Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004004.1 Hibiscus syriacus cultivar Beakdansim tig00008727_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: 52837
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:309 original size:22 final size:21
Alignment explanation
Indices: 284--324 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
274 CCAGATGTCC
284 AGAGGG-AACCGATTCTCCCCCA
1 AGAGGGTAA-CGATTC-CCCCCA
306 AGAGGGTAACGATTCCCCC
1 AGAGGGTAACGATTCCCCC
325 TGAATGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 12 0.67
23 2 0.11
ACGTcount: A:0.27, C:0.34, G:0.24, T:0.15
Consensus pattern (21 bp):
AGAGGGTAACGATTCCCCCCA
Found at i:4145 original size:11 final size:12
Alignment explanation
Indices: 4115--4140 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4105 GGATTAAAAG
4115 TGCATTTTTAAA
1 TGCATTTTTAAA
4127 TGCATTTTTAAA
1 TGCATTTTTAAA
4139 TG
1 TG
4141 GTTTTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.50
Consensus pattern (12 bp):
TGCATTTTTAAA
Found at i:8273 original size:21 final size:21
Alignment explanation
Indices: 8249--8304 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
8239 TTTACACTTA
*
8249 GGGAATCGAATCCCTATGAGG
1 GGGAACCGAATCCCTATGAGG
*
8270 GGGAACCGATTCCCTATGAGG
1 GGGAACCGAATCCCTATGAGG
* *
8291 GGGTACCGATTCCC
1 GGGAACCGAATCCC
8305 CCACGCTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.25, G:0.32, T:0.20
Consensus pattern (21 bp):
GGGAACCGAATCCCTATGAGG
Found at i:12220 original size:3 final size:3
Alignment explanation
Indices: 12212--12236 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12202 GACCGAAACG
12212 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
12237 TTGGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:13750 original size:14 final size:14
Alignment explanation
Indices: 13731--13758 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13721 TTTTCGTTTC
13731 CCTAAAATTTTATA
1 CCTAAAATTTTATA
13745 CCTAAAATTTTATA
1 CCTAAAATTTTATA
13759 AGTACACTAA
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:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
CCTAAAATTTTATA
Found at i:20499 original size:2 final size:2
Alignment explanation
Indices: 20492--20524 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20482 GTACACAAAT
20492 TA TA 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 TA TA T
20525 TATTACATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21672 original size:14 final size:14
Alignment explanation
Indices: 21653--21679 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21643 GATTGATAAT
21653 TTTAAAAATTAACC
1 TTTAAAAATTAACC
21667 TTTAAAAATTAAC
1 TTTAAAAATTAAC
21680 AATATATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTAAAAATTAACC
Found at i:22347 original size:2 final size:2
Alignment explanation
Indices: 22340--22365 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22330 TCCTCCATTA
22340 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
22366 CAATAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25394 original size:20 final size:21
Alignment explanation
Indices: 25348--25399 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
25338 TAGTAAGTAA
* * *
25348 ATTTATTAATTTAATTATCAT
1 ATTTAATAATTTAATTATAAC
*
25369 AATTAATAATTT-ATTATAAC
1 ATTTAATAATTTAATTATAAC
*
25389 ATTTAAAAATT
1 ATTTAATAATT
25400 AATCATATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTAATAATTTAATTATAAC
Found at i:25456 original size:19 final size:19
Alignment explanation
Indices: 25432--25473 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
25422 TATTATAAAC
25432 TCAAAATCTCACAATTTCA
1 TCAAAATCTCACAATTTCA
* *
25451 TCAAAATCTTATAATTTCA
1 TCAAAATCTCACAATTTCA
25470 TCAA
1 TCAA
25474 TGGTAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (19 bp):
TCAAAATCTCACAATTTCA
Found at i:27931 original size:698 final size:698
Alignment explanation
Indices: 27010--28406 Score: 2758
Period size: 698 Copynumber: 2.0 Consensus size: 698
27000 TATAAAATTA
*
27010 TTTTTTTATCAATACATACATCTAATTATATTTCAGACAATTTTAAGGTATATTAGCAAAAGTGC
1 TTTTTTTAACAATACATACATCTAATTATATTTCAGACAATTTTAAGGTATATTAGCAAAAGTGC
27075 ATTTACATTGCCTCTTAATTTTTTAATTTGTATTTTTATGACCTTATATTAAAAGAATATTAAAA
66 ATTTACATTGCCTCTTAATTTTTTAATTTGTATTTTTATGACCTTATATTAAAAGAATATTAAAA
*
27140 AATAAAAAAAGTATTAGAGCTTATGATGTGAAAATTATAAGGCATTTCGTACCATAAGTAGTAAA
131 AATAAAAAAAGTATTAGAGCTTATGATGTGAAAATTATAAGGCATTTCGTACAATAAGTAGTAAA
27205 ATTAGGTTGAAGAGAGACAGCTGAAGATTTTTTATGAAAATATTTAAATATTTTAATACTTTTTG
196 ATTAGGTTGAAGAGAGACAGCTGAAGATTTTTTATGAAAATATTTAAATATTTTAATACTTTTTG
27270 TTTAATTTCAATTAATAATTAATAATTTATCATTTTATAGCATATTGTACCTGATCAAATATCTT
261 TTTAATTTCAATTAATAATTAATAATTTATCATTTTATAGCATATTGTACCTGATCAAATATCTT
27335 TCACACCTCGAAGTCTTTGGAGAAACCTTTCACAAATTTTCATTGCACCTCGTAATCTCTGGAGT
326 TCACACCTCGAAGTCTTTGGAGAAACCTTTCACAAATTTTCATTGCACCTCGTAATCTCTGGAGT
27400 ACCTTCTCGGAATTAGTATCCTGAAATAACGACTCCAAAAAAGGAGTATCAAACACTCAATACCC
391 ACCTTCTCGGAATTAGTATCCTGAAATAACGACTCCAAAAAAGGAGTATCAAACACTCAATACCC
27465 CTTAAGAATTGTGGAAGACATAAAGAGAAACGTCTTCTGAAGAATGATCTTGAAGATCTAATCTC
456 CTTAAGAATTGTGGAAGACATAAAGAGAAACGTCTTCTGAAGAATGATCTTGAAGATCTAATCTC
27530 GAAAAATAGCAACCTATTGACATAATCTTTGACAGGCCCACGTGACTTATCCTAGTCGAATCTAT
521 GAAAAATAGCAACCTATTGACATAATCTTTGACAGGCCCACGTGACTTATCCTAGTCGAATCTAT
27595 TGTGATTTTGTAATATCCTCAACACCGGGTTAGTGACCAAATTGTAAAACTTTAGAATTTAGTGA
586 TGTGATTTTGTAATATCCTCAACACCGGGTTAGTGACCAAATTGTAAAACTTTAGAATTTAGTGA
27660 CTAAAGTAGATAAATTGAACAATTCAAGGACTTATATGAAAAATTTTG
651 CTAAAGTAGATAAATTGAACAATTCAAGGACTTATATGAAAAATTTTG
27708 TTTTTTTAACAATACATACATCTAATTATATTTCAGACAATTTTAAGGTATATTAGCAAAAGTGC
1 TTTTTTTAACAATACATACATCTAATTATATTTCAGACAATTTTAAGGTATATTAGCAAAAGTGC
*
27773 ATTTACATTTCCTCTTAATTTTTTAATTTGTATTTTTATGACCTTATATTAAAAGAATATTAAAA
66 ATTTACATTGCCTCTTAATTTTTTAATTTGTATTTTTATGACCTTATATTAAAAGAATATTAAAA
27838 AATAAAAAAAGTATTAGAGCTTATGATGTGAAAATTATAAGGCATTTCGTACAATAAGTAGTAAA
131 AATAAAAAAAGTATTAGAGCTTATGATGTGAAAATTATAAGGCATTTCGTACAATAAGTAGTAAA
27903 ATTAGGTTGAAGAGAGACAGCTGAAGATTTTTTATGAAAATATTTAAATATTTTAATACTTTTTG
196 ATTAGGTTGAAGAGAGACAGCTGAAGATTTTTTATGAAAATATTTAAATATTTTAATACTTTTTG
27968 TTTAATTTCAATTAATAATTAATAATTTATCATTTTATAGCATATTGTACCTGATCAAATATCTT
261 TTTAATTTCAATTAATAATTAATAATTTATCATTTTATAGCATATTGTACCTGATCAAATATCTT
28033 TCACACCTCGAAGTCTTTGGAGAAACCTTTCACAAATTTTCATTGCACCTCGTAATCTCTGGAGT
326 TCACACCTCGAAGTCTTTGGAGAAACCTTTCACAAATTTTCATTGCACCTCGTAATCTCTGGAGT
28098 ACCTTCTCGGAATTAGTATCCTGAAATAACGACTCCAAAAAAGGAGTATCAAACACTCAATACCC
391 ACCTTCTCGGAATTAGTATCCTGAAATAACGACTCCAAAAAAGGAGTATCAAACACTCAATACCC
28163 CTTAAGAATTGTGGAAGACATAAAGAGAAACGTCTTCTGAAGAATGATCTTGAAGATCTAATCTC
456 CTTAAGAATTGTGGAAGACATAAAGAGAAACGTCTTCTGAAGAATGATCTTGAAGATCTAATCTC
28228 GAAAAATAGCAACCTATTGACATAATCTTTGACAGGCCCACGTGACTTATCCTAGTCGAATCTAT
521 GAAAAATAGCAACCTATTGACATAATCTTTGACAGGCCCACGTGACTTATCCTAGTCGAATCTAT
*
28293 TGTGATTTTGTAATATCCTCAACATCGGGTTAGTGACCAAATTGTAAAACTTTAGAATTTAGTGA
586 TGTGATTTTGTAATATCCTCAACACCGGGTTAGTGACCAAATTGTAAAACTTTAGAATTTAGTGA
28358 CTAAAGTAGATAAATTGAACAATTCAAGGACTTATATGAAAAATTTTG
651 CTAAAGTAGATAAATTGAACAATTCAAGGACTTATATGAAAAATTTTG
28406 T
1 T
28407 GTAGGACTAA
Statistics
Matches: 695, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
698 695 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (698 bp):
TTTTTTTAACAATACATACATCTAATTATATTTCAGACAATTTTAAGGTATATTAGCAAAAGTGC
ATTTACATTGCCTCTTAATTTTTTAATTTGTATTTTTATGACCTTATATTAAAAGAATATTAAAA
AATAAAAAAAGTATTAGAGCTTATGATGTGAAAATTATAAGGCATTTCGTACAATAAGTAGTAAA
ATTAGGTTGAAGAGAGACAGCTGAAGATTTTTTATGAAAATATTTAAATATTTTAATACTTTTTG
TTTAATTTCAATTAATAATTAATAATTTATCATTTTATAGCATATTGTACCTGATCAAATATCTT
TCACACCTCGAAGTCTTTGGAGAAACCTTTCACAAATTTTCATTGCACCTCGTAATCTCTGGAGT
ACCTTCTCGGAATTAGTATCCTGAAATAACGACTCCAAAAAAGGAGTATCAAACACTCAATACCC
CTTAAGAATTGTGGAAGACATAAAGAGAAACGTCTTCTGAAGAATGATCTTGAAGATCTAATCTC
GAAAAATAGCAACCTATTGACATAATCTTTGACAGGCCCACGTGACTTATCCTAGTCGAATCTAT
TGTGATTTTGTAATATCCTCAACACCGGGTTAGTGACCAAATTGTAAAACTTTAGAATTTAGTGA
CTAAAGTAGATAAATTGAACAATTCAAGGACTTATATGAAAAATTTTG
Found at i:34845 original size:19 final size:20
Alignment explanation
Indices: 34811--34848 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
34801 CGTGCATAAG
*
34811 TGATATATGTTTATATGTTT
1 TGATACATGTTTATATGTTT
34831 TGATACATG-TTATATGTT
1 TGATACATGTTTATATGTT
34849 ACATGTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.26, C:0.03, G:0.16, T:0.55
Consensus pattern (20 bp):
TGATACATGTTTATATGTTT
Found at i:35110 original size:23 final size:22
Alignment explanation
Indices: 35078--35120 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
35068 AGTCAAGGGT
35078 TACATAGGTCATTCGGGACATA
1 TACATAGGTCATTCGGGACATA
*
35100 TACATGAGGTCCTTCGGGACA
1 TACAT-AGGTCATTCGGGACA
35121 AATTTCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (22 bp):
TACATAGGTCATTCGGGACATA
Found at i:36205 original size:30 final size:30
Alignment explanation
Indices: 36153--36216 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
36143 TTTATTTTAA
*
36153 AAAAAATTAAATAAACCTTCAAATTCGACC
1 AAAAAATTAAATAAACCTTCAAACTCGACC
* * *
36183 AAAAAATTAATTAAGTCC-TCAAACTCGATC
1 AAAAAATTAAATAA-ACCTTCAAACTCGACC
36213 AAAA
1 AAAA
36217 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.53, C:0.19, G:0.05, T:0.23
Consensus pattern (30 bp):
AAAAAATTAAATAAACCTTCAAACTCGACC
Found at i:36700 original size:39 final size:39
Alignment explanation
Indices: 36656--36732 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
36646 GGTTAGATTC
*
36656 AACTTAAAATGTTATATTCTTT-ATAACATTTGCAGTTGT
1 AACTTAAAATGTTACATT-TTTCATAACATTTGCAGTTGT
* *
36695 AACTTAAAATGTTACATTTTTCATAATATTTTCAGTTG
1 AACTTAAAATGTTACATTTTTCATAACATTTGCAGTTG
36733 CCAAACGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 3 0.09
39 31 0.91
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (39 bp):
AACTTAAAATGTTACATTTTTCATAACATTTGCAGTTGT
Found at i:38540 original size:64 final size:65
Alignment explanation
Indices: 38416--38571 Score: 210
Period size: 64 Copynumber: 2.4 Consensus size: 65
38406 TACACTAGGG
* * * * *
38416 GTGCATCGATGCATAAAATACATTCGATGTTTCAAACAAGTCTGGAGTGCATCGATGCATG-GTC
1 GTGCATCGATACACAAAATGCATTCGATGTTTCAAACAAGTCAGGAGTGCATCGATGCATGCCT-
38480 T
65 T
* *
38481 GTGCATCGGTACACAAAATGCATTCGATG-TTCAAA-ATATTCAGGAGTGCATCGATGCATGCCT
1 GTGCATCGATACACAAAATGCATTCGATGTTTCAAACA-AGTCAGGAGTGCATCGATGCATGCCT
38544 T
65 T
38545 GTGCATCGATACACAAAATGCATTCGA
1 GTGCATCGATACACAAAATGCATTCGA
38572 AATGGGTGTG
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
63 1 0.01
64 54 0.67
65 26 0.32
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (65 bp):
GTGCATCGATACACAAAATGCATTCGATGTTTCAAACAAGTCAGGAGTGCATCGATGCATGCCTT
Found at i:39201 original size:17 final size:17
Alignment explanation
Indices: 39179--39212 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39169 GATAGAGAGT
*
39179 AATATTTTTAATAATTA
1 AATATTTATAATAATTA
*
39196 AATATTTATATTAATTA
1 AATATTTATAATAATTA
39213 TTTTATATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATTTATAATAATTA
Found at i:39214 original size:13 final size:13
Alignment explanation
Indices: 39194--39252 Score: 59
Period size: 12 Copynumber: 4.6 Consensus size: 13
39184 TTTTAATAAT
39194 TAAA-TATTTATA
1 TAAATTATTTATA
*
39206 TTAATTATTTTATA
1 TAAATTA-TTTATA
*
39220 TAAAGTATTTATA
1 TAAATTATTTATA
**
39233 TGCATT-TTTATA
1 TAAATTATTTATA
39245 TAAATTAT
1 TAAATTAT
39253 CTCTATTCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
12 13 0.36
13 12 0.33
14 11 0.31
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (13 bp):
TAAATTATTTATA
Found at i:39246 original size:27 final size:26
Alignment explanation
Indices: 39194--39249 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
39184 TTTTAATAAT
*
39194 TAAATATTTATATTAATTATTTTATA
1 TAAATATTTATATGAATTATTTTATA
*
39220 TAAAGTATTTATATGCA-T-TTTTATA
1 TAAA-TATTTATATGAATTATTTTATA
39245 TAAAT
1 TAAAT
39250 TATCTCTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 11 0.41
26 5 0.19
27 10 0.37
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (26 bp):
TAAATATTTATATGAATTATTTTATA
Found at i:39263 original size:25 final size:25
Alignment explanation
Indices: 39213--39265 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
39203 ATATTAATTA
*
39213 TTTTATATAAAGTATTTATATGCAT
1 TTTTATATAAAGTATCTATATGCAT
* * *
39238 TTTTATATAAATTATCTCTATTCAT
1 TTTTATATAAAGTATCTATATGCAT
39263 TTT
1 TTT
39266 AAATATGCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.57
Consensus pattern (25 bp):
TTTTATATAAAGTATCTATATGCAT
Found at i:40348 original size:2 final size:2
Alignment explanation
Indices: 40341--40370 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
40331 TTTAAATCCA
40341 CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
40371 CCTGAGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:43239 original size:2 final size:2
Alignment explanation
Indices: 43234--43271 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
43224 TTTTATCAAA
43234 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
43272 TTAATATCAT
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:44494 original size:19 final size:18
Alignment explanation
Indices: 44472--44521 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
44462 AGAAAATTAT
44472 TAATAAAAATAAAAATATC
1 TAAT-AAAATAAAAATATC
*
44491 TAAT-TAATAAAAATATC
1 TAATAAAATAAAAATATC
*
44508 TAAGACAAATAAAA
1 TAATA-AAATAAAA
44522 TCTAGACCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 15 0.58
19 11 0.42
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (18 bp):
TAATAAAATAAAAATATC
Found at i:45311 original size:24 final size:24
Alignment explanation
Indices: 45284--45338 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
45274 TTATTTAACG
*
45284 TTCGTTTAAATGTTTGTGAACACA
1 TTCGTTTAAATGTTCGTGAACACA
* * *
45308 TTCGTTT-AGTGTTCGTGGACATA
1 TTCGTTTAAATGTTCGTGAACACA
45331 TTCGTTTA
1 TTCGTTTA
45339 GTATTCGCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (24 bp):
TTCGTTTAAATGTTCGTGAACACA
Found at i:45320 original size:23 final size:23
Alignment explanation
Indices: 45301--45385 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
45291 AAATGTTTGT
* *
45301 GAACACATTCGTTTAGTGTTCGT
1 GAACATATTCGTTTAGTGTTCGC
* *
45324 GGACATATTCGTTTAGTATTCGC
1 GAACATATTCGTTTAGTGTTCGC
* *
45347 GAACATGTTCATTTAGTGTTCGC
1 GAACATATTCGTTTAGTGTTCGC
*
45370 GAACATGTTCGTTTAG
1 GAACATATTCGTTTAG
45386 AATAAAAAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (23 bp):
GAACATATTCGTTTAGTGTTCGC
Found at i:52648 original size:14 final size:13
Alignment explanation
Indices: 52629--52659 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
52619 CCGTTATCAA
52629 TTTTTCGGTATTAT
1 TTTTTCGGTA-TAT
52643 TTTTTCGGTATAT
1 TTTTTCGGTATAT
52656 TTTT
1 TTTT
52660 CCGCTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.13, C:0.06, G:0.13, T:0.68
Consensus pattern (13 bp):
TTTTTCGGTATAT
Done.