTATATACTTTA-CACTT-TATACTT
1 TATACTTTAATAC-TTATATTATATA-TTTAGTACTTATATACTT
5754 TATA
1 TATA
5758 TATACAGATA
Statistics
Matches: 69, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
41 3 0.04
42 23 0.33
43 36 0.52
44 7 0.10
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.53
Consensus pattern (43 bp):
TATACTTTAATACTTATATTATATATTTAGTACTTATATACTT
Found at i:5733 original size:28 final size:28
Alignment explanation
Indices: 5688--5758 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
5678 ATACTTATAT
5688 TTTATAC-TTAGTACTTATAT-CCAAACAC
1 TTTATACTTTA-TA-TTATATACCAAACAC
***
5716 TTTATTACTTTATATTATATACTTTACAC
1 TTTA-TACTTTATATTATATACCAAACAC
5745 TTTATACTTTATAT
1 TTTATACTTTATAT
5759 ATACAGATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 20 0.54
29 14 0.38
30 3 0.08
ACGTcount: A:0.32, C:0.15, G:0.01, T:0.51
Consensus pattern (28 bp):
TTTATACTTTATATTATATACCAAACAC
Found at i:5756 original size:7 final size:7
Alignment explanation
Indices: 5638--5757 Score: 63
Period size: 7 Copynumber: 16.9 Consensus size: 7
5628 TAGTTTAATA
5638 TTTATA-
1 TTTATAC
*
5644 TTATATAT
1 TT-TATAC
5652 TTTAGTAC
1 TTTA-TAC
5660 TTATATAC
1 TT-TATAC
5668 TTTATA-
1 TTTATAC
5674 TTTAATAC
1 TTT-ATAC
*
5682 -TTATAT
1 TTTATAC
5688 TTTATAC
1 TTTATAC
5695 -TTAGTAC
1 TTTA-TAC
5702 -TTATATC
1 TTTATA-C
*** *
5709 CAAACAC
1 TTTATAC
5716 TTTATTAC
1 TTTA-TAC
5724 TTTATA-
1 TTTATAC
5730 TTATATAC
1 TT-TATAC
*
5738 TTTACAC
1 TTTATAC
5745 TTTATAC
1 TTTATAC
5752 TTTATA
1 TTTATA
5758 TATACAGATA
Statistics
Matches: 89, Mismatches: 12, Indels: 25
0.71 0.10 0.20
Matches are distributed among these distances:
6 15 0.17
7 51 0.57
8 21 0.24
9 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (7 bp):
TTTATAC
Found at i:6659 original size:473 final size:470
Alignment explanation
Indices: 5769--6705 Score: 1485
Period size: 473 Copynumber: 2.0 Consensus size: 470
5759 ATACAGATAC
*
5769 ATATACTTATACTTATAGTTTATATAGTATATAAAGTACCAAATTGAACAAACATGAATTCGAAA
1 ATATACTTATAATTATAGTTTATATAGTATATAAAGTACCAAATTGAACAAACATGAATTCGAAA
*
5834 TAAAAAAAATTGATAAATTAAACAACACGCATTGATGAGGGATGAAATTGAATTAATTATAAAAT
66 T-AAAAAAATTGAAAAATTAAACAACACGCATTGAT-AGGGATGAAATTGAATTAATTATAAAAT
* * *
5899 GTGAAGCTGATATTAATATAAAAAGGACTAAATTGCATACATTTAAAAATTTGGTGAACATAATT
129 GTGAAGATGATATTAATATAAAAAGGACTAAATTACATACATTTAAAAAGTTGGTGAACATAATT
5964 TGAAAATAAATTTATTATGATTCACATTTTATAGGGTTTTAAGTAAATTAAAAAATAAATAAGTA
194 TGAAAATAAATTTATTATGATTCACATTTTATAGGGTTTTAAGTAAATTAAAAAATAAATAAGTA
* *
6029 TGAGCCAATTTCAGATACAAATATAATTTGAAGGACTAAATTGAATAAATATGAAATTAAAATTA
259 TGAGCCAATTTCAGATACAAATATAATTTGAAGGACTAAATTGAACAAATATGAAATAAAAATTA
*
6094 AAATTAAAATACAATAAACAACATAAAAGGATCAAATAAAAAAATTGTAAAATGTGAGGAAAAAT
324 AAATTAAAATACAATAAACAACATAAAAGAATCAAATAAAAAAATTGTAAAATGTGAGGAAAAAT
* * *
6159 TAAAAAATGGATTGAATTACATTAATTTCAAAAGTTGGGGAAAATTAAAACAATTATAATGTATA
389 TAAAAAATAGATTGAATTACATTAATTTCAAAAGTTGGGAAAAATTAAAACAATTATAATATATA
6224 T-TATATAAATATACAT
454 TATATATAAATATACAT
*
6240 ATATACTTATAATTATAGTTTATATATGTATATAAAGTACCAAATTGAACAAACATGAAATTGGA
1 ATATACTTATAATTATAGTTTATATA-GTATATAAAGTACCAAATTGAACAAACATG-AATTCGA
* *
6305 AAT-AAAAAATTGAAAAATTAAATAACACGCATTGAT-GGTATGAAATTGAATTAATTATAAAAT
64 AATAAAAAAATTGAAAAATTAAACAACACGCATTGATAGGGATGAAATTGAATTAATTATAAAAT
* *
6368 GTGAAGATGATATTAATATAAAAAATGGACTAAATTATATACATTTTAAAAGTTGGTG-A-ATAA
129 GTGAAGATGATATTAATAT-AAAAA-GGACTAAATTACATACATTTAAAAAGTTGGTGAACATAA
* *
6431 TTTGAAAA-GAATTTATTATGTGATT-ATATTTTATAGGGTTTTAAGTAAATTACAAAAATATAA
192 TTTGAAAATAAATTTATTA--TGATTCACATTTTATAGGGTTTTAAGTAAATT--AAAAA-ATAA
* * *
6494 ATAAGTAT-AGGTCAATTTCAGATACAAATATAATTTGAAGGACTGAATTGAACGAATATGAAAT
252 ATAAGTATGA-GCCAATTTCAGATACAAATATAATTTGAAGGACTAAATTGAACAAATATGAAAT
*
6558 AACAAATTAAAATTTAAATACAATAAACAACATAAAAGAATCAAATAAAAAAATTGTAAAATGTG
316 AA-AAATTAAAATTAAAATACAATAAACAACATAAAAGAATCAAATAAAAAAATTGTAAAATGTG
**
6623 AGGAAAAATTGTAAAATAGATTGAATTACATTAATTTCAAAAGTTGGGAAAAATTAAAACAATTA
380 AGGAAAAATTAAAAAATAGATTGAATTACATTAATTTCAAAAGTTGGGAAAAATTAAAACAATTA
6688 TAATATATATATATATAA
445 TAATATATATATATATAA
6706 TGTATTAATC
Statistics
Matches: 430, Mismatches: 24, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
468 9 0.02
469 81 0.19
470 11 0.03
471 90 0.21
472 93 0.22
473 139 0.32
474 7 0.02
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (470 bp):
ATATACTTATAATTATAGTTTATATAGTATATAAAGTACCAAATTGAACAAACATGAATTCGAAA
TAAAAAAATTGAAAAATTAAACAACACGCATTGATAGGGATGAAATTGAATTAATTATAAAATGT
GAAGATGATATTAATATAAAAAGGACTAAATTACATACATTTAAAAAGTTGGTGAACATAATTTG
AAAATAAATTTATTATGATTCACATTTTATAGGGTTTTAAGTAAATTAAAAAATAAATAAGTATG
AGCCAATTTCAGATACAAATATAATTTGAAGGACTAAATTGAACAAATATGAAATAAAAATTAAA
ATTAAAATACAATAAACAACATAAAAGAATCAAATAAAAAAATTGTAAAATGTGAGGAAAAATTA
AAAAATAGATTGAATTACATTAATTTCAAAAGTTGGGAAAAATTAAAACAATTATAATATATATA
TATATAAATATACAT
Found at i:6765 original size:2 final size:2
Alignment explanation
Indices: 6754--6790 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
6744 TACATGCATC
6754 AT AT -T AT 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
6791 GATGCATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:7226 original size:21 final size:21
Alignment explanation
Indices: 7195--7234 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
7185 TTTTTGAAGA
7195 AAAATCATCCCCAAATGGCTCT
1 AAAATCAT-CCCAAATGGCTCT
*
7217 AAAA-CATCCCTAATGGCT
1 AAAATCATCCCAAATGGCT
7235 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 3 0.18
22 4 0.24
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.23
Consensus pattern (21 bp):
AAAATCATCCCAAATGGCTCT
Found at i:7489 original size:34 final size:32
Alignment explanation
Indices: 7450--7519 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
7440 TTTTGTAAAG
*
7450 GGGAAAGGTTCTAGCTAAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAG-TAAGCCCGTG-AAAAACTA
* *
7484 GGGAAAGGTTCTAGTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGTAAGCCCGTGAAAAACTA
7516 GGGA
1 GGGA
7520 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 8 0.24
34 14 0.42
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGTAAGCCCGTGAAAAACTA
Found at i:7921 original size:2 final size:2
Alignment explanation
Indices: 7914--8274 Score: 135
Period size: 2 Copynumber: 183.0 Consensus size: 2
7904 AACTATAAAG
* *
7914 TA TA TA TA -A TA TA TA CTA TA TA TA AA CTA TA AA GTA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * *
7956 -A TT TA TA CTA -A AA CTT TA TA TA TA T- TA TA TA CTT TA TA T-
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
7995 TA TA T- TC T- 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
* * * * * *
8035 AA GT- TT TA GTA TA AA GTA TA TA AA TA TA AA TA -A TA TA -A AA
1 TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
8075 TA TA AA TA T- TA TA TA -A TA TA TA TA TA TA AA GTA TA -A CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * *
8116 AA CTA -A AA AA TA -A GTA TA TA -A TA TA AA TA TA TA GTA TA TA
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * *
8156 TA TC TA TA TA TA TA TA TA TA TA TA TA -A GTA TA -A TA TA AA GCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* *
8198 TA TA -A GTA T- TA -A TA -A GTA TA TA -A GTA T- TA AA TA TA AA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA
8235 GTA TA TA -A GTA TA TA TA TA TA T- 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
8275 ATTTTAGTAT
Statistics
Matches: 273, Mismatches: 39, Indels: 94
0.67 0.10 0.23
Matches are distributed among these distances:
1 26 0.10
2 224 0.82
3 23 0.08
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (2 bp):
TA
Found at i:8068 original size:145 final size:141
Alignment explanation
Indices: 7907--8241 Score: 311
Period size: 145 Copynumber: 2.3 Consensus size: 141
7897 AAATGTAAAC
* **
7907 TATAAAGTATATATAATATATACTATATATAAACTATAAAGTATATATAATTTAT-ACTA-AAAC
1 TATAAA-TATAAATAATATATA-TATATATAAA-TATAAAGTATATATAAAGTATAACTATAAAC
** * * * * * **
7970 T-TTATATATATTATATACTTTATATTATATTCTTATATATATATATATATATATATATATATAT
63 TAAAAAATA-AGTATATAATATA-AATATA-TAGTATATATATATATATATATATATATATATAT
* * *
8034 AAAGTTTTAGTATAAAGTA
125 -AAG-TATAATATAAAGCA
* * * *
8053 TATAAATATAAATAATATAAAATATAAATATTATATAATATATATATATAAAGTATAACTATAAA
1 TATAAATATAAATAATAT-ATATATATATA-AATATAA-A-GTATATATAAAGTATAACTATAAA
*
8118 CTAAAAAATAAGTATATAATATAAATATATAGTATATATATCTATATATATATATATATATATAA
62 CTAAAAAATAAGTATATAATATAAATATATAGTATATATATATATATATATATATATATATATAA
8183 GTATAATATAAAGCA
127 GTATAATATAAAGCA
* *
8198 TATAAGTATTAATAAGTATATA-AGTAT-TAAATATAAAGTATATA
1 TATAAATATAAATAA-TATATATA-TATATAAATATAAAGTATATA
8242 AGTATATATA
Statistics
Matches: 154, Mismatches: 26, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
141 6 0.04
142 1 0.01
143 6 0.04
144 3 0.02
145 51 0.33
146 16 0.10
147 43 0.28
148 9 0.06
149 15 0.10
150 4 0.03
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (141 bp):
TATAAATATAAATAATATATATATATATAAATATAAAGTATATATAAAGTATAACTATAAACTAA
AAAATAAGTATATAATATAAATATATAGTATATATATATATATATATATATATATATATAAGTAT
AATATAAAGCA
Found at i:8359 original size:8 final size:8
Alignment explanation
Indices: 8346--8474 Score: 127
Period size: 8 Copynumber: 17.1 Consensus size: 8
8336 ATAAAGACCA
8346 AAGTATAT
1 AAGTATAT
8354 AAGTATAT
1 AAGTATAT
*
8362 AAATATA-
1 AAGTATAT
8369 AAGTATAT
1 AAGTATAT
8377 ATATGTATAT
1 A-A-GTATAT
8387 AA-TAATAT
1 AAGT-ATAT
8395 AAGTATAT
1 AAGTATAT
8403 AAG--TAT
1 AAGTATAT
8409 AA-TATA-
1 AAGTATAT
8415 AAGTATAT
1 AAGTATAT
8423 AAGTAT-T
1 AAGTATAT
8430 AA--ATAT
1 AAGTATAT
8436 AAGTATAT
1 AAGTATAT
8444 AAGTAT-T
1 AAGTATAT
*
8451 AAATATA-
1 AAGTATAT
*
8458 AAGCATAT
1 AAGTATAT
8466 AAGTATAT
1 AAGTATAT
8474 A
1 A
8475 TATAACTATA
Statistics
Matches: 101, Mismatches: 6, Indels: 28
0.75 0.04 0.21
Matches are distributed among these distances:
5 2 0.02
6 10 0.10
7 27 0.27
8 52 0.51
9 3 0.03
10 7 0.07
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.36
Consensus pattern (8 bp):
AAGTATAT
Found at i:8395 original size:41 final size:41
Alignment explanation
Indices: 8350--8485 Score: 120
Period size: 43 Copynumber: 3.1 Consensus size: 41
8340 AGACCAAAGT
8350 ATATAAGTATATAAATATAAAGTATATATATGTATATAATA
1 ATATAAGTATATAAATATAAAGTATATATATGTATATAATA
8391 ATATAAGTATATAAGTATAATATAAAGTATATAAGTAT-TAAATATAAGT-
1 ATATAAG--TAT-A-TA-AATATAAAGTATAT-A-TATGT--ATATAA-TA
*
8440 ATATAAGTAT-TAAATATAAAGCATATA-A-GTATATATATA
1 ATATAAGTATATAAATATAAAGTATATATATGTATATA-ATA
8479 ACTATAA
1 A-TATAA
8486 AGTGTAATAT
Statistics
Matches: 80, Mismatches: 1, Indels: 29
0.73 0.01 0.26
Matches are distributed among these distances:
38 6 0.08
39 2 0.03
40 7 0.09
41 7 0.09
42 1 0.01
43 16 0.20
44 3 0.04
45 2 0.03
46 14 0.17
47 5 0.06
48 3 0.04
49 13 0.16
50 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (41 bp):
ATATAAGTATATAAATATAAAGTATATATATGTATATAATA
Found at i:8500 original size:43 final size:43
Alignment explanation
Indices: 8349--8488 Score: 144
Period size: 41 Copynumber: 3.2 Consensus size: 43
8339 AAGACCAAAG
* *
8349 TATATAAGTATATAAATATAAAGTATATATATGTATATAATAATATAAG
1 TATATAAGTA-ATAAATATAAAGCATATA-A-GTAT-T-A-AATATAAC
* *
8398 TATATAAGT-AT-AATATAAAGTATATAAGTATTAAATATAAG
1 TATATAAGTAATAAATATAAAGCATATAAGTATTAAATATAAC
* *
8439 TATATAAGTATTAAATATAAAGCATATAAGTA-TATATATAAC
1 TATATAAGTAATAAATATAAAGCATATAAGTATTAAATATAAC
8481 TATA-AAGT
1 TATATAAGT
8489 GTAATATATA
Statistics
Matches: 85, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
41 21 0.25
42 14 0.16
43 19 0.22
44 4 0.05
45 1 0.01
46 15 0.18
47 2 0.02
49 9 0.11
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (43 bp):
TATATAAGTAATAAATATAAAGCATATAAGTATTAAATATAAC
Found at i:8598 original size:18 final size:17
Alignment explanation
Indices: 8575--8648 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 17
8565 ATTTAATTAA
8575 ATAAAGTATAAGTATAAT
1 ATAAAGTATAAGTAT-AT
*
8593 ATAAAGTA-CA-TATAAT
1 ATAAAGTATAAGTAT-AT
8609 ATAAAGTATATAAGTATAT
1 ATAAAG--TATAAGTATAT
*
8628 ATAAACTATAAAGTATAT
1 ATAAAGTAT-AAGTATAT
8646 ATA
1 ATA
8649 TTATATACTT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
16 12 0.25
17 4 0.08
18 21 0.44
19 8 0.17
20 3 0.06
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (17 bp):
ATAAAGTATAAGTATAT
Found at i:8653 original size:16 final size:16
Alignment explanation
Indices: 8005--8620 Score: 104
Period size: 16 Copynumber: 38.4 Consensus size: 16
7995 TATATTCTTA
*
8005 TATATATATATATATA-
1 TATATATA-ATATAAAG
8021 TATATATATATATAAAG
1 TATATATA-ATATAAAG
*
8038 T-T-T-TAGTATAAAG
1 TATATATAATATAAAG
8051 TATATA-AATATAAA-
1 TATATATAATATAAAG
*
8065 TAATATAAAATATAAA-
1 T-ATATATAATATAAAG
*
8081 TATTATATAATATATA-
1 TA-TATATAATATAAAG
*
8097 TATATA-AAGTAT-AAC
1 TATATATAA-TATAAAG
* * *
8112 TATAAACTAAAAAATAAG
1 TATATA-TAATATA-AAG
*
8130 TATATAATATAAATATATAG
1 --TAT-ATAT-AATATAAAG
* *
8150 TATATATATCTATATA-
1 TATATATA-ATATAAAG
8166 TATATATATATATATAAG
1 TATATATA-ATATA-AAG
*
8184 TATAATATAAAGCATATAAG
1 TAT-ATAT-AA-TATA-AAG
8204 TAT-TAATAAGTATATAAG
1 TATAT-ATAA-TATA-AAG
8222 TAT-TA-AATATAAAG
1 TATATATAATATAAAG
* *
8236 TATATA-AGTATATA-
1 TATATATAATATAAAG
*
8250 TATATATTATATATATA-
1 TATATA-TA-ATATAAAG
**
8267 TATATATAAT-TTTAG
1 TATATATAATATAAAG
* * *
8282 TATAAAGT-GTATATA-
1 TATATA-TAATATAAAG
*
8297 CATATATAATATAAAG
1 TATATATAATATAAAG
**
8313 TA-AGTATGTTATATAA-
1 TATA-TATAATATA-AAG
8329 -A-ATA-AATATAAAG
1 TATATATAATATAAAG
* *
8342 -ACCA-A-AGTATATAAG
1 TA-TATATAATATA-AAG
8357 TATATA-AATATAAAG
1 TATATATAATATAAAG
*
8372 TATATATATGTATATAA-
1 TATATATA-ATATA-AAG
8389 TA-ATATAAGTATATAAG
1 TATATATAA-TATA-AAG
8406 TATAATATAAAGTATATAAG
1 TAT-ATAT-AA-TATA-AAG
8426 TAT-TA-AATAT-AAG
1 TATATATAATATAAAG
*
8439 TATATA-AGTATTAAA-
1 TATATATAATA-TAAAG
* **
8454 TATAAAGCATAT-AAG
1 TATATATAATATAAAG
8469 TATATATATAACTATAAAG
1 --TATATATAA-TATAAAG
*
8488 TGTAATATATATATAAAG
1 TAT-ATATA-ATATAAAG
* *
8506 T-T-T-TAGTATAAGG
1 TATATATAATATAAAG
8519 TATATA-ATATATAAA-
1 TATATATA-ATATAAAG
**
8534 TATA-A-GGTATAAA-
1 TATATATAATATAAAG
*
8547 TATAT-TTATATTACACA-
1 TATATATAATA-TA-A-AG
*
8564 TATTTAATTAA-ATAAAG
1 TATAT-A-TAATATAAAG
8581 TATAAGTATAATATAAAG
1 TAT-A-TATAATATAAAG
*
8599 TACATATAATATAAAG
1 TATATATAATATAAAG
8615 TATATA
1 TATATA
8621 AGTATATATA
Statistics
Matches: 463, Mismatches: 61, Indels: 152
0.68 0.09 0.22
Matches are distributed among these distances:
12 2 0.00
13 36 0.08
14 44 0.10
15 92 0.20
16 120 0.26
17 59 0.13
18 54 0.12
19 17 0.04
20 33 0.07
21 6 0.01
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (16 bp):
TATATATAATATAAAG
Found at i:8793 original size:25 final size:23
Alignment explanation
Indices: 8753--9294 Score: 214
Period size: 24 Copynumber: 23.9 Consensus size: 23
8743 ACTAAAACTT
* *
8753 TATATA-TATATATTTATAGTTTA
1 TATATACTTTATATTTATA-TATA
8776 TATATACTTTATAGTTTATATATA
1 TATATACTTTATA-TTTATATATA
8800 TACTATACTTTATATTTATACT-TA
1 TA-TATACTTTATATTTATA-TATA
8824 TACTTATA-TTTAATACTTTGATATTATA
1 TA--TATACTTT-ATA-TTT-ATA-TATA
*
8852 TTATATAC-TTATATACT-TATAT-
1 -TATATACTTTATAT-TTATATATA
* *
8874 TATATGCTTGTATACTTTAGTCT-TA
1 TATATACTT-TATA-TTTA-TATATA
*
8899 TAATTATACTTTATATATATA-ATA
1 T-A-TATACTTTATATTTATATATA
*
8923 TACTTATACTTTATATTATATATGTA
1 TA--TATACTTTATATT-TATATATA
* * * *
8949 TATATACTTTATACTAAAACTTTA
1 TATATACTTTATATTTATA-TATA
* * *
8973 TATATA-TATATATATACATATA
1 TATATACTTTATATTTATATATA
* *
8995 TACATAC-TTATACTT-TATATA
1 TATATACTTTATATTTATATATA
*
9016 TATATACTTATATACTT-TATAT-
1 TATATACTT-TATATTTATATATA
*
9038 TATATACTTTAGT-CTT-TATA-A
1 TATATACTTTA-TATTTATATATA
9059 T-TATACTTTATATATT-TATAT-
1 TATATACTTTATAT-TTATATATA
*
9080 TA-ATACTATAT-TTTATTATATA
1 TATATACTTTATATTTA-TATATA
*
9102 CTTATATACTTTATA-TTATATGCT-
1 --TATATACTTTATATTTATAT-ATA
* *
9126 TATATACTTTA-GTCT-TATA-A
1 TATATACTTTATATTTATATATA
*
9146 T-TATACTTTATA--TATAAATA
1 TATATACTTTATATTTATATATA
9166 CT-TATACTTTATATTTATATATA
1 -TATATACTTTATATTTATATATA
* *
9189 CTTTATA-TTATATACTTATATACT-
1 -TATATACTT-TATATTTATATA-TA
* *
9213 T-TAGT-CTTTATAATTATA-CT-
1 TATA-TACTTTATATTTATATATA
* *
9233 T-TATA--TTAT-TATATATGTA
1 TATATACTTTATATTTATATATA
*
9252 TATATACTTTATATATATATATA
1 TATATACTTTATATTTATATATA
9275 TATA-A-TTTATAGTTTATATA
1 TATATACTTTATA-TTTATATA
9295 CAAACTTATA
Statistics
Matches: 409, Mismatches: 47, Indels: 127
0.70 0.08 0.22
Matches are distributed among these distances:
17 4 0.01
18 6 0.01
19 17 0.04
20 20 0.05
21 68 0.17
22 60 0.15
23 64 0.16
24 85 0.21
25 49 0.12
26 16 0.04
27 16 0.04
28 2 0.00
29 2 0.00
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATACTTTATATTTATATATA
Found at i:8817 original size:6 final size:6
Alignment explanation
Indices: 8755--9293 Score: 107
Period size: 6 Copynumber: 81.8 Consensus size: 6
8745 TAAAACTTTA
* * *
8755 TATATA TATATT TATAGTT TATA-- TATACTT TATAGTT TATATA TATA-C
1 TATATT TATATT TATA-TT TATATT TATA-TT TATA-TT TATATT TATATT
* *
8803 TATACTT TATATT TATACT TATACT TATATT TAATACTT TGATA-T TATATT
1 TATA-TT TATATT TATATT TATATT TATATT T-ATA-TT T-ATATT TATATT
* * * *
8854 ATATACTT ATATACT TATATT ATATGCTT GTATACTT TAGT-CT TATAAT
1 -TATA-TT -TATATT TATATT -TAT-ATT -TATA-TT TA-TATT TATATT
* * * *
8903 TATACTT TATATA TATA-A TATACT TATACTT TATATT ATATATG TATA--
1 TATA-TT TATATT TATATT TATATT TATA-TT TATATT -TATATT TATATT
* * * * ** * * *
8951 TATACTT TATACT AAAACTT TATATAT ATATATA TATACA TATATA CATACT
1 TATA-TT TATATT TATA-TT TATAT-T -TATATT TATATT TATATT TATATT
*
9003 TATACTT TATATAT ATATACTT ATATACTT TATATT ATATACTT TAGTCTT
1 TATA-TT TATAT-T -TATA-TT -TATA-TT TATATT -TATA-TT TA-TATT
* * *
9054 TATAAT TATACTTT ATATATT TATATT AATA-C TATATT T-TATT ATATACTT
1 TATATT TATA--TT -TATATT TATATT TATATT TATATT TATATT -TATA-TT
*
9105 ATATACTT TATA-T TATATGCT TATATACT T-TAGTCT TATAAT TATACTT
1 -TATA-TT TATATT TATAT--T TATAT--T TATA-T-T TATATT TATA-TT
* *
9154 TATATAT AAATACT TATACTT TATATT TATA-- TATACTT TATATT ATATACTT
1 TATAT-T -TATATT TATA-TT TATATT TATATT TATA-TT TATATT -TATA-TT
* * * * *
9206 ATATACTT TAGTCTT TATAAT TATACTT TATATTAT TATATA TGTATA
1 -TATA-TT TA-TATT TATATT TATA-TT TATA-T-T TATATT TATATT
*
9254 TATACTT TATATAT ATATATA TATAATT TATAGTT TATAT
1 TATA-TT TATAT-T -TATATT TAT-ATT TATA-TT TATAT
9294 ACAAACTTAT
Statistics
Matches: 411, Mismatches: 60, Indels: 124
0.69 0.10 0.21
Matches are distributed among these distances:
4 12 0.03
5 25 0.06
6 141 0.34
7 139 0.34
8 89 0.22
9 5 0.01
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (6 bp):
TATATT
Found at i:8917 original size:2 final size:2
Alignment explanation
Indices: 8910--9043 Score: 57
Period size: 2 Copynumber: 66.0 Consensus size: 2
8900 AATTATACTT
* *
8910 TA TA TA TA TA -A TA TA CT- TA TA CTT TA TA T- TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * *
8951 TA TA CTT TA TA CTA -A AA CTT TA TA TA TA TA TA TA TA TA CA TA
1 TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
8993 TA TA CA TA CT- TA TA CTT TA TA TA TA TA TA CT- TA TA TA CTT TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA
9035 TA T- TA TA TA
1 TA TA TA TA TA
9044 CTTTAGTCTT
Statistics
Matches: 99, Mismatches: 17, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
1 7 0.07
2 83 0.84
3 9 0.09
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:8952 original size:8 final size:7
Alignment explanation
Indices: 8752--9277 Score: 99
Period size: 8 Copynumber: 73.1 Consensus size: 7
8742 TACTAAAACT
8752 TTATATA
1 TTATATA
8759 -TATATA
1 TTATATA
8765 TT-TATA
1 TTATATA
8771 GTT-TATA
1 -TTATATA
8778 -TATACT-
1 TTATA-TA
8784 TTATAGT-
1 TTATA-TA
8791 TTATATA
1 TTATATA
8798 TATACTATA
1 T-TA-TATA
8807 CTT-TATA
1 -TTATATA
8814 TT-TATA
1 TTATATA
*
8820 CTTATA-C
1 -TTATATA
8827 TTATAT-
1 TTATATA
8833 TTA-ATA
1 TTATATA
8839 CTT-TGATA
1 -TTAT-ATA
8847 -T-TATA
1 TTATATA
8852 TTATATA
1 TTATATA
8859 CTTATATA
1 -TTATATA
*
8867 CT-TATA
1 TTATATA
*
8873 TTATATGC
1 TTATAT-A
*
8881 TTGTATA
1 TTATATA
*
8888 CTT-TAGTC
1 -TTATA-TA
8896 TTATA-A
1 TTATATA
8902 TTATACT-
1 TTATA-TA
8909 TTATATA
1 TTATATA
8916 TATAATATA
1 T-T-ATATA
*
8925 CTTATA-C
1 -TTATATA
8932 TT-TATA
1 TTATATA
8938 TTATATA
1 TTATATA
8945 TGTATATA
1 T-TATATA
*
8953 TACTTTATA
1 T--TATATA
* *
8962 CTA-AAA
1 TTATATA
8968 CTTTATATA
1 --TTATATA
8977 TATATATA
1 T-TATATA
*
8985 TATACATA
1 T-TATATA
*
8993 TATACATA
1 T-TATATA
9001 CTTATACT-
1 -TTATA-TA
9009 TTATATA
1 TTATATA
9016 -TATATA
1 TTATATA
9022 CTTATATA
1 -TTATATA
9030 CTT-TATA
1 -TTATATA
9037 TTATATA
1 TTATATA
*
9044 CTT-TAGTC
1 -TTATA-TA
9052 TT-TATAA
1 TTATAT-A
9059 TTATACT-
1 TTATA-TA
9066 TTATATA
1 TTATATA
9073 TT-TATA
1 TTATATA
9079 TTA-ATA
1 TTATATA
*
9085 CTATATTTTA
1 -T-TA-TATA
9095 TTATATA
1 TTATATA
9102 CTTATATA
1 -TTATATA
9110 CTT-TATA
1 -TTATATA
*
9117 TTATATGC
1 TTATAT-A
9125 TTATATA
1 TTATATA
*
9132 CTT-TAGTC
1 -TTATA-TA
9140 TTATA-A
1 TTATATA
9146 TTATACT-
1 TTATA-TA
9153 TTATATA
1 TTATATA
*
9160 -TAAATA
1 TTATATA
9166 CTTATACT-
1 -TTATA-TA
9174 TTATAT-
1 TTATATA
9180 TTATATA
1 TTATATA
*
9187 TACTTTATA
1 T--TATATA
9196 TTATATA
1 TTATATA
9203 CTTATATA
1 -TTATATA
*
9211 CTT-TAGTC
1 -TTATA-TA
9219 TT-TATAA
1 TTATAT-A
9226 TTATACT-
1 TTATA-TA
9233 TTATATTA
1 TTATA-TA
9241 TTATATA
1 TTATATA
9248 TGTATATA
1 T-TATATA
*
9256 -TACTTTA
1 TTA-TATA
9263 -TATATA
1 TTATATA
9269 TATATATA
1 T-TATATA
9277 T
1 T
9278 AATTTATAGT
Statistics
Matches: 402, Mismatches: 37, Indels: 159
0.67 0.06 0.27
Matches are distributed among these distances:
5 8 0.02
6 93 0.23
7 133 0.33
8 134 0.33
9 30 0.07
10 4 0.01
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (7 bp):
TTATATA
Found at i:9091 original size:17 final size:18
Alignment explanation
Indices: 8998--9209 Score: 78
Period size: 21 Copynumber: 10.6 Consensus size: 18
8988 ACATATATAC
8998 ATACTTATACTTTATATATAT
1 ATACTTATA-TTT-TAT-TAT
9019 ATACTTATATACTTTATATTAT
1 ATAC-T-TATA-TTT-TATTAT
*
9041 ATACTT-TAGTCTTTATAATT
1 ATACTTATA-T-TTTATTA-T
9061 ATACTTTATATATTTA-TATT
1 ATAC-TTATAT-TTTATTA-T
9081 AATAC-TATATTTTATTAT
1 -ATACTTATATTTTATTAT
9099 ATACTTATATACTTTATATTAT
1 ATAC-T-TATA-TTT-TATTAT
*
9121 ATGCTTATATACTTTAGTCT-T
1 ATACTTATAT--TTTA-T-TAT
* *
9142 ATAATTATACTTTATATATAA
1 ATACTTATA-TTT-TAT-TAT
9163 ATACTTATACTTTATATT-T
1 ATACTTATA-TTT-TATTAT
9182 ATA--TATACTTTATATTAT
1 ATACTTATA-TTT-TATTAT
9200 ATACTTATAT
1 ATACTTATAT
9210 ACTTTAGTCT
Statistics
Matches: 157, Mismatches: 11, Indels: 48
0.73 0.05 0.22
Matches are distributed among these distances:
17 17 0.11
18 9 0.06
19 19 0.12
20 30 0.19
21 49 0.31
22 21 0.13
23 12 0.08
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.54
Consensus pattern (18 bp):
ATACTTATATTTTATTAT
Found at i:9232 original size:167 final size:154
Alignment explanation
Indices: 8852--9285 Score: 470
Period size: 157 Copynumber: 2.7 Consensus size: 154
8842 TGATATTATA
* *
8852 TTATATACTTATATAC-TTATATTATATGCTTGTATACTTTAGTC-TTATAATTATACTTTATAT
1 TTATATA--TATATACTTTATATTATATACTTATATACTTTAGTCTTTATAATTATACTTTATAT
*
8915 A--TATAATATACTTATACTTTATATTATATATGTATATATACTTTATACTAAAACTTTATATAT
64 ATTTATATTATAC-TATA-TTT-TATTATATA--TATATATACTTTATACTAAAACTTTATATAT
*
8978 ATATATATATACATATATACATACTTATACT
124 ATATATATATACATATATAAATACTTATACT
9009 TTATATATATATACTTATATACTT-TATA-TTATATACTTTAGTCTTTATAATTATACTTTATAT
1 TTATATATATATACTT-TATA-TTATATACTTATATACTTTAGTCTTTATAATTATACTTTATAT
* ** *
9072 ATTTATATTAATACTATATTTTATTATATACT-TATATACTTTATATTATATGCTTATATACTTT
64 ATTTATATT-ATACTATATTTTATTATATA-TATATATACTTTATACTA-AAACTT-TATA-TAT
*
9136 AGTCTTATAATTATACTTTATATATAAATACTTATACT
124 A-T-ATAT-A-TATAC---ATATATAAATACTTATACT
9174 TTATATTTATATATACTTTATATTATATACTTATATACTTTAGTCTTTATAATTATACTTTATAT
1 TTATA--TATATATACTTTATATTATATACTTATATACTTTAGTCTTTATAATTATACTTTATA-
* *
9239 TATTATATATGTATA-TATACTTTATATATATATATATATAATTTATA
63 TATT-TATAT-TATACTATATTTTAT-TATATATATATATACTTTATA
9286 GTTTATATAC
Statistics
Matches: 239, Mismatches: 12, Indels: 40
0.82 0.04 0.14
Matches are distributed among these distances:
155 22 0.09
156 20 0.08
157 47 0.20
158 8 0.03
159 10 0.04
160 7 0.03
161 1 0.00
162 5 0.02
165 25 0.10
166 8 0.03
167 45 0.19
168 14 0.06
169 26 0.11
170 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (154 bp):
TTATATATATATACTTTATATTATATACTTATATACTTTAGTCTTTATAATTATACTTTATATAT
TTATATTATACTATATTTTATTATATATATATATACTTTATACTAAAACTTTATATATATATATA
TATACATATATAAATACTTATACT
Found at i:9245 original size:101 final size:101
Alignment explanation
Indices: 8903--9294 Score: 259
Period size: 101 Copynumber: 3.8 Consensus size: 101
8893 GTCTTATAAT
8903 TATACTTTATA-TATATAATATACTTATACTTTA-TATTATATATGTATATATACTTTATACTA-
1 TATACTTTATATTATATAAT-TA--TATA-TTTAGTATTATATA--TATATATACTTTATA-TAT
* * * * *
8965 AAACT-T-TATATATATATATATATACA-TATA-TACATAC-T-
59 AAA-TATATATATTTATATTTATATATATTTTATTATATACTTA
*
9003 TATACTTTATATATATATACTTATATACTTTA-TATTATATACT-T-TAGT-CTTTATA-ATTAT
1 TATACTTTATAT-TATATAATTATATA-TTTAGTATTATATA-TATATA-TACTTTATATA-TA-
* * *
9063 ACTTTATATATTTATATTAATACTATATTTTATTATATACTTA
60 AATATATATATTTATATTTATA-TATATTTTATTATATACTTA
** *
9106 TATACTTTATATTATATGCTTATATACTTTAGT-CT-TATA-AT-TATACTTTATATATAAATAC
1 TATACTTTATATTATATAATTATATA-TTTAGTATTATATATATATATACTTTATATATAAATA-
9167 T-TATACTTTATATTTATATATACTTTATATTATATACTTA
64 TATATA-TTTATATTTATATATA-TTT-TATTATATACTTA
* * *
9207 TATACTTTAGTCTT-TATAATTATACT-TTATATTATTATATATGTATATATACTTTATATATAT
1 TATACTTTA-TATTATATAATTATA-TATT-TAGTATTATATA--TATATATACTTTATATATAA
9270 ATATATATAATTTATAGTTTATATA
61 ATATATAT-ATTTATA-TTTATATA
9295 CAAACTTATA
Statistics
Matches: 239, Mismatches: 20, Indels: 58
0.75 0.06 0.18
Matches are distributed among these distances:
94 1 0.00
96 11 0.05
97 4 0.02
98 14 0.06
99 32 0.13
100 43 0.18
101 46 0.19
102 32 0.13
103 17 0.07
106 3 0.01
107 27 0.11
108 9 0.04
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.53
Consensus pattern (101 bp):
TATACTTTATATTATATAATTATATATTTAGTATTATATATATATATACTTTATATATAAATATA
TATATTTATATTTATATATATTTTATTATATACTTA
Found at i:9425 original size:20 final size:21
Alignment explanation
Indices: 9400--9455 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
9390 AATACAATTC
9400 ATATATAATTTTTATA-TAAA
1 ATATATAATTTTTATATTAAA
9420 ATATAT-A-TTTTATATTAAA
1 ATATATAATTTTTATATTAAA
*
9439 ACTATATAATTTATATA
1 A-TATATAATTTTTATA
9456 GTTCAATAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 7 0.23
19 6 0.19
20 11 0.35
21 1 0.03
22 6 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATATAATTTTTATATTAAA
Found at i:9840 original size:73 final size:73
Alignment explanation
Indices: 9752--9916 Score: 235
Period size: 73 Copynumber: 2.3 Consensus size: 73
9742 TATCTAAGTC
* * *
9752 ATAGGTGCCAATACCCTTATGTTGA-TTTTGGCTCCGAGAAAAACAGAATGCCAAATGGGTACCG
1 ATAGGTACCAATACCCTTATGTT-ATTTTTGGCTCCAAGAAAAACAGAATGCCAAATGGGGACCG
9816 ATACCCCTCT
65 ATACCCC-CT
* *
9826 -TAGGTACCAATACCCTTGTGTTATTTTTGGCTCCAAGAAAAACAGAATGCCCAATGGGGACCGA
1 ATAGGTACCAATACCCTTATGTTATTTTTGGCTCCAAGAAAAACAGAATGCCAAATGGGGACCGA
9890 TACCCCCT
66 TACCCCCT
* *
9898 AGAGGTACCGATACCCTTA
1 ATAGGTACCAATACCCTTA
9917 GTCATTTAAC
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
72 3 0.04
73 78 0.96
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (73 bp):
ATAGGTACCAATACCCTTATGTTATTTTTGGCTCCAAGAAAAACAGAATGCCAAATGGGGACCGA
TACCCCCT
Found at i:11709 original size:21 final size:21
Alignment explanation
Indices: 11683--11725 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
11673 CTTTTGATGA
11683 GCTGTTAGAGGAATATACTGG
1 GCTGTTAGAGGAATATACTGG
11704 GCTGTTAGAGGAATATACTGG
1 GCTGTTAGAGGAATATACTGG
11725 G
1 G
11726 TTGACTTCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.35, T:0.28
Consensus pattern (21 bp):
GCTGTTAGAGGAATATACTGG
Found at i:14312 original size:17 final size:17
Alignment explanation
Indices: 14270--14312 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
14260 AAAGATTGTC
*
14270 AAACTTTTTGATAGAAA
1 AAACGTTTTGATAGAAA
*
14287 AAACTTTTTGATAGAAA
1 AAACGTTTTGATAGAAA
*
14304 AAAGGTTTT
1 AAACGTTTT
14313 TCAAAAGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (17 bp):
AAACGTTTTGATAGAAA
Found at i:14313 original size:18 final size:17
Alignment explanation
Indices: 14270--14306 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
14260 AAAGATTGTC
14270 AAACTTTTTGATAGAAA
1 AAACTTTTTGATAGAAA
14287 AAACTTTTTGATAGAAA
1 AAACTTTTTGATAGAAA
14304 AAA
1 AAA
14307 GGTTTTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (17 bp):
AAACTTTTTGATAGAAA
Found at i:15629 original size:20 final size:21
Alignment explanation
Indices: 15569--15629 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
15559 TTTTTGTGCA
* *
15569 CTAGGTATCGATACCCCCTTT
1 CTAGGTATCGATACCTCCTTG
*
15590 ATAGGTATCGATACCTCCTTG
1 CTAGGTATCGATACCTCCTTG
*
15611 CTAGGTATCGGTA-CTCCTT
1 CTAGGTATCGATACCTCCTT
15630 CAACATGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 6 0.17
21 29 0.83
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (21 bp):
CTAGGTATCGATACCTCCTTG
Found at i:18197 original size:73 final size:72
Alignment explanation
Indices: 18061--18222 Score: 229
Period size: 73 Copynumber: 2.2 Consensus size: 72
18051 CCTAAGTTAT
**
18061 AGGTACCGATACCCTTATGTTGATTTTGGCTCTGAGAAAAACAGAATGCCAAATGGGTACCGATA
1 AGGTACCGATACCCTTATGTTGATTTTGGCTCCAAGAAAAACAGAATGCCAAATGGGTACCGATA
18126 CCCTTCATA
66 CCC--CATA
* *
18135 AGGTACCGATACCCTTGTGTT-ATTTTTGGCTCCAAG-AAAACAGAATGCCCAATGGGTACCGAT
1 AGGTACCGATACCCTTATGTTGA-TTTTGGCTCCAAGAAAAACAGAATGCCAAATGGGTACCGAT
*
18198 ACCCCCTA
65 ACCCCATA
*
18206 GGGTACCGATACCCTTA
1 AGGTACCGATACCCTTA
18223 GTCATTTAAC
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
71 18 0.22
73 31 0.39
74 31 0.39
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (72 bp):
AGGTACCGATACCCTTATGTTGATTTTGGCTCCAAGAAAAACAGAATGCCAAATGGGTACCGATA
CCCCATA
Found at i:18925 original size:9 final size:9
Alignment explanation
Indices: 18903--18970 Score: 54
Period size: 9 Copynumber: 7.8 Consensus size: 9
18893 ACTTAATAGT
*
18903 ATATATATT
1 ATATATATA
* *
18912 TTATACATA
1 ATATATATA
18921 ATATATATA
1 ATATATATA
*
18930 ATTTATAT-
1 ATATATATA
18938 ATAATATATA
1 AT-ATATATA
18948 ATA-ATATA
1 ATATATATA
18956 A-ATATA-A
1 ATATATATA
18963 ACTATATA
1 A-TATATA
18971 GTTTATATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
7 3 0.06
8 11 0.23
9 31 0.66
10 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATATATA
Found at i:18962 original size:11 final size:11
Alignment explanation
Indices: 18921--18962 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
18911 TTTATACATA
18921 ATATATATAAT
1 ATATATATAAT
*
18932 TTATATATAAT
1 ATATATATAAT
18943 ATATA-ATAAT
1 ATATATATAAT
*
18953 ATAAATATAA
1 ATATATATAA
18963 ACTATATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATATATAAT
Found at i:19012 original size:22 final size:21
Alignment explanation
Indices: 18896--19015 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 21
18886 TCGATTAACT
18896 TAATAGTATATATATTTTATACA
1 TAATA-TATATATA-TTTATACA
*
18919 TAATATATATA-ATTTATATA
1 TAATATATATATATTTATACA
* *
18939 TAATATATA-ATA-ATATAAA
1 TAATATATATATATTTATACA
* *
18958 T-ATAAACTATATAGTTTATATTA
1 TAATATA-TATATA-TTTATA-CA
*
18981 TCAA-ACTATATA-GTTTATACA
1 T-AATA-TATATATATTTATACA
19002 TAATATATATATAT
1 TAATATATATATAT
19016 AAACAATTGT
Statistics
Matches: 76, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
18 4 0.05
19 9 0.12
20 28 0.37
21 5 0.07
22 16 0.21
23 7 0.09
24 5 0.07
25 2 0.03
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (21 bp):
TAATATATATATATTTATACA
Found at i:21268 original size:2 final size:2
Alignment explanation
Indices: 21263--21301 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
21253 AAAAAATTAG
*
21263 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21302 AAACTTCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25849 original size:7 final size:7
Alignment explanation
Indices: 25839--25890 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
25829 TAAATTTCTT
25839 ATTTAAA
1 ATTTAAA
25846 ATTTATAA
1 ATTTA-AA
25854 ATTTAAA
1 ATTTAAA
25861 A-TT--A
1 ATTTAAA
25865 ATTT-AA
1 ATTTAAA
25871 ATTTAAA
1 ATTTAAA
*
25878 ATAT-AA
1 ATTTAAA
25884 ATTTAAA
1 ATTTAAA
25891 TTGACTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 12 0.32
7 15 0.39
8 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTTAAA
Found at i:25849 original size:14 final size:15
Alignment explanation
Indices: 25839--25890 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 15
25829 TAAATTTCTT
25839 ATTTAAAATTTATAA
1 ATTTAAAATTTATAA
*
25854 ATTTAAAATTAATTTAA
1 ATTTAAAATT--TATAA
25871 ATTTAAAA--TATAA
1 ATTTAAAATTTATAA
25884 ATTTAAA
1 ATTTAAA
25891 TTGACTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 11 0.33
15 10 0.30
17 12 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTAAAATTTATAA
Found at i:25869 original size:19 final size:18
Alignment explanation
Indices: 25851--25892 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 18
25841 TTAAAATTTA
25851 TAAATTTAAAAT-TAATT
1 TAAATTTAAAATATAATT
25868 TAAATTTAAAATATAAATT
1 TAAATTTAAAATAT-AATT
25887 TAAATT
1 TAAATT
25893 GACTAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 12 0.52
18 1 0.04
19 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTTAAAATATAATT
Found at i:25891 original size:6 final size:6
Alignment explanation
Indices: 25851--25892 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
25841 TTAAAATTTA
* *
25851 TAAATT TAAAAT T-AATT TAAATT TAAAATA TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT
25893 GACTAAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 4 0.13
6 21 0.70
7 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:26282 original size:14 final size:14
Alignment explanation
Indices: 26263--26294 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
26253 AGCTATAGTA
26263 TATTATCATAAATT
1 TATTATCATAAATT
*
26277 TATTATCATAACTT
1 TATTATCATAAATT
26291 TATT
1 TATT
26295 TCAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATCATAAATT
Found at i:27229 original size:160 final size:158
Alignment explanation
Indices: 26960--27282 Score: 477
Period size: 160 Copynumber: 2.0 Consensus size: 158
26950 TAATAAAAAT
* * *
26960 AATT-ATTTATAATTAATTTGAAAAAAATTGTTGACGTAGCATCACACGTAGACATGTCATGTTA
1 AATTGATTTATAATTAATTTGAAAAAAATTGTTGACGTAGCATCACACGCAGACATGCCACGTTA
* *
27024 GCATCTCCATCCACATGTTCTTGCTTAGTCAACTACAAAAATTGACCATTATTTGACTAACGATT
66 GCATCTCCATCCACATGTTCTTGCTTAGTCAAATACAAAAATTGACCATTAATTGACTAACGATT
* *
27089 TTTATCTAACGAGGGTATTTTTTGACCCA
131 TTGATCCAACGA-GGTATTTTTTGACCCA
* * *
27118 AATTGATTTATAATTAATTTGAAAAAAAATTGTTGACGTGGCATCACACGCGGACGTGCCACGTT
1 AATTGATTTATAATTAATTTG-AAAAAAATTGTTGACGTAGCATCACACGCAGACATGCCACGTT
* ** * * *
27183 AGCATCTCCCTCCATGTGTTCTTGCTTAGTCAAATATAAGAATTGACCGTTAATTGACTAACGAT
65 AGCATCTCCATCCACATGTTCTTGCTTAGTCAAATACAAAAATTGACCATTAATTGACTAACGAT
27248 TTTGATCCAACGAGGTATTTTTTGACCCA
130 TTTGATCCAACGAGGTATTTTTTGACCCA
27277 AATTGA
1 AATTGA
27283 AACATTAAGG
Statistics
Matches: 147, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
158 4 0.03
159 38 0.26
160 105 0.71
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (158 bp):
AATTGATTTATAATTAATTTGAAAAAAATTGTTGACGTAGCATCACACGCAGACATGCCACGTTA
GCATCTCCATCCACATGTTCTTGCTTAGTCAAATACAAAAATTGACCATTAATTGACTAACGATT
TTGATCCAACGAGGTATTTTTTGACCCA
Found at i:33778 original size:2 final size:2
Alignment explanation
Indices: 33771--33817 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
33761 CAATACTAAC
33771 AT AT AT AT AT AT 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 AT AT
33813 AT AT A
1 AT AT A
33818 AATTTATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34591 original size:46 final size:46
Alignment explanation
Indices: 34536--34662 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
34526 GTAAGCATGC
34536 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
* *
34582 AACTAAGCTTATGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
34628 AAATAAGCTTACGAGCTTATAGG-A-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTAT-GGTATTAAATGGTAAG
34663 AAATTTTATA
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
45 11 0.14
46 63 0.83
47 2 0.03
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
Found at i:36965 original size:11 final size:11
Alignment explanation
Indices: 36949--36999 Score: 75
Period size: 11 Copynumber: 4.6 Consensus size: 11
36939 TAAATAGAAA
36949 AAAAAAAAAAG
1 AAAAAAAAAAG
36960 AAAAAAAAAAG
1 AAAAAAAAAAG
*
36971 AAAAACAAAAG
1 AAAAAAAAAAG
*
36982 AAAAGAAAAAG
1 AAAAAAAAAAG
*
36993 AGAAAAA
1 AAAAAAA
37000 TGATGAGAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:36967 original size:16 final size:16
Alignment explanation
Indices: 36946--36999 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 16
36936 ATATAAATAG
36946 AAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAGAA
*
36962 AAAAAAAAGAAAAACAA
1 AAAAAAAA-AAAAAGAA
*
36979 AAGAAAAGAAAAAGAGAA
1 AA-AAAA-AAAAAAAGAA
36997 AAA
1 AAA
37000 TGATGAGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.25
17 10 0.31
18 12 0.38
19 2 0.06
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAA
Found at i:36992 original size:6 final size:6
Alignment explanation
Indices: 36948--36998 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
36938 ATAAATAGAA
* *
36948 AAAAAA AAAAAG AAAAA- AAAAAG AAAAA- CAAAAG -AAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
36993 AGAAAA
1 A-AAAA
36999 ATGATGAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 14 0.36
6 21 0.54
7 4 0.10
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Done.