Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000413.1 Hibiscus syriacus cultivar Beakdansim tig00000759_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: 119521
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10043 original size:21 final size:22
Alignment explanation
Indices: 10002--10054 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
9992 AAGTTCCCTG
10002 GGTATCGATACCCTCCACATA-
1 GGTATCGATACCCTCCACATAT
**
10023 GGTATCGATACCC-CTTTCATAT
1 GGTATCGATACCCTC-CACATAT
10045 GGTATCGATA
1 GGTATCGATA
10055 TTGTTCATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
22 10 0.36
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
GGTATCGATACCCTCCACATAT
Found at i:18722 original size:20 final size:20
Alignment explanation
Indices: 18699--18740 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
18689 TTGAAGCAAT
18699 AAAAATA-AAAAATATTTTAA
1 AAAAATATAAAAATA-TTTAA
* *
18719 AAAAGTATTAAAATATTTAA
1 AAAAATATAAAAATATTTAA
18739 AA
1 AA
18741 TTATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAATATAAAAATATTTAA
Found at i:19445 original size:87 final size:87
Alignment explanation
Indices: 19297--19459 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
19287 TATATTATAT
* *
19297 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATATAATAGAT
1 TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATATAATAGAT
19362 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
19384 TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCACTTATATAATGTAATAGGT
1 TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATATAATAGAT
19449 AGCGCTTATAT
66 AGCGCTTATAT
19460 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (87 bp):
TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACACTTATATAATATAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:19902 original size:182 final size:182
Alignment explanation
Indices: 19594--20434 Score: 1438
Period size: 182 Copynumber: 4.6 Consensus size: 182
19584 ATGCGTTCAC
** * *
19594 ATTTTGTCATTTATAGACCGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACAT
1 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
*
19659 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCG
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
* *
19724 ATTCTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCT
131 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCT
*
19776 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAA
1 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
*
19841 TTTTATAAAATATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
19906 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCT
131 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCT
19958 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
1 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
* *
20023 TTTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATT-AATTTCAAAA--GTC
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTC
*
20085 GATACTTATAATAAATTATCGACATTTTCAACATAACCGGTAGCGCTTTACCT
130 GATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCT
*
20138 GTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
1 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
* *
20203 TTTTATAACGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAATTGTCG
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
* *
20267 ATACGTATAATAAATTATCGACACTTTCAACGTAACCGGTAGCGCTTTACCT
131 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCT
* * *
20319 GTTTTTTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
1 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
* **
20384 TTTTATAAAGTATCGACACTTTATTGACAATATAACTTCTTCTCTTTTAAA
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
20435 AAAGGTAAAA
Statistics
Matches: 627, Mismatches: 27, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
178 2 0.00
179 18 0.03
180 153 0.24
181 148 0.24
182 304 0.48
183 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCG
ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCT
Found at i:20393 original size:361 final size:363
Alignment explanation
Indices: 19594--20434 Score: 1445
Period size: 361 Copynumber: 2.3 Consensus size: 363
19584 ATGCGTTCAC
** * *
19594 ATTTTGTCATTTATAGACCGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACAT
1 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
19659 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCG
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAG-GTCG
* *
19724 ATTCTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTATTTTGTCATTTC
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTATTTTGTCATTTC
19789 GAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAATTTTATAAAATAT
195 GAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAATTTTATAAAATAT
*
19854 CGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATAATAA
260 CGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAA
19919 ATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCT
325 ATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCT
19958 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
1 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
* *
20023 TTTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCTTCTCTTATTAATTTC-AAAA-GTCG
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCTAAAAGGTCG
* *
20086 ATACTTATAATAAATTATCGACATTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTC
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTATTTTGTCATTTC
* **
20151 GAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAACGTAT
195 GAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAATTTTATAAAATAT
*
20216 CGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAATTGTCGATACGTATAATAA
260 CGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAA
*
20280 ATTATCGACACTTTCAACGTAACCGGTAGCGCTTTACCT
325 ATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCT
* * *
20319 GTTTTTTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
1 ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
* **
20384 TTTTATAAAGTATCGACACTTTATTGACAATATAACTTCTTCTCTTTTAAA
66 TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
20435 AAAGGTAAAA
Statistics
Matches: 452, Mismatches: 24, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
360 4 0.01
361 181 0.40
362 150 0.33
364 110 0.24
365 7 0.02
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (363 bp):
ATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAT
TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTATTTTGTCATTTCG
AGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACAATTTTATAAAATATC
GACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAA
TTATCGACACTTTCAACATAACCGGTAGCGCTTTACCT
Found at i:24336 original size:20 final size:19
Alignment explanation
Indices: 24290--24348 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
24280 TCCGGTAGCG
* *
24290 TTTTACCGGTTTCATCATT
1 TTTTACCAGTTTTATCATT
*
24309 TTGATACCAGTTTTATCATAT
1 TT-TTACCAGTTTTATCAT-T
* *
24330 TTTTACCTGTTATATCATT
1 TTTTACCAGTTTTATCATT
24349 GTTGATCGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.22, C:0.17, G:0.08, T:0.53
Consensus pattern (19 bp):
TTTTACCAGTTTTATCATT
Found at i:24518 original size:182 final size:181
Alignment explanation
Indices: 24081--24548 Score: 625
Period size: 182 Copynumber: 2.6 Consensus size: 181
24071 ACGAAAGTAT
* * *
24081 CGACACTTTTAATATA-TCTGGTATCATTTTACCGGTTTTATCATTTTGATA-TCGGTTTTATCA
1 CGACACTTTAAATATATTC-GGTACCGTTTTACCGGTTTTATCATTTTGATACT-GGTTTTATCA
* * * *
24144 TATTTTTACCTGTTAAATCGTTGTTTGATCGATACATTTTTTTTAAAGTATCGACACTTTATAGG
64 TATTTTTACCTGTTATATCATTG-TTGATCGATACA-TTTTTTGAAAGTATCGACACTTTATAGA
* * **
24209 CGCTAAAACTGCTTCTCATTTAAATTCACAAAGTGTCGATCCTTATATAAAGTTT
127 CGCTAAAACTGCTTCTCATTTAAATTAACAAAGTGTCGATCCTTATATAAAATAC
* * * * **
24264 CGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTCATCATTTTGATACCAGTTTTATCATA
1 CGACACTTTAAATATATTCGGTACCGTTTTACCGGTTTTATCATTTTGATACTGGTTTTATCATA
*
24329 TTTTTACCTGTTATATCATTGTTGATCGATATATTTTTTGAAAGTATCGACACTTTATAGACGCT
66 TTTTTACCTGTTATATCATTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTATAGACGCT
* *
24394 AAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATTAAAATAC
131 AAAACTGCTTCTCATTTAAATTAACAAAGTGTCGATCCTTATA-TAAAATAC
* * ** *
24446 CGACACTTTAAATATATTCGGTACCGCTTTACCGGTTTTACCATTTCAATACTGGTTTTGTCATA
1 CGACACTTTAAATATATTCGGTACCGTTTTACCGGTTTTATCATTTTGATACTGGTTTTATCATA
* * *
24511 GTTTTACCTGTTATATCATTGTGGATCTATACATTTTT
66 TTTTTACCTGTTATATCATTGTTGATCGATACATTTTT
24549 AATTTGGATC
Statistics
Matches: 249, Mismatches: 33, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
181 70 0.28
182 104 0.42
183 74 0.30
184 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (181 bp):
CGACACTTTAAATATATTCGGTACCGTTTTACCGGTTTTATCATTTTGATACTGGTTTTATCATA
TTTTTACCTGTTATATCATTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTATAGACGCT
AAAACTGCTTCTCATTTAAATTAACAAAGTGTCGATCCTTATATAAAATAC
Found at i:26251 original size:3 final size:3
Alignment explanation
Indices: 26243--26268 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
26233 GAATTCATAT
26243 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
26269 TGTTGCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:27537 original size:33 final size:33
Alignment explanation
Indices: 27499--27606 Score: 164
Period size: 33 Copynumber: 3.3 Consensus size: 33
27489 AAAGAAGGAA
* *
27499 GGAAGAAGAGAGGTTG-ATGCGTGAGAAGCAGCG
1 GGAAGAAGAGAGATTGCA-GCGCGAGAAGCAGCG
* *
27532 TGAAGAAGAGAGATTGCAGCGCGAGAAGCAGTG
1 GGAAGAAGAGAGATTGCAGCGCGAGAAGCAGCG
27565 GGAAGAAGAGAGATTGCAGCGCGAGAAGCAGCG
1 GGAAGAAGAGAGATTGCAGCGCGAGAAGCAGCG
27598 GGAAGAAGA
1 GGAAGAAGA
27607 AAGAAGAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 67 0.99
34 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.43, T:0.09
Consensus pattern (33 bp):
GGAAGAAGAGAGATTGCAGCGCGAGAAGCAGCG
Found at i:35954 original size:36 final size:36
Alignment explanation
Indices: 35903--35986 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
35893 TGATGTAAAA
* *
35903 ATCGATGATCTTATATTATCAACGTTTAATTCTTTC
1 ATCGATGATCCTATATTATCAACGTTCAATTCTTTC
* * *
35939 ATCGATAATCCTATATTATCGATGTTCAATTCTTTC
1 ATCGATGATCCTATATTATCAACGTTCAATTCTTTC
*
35975 ATCAATGATCCT
1 ATCGATGATCCT
35987 CTGTTGTCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (36 bp):
ATCGATGATCCTATATTATCAACGTTCAATTCTTTC
Found at i:36000 original size:36 final size:36
Alignment explanation
Indices: 35914--36011 Score: 106
Period size: 36 Copynumber: 2.7 Consensus size: 36
35904 TCGATGATCT
* * *
35914 TATATTATCAACGTTTAATTCTTTCATCGATAATCC
1 TATATTATCAATGTTCAATTCTTTCATCAATAATCC
* *
35950 TATATTATCGATGTTCAATTCTTTCATCAATGATCC
1 TATATTATCAATGTTCAATTCTTTCATCAATAATCC
* * * **
35986 TCTGTTGTCAATGTTCTTTTCTTTCA
1 TATATTATCAATGTTCAATTCTTTCA
36012 CGGATAACCC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.48
Consensus pattern (36 bp):
TATATTATCAATGTTCAATTCTTTCATCAATAATCC
Found at i:41810 original size:21 final size:21
Alignment explanation
Indices: 41784--41850 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
41774 GATTTACATA
41784 TTCGCATTGCGATAGTCAAAG
1 TTCGCATTGCGATAGTCAAAG
* **
41805 TTCGCATTGTGATCTTCCAAA-
1 TTCGCATTGCGATAGT-CAAAG
*
41826 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCAAAG
41845 TTCGCA
1 TTCGCA
41851 ACGAGTGGTG
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
18 3 0.09
19 11 0.31
21 17 0.49
22 4 0.11
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCAAAG
Found at i:42449 original size:6 final size:6
Alignment explanation
Indices: 42440--42466 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
42430 CGCCGTCTCG
42440 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
42467 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:42594 original size:21 final size:21
Alignment explanation
Indices: 42568--42678 Score: 95
Period size: 21 Copynumber: 5.3 Consensus size: 21
42558 ATTTTGGACT
*
42568 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
42589 ATCGCAAAGCTAACTTCGACT--
1 ATCGC-AA-CGAACTTGGAATAA
42610 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
42631 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
42652 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
42673 ATCGCA
1 ATCGCA
42679 TCGCGAACTT
Statistics
Matches: 70, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
19 18 0.26
20 2 0.03
21 30 0.43
22 2 0.03
23 18 0.26
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:42626 original size:42 final size:42
Alignment explanation
Indices: 42564--42740 Score: 277
Period size: 42 Copynumber: 4.3 Consensus size: 42
42554 TGCGATTTTG
* *
42564 GACTATCGCAACGAATTTGGAATAAATCGCAAAGCTAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
42606 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
42648 GACTATCGCAACGAATTTGGAATAAATCGCATCGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
42690 GACTATCGCAACGAATTTGG-A-AAATCGTAACGCAAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
42730 GACTATCGCAA
1 GACTATCGCAA
42741 TGCGATAGTC
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 26 0.21
41 1 0.01
42 99 0.79
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:43900 original size:2 final size:2
Alignment explanation
Indices: 43893--43929 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
43883 GATAAACAAT
43893 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43930 AAATTACATA
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):
TA
Found at i:44374 original size:2 final size:2
Alignment explanation
Indices: 44367--44412 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
44357 ACTCGGAAAC
44367 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
44409 AT AT
1 AT AT
44413 TCGAGAGGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50981 original size:22 final size:21
Alignment explanation
Indices: 50939--50983 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
50929 AAATTTATCA
* *
50939 TAAATAAATCTTATTACCTAT
1 TAAATAAATCCTACTACCTAT
50960 TAAATAAATTCCTACTACCTAT
1 TAAATAAA-TCCTACTACCTAT
50982 TA
1 TA
50984 TTTTAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATAAATCCTACTACCTAT
Found at i:51421 original size:13 final size:13
Alignment explanation
Indices: 51403--51427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51393 TGAAAAAAAA
51403 TTTAATAATAAAC
1 TTTAATAATAAAC
51416 TTTAATAATAAA
1 TTTAATAATAAA
51428 AAAAGAAAAT
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTAATAATAAAC
Found at i:51532 original size:7 final size:7
Alignment explanation
Indices: 51520--51548 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
51510 TAACCCTATT
51520 TCTTTTC
1 TCTTTTC
51527 TCTTTTC
1 TCTTTTC
51534 TCTTTTC
1 TCTTTTC
51541 TCTTTTC
1 TCTTTTC
51548 T
1 T
51549 ACGAGTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (7 bp):
TCTTTTC
Found at i:51873 original size:21 final size:21
Alignment explanation
Indices: 51844--51896 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
51834 ATTTTGACTA
51844 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
51865 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
51886 TCGCAATGCGA
1 TCGCATTGCGA
51897 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:51911 original size:20 final size:20
Alignment explanation
Indices: 51886--51950 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
51876 TTTTCCTAAT
51886 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
51906 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
*
51926 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
51946 T-GCAA
1 TCGCAA
51951 ACGTTGTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 4 0.10
20 36 0.90
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:52150 original size:19 final size:19
Alignment explanation
Indices: 52126--52258 Score: 115
Period size: 19 Copynumber: 7.4 Consensus size: 19
52116 GCAACGAGAT
52126 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52145 AATCGCAA--CG---TGAA
1 AATCGCAATGCGAAATGAA
*
52159 AATCGCAACGCGAATATGAA
1 AATCGCAATGCGAA-ATGAA
* ** *
52179 TATCGCACCGCGGAAATGAC
1 AATCGCAATGC-GAAATGAA
*
52199 TATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
52218 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
52232 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52251 AATCGCAA
1 AATCGCAA
52259 CGACAAAATC
Statistics
Matches: 93, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 32 0.34
20 26 0.28
21 3 0.03
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:52160 original size:14 final size:14
Alignment explanation
Indices: 52141--52168 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52131 CAATGCGAAA
52141 TGAAAATCGCAACG
1 TGAAAATCGCAACG
52155 TGAAAATCGCAACG
1 TGAAAATCGCAACG
52169 CGAATATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:52163 original size:33 final size:33
Alignment explanation
Indices: 52113--52279 Score: 190
Period size: 33 Copynumber: 4.8 Consensus size: 33
52103 CTTAATGTCT
*
52113 ATCGCAACGAGATAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
* * *
52146 ATCGCAACGTGAAAATCGCAACGCGAATATGAAT
1 ATCGCAACGAGAAAATCGCAATGCGAA-ATGAAA
* *
52180 ATCGCACCGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAACG-AG-AA--A--ATCGCAATGCGAAATGAAA
*
52219 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
* *
52252 ATCGCAACGACAAAATCGCAACGCGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAA
52280 CTAAATTCGC
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
33 68 0.60
34 13 0.12
35 2 0.02
36 2 0.02
37 1 0.01
38 2 0.02
39 13 0.12
40 12 0.11
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:52395 original size:19 final size:19
Alignment explanation
Indices: 52285--52387 Score: 153
Period size: 19 Copynumber: 5.7 Consensus size: 19
52275 CGAAACTAAA
52285 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
52304 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
52323 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
52342 TTCGCGTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
52357 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
52375 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
52388 AGTCATTTTT
Statistics
Matches: 76, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 60 0.79
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:52515 original size:14 final size:14
Alignment explanation
Indices: 52494--52530 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
52484 CATCAATTAA
52494 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
52508 ATAAATCATCTTTT
1 ACAAATCAACTTTT
52522 ACAAATCAA
1 ACAAATCAA
52531 TTAAACAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:52856 original size:20 final size:20
Alignment explanation
Indices: 52775--52923 Score: 111
Period size: 20 Copynumber: 7.3 Consensus size: 20
52765 ATGGACATTA
* * *
52775 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
* * *
52795 TTACGATTTACAGATACACG
1 TTGCGATTTACGGATACGCG
* * *
52815 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCG
*
52835 TTACGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
* * *
52855 TTGTGATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
* *
52876 TTGTGATTTATGGATACGCG
1 TTGCGATTTACGGATACGCG
**
52896 TTGCGATTTTACGGATACTAG
1 TTGCGA-TTTACGGATACGCG
52917 TTGCGAT
1 TTGCGAT
52924 AGTCAGAATC
Statistics
Matches: 100, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
20 66 0.66
21 34 0.34
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:52867 original size:21 final size:21
Alignment explanation
Indices: 52841--52913 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
52831 CTCGTTACGA
52841 TTTACGGATACGCGTTGTGAT
1 TTTACGGATACGCGTTGTGAT
* *
52862 TTTACGTAT-TGTCGTTGTGA-
1 TTTACGGATACG-CGTTGTGAT
* *
52882 TTTATGGATACGCGTTGCGAT
1 TTTACGGATACGCGTTGTGAT
52903 TTTACGGATAC
1 TTTACGGATAC
52914 TAGTTGCGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.41
Consensus pattern (21 bp):
TTTACGGATACGCGTTGTGAT
Found at i:52884 original size:41 final size:41
Alignment explanation
Indices: 52775--52908 Score: 191
Period size: 40 Copynumber: 3.3 Consensus size: 41
52765 ATGGACATTA
* *
52775 TTGCGA-TTTACGTATTCTCGTTACGATTTACAGATACACG
1 TTGCGATTTTACGTATTCTCGTTACGATTTACGGATACGCG
52815 TTGCGA-TTTACGTATTCTCGTTACGATTTACGGATACGCG
1 TTGCGATTTTACGTATTCTCGTTACGATTTACGGATACGCG
* * ** *
52855 TTGTGATTTTACGTATTGTCGTTGTGATTTATGGATACGCG
1 TTGCGATTTTACGTATTCTCGTTACGATTTACGGATACGCG
52896 TTGCGATTTTACG
1 TTGCGATTTTACG
52909 GATACTAGTT
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 43 0.51
41 42 0.49
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.41
Consensus pattern (41 bp):
TTGCGATTTTACGTATTCTCGTTACGATTTACGGATACGCG
Found at i:54678 original size:14 final size:14
Alignment explanation
Indices: 54661--54717 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
54651 GATAAACATA
54661 GTTAATTAAATTTT
1 GTTAATTAAATTTT
*
54675 GTTAATCAAATTATT
1 GTTAATTAAATT-TT
*
54690 -TAACTATTTAAATTTT
1 GT---TAATTAAATTTT
54706 GTTAATTAAATT
1 GTTAATTAAATT
54718 ACTTATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.62
15 2 0.06
16 2 0.06
17 9 0.26
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (14 bp):
GTTAATTAAATTTT
Found at i:56337 original size:32 final size:31
Alignment explanation
Indices: 56294--56378 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
56284 AGAAAGTTTG
* *
56294 GGGCCACAGGGCCTACCTAAGAATACATCTTA
1 GGGCCGCAGGGCCTACCTAAGAAT-CATCTCA
* * *
56326 GGGCCGTAGGGCCTATCC-GAGAATGATCTCA
1 GGGCCGCAGGGCCTA-CCTAAGAATCATCTCA
*
56357 GGGCCGCAGAGCCTACCTAAGA
1 GGGCCGCAGGGCCTACCTAAGA
56379 GTCACATTAG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
30 2 0.05
31 21 0.49
32 18 0.42
33 2 0.05
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.16
Consensus pattern (31 bp):
GGGCCGCAGGGCCTACCTAAGAATCATCTCA
Found at i:62227 original size:39 final size:33
Alignment explanation
Indices: 62149--62215 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
62139 ATTAACGGTC
* *
62149 AAAATTAACGATGAGTAATTAAAATCAGAATAA
1 AAAATTAACGATGAGTAATCAAAATCAAAATAA
62182 AAAATTAACGATGAGTAATCAAAATCAAAATAA
1 AAAATTAACGATGAGTAATCAAAATCAAAATAA
62215 A
1 A
62216 TGAAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.22
Consensus pattern (33 bp):
AAAATTAACGATGAGTAATCAAAATCAAAATAA
Found at i:72198 original size:274 final size:269
Alignment explanation
Indices: 71798--72341 Score: 984
Period size: 275 Copynumber: 2.0 Consensus size: 269
71788 TTAAAATAGA
71798 ATATTTTTTATTTATAACAAAATATTGAGGGCTAAAGTACTTTTAAATTAAAAGTTAAAGTGATT
1 ATATTTTTTATTTATAACAAAATATTGAGGGCTAAAGTACTTTTAAATTAAAAGTTAAAGTGATT
71863 GTTTAGTCAAAAAAATAATAATTTTTACCTAAAAATTAAATTTTAGAGATCAAAACATTT-AAAA
66 GTTTAGTCAAAAAAATAATAATTTTTACCTAAAAATTAAATTTTAGAGATCAAAACATTTAAAAA
71927 AATTAAGAATAAAAAAATTATTTAGTTAAATATTTGTATTTTTTAAAATAGTATGTCTTCTATTT
131 AATTAAGAATAAAAAAATTATTTAGTTAAATATTTGTATTTTTTAAAATAGTATGTCTTCTATTT
71992 ATCCATATTATAAATTTGATAAAATTTAATAAATATATGTGTGTTATATATGCCTCTTCACCAAA
196 ATCCATATTATAAATTTGATAAAATTTAATAAATATATGTGTGTTATATATGCCTCTTCACCAAA
*
72057 TTCAATATG
261 TCCAATATG
72066 ATATTTTTTATTTATAACAAAATATTGAGGGCTAAAGTACTTTTAAATTAAAAATTAAAAGTTAA
1 ATATTTTTTATTTATAACAAAATATTGAGGGCTAAAGTAC--TT---TT--AAATTAAAAGTTAA
* *
72131 AGTGATTGTTTAGTC-AAAAATTAATAATTTTTACCTAAAAATTAAATTTTAGTGATCAAAACAT
59 AGTGATTGTTTAGTCAAAAAAATAATAATTTTTACCTAAAAATTAAATTTTAGAGATCAAAACAT
72195 TTAAAAAAATTAAGAATAAAAAAATTATTTAGTTAAATATTTGTATTTTTTAAAATAGTATGTCT
124 TTAAAAAAATTAAGAATAAAAAAATTATTTAGTTAAATATTTGTATTTTTTAAAATAGTATGTCT
72260 TCTATTTATCCATATTATAAATTTGATAAAATTTAATAAATATATGTGTGTTATATATGCCTCTT
189 TCTATTTATCCATATTATAAATTTGATAAAATTTAATAAATATATGTGTGTTATATATGCCTCTT
72325 CACCAAATCCAATATG
254 CACCAAATCCAATATG
72341 A
1 A
72342 AAGGATGATG
Statistics
Matches: 265, Mismatches: 3, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
268 40 0.15
270 2 0.01
273 2 0.01
274 49 0.18
275 172 0.65
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.41
Consensus pattern (269 bp):
ATATTTTTTATTTATAACAAAATATTGAGGGCTAAAGTACTTTTAAATTAAAAGTTAAAGTGATT
GTTTAGTCAAAAAAATAATAATTTTTACCTAAAAATTAAATTTTAGAGATCAAAACATTTAAAAA
AATTAAGAATAAAAAAATTATTTAGTTAAATATTTGTATTTTTTAAAATAGTATGTCTTCTATTT
ATCCATATTATAAATTTGATAAAATTTAATAAATATATGTGTGTTATATATGCCTCTTCACCAAA
TCCAATATG
Found at i:73223 original size:24 final size:24
Alignment explanation
Indices: 73206--73293 Score: 124
Period size: 24 Copynumber: 3.7 Consensus size: 24
73196 ATCATAACAT
*
73206 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAG
*
73230 AATTCAGGTCAAGTATTCA-ATCAG
1 AATCCAGGTCAAGTA-TCAGATCAG
*
73254 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
*
73278 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
73294 TATAATAGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 2 0.04
24 52 0.91
25 3 0.05
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAG
Found at i:77907 original size:24 final size:24
Alignment explanation
Indices: 77880--77958 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
77870 TATATCAAAA
*
77880 ATCATAACATAATCCAGGTCAAGT
1 ATCATAACAAAATCCAGGTCAAGT
* *
77904 ATCAGATCAAAATCCAGGTCAAGT
1 ATCATAACAAAATCCAGGTCAAGT
* * *
77928 ATTCA-ATCAGAATCCAGGTCAGGT
1 A-TCATAACAAAATCCAGGTCAAGT
*
77952 ATTATAA
1 ATCATAA
77959 TAGAAATCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.04
24 41 0.89
25 3 0.07
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCATAACAAAATCCAGGTCAAGT
Found at i:77963 original size:24 final size:24
Alignment explanation
Indices: 77890--77954 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
77880 ATCATAACAT
*
77890 AATCCAGGTCAAGTA-TCAGATCAA
1 AATCCAGGTCAAGTATTCA-ATCAG
77914 AATCCAGGTCAAGTATTCAATCAG
1 AATCCAGGTCAAGTATTCAATCAG
*
77938 AATCCAGGTCAGGTATT
1 AATCCAGGTCAAGTATT
77955 ATAATAGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 35 0.92
25 3 0.08
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
AATCCAGGTCAAGTATTCAATCAG
Found at i:80454 original size:18 final size:18
Alignment explanation
Indices: 80431--80469 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
80421 GCCGGTTAAC
*
80431 GGTCAACGGGTCGGGTTG
1 GGTCAACGGGTCGGGTCG
80449 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
80467 GGT
1 GGT
80470 TATGACTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.18, G:0.51, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:81380 original size:22 final size:24
Alignment explanation
Indices: 81331--81382 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
81321 CCTATTAAAT
* *
81331 TTTTTAATAAAATTCATACAATTT
1 TTTTTAAAAAAATTCATACAATTA
*
81355 TTTTTAAAAAAATT-ATTC-ATTA
1 TTTTTAAAAAAATTCATACAATTA
81377 TTTTTA
1 TTTTTA
81383 TTTCTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.36
23 3 0.12
24 13 0.52
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTTAAAAAAATTCATACAATTA
Found at i:81540 original size:15 final size:15
Alignment explanation
Indices: 81517--81554 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
81507 TTATAAAATC
* *
81517 ATATCATTTTAATAA
1 ATATTATTTAAATAA
81532 ATATTATTTAAATAA
1 ATATTATTTAAATAA
81547 ATATTATT
1 ATATTATT
81555 CCCATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTATTTAAATAA
Found at i:86723 original size:17 final size:18
Alignment explanation
Indices: 86701--86735 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
86691 GGACCCTGAA
86701 ATCCAAACAACA-AAAAG
1 ATCCAAACAACATAAAAG
*
86718 ATCCAAACTACATAAAAG
1 ATCCAAACAACATAAAAG
86736 TGGCTGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.23, G:0.06, T:0.11
Consensus pattern (18 bp):
ATCCAAACAACATAAAAG
Found at i:87248 original size:21 final size:21
Alignment explanation
Indices: 87222--87295 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
87212 GTTTCCAAAT
* *
87222 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCGAACTTAGACTA
87243 TCGCAATGCGAACTTAGACTA
1 TCGCAATGCGAACTTAGACTA
**
87264 TCGCAATGCGAACTTCTACTA
1 TCGCAATGCGAACTTAGACTA
*
87285 TCGCATTGCGA
1 TCGCAATGCGA
87296 TTTACATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGAACTTAGACTA
Found at i:87350 original size:21 final size:21
Alignment explanation
Indices: 87307--87371 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
87297 TTACATATTT
* *
87307 GCATTGCGATAGT-CGACATC
1 GCATTGCGATAGTCCAAAATC
87327 GCATTGCGATAGTCCAAAATC
1 GCATTGCGATAGTCCAAAATC
*
87348 GCATTGAGATAGTCCAAAATC
1 GCATTGCGATAGTCCAAAATC
87369 GCA
1 GCA
87372 ACGACTGGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 13 0.32
21 28 0.68
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (21 bp):
GCATTGCGATAGTCCAAAATC
Found at i:87465 original size:6 final size:6
Alignment explanation
Indices: 87454--87499 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
87444 GACACGTATT
*
87454 ACCACG ACCACG ACCACG ATCACG ACCACG ACCACG ACCACG ACCA
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCA
87500 AAAAACTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.35, C:0.48, G:0.15, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:99313 original size:60 final size:59
Alignment explanation
Indices: 99215--99395 Score: 170
Period size: 60 Copynumber: 3.0 Consensus size: 59
99205 GCATCGTATA
* * *
99215 TCTTCAAAGTATGACTCTTATT-TAAATTGATTCC-TAAACTTTTAAATATTTCAATTTCAT
1 TCTT-AAAGTATGACT-TCATTCTAAATT-AGTCCTTAAACTTTTAAACATTTCAATTTCAT
* *
99275 TCTTAAAGTATGACTATCATTCTAAATTAGTCCTTAAACTTTTAAACATTTTAACTTCAT
1 TCTTAAAGTATGACT-TCATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCAT
* * * * * * *
99335 CCCTAAATTATGGCCTTCATTCTAAATTGGT-CTATAAACTTTCTGAACATTCCAATTTCAT
1 TCTTAAAGTAT-GACTTCATTCTAAATTAGTCCT-TAAACTTT-TAAACATTTCAATTTCAT
99396 CCCAAACTAT
Statistics
Matches: 101, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
59 21 0.21
60 63 0.62
61 17 0.17
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (59 bp):
TCTTAAAGTATGACTTCATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCAT
Found at i:99899 original size:27 final size:28
Alignment explanation
Indices: 99866--99927 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
99856 AAATTAAATT
*
99866 ATTTAATTATTATT-T-TTAAAAATTATA
1 ATTTAATTATAATTCTATT-AAAATTATA
99893 ATTTAATTATAATTCTATTAAAATTATA
1 ATTTAATTATAATTCTATTAAAATTATA
99921 A-TTAATT
1 ATTTAATT
99928 TAAGTAGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 19 0.59
28 11 0.34
29 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTAATTATAATTCTATTAAAATTATA
Found at i:100693 original size:16 final size:17
Alignment explanation
Indices: 100665--100696 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
100655 TATTAAAATT
100665 ATAATTAAATTTTAAAA
1 ATAATTAAATTTTAAAA
100682 ATAATT-AATTTTAAA
1 ATAATTAAATTTTAAA
100697 TAAATCCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATTAAATTTTAAAA
Found at i:101375 original size:30 final size:30
Alignment explanation
Indices: 101340--101409 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
101330 ATTTTTAAAT
101340 GTGTTCATTTTCGTTTAATTT-TTTGATATA
1 GTGTTCATTTTCGTTT-ATTTATTTGATATA
* **
101370 GTGTTCATGTTCGTTTATTTATTTTTTATA
1 GTGTTCATTTTCGTTTATTTATTTGATATA
101400 GTGTTCATTT
1 GTGTTCATTT
101410 CATTCATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.61
Consensus pattern (30 bp):
GTGTTCATTTTCGTTTATTTATTTGATATA
Found at i:107424 original size:47 final size:47
Alignment explanation
Indices: 107359--107460 Score: 195
Period size: 47 Copynumber: 2.2 Consensus size: 47
107349 ATTTATAATT
107359 AAATTTATGATTATAAGACGTTGCATTGTTGAACTTTTCGATTATTA
1 AAATTTATGATTATAAGACGTTGCATTGTTGAACTTTTCGATTATTA
*
107406 AAATTTATGATTATAAGACGTTGTATTGTTGAACTTTTCGATTATTA
1 AAATTTATGATTATAAGACGTTGCATTGTTGAACTTTTCGATTATTA
107453 AAATTTAT
1 AAATTTAT
107461 AAAATGATCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (47 bp):
AAATTTATGATTATAAGACGTTGCATTGTTGAACTTTTCGATTATTA
Found at i:108968 original size:39 final size:38
Alignment explanation
Indices: 108925--109099 Score: 197
Period size: 39 Copynumber: 4.5 Consensus size: 38
108915 AGGTGACAGC
* * *
108925 GGCTTAGGTGTTGCCTTGGGTGGAGGAGGATAAGTTGGT
1 GGCTT-GGTGGTGCCTTGGGCGGAGGAGCATAAGTTGGT
* * * *
108964 GGCTTGGGTAGTACCTTGGGCGGAGGTGCATAAGTCGGT
1 GGCTT-GGTGGTGCCTTGGGCGGAGGAGCATAAGTTGGT
* * * *
109003 GGCTTGGTTGGTACCTTTGGTGGAGGAGGATAAGTTGGT
1 GGCTTGG-TGGTGCCTTGGGCGGAGGAGCATAAGTTGGT
*
109042 GGCTTGGGTGGTGCTTTGGGCGGAGGAGCATAAGTTGGT
1 GGCTT-GGTGGTGCCTTGGGCGGAGGAGCATAAGTTGGT
109081 GGCTTGGTAGGTGCCTTGG
1 GGCTTGGT-GGTGCCTTGG
109100 ATGGTGTTGG
Statistics
Matches: 113, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
38 5 0.04
39 106 0.94
40 2 0.02
ACGTcount: A:0.14, C:0.11, G:0.46, T:0.30
Consensus pattern (38 bp):
GGCTTGGTGGTGCCTTGGGCGGAGGAGCATAAGTTGGT
Found at i:109025 original size:78 final size:78
Alignment explanation
Indices: 108938--109099 Score: 252
Period size: 78 Copynumber: 2.1 Consensus size: 78
108928 TTAGGTGTTG
*
108938 CCTTGGGTGGAGGAGGATAAGTTGGTGGCTTGGGTAGTACCTTGGGCGGAGGTGCATAAGTCGGT
1 CCTTGGGTGGAGGAGGATAAGTTGGTGGCTTGGGTAGTACCTTGGGCGGAGGAGCATAAGTCGGT
*
109003 GGCTTGGTTGGTA
66 GGCTTGGTAGGTA
* * * * *
109016 CCTTTGGTGGAGGAGGATAAGTTGGTGGCTTGGGTGGTGCTTTGGGCGGAGGAGCATAAGTTGGT
1 CCTTGGGTGGAGGAGGATAAGTTGGTGGCTTGGGTAGTACCTTGGGCGGAGGAGCATAAGTCGGT
*
109081 GGCTTGGTAGGTG
66 GGCTTGGTAGGTA
109094 CCTTGG
1 CCTTGG
109100 ATGGTGTTGG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.14, C:0.11, G:0.46, T:0.29
Consensus pattern (78 bp):
CCTTGGGTGGAGGAGGATAAGTTGGTGGCTTGGGTAGTACCTTGGGCGGAGGAGCATAAGTCGGT
GGCTTGGTAGGTA
Found at i:112257 original size:29 final size:29
Alignment explanation
Indices: 112198--112258 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
112188 ATAATACCCA
* * * * *
112198 TTTTTAAATTATTTAGTTAAATGATATAT
1 TTTTTAAATTATTTAATAAAATAACACAT
112227 TTTTTAAATTATTTAATAAAATAACACAT
1 TTTTTAAATTATTTAATAAAATAACACAT
112256 TTT
1 TTT
112259 CATAACTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (29 bp):
TTTTTAAATTATTTAATAAAATAACACAT
Done.