Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003334.1 Hibiscus syriacus cultivar Beakdansim tig00007018_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: 103804
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:4082 original size:2 final size:2
Alignment explanation
Indices: 4075--4103 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4065 TAAATTTAGT
4075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4104 TAATCATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4704 original size:3 final size:3
Alignment explanation
Indices: 4696--4731 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
4686 TTATCCTTGT
*
4696 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4732 TCAATTCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7408 original size:2 final size:2
Alignment explanation
Indices: 7326--7389 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
7316 TTATTTTTTA
7326 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
7368 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
7390 TTAAAGTTCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7662 original size:13 final size:13
Alignment explanation
Indices: 7646--7670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7636 ATTATAAAAA
7646 AAAATAAAAAATG
1 AAAATAAAAAATG
7659 AAAATAAAAAAT
1 AAAATAAAAAAT
7671 ATATATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAATAAAAAATG
Found at i:7674 original size:2 final size:2
Alignment explanation
Indices: 7669--7719 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
7659 AAAATAAAAA
7669 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
7711 AT AT AT AT A
1 AT AT AT AT A
7720 ATAAACTAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10328 original size:20 final size:21
Alignment explanation
Indices: 10299--10341 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
10289 ATTTCCATAT
* *
10299 TGTAATAGGGAA-CGATTCCC
1 TGTAACAGGGAATCGATACCC
10319 TGTAACAGGGAATCGATACCC
1 TGTAACAGGGAATCGATACCC
10340 TG
1 TG
10342 CTACAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (21 bp):
TGTAACAGGGAATCGATACCC
Found at i:10832 original size:16 final size:15
Alignment explanation
Indices: 10799--10857 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 15
10789 ACACATATAC
10799 ATTTATCATGAA-CAT
1 ATTTATCAT-AATCAT
10814 ATTTATCAGTAATCAT
1 ATTTATCA-TAATCAT
10830 ATTATTATCACTAATTCAT
1 A-T-TTATCA-TAA-TCAT
10849 -TTTATCATA
1 ATTTATCATA
10858 TAATCATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 12 0.32
16 11 0.29
17 2 0.05
18 9 0.24
19 4 0.11
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (15 bp):
ATTTATCATAATCAT
Found at i:10848 original size:19 final size:18
Alignment explanation
Indices: 10816--10866 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
10806 ATGAACATAT
*
10816 TTATCAGTAATCATATTA
1 TTATCACTAATCATATTA
*
10834 TTATCACTAATTCATTTTA
1 TTATCACTAA-TCATATTA
*
10853 TCAT-A-TAATCATAT
1 TTATCACTAATCATAT
10867 ATTGAACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 5 0.18
17 3 0.11
18 10 0.36
19 10 0.36
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (18 bp):
TTATCACTAATCATATTA
Found at i:11138 original size:23 final size:22
Alignment explanation
Indices: 11112--11156 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11102 CTGAGTGGCA
11112 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
* * *
11135 TATGTATTTTTCCCGAATGACC
1 TATGAATTTGTCCCGAAGGACC
11157 ACTGTATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:11143 original size:22 final size:22
Alignment explanation
Indices: 11118--11177 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
11108 GGCATATGAA
11118 ATTTGTCCCGAAGGACCTA-TGT
1 ATTTGTCCCGAAGGACC-ACTGT
* *
11140 ATTTTTCCCGAATGACCACTGT
1 ATTTGTCCCGAAGGACCACTGT
* *
11162 ATATGTCCCAAAGGAC
1 ATTTGTCCCGAAGGAC
11178 GCGTAGACCT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCACTGT
Found at i:11658 original size:2 final size:2
Alignment explanation
Indices: 11614--11645 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11604 ACATATAAGA
11614 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
11646 TCATTTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16464 original size:22 final size:22
Alignment explanation
Indices: 16439--16499 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
16429 GGCATATGAA
16439 ATTTGTCCCGAAGGACCTA-TGT
1 ATTTGTCCCGAAGGACC-ACTGT
*
16461 ATTTGTCCCGATGGACCACTGT
1 ATTTGTCCCGAAGGACCACTGT
* * *
16483 ATATATCCTGAAGGACC
1 ATTTGTCCCGAAGGACC
16500 GCATAGACCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCACTGT
Found at i:23118 original size:17 final size:17
Alignment explanation
Indices: 23071--23116 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
23061 TAATTAAATA
*
23071 ATTAAACAATTTAATTT
1 ATTAAATAATTTAATTT
* *
23088 TTTAATTAATTTAATTT
1 ATTAAATAATTTAATTT
23105 GATTAAATAATT
1 -ATTAAATAATT
23117 AAAGACCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTAAATAATTTAATTT
Found at i:31938 original size:29 final size:30
Alignment explanation
Indices: 31906--31963 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
31896 TTTTTTTCAA
*
31906 AATTACGAAAATAGCACCATTTT-AAAATT
1 AATTACCAAAATAGCACCATTTTCAAAATT
* * *
31935 AATTACCAATATAGTACTATTTTCAAAAT
1 AATTACCAAAATAGCACCATTTTCAAAAT
31964 ATTTACTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (30 bp):
AATTACCAAAATAGCACCATTTTCAAAATT
Found at i:33933 original size:22 final size:21
Alignment explanation
Indices: 33879--33942 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
33869 AGTCGAGGGT
33879 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
* *
33900 CTCATAGGTCCTTCGAGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
33922 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
33943 AATTTCATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:34118 original size:22 final size:23
Alignment explanation
Indices: 34075--34119 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
34065 AGTCTTTGCA
* * *
34075 TTATTATATGATATTATGTATGT
1 TTATTATATGAAATGATATATGT
34098 TTATT-TATGAAATGATATATGT
1 TTATTATATGAAATGATATATGT
34120 GCTATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (23 bp):
TTATTATATGAAATGATATATGT
Found at i:34518 original size:30 final size:30
Alignment explanation
Indices: 34479--34545 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
34469 TTGTAAAACC
34479 ATATGATCGAGTTTTGTAATGTTTTAAACGT
1 ATAT-ATCGAGTTTTGTAATGTTTTAAACGT
34510 ATATATCGAGTTTTGTAATGTTTTAAACGT
1 ATATATCGAGTTTTGTAATGTTTTAAACGT
34540 ATATAT
1 ATATAT
34546 GTAAATGGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.46
Consensus pattern (30 bp):
ATATATCGAGTTTTGTAATGTTTTAAACGT
Found at i:34726 original size:22 final size:22
Alignment explanation
Indices: 34690--34733 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
34680 TAGCATTCGG
** *
34690 TACTGTTCATGGTACTATTCAT
1 TACTGTTCACAGTACCATTCAT
34712 TACTGTTCACAGTACCATTCAT
1 TACTGTTCACAGTACCATTCAT
34734 ACATTATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (22 bp):
TACTGTTCACAGTACCATTCAT
Found at i:36211 original size:424 final size:423
Alignment explanation
Indices: 35423--36271 Score: 1653
Period size: 424 Copynumber: 2.0 Consensus size: 423
35413 AATTAAAAAA
*
35423 AATCATAGAACAAAATTTATATATATAAATGATAACACCATTAGTTGTTACTACTAAAATGATCA
1 AATCATAGAACAAAATTTATATATATAAATGATAACACCATTAGTTGTTACTACTAAAATGATAA
35488 TATAAATTAGTTTAAAAATGATAATATAAATATTTTTATAATTTATATAATCATACAATTAGGAT
66 TATAAATTAGTTTAAAAATGATAATATAAATATTTTTATAATTTATATAATCATACAATTAGGAT
35553 CACATAACAATCTACTTAATCATATTTAATAAATAATACACTTATATGTCAATGAAATATTTTTA
131 CACATAACAATCTACTTAATCATATTTAATAAATAATACACTTATATGTCAATGAAATATTTTTA
35618 ATTTGTGTTACATAAATTTTTTGAACTCATAATTAAAAAATAAGTATTTAAATATATTAACATAT
196 ATTTGTGTTACATAAATTTTTTGAACTCATAATTAAAAAATAAGTATTTAAATATATTAACATAT
35683 AAAATATATATAATCTTAATTAATAAACCTTAATAATAAATATTAACCTAATGAAATTTAACATT
261 AAAATATATATAATCTTAATTAATAAACCTTAATAATAAATATTAACCTAATGAAATTTAACATT
35748 AGTGTATAAGTGGATTCATTATATATATAGAGATAATATAAAAAAGTAGAGGAATACTCATTTTA
326 AGTGTATAAGTGGATTCATTATATATATAGAGATAATATAAAAAAGTAGAGGAATACTCATTTTA
*
35813 GTTTTTATTTCACATTATAAAAAAAACATAATCT
391 GTTTTTATCTCACATTAT-AAAAAAACATAATCT
35847 AATCATAGAACAAAATTTATATATATAAATGATAACACCATTAGTTGTTACTACTAAAATGATAA
1 AATCATAGAACAAAATTTATATATATAAATGATAACACCATTAGTTGTTACTACTAAAATGATAA
35912 TATAAATTAGTTTAAAAATGATAATATAAATATTTTTATAATTTATATAATCATACAATTAGGAT
66 TATAAATTAGTTTAAAAATGATAATATAAATATTTTTATAATTTATATAATCATACAATTAGGAT
35977 CACATAACAATCTACTTAATCATATTTAATAAATAATACACTTATATGTCAATGAAATATTTTTA
131 CACATAACAATCTACTTAATCATATTTAATAAATAATACACTTATATGTCAATGAAATATTTTTA
36042 ATTTGTGTTACATAAATTTTTTGAACTCATAATTAAAAAATAAGTATTTAAATATATTAACATAT
196 ATTTGTGTTACATAAATTTTTTGAACTCATAATTAAAAAATAAGTATTTAAATATATTAACATAT
36107 AAAATATATATAATCTTAATTAATAAACCTTAATAATAAATATTAACCTAATGAAATTTAACATT
261 AAAATATATATAATCTTAATTAATAAACCTTAATAATAAATATTAACCTAATGAAATTTAACATT
*
36172 AGTGTATAAGTGGATTCATTATATATATAGAGATAATATAAAAAAGTTGAGGAATACTCATTTTA
326 AGTGTATAAGTGGATTCATTATATATATAGAGATAATATAAAAAAGTAGAGGAATACTCATTTTA
*
36237 GTTTTTATCTCACATTATAAAAAACCATAATCT
391 GTTTTTATCTCACATTATAAAAAAACATAATCT
36270 AA
1 AA
36272 ACACTCCAAT
Statistics
Matches: 421, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
423 16 0.04
424 405 0.96
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (423 bp):
AATCATAGAACAAAATTTATATATATAAATGATAACACCATTAGTTGTTACTACTAAAATGATAA
TATAAATTAGTTTAAAAATGATAATATAAATATTTTTATAATTTATATAATCATACAATTAGGAT
CACATAACAATCTACTTAATCATATTTAATAAATAATACACTTATATGTCAATGAAATATTTTTA
ATTTGTGTTACATAAATTTTTTGAACTCATAATTAAAAAATAAGTATTTAAATATATTAACATAT
AAAATATATATAATCTTAATTAATAAACCTTAATAATAAATATTAACCTAATGAAATTTAACATT
AGTGTATAAGTGGATTCATTATATATATAGAGATAATATAAAAAAGTAGAGGAATACTCATTTTA
GTTTTTATCTCACATTATAAAAAAACATAATCT
Found at i:36630 original size:17 final size:17
Alignment explanation
Indices: 36608--36654 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
36598 TGATTAAGCA
36608 CTGAATGATTCAATGGC
1 CTGAATGATTCAATGGC
*
36625 CTGAATAATTCAATGGC
1 CTGAATGATTCAATGGC
36642 CTGAATGATTCAA
1 CTGAATGATTCAA
36655 AGGCTCTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (17 bp):
CTGAATGATTCAATGGC
Found at i:37275 original size:102 final size:102
Alignment explanation
Indices: 37138--37338 Score: 321
Period size: 102 Copynumber: 2.0 Consensus size: 102
37128 ATCACTCAAC
* * *
37138 AGTTTACTCAGTAACGAGGTCCTTATGTAGATTATTTTAATAATGAAACATGTCACACGTTTACT
1 AGTTTACTCAGTAACGAGGTCCTTATGTAGATTATTTTAATAATAAAACATATAACACGTTTACT
*
37203 CACTGAATTTTACCCTCTCTCCTATTTCACTCACAAT
66 CACTGAATTTTACCCTCTCTCATATTTCACTCACAAT
* * * *
37240 AGTTTACTCAGTAACGGGGTGCTTATGTGGGTTATTTTAATAATAAAACATATAACACGTTTACT
1 AGTTTACTCAGTAACGAGGTCCTTATGTAGATTATTTTAATAATAAAACATATAACACGTTTACT
*
37305 CACTGAATTTTACTCTCTCTCATATTTCACTCAC
66 CACTGAATTTTACCCTCTCTCATATTTCACTCAC
37339 TGTAATTTTA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (102 bp):
AGTTTACTCAGTAACGAGGTCCTTATGTAGATTATTTTAATAATAAAACATATAACACGTTTACT
CACTGAATTTTACCCTCTCTCATATTTCACTCACAAT
Found at i:37569 original size:37 final size:37
Alignment explanation
Indices: 37528--37598 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
37518 TGGGTGTGGT
37528 TCCTTAACGATTATATAATATTTTTTCTGGGTTTAGA
1 TCCTTAACGATTATATAATATTTTTTCTGGGTTTAGA
*
37565 TCCTTAATGATTATATAATATTTTTTCTGGGTTT
1 TCCTTAACGATTATATAATATTTTTTCTGGGTTT
37599 TTTTTACACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (37 bp):
TCCTTAACGATTATATAATATTTTTTCTGGGTTTAGA
Found at i:41439 original size:2 final size:2
Alignment explanation
Indices: 41428--41456 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41418 GGCTCCAGAA
41428 AT AT -T 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
41457 TAGCAATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:43196 original size:17 final size:17
Alignment explanation
Indices: 43176--43244 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 17
43166 TAATATATAT
43176 ATATTATTATTAATAAA
1 ATATTATTATTAATAAA
43193 ATATT-TTA-TAAT-AA
1 ATATTATTATTAATAAA
**
43207 ATAAAATT-TTAA-AATA
1 ATATTATTATTAATAA-A
43223 A-A-TATTATTAATAAA
1 ATATTATTATTAATAAA
43238 ATGATTA
1 AT-ATTA
43245 ATTAATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 17
0.67 0.05 0.28
Matches are distributed among these distances:
14 8 0.20
15 17 0.43
16 7 0.17
17 6 0.15
18 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (17 bp):
ATATTATTATTAATAAA
Found at i:43201 original size:19 final size:19
Alignment explanation
Indices: 43164--43213 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
43154 TTTTTTAAGG
* *
43164 ATTAATATATATATATTATT
1 ATTAATA-AAATATATTATA
*
43184 ATTAATAAAATATTTTATA
1 ATTAATAAAATATATTATA
*
43203 ATAAATAAAAT
1 ATTAATAAAAT
43214 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAATAAAATATATTATA
Found at i:46733 original size:15 final size:16
Alignment explanation
Indices: 46700--46734 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
46690 ACTAGTTATC
*
46700 TTAAAAAATTACTTCA
1 TTAAAAAATTACTTAA
46716 TTAAAAAATTAC-TAA
1 TTAAAAAATTACTTAA
46731 TTAA
1 TTAA
46735 TTTACTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAAAATTACTTAA
Found at i:47149 original size:11 final size:12
Alignment explanation
Indices: 47130--47158 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
47120 TAACTTACGA
47130 TCAACTCACAGT
1 TCAACTCACAGT
47142 TCAA-TCACAGT
1 TCAACTCACAGT
47153 TCAACT
1 TCAACT
47159 ACACCATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.34, C:0.31, G:0.07, T:0.28
Consensus pattern (12 bp):
TCAACTCACAGT
Found at i:48239 original size:31 final size:32
Alignment explanation
Indices: 48170--48248 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 32
48160 AAAAATTTAT
* *
48170 GTACTAAAATGAAACAAAAAGTTAACATCGGG
1 GTACTAAAATGAAACAAAAAGTTAACAACGAG
*
48202 GTACTAAAATGAAATAAAAAGTTAACAAC-AG
1 GTACTAAAATGAAACAAAAAGTTAACAACGAG
48233 GTACTAAAATGTAAAC
1 GTACTAAAATG-AAAC
48249 TTTAAGTATG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 12 0.29
32 30 0.71
ACGTcount: A:0.53, C:0.11, G:0.15, T:0.20
Consensus pattern (32 bp):
GTACTAAAATGAAACAAAAAGTTAACAACGAG
Found at i:51454 original size:18 final size:18
Alignment explanation
Indices: 51431--51466 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51421 CCATACTCGT
*
51431 GTAAATCGTAAACTAGAC
1 GTAAATCGTAAACGAGAC
51449 GTAAATCGTAAACGAGAC
1 GTAAATCGTAAACGAGAC
51467 CGAAGCCATT
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:0.44, C:0.17, G:0.19, T:0.19
Consensus pattern (18 bp):
GTAAATCGTAAACGAGAC
Found at i:61861 original size:156 final size:156
Alignment explanation
Indices: 61566--61873 Score: 465
Period size: 156 Copynumber: 2.0 Consensus size: 156
61556 TTAAATGAGC
*
61566 ATGTTCGTGAATGTTAAGTGAATATGTTTACAAACATTAAACGAATATGTTCGTGAACGCTAAAC
1 ATGTTCGTGAATGTTAAGTGAACATGTTTACAAACATTAAACGAATATGTTCGTGAACGCTAAAC
* * *
61631 AAATGAACACAAATAATTTAAAAAATAAGTAACCAAACACGATATTGAAAATTTAAACAAACACG
66 AAATGAACACAAATAATTTAAAAAATAAGTAAACAAACACGATATTAAAAATTTAAACAAACACA
61696 AACAAAAACATGAATACGAAATGGAT
131 AACAAAAACATGAATACGAAATGGAT
* * *
61722 ATGTTTGTGAATGTTAAGTGTACATGTTTACAAACATTAAACGAATATGTTCGTGAATGCTAAAC
1 ATGTTCGTGAATGTTAAGTGAACATGTTTACAAACATTAAACGAATATGTTCGTGAACGCTAAAC
* * * * * * *
61787 GAATGAACACGAATAATTTTAAAAATAAGTAAACGAACACGATATTAAAAATTTAAATAGACCCT
66 AAATGAACACAAATAATTTAAAAAATAAGTAAACAAACACGATATTAAAAATTTAAACAAACAC-
*
61852 AAAC-CAAACATGAATACGAAAT
130 AAACAAAAACATGAATACGAAAT
61874 ACTATTAAAA
Statistics
Matches: 136, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
156 133 0.98
157 3 0.02
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.26
Consensus pattern (156 bp):
ATGTTCGTGAATGTTAAGTGAACATGTTTACAAACATTAAACGAATATGTTCGTGAACGCTAAAC
AAATGAACACAAATAATTTAAAAAATAAGTAAACAAACACGATATTAAAAATTTAAACAAACACA
AACAAAAACATGAATACGAAATGGAT
Found at i:63247 original size:18 final size:19
Alignment explanation
Indices: 63199--63245 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
63189 AAAATTTTAG
63199 AATATAAAAATAAATTTTC
1 AATATAAAAATAAATTTTC
*
63218 AATATAAAAATAAATTTTT
1 AATATAAAAATAAATTTTC
*
63237 AATAGAAAA
1 AATATAAAA
63246 TACATGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AATATAAAAATAAATTTTC
Found at i:68056 original size:2 final size:2
Alignment explanation
Indices: 68051--68088 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
68041 TATATTGTTA
68051 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
68089 CTTGCTCTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71518 original size:20 final size:20
Alignment explanation
Indices: 71493--71548 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
71483 CCTATTCATC
*
71493 GGTAATCTTTTATTCCCATT
1 GGTAATCTTATATTCCCATT
71513 GGTAATCTTATATTCCCATT
1 GGTAATCTTATATTCCCATT
71533 GGTAATCTTATATTCC
1 GGTAATCTTATATTCC
71549 GTGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (20 bp):
GGTAATCTTATATTCCCATT
Found at i:71850 original size:2 final size:2
Alignment explanation
Indices: 71845--71880 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
71835 TTCTTCATAA
71845 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
71881 TAAGGTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72101 original size:15 final size:15
Alignment explanation
Indices: 72081--72122 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
72071 AATAAAATTA
72081 TTTGATTAATTCAGT
1 TTTGATTAATTCAGT
72096 TTTGATTAATTCAGT
1 TTTGATTAATTCAGT
72111 TTTGATTAATTC
1 TTTGATTAATTC
72123 GATTTAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.55
Consensus pattern (15 bp):
TTTGATTAATTCAGT
Found at i:81061 original size:117 final size:117
Alignment explanation
Indices: 80878--81096 Score: 325
Period size: 117 Copynumber: 1.9 Consensus size: 117
80868 AACTATAATA
* *
80878 AAAAAATAATTTGAACCATTGATGTTTTGATTTAATCAATTAGACTAACCAACTATTTAAATGTT
1 AAAAAATAATTTGAACCACTGATGTTTCGATTTAATCAATTAGACTAACCAACTATTTAAATGTT
*
80943 TCAATCAAACCACTAACCGTTAACTTTTAACGGAAGACCATTCAACTGTGAT
66 TCAATCAAACCACTAACCGCTAACTTTTAACGGAAGACCATTCAACTGTGAT
* * * *
80995 AAAAAATCATTTGGACCACT-ATTGTTTCGATTTAATCAATTAGAC-CACCAAATTATTTAAATG
1 AAAAAATAATTTGAACCACTGA-TGTTTCGATTTAATCAATTAGACTAACC-AACTATTTAAATG
* *
81058 TTTCAATCAAGCCACTGACCGCTAACTTTTAACGGAAGA
64 TTTCAATCAAACCACTAACCGCTAACTTTTAACGGAAGA
81097 GATGAAGCGG
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
116 4 0.04
117 87 0.96
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (117 bp):
AAAAAATAATTTGAACCACTGATGTTTCGATTTAATCAATTAGACTAACCAACTATTTAAATGTT
TCAATCAAACCACTAACCGCTAACTTTTAACGGAAGACCATTCAACTGTGAT
Found at i:81549 original size:22 final size:24
Alignment explanation
Indices: 81521--81576 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
81511 CTTCAAATAG
81521 TATATTTTT-TA-TTAACTTAAAA
1 TATATTTTTATAGTTAACTTAAAA
*
81543 TATATTTGTTATATGTTAACTTCAAA
1 TATATTT-TTATA-GTTAACTTAAAA
81569 TATATTTT
1 TATATTTT
81577 ATTTAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.24
23 2 0.07
24 2 0.07
25 1 0.03
26 17 0.59
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (24 bp):
TATATTTTTATAGTTAACTTAAAA
Found at i:81636 original size:29 final size:30
Alignment explanation
Indices: 81577--81651 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 30
81567 AATATATTTT
* * *
81577 ATTTAAATAATATATTTTATTCTTTTATTA
1 ATTTAAATAATATAATTTATTATCTTATTA
* *
81607 ATTTAAA-AATATAATTTGTTATCTTCTTA
1 ATTTAAATAATATAATTTATTATCTTATTA
*
81636 ACTTAATATATATATA
1 ATTTAA-ATA-ATATA
81652 TATATATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 22 0.61
30 8 0.22
31 1 0.03
32 5 0.14
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.53
Consensus pattern (30 bp):
ATTTAAATAATATAATTTATTATCTTATTA
Found at i:81648 original size:2 final size:2
Alignment explanation
Indices: 81641--81688 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
81631 TCTTAACTTA
81641 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
81683 AT AT AT
1 AT AT AT
81689 TTTTTTATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81817 original size:29 final size:27
Alignment explanation
Indices: 81742--81902 Score: 110
Period size: 30 Copynumber: 5.6 Consensus size: 27
81732 TAAATAAAAG
* * *
81742 AATAAAATATATAATTTGAAGATAAAT-T
1 AATAAAATATAT--TTTTAAGTTAAATAA
81770 AATAACATATATATTTTTAAGTTAATATAA
1 AATAA-A-ATATATTTTTAAGTTAA-ATAA
81800 GAATAAAATATATTTTTAAAGTTAAGATAA
1 -AATAAAATATATTTTT-AAGTTAA-ATAA
** * *
81830 GAATAAAATGCAGTTTTAAATTAAAATTAA
1 -AATAAAATATATTTTTAAGTT-AAA-TAA
* *
81860 AATAAAATATATTTAATAAGTTGAATAA
1 AATAAAATATATTT-TTAAGTTAAATAA
*
81888 AA-AATATATATTTTT
1 AATAAAATATATTTTT
81903 CTGTCATTAA
Statistics
Matches: 108, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.01
27 10 0.09
28 19 0.18
29 31 0.29
30 42 0.39
31 5 0.05
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (27 bp):
AATAAAATATATTTTTAAGTTAAATAA
Found at i:81824 original size:30 final size:30
Alignment explanation
Indices: 81726--81873 Score: 119
Period size: 30 Copynumber: 5.0 Consensus size: 30
81716 TATTATTACC
* * *
81726 TTAAAGTAAATAAAAGAATAAAATATATAAT
1 TTAAAGTTAATATAAGAATAAAATATAT-TT
* * *
81757 TTGAAGATAA-AT--TAATAACATATATATTT
1 TTAAAGTTAATATAAGAATAA-A-ATATATTT
81786 TT-AAGTTAATATAAGAATAAAATATATTT
1 TTAAAGTTAATATAAGAATAAAATATATTT
* ** *
81815 TTAAAGTTAAGATAAGAATAAAATGCAGTT
1 TTAAAGTTAATATAAGAATAAAATATATTT
*
81845 TTAAA-TTAAAATTAA-AATAAAATATATTT
1 TTAAAGTTAATA-TAAGAATAAAATATATTT
81874 AATAAGTTGA
Statistics
Matches: 94, Mismatches: 16, Indels: 16
0.75 0.13 0.13
Matches are distributed among these distances:
28 11 0.12
29 32 0.34
30 39 0.41
31 12 0.13
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (30 bp):
TTAAAGTTAATATAAGAATAAAATATATTT
Found at i:90076 original size:41 final size:41
Alignment explanation
Indices: 90019--90096 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
90009 AATCACTGTC
*
90019 ATAAGTATCACATAGCCGATCCACCTCCATTCACATATCCA
1 ATAAGTATCACATAGCCCATCCACCTCCATTCACATATCCA
*
90060 ATAAGTATCACATAGCCCATCCCCCTCCATTCACATA
1 ATAAGTATCACATAGCCCATCCACCTCCATTCACATA
90097 GCCCAAAGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.24
Consensus pattern (41 bp):
ATAAGTATCACATAGCCCATCCACCTCCATTCACATATCCA
Found at i:90886 original size:2 final size:2
Alignment explanation
Indices: 90879--90949 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
90869 GTATACTTAA
90879 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
90921 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90950 TAATAAATAA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:90953 original size:6 final size:7
Alignment explanation
Indices: 90878--90959 Score: 80
Period size: 8 Copynumber: 11.3 Consensus size: 7
90868 AGTATACTTA
90878 AATATAT
1 AATATAT
90885 -ATATAT
1 AATATAT
90891 -ATATAT
1 AATATAT
90897 ATATATAT
1 A-ATATAT
90905 ATATATAT
1 A-ATATAT
90913 ATATATAT
1 A-ATATAT
90921 ATATATAT
1 A-ATATAT
90929 ATATATAT
1 A-ATATAT
90937 ATATATAT
1 A-ATATAT
90945 AATAT-T
1 AATATAT
*
90951 AATAAAT
1 AATATAT
90958 AA
1 AA
90960 ATAAAGGTAA
Statistics
Matches: 71, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
6 17 0.24
7 7 0.10
8 47 0.66
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AATATAT
Found at i:92255 original size:15 final size:15
Alignment explanation
Indices: 92212--92255 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
92202 GATTATCAAT
92212 AAAAAATATAAAGAAA
1 AAAAAATATAAA-AAA
*
92228 AAAAAATCTAAAACAA
1 AAAAAATATAAAA-AA
92244 AAAAAAT-TAAAA
1 AAAAAATATAAAA
92256 TTTTCAGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (15 bp):
AAAAAATATAAAAAA
Found at i:93348 original size:23 final size:23
Alignment explanation
Indices: 93303--93350 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
93293 TTTTGTTAGA
* *
93303 TTTGTTTAATGTTTACGAGCATG
1 TTTGTTTAACGTTTACGAACATG
**
93326 TTTGTTTAACGTTTGTGAACATG
1 TTTGTTTAACGTTTACGAACATG
93349 TT
1 TT
93351 CATTTATATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (23 bp):
TTTGTTTAACGTTTACGAACATG
Found at i:97168 original size:16 final size:16
Alignment explanation
Indices: 97149--97198 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
97139 ATTGACACAT
97149 AAATTAAAGTATTTAA
1 AAATTAAAGTATTTAA
* **
97165 AAATT-GA-TACAT-A
1 AAATTAAAGTATTTAA
97178 AAATTAAAGTATTTAA
1 AAATTAAAGTATTTAA
97194 AAATT
1 AAATT
97199 TAGAGGTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 6 0.24
14 4 0.16
15 4 0.16
16 11 0.44
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (16 bp):
AAATTAAAGTATTTAA
Found at i:97169 original size:28 final size:29
Alignment explanation
Indices: 97137--97198 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
97127 GATAATAATC
97137 AAATTGACACAT-AAATTAAAGTATTTAA
1 AAATTGACACATAAAATTAAAGTATTTAA
*
97165 AAATTGATACATAAAATTAAAGTATTTAA
1 AAATTGACACATAAAATTAAAGTATTTAA
97194 AAATT
1 AAATT
97199 TAGAGGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (29 bp):
AAATTGACACATAAAATTAAAGTATTTAA
Found at i:103088 original size:31 final size:27
Alignment explanation
Indices: 103046--103117 Score: 74
Period size: 31 Copynumber: 2.5 Consensus size: 27
103036 GTCGAGCTTT
*
103046 ACGAGTAACGAGTCAAGCCACAAGTTTTCTCA
1 ACGAGCAACGAGTCAAG-CA-AAG-TTT-T-A
*
103078 ACGAGC-ACGAGTCGAGCAAAGTTTTA
1 ACGAGCAACGAGTCAAGCAAAGTTTTA
103104 ACGAGCAACGAGTC
1 ACGAGCAACGAGTC
103118 GAGTTGAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
26 7 0.19
27 8 0.22
28 3 0.08
29 3 0.08
30 2 0.05
31 9 0.24
32 5 0.14
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (27 bp):
ACGAGCAACGAGTCAAGCAAAGTTTTA
Done.