Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009298.1 Hibiscus syriacus cultivar Beakdansim tig00113010_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: 52564
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:726 original size:29 final size:30
Alignment explanation
Indices: 693--776 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
683 TTTCAATTCA
* * *
693 TTAAATTTCTGTTTGTATTATTTT-GTCTT
1 TTAAATTTCTGTTTATATTATTTTAGCCTC
* * *
722 TTAAATTTCTATTTTTACTATTTTAGCCTC
1 TTAAATTTCTGTTTATATTATTTTAGCCTC
* *
752 TTAACTTTCTGTTTATGTTATTTTA
1 TTAAATTTCTGTTTATATTATTTTA
777 ATCCTTTAAG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 21 0.48
30 23 0.52
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.62
Consensus pattern (30 bp):
TTAAATTTCTGTTTATATTATTTTAGCCTC
Found at i:1071 original size:16 final size:18
Alignment explanation
Indices: 1033--1072 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
1023 ACGCAAACCA
1033 ATTTTTATCTTAAAAATG
1 ATTTTTATCTTAAAAATG
*
1051 A-TTTT-TCTT-AAAATT
1 ATTTTTATCTTAAAAATG
1066 ATTTTTA
1 ATTTTTA
1073 AAAGATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 5
0.76 0.04 0.20
Matches are distributed among these distances:
15 6 0.32
16 8 0.42
17 4 0.21
18 1 0.05
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (18 bp):
ATTTTTATCTTAAAAATG
Found at i:2107 original size:32 final size:31
Alignment explanation
Indices: 2053--2118 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
2043 AATGATTTAT
* *
2053 TTTCTTTTGTTTGTGTACACTAA-TTAATTTC
1 TTTCTTTTGTTTATGTAAACTAACTT-ATTTC
2084 TTTCATTTTGTTTATGTAAACTAACTTATTTC
1 TTTC-TTTTGTTTATGTAAACTAACTTATTTC
2116 TTT
1 TTT
2119 TTATTGTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 4 0.13
32 25 0.81
33 2 0.06
ACGTcount: A:0.21, C:0.12, G:0.08, T:0.59
Consensus pattern (31 bp):
TTTCTTTTGTTTATGTAAACTAACTTATTTC
Found at i:5292 original size:100 final size:101
Alignment explanation
Indices: 5119--5336 Score: 348
Period size: 100 Copynumber: 2.2 Consensus size: 101
5109 ACATGAATCC
* * *
5119 TTCAGCTAGCCTGATAAAGGTGATTATAAGATATACGTACAATAAAGCTTGAGTTGTACCTCTAG
1 TTCAGCTAGCCTGATAAAGGTGATTATAAGATATACATACAATAAAGCTTGAGCTATACCTCTAG
*
5184 AGCAATTGGTTAAACGC-CCGACTTTATGGATAAGA
66 AGCAATTGGTTAAACACTCCGACTTTATGGATAAGA
*
5219 TTCAGCTAGCCTGATAAAGGTGATTATAAGATATACATACAATAAAGCTTGAGCTATCCCTCTAG
1 TTCAGCTAGCCTGATAAAGGTGATTATAAGATATACATACAATAAAGCTTGAGCTATACCTCTAG
**
5284 AGCAATTGGTTAAACACTCCGGTTTTATGGATAAGA
66 AGCAATTGGTTAAACACTCCGACTTTATGGATAAGA
* *
5320 TTCATCTAGCCAGATAA
1 TTCAGCTAGCCTGATAA
5337 TGGAAAATTA
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
100 77 0.71
101 31 0.29
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (101 bp):
TTCAGCTAGCCTGATAAAGGTGATTATAAGATATACATACAATAAAGCTTGAGCTATACCTCTAG
AGCAATTGGTTAAACACTCCGACTTTATGGATAAGA
Found at i:6418 original size:66 final size:66
Alignment explanation
Indices: 6299--6440 Score: 169
Period size: 66 Copynumber: 2.1 Consensus size: 66
6289 TTTTCTAAAA
* * * **
6299 AAACAAAATTTTGTCTCTTTTGAGACAATTTCTTTTTAAGAAAAATCTTTGAGTTTGTTT-TTTT
1 AAACAAAATTTTGTCTCTTTTGAGACAACTTCTTTTGAAGAAAAATCTCTGAGTAGGTTTCTTTT
6363 GG
66 -G
* * * **
6365 AAACAAAATTTTGTCTCTTTTGAGATAGCTTCTTTTGAAGCATCATCTCTGAGTAGGTTTCTTTT
1 AAACAAAATTTTGTCTCTTTTGAGACAACTTCTTTTGAAGAAAAATCTCTGAGTAGGTTTCTTTT
6430 G
66 G
6431 AAACCAAAAT
1 AAA-CAAAAT
6441 CCTTAGATGG
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
66 54 0.84
67 10 0.16
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.44
Consensus pattern (66 bp):
AAACAAAATTTTGTCTCTTTTGAGACAACTTCTTTTGAAGAAAAATCTCTGAGTAGGTTTCTTTT
G
Found at i:6772 original size:134 final size:127
Alignment explanation
Indices: 6457--6765 Score: 359
Period size: 134 Copynumber: 2.4 Consensus size: 127
6447 ATGGCTAAGA
* * *
6457 TTCATCATAGTATGAGCAGTGTCAT-CCCCGACCAGATCTCCTTATTATATAGGAGTTGTGTCAA
1 TTCATCAT-GTATGAGCAGTGTCATCCCCCGACCAGATCTCCTCATTATATAGGAGCTATGTCAA
* * * *** * *
6521 CCCGATAACCATTCGTCCTCATCACGTAGGAGCCGTGTTATCACCTTTAGATGACCAGAACTC
65 CCAGATAACCAGTCGTCCTCATCACATAGGAAAAGAGTTATCACCTTTAGATGACAAGAACTC
* * * * * *
6584 TTCATCACGTATGAGTAGTGTCATCACCTGACCAGATTTTCTCATTATATAGGAGCTATGTCAAT
1 TTCATCATGTATGAGCAGTGTCATCCCCCGACCAGATCTCCTCATTATATAGGAGCTATGTCAA-
* *
6649 CTAGATAACCAGTCGTCCTCATCACATAGGAAAAGAGTTATCACCCTTCCTAAAGATAGGCAAGA
65 CCAGATAACCAGTCGTCCTCATCACATAGGAAAAGAGTTATCA-CCTT--T--AGAT-GACAAGA
6714 ACTC
124 ACTC
*
6718 TTCATCATGTATGAGCAGTGTCATCCCCCGACTAGATCTCCTCATTAT
1 TTCATCATGTATGAGCAGTGTCATCCCCCGACCAGATCTCCTCATTAT
6766 GCAGGAGTCG
Statistics
Matches: 148, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
126 15 0.10
127 39 0.26
128 35 0.24
129 4 0.03
131 1 0.01
133 4 0.03
134 50 0.34
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (127 bp):
TTCATCATGTATGAGCAGTGTCATCCCCCGACCAGATCTCCTCATTATATAGGAGCTATGTCAAC
CAGATAACCAGTCGTCCTCATCACATAGGAAAAGAGTTATCACCTTTAGATGACAAGAACTC
Found at i:7001 original size:9 final size:9
Alignment explanation
Indices: 6972--7014 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 9
6962 GGGTCGAAAA
6972 AATATTATT
1 AATATTATT
6981 AAATATTATT
1 -AATATTATT
6991 ATTACTATTATT
1 A--A-TATTATT
7003 AATATTATT
1 AATATTATT
7012 AAT
1 AAT
7015 TTACATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 11 0.37
10 10 0.33
11 1 0.03
12 8 0.27
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (9 bp):
AATATTATT
Found at i:12595 original size:38 final size:38
Alignment explanation
Indices: 12553--12645 Score: 159
Period size: 38 Copynumber: 2.4 Consensus size: 38
12543 TCAGATATGG
*
12553 TCTTGGAAGATTATATAATAAATTTGTTTAGGGTGATC
1 TCTTGGAAGATTATATAATAAATTTGTTTAGGATGATC
*
12591 TCTTGGAAGATTATACAATAAATTTGTTTAGGATGATC
1 TCTTGGAAGATTATATAATAAATTTGTTTAGGATGATC
*
12629 TCTTGGAAGACTATATA
1 TCTTGGAAGATTATATA
12646 TAGGGTTGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (38 bp):
TCTTGGAAGATTATATAATAAATTTGTTTAGGATGATC
Found at i:18949 original size:25 final size:25
Alignment explanation
Indices: 18912--18969 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
18902 TCCATGCCCA
18912 TAATAATACTTGACTAGAGATCTTT
1 TAATAATACTTGACTAGAGATCTTT
*
18937 TAATAATATTTGACTAGAGATCTTT
1 TAATAATACTTGACTAGAGATCTTT
18962 TAATAATA
1 TAATAATA
18970 ACAATTATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (25 bp):
TAATAATACTTGACTAGAGATCTTT
Found at i:25586 original size:21 final size:21
Alignment explanation
Indices: 25545--25585 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
25535 TTCATTATAA
*
25545 ATTCTCTTCAAACTTTAAAAT
1 ATTCTCTTCAAACCTTAAAAT
*
25566 ATTCTCTATCAACCCTTAAA
1 ATTCTCT-TCAAACCTTAAA
25586 TCATAAGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTCTCTTCAAACCTTAAAAT
Found at i:34402 original size:21 final size:20
Alignment explanation
Indices: 34378--34418 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34368 AATAATTTTT
*
34378 AAAAGAATTATCATATTAATC
1 AAAAG-ATTACCATATTAATC
*
34399 AAAAGGTTACCATATTAATC
1 AAAAGATTACCATATTAATC
34419 TTCATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (20 bp):
AAAAGATTACCATATTAATC
Found at i:35313 original size:13 final size:13
Alignment explanation
Indices: 35284--35318 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
35274 ATAACTAATA
*
35284 ATATTAAAT-ATT
1 ATATTAAATAAAT
35296 ATATTAAATAAAT
1 ATATTAAATAAAT
35309 ATATTAAATA
1 ATATTAAATA
35319 TTTATGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:38318 original size:8 final size:8
Alignment explanation
Indices: 38305--38345 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
38295 CTCATTTTCA
38305 GAGAATTT
1 GAGAATTT
38313 GAGAATTT
1 GAGAATTT
*
38321 -AGAGTTT
1 GAGAATTT
*
38328 GGGAATTT
1 GAGAATTT
38336 GAGAATTT
1 GAGAATTT
38344 GA
1 GA
38346 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:39119 original size:128 final size:128
Alignment explanation
Indices: 38413--39402 Score: 1881
Period size: 126 Copynumber: 7.8 Consensus size: 128
38403 CTATAATCGG
38413 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
38478 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
38541 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
38605 TATCATTGCCCTATTATGTCATTCATGT-CCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
38667 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
38732 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAG--ATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
38793 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
38858 TATCATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
38920 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
38985 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
39048 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
39113 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
39176 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTT--TCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
39239 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
39302 TTCACCATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTT--TCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
39365 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
39403 ATAACTTAAA
Statistics
Matches: 855, Mismatches: 2, Indels: 12
0.98 0.00 0.01
Matches are distributed among these distances:
125 10 0.01
126 352 0.41
127 243 0.28
128 250 0.29
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (128 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:39366 original size:507 final size:505
Alignment explanation
Indices: 38413--39400 Score: 1872
Period size: 507 Copynumber: 1.9 Consensus size: 505
38403 CTATAATCGG
38413 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
*
38478 TATCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
38543 CACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
131 CACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
38608 CATTGCCCTATTATGTCATTCATGTCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
196 CATTGCCCTATTATGTCACTCATGTCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
38673 ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCAT
261 ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTC-TCAGAGAATATGTTATCAT
* *
38738 TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATCAGTACCTATTATTTCACTATTC
325 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATCAGTACCTATTATTTCACCATTC
38803 ACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCC
390 ACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTC-TCAGAGAATATGTTATCATTGCC
38868 CTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTAT
454 CTATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTAT
38920 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
38985 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
66 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
39050 CACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
131 CACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
39115 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
195 TCATTGCCCTATTATGTCACTCATGT-CCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
39180 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTT-TCAGAGAATATGTTATCA
259 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCTCAGAGAATATGTTATCA
39244 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACCA
324 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAG--ATATCAGTACCTATTATTTCACCA
39309 TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTT-TCAGAGAATATGTTATCATTG
387 TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCTCAGAGAATATGTTATCATTG
39373 CCCTATTATGTCACTCATGTCCCTCGGG
452 CCCTATTATGTCACTCATGTCCCTCGGG
39401 GAATAACTTA
Statistics
Matches: 473, Mismatches: 4, Indels: 8
0.98 0.01 0.02
Matches are distributed among these distances:
507 260 0.55
508 63 0.13
509 150 0.32
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (505 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTT
CACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACT
ATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCTCAGAGAATATGTTATCATT
GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATCAGTACCTATTATTTCACCATTCA
CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCTCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTCATGTCCCTCGGGACACTAGATATATCAGTACCTATTAT
Found at i:39848 original size:33 final size:34
Alignment explanation
Indices: 39787--39882 Score: 124
Period size: 34 Copynumber: 2.9 Consensus size: 34
39777 AAATTTAATG
*
39787 TTAAATTTCGAATACTA-TATTTTATATTTTAAAT
1 TTAAATTTCGAATAATATTATTTT-TATTTTAAAT
* *
39821 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATTATTTTTATTTTAAAT
* *
39854 TTAAATTTCGAATAATATAATTTGTATTT
1 TTAAATTTCGAATAATATTATTTTTATTT
39883 AAAAACATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
33 23 0.42
34 32 0.58
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.56
Consensus pattern (34 bp):
TTAAATTTCGAATAATATTATTTTTATTTTAAAT
Found at i:40422 original size:21 final size:21
Alignment explanation
Indices: 40398--40491 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
40388 TATGGTATAA
*
40398 AACCCTGCGGGCTAGGTATGT
1 AACCCTGCGGGCTAGGAATGT
*
40419 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
*
40440 AA-CATGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
40461 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
40482 AACCCTGCGG
1 AACCCTGCGG
40492 AGATGGCATA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 3 0.05
21 61 0.92
22 2 0.03
ACGTcount: A:0.21, C:0.24, G:0.35, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:40521 original size:21 final size:21
Alignment explanation
Indices: 40495--40542 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
40485 CCTGCGGAGA
*
40495 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
40516 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
40537 GGGCAT
1 TGGCAT
40543 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:42281 original size:15 final size:14
Alignment explanation
Indices: 42260--42329 Score: 54
Period size: 15 Copynumber: 4.9 Consensus size: 14
42250 AATAATTCTA
42260 AATAAATAATAATT
1 AATAAATAATAATT
* *
42274 ATATAAATATTATTT
1 A-ATAAATAATAATT
* *
42289 AATAAAAAAATATTT
1 AAT-AAATAATAATT
42304 ACATAAAT-AT-ATT
1 A-ATAAATAATAATT
*
42317 AATAAAAAATAAT
1 AATAAATAATAAT
42330 AACTATTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
12 5 0.11
13 5 0.11
14 7 0.16
15 25 0.57
16 2 0.05
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAAATAATAATT
Found at i:42323 original size:28 final size:30
Alignment explanation
Indices: 42267--42329 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
42257 CTAAATAAAT
*
42267 AATAATTATATAAATATTATTTAATAAAAA
1 AATAATTACATAAATATTATTTAATAAAAA
*
42297 AATATTTACATAAATA-TA-TTAAT-AAAA
1 AATAATTACATAAATATTATTTAATAAAAA
42324 AATAAT
1 AATAAT
42330 AACTATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 9 0.30
28 5 0.17
29 2 0.07
30 14 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
AATAATTACATAAATATTATTTAATAAAAA
Found at i:44781 original size:6 final size:7
Alignment explanation
Indices: 44756--44800 Score: 56
Period size: 7 Copynumber: 6.4 Consensus size: 7
44746 CCAAATAATT
*
44756 TTTTTCT
1 TTTTTCA
*
44763 TTTTTACT
1 TTTTT-CA
44771 TTTTTCA
1 TTTTTCA
44778 TTTTTCA
1 TTTTTCA
44785 TTTTTCA
1 TTTTTCA
44792 TTTTT-A
1 TTTTTCA
44798 TTT
1 TTT
44801 ATTTATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
6 4 0.11
7 25 0.69
8 7 0.19
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCA
Found at i:46365 original size:17 final size:17
Alignment explanation
Indices: 46343--46377 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
46333 TAACAACTCG
46343 ATGTGGTA-AAAAGTTAA
1 ATGTGGTACAAAA-TTAA
46360 ATGTGGTACAAAATTAA
1 ATGTGGTACAAAATTAA
46377 A
1 A
46378 GAACCAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.29
Consensus pattern (17 bp):
ATGTGGTACAAAATTAA
Found at i:47186 original size:3 final size:3
Alignment explanation
Indices: 47180--47215 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
47170 GTAATAGTAC
47180 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47216 GGTTGTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Done.