Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003436.1 Hibiscus syriacus cultivar Beakdansim tig00007243_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: 78460
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7466 original size:33 final size:33
Alignment explanation
Indices: 7427--7517 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
7417 ATGAAAAAGG
7427 AAATAAAAAATATTAATATAAGAATAATAAAA-T
1 AAATAAAAAATATTAATA-AAGAATAATAAAATT
* *
7460 AAATAAAATAGATTAATAAAG-ATAAATAAAATT
1 AAATAAAAAATATTAATAAAGAAT-AATAAAATT
* * *
7493 GAGTAAAAAATAATAATAAA-AATAA
1 AAATAAAAAATATTAATAAAGAATAA
7518 AAACACAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
31 2 0.04
32 12 0.25
33 34 0.71
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.25
Consensus pattern (33 bp):
AAATAAAAAATATTAATAAAGAATAATAAAATT
Found at i:7514 original size:13 final size:13
Alignment explanation
Indices: 7496--7551 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 13
7486 TAAAATTGAG
7496 TAAAAAATAATAA
1 TAAAAAATAATAA
*
7509 T-AAAAATAAAAA
1 TAAAAAATAATAA
* *
7521 CACAAAATAA-AA
1 TAAAAAATAATAA
7533 TAAAATAA-AATAA
1 TAAAA-AATAATAA
7546 TAAAAA
1 TAAAAA
7552 GGGTAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 18 0.51
13 17 0.49
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAAAATAATAA
Found at i:7550 original size:23 final size:22
Alignment explanation
Indices: 7427--7550 Score: 85
Period size: 23 Copynumber: 5.5 Consensus size: 22
7417 ATGAAAAAGG
* *
7427 AAATAA-AAAAT-ATTAATATA
1 AAATAATAAAATAAATAAAATA
7447 AGAATAATAAAATAAATAAAATA
1 A-AATAATAAAATAAATAAAATA
* * *
7470 GATTAATAAAGATAAATAAAATT
1 AAATAATAAA-ATAAATAAAATA
* *
7493 GAGTAA-AAAATAATAATAAAAATA
1 AAATAATAAAAT-A-AAT-AAAATA
*
7517 AAA-ACACAAAATAAAATAAAATA
1 AAATA-ATAAAAT-AAATAAAATA
7540 AAATAATAAAA
1 AAATAATAAAA
7551 AGGGTAAATT
Statistics
Matches: 84, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.01
21 7 0.08
22 17 0.20
23 41 0.49
24 11 0.13
25 7 0.08
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (22 bp):
AAATAATAAAATAAATAAAATA
Found at i:19352 original size:62 final size:62
Alignment explanation
Indices: 19255--19375 Score: 208
Period size: 62 Copynumber: 2.0 Consensus size: 62
19245 ATAGCATCCC
* *
19255 AAACATCAAGATCGATGGATTGGATGAACAACATCATCATATTCTTCCAATATGAATAACCT
1 AAACATCAAGATCGATGGATTGAATGAACAACATCATCATATTCTTCCAATAGGAATAACCT
19317 AAACATCAAGATCGATGGATTGAAT-AGACAACATCATCATATTCTTCCAATAGGAATAA
1 AAACATCAAGATCGATGGATTGAATGA-ACAACATCATCATATTCTTCCAATAGGAATAA
19376 TTTGCACCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
61 1 0.02
62 55 0.98
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (62 bp):
AAACATCAAGATCGATGGATTGAATGAACAACATCATCATATTCTTCCAATAGGAATAACCT
Found at i:23524 original size:16 final size:17
Alignment explanation
Indices: 23486--23551 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 17
23476 ACATCATCCA
*
23486 TAAATATAATTAAATATT
1 TAAATA-AATAAAATATT
23504 T-AATAAATAAAAT-TT
1 TAAATAAATAAAATATT
23519 TAAAT-AAT-AAATGACTT
1 TAAATAAATAAAAT-A-TT
*
23536 TAAAAGAAATAAAATA
1 T-AAATAAATAAAATA
23552 GTATATTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
14 4 0.10
15 6 0.15
16 10 0.26
17 7 0.18
18 4 0.10
19 4 0.10
20 4 0.10
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (17 bp):
TAAATAAATAAAATATT
Found at i:25232 original size:19 final size:17
Alignment explanation
Indices: 25190--25224 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25180 AATAGGAGTC
25190 TAATTTTTTTTAATATT
1 TAATTTTTTTTAATATT
25207 TAATTTTTTGTT-ATATT
1 TAATTTTTT-TTAATATT
25224 T
1 T
25225 TTTATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TAATTTTTTTTAATATT
Found at i:26552 original size:10 final size:10
Alignment explanation
Indices: 26537--26584 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
26527 TTTTTTTAAT
*
26537 GATTAAATTA
1 GATTAAAGTA
26547 GATTAAAGTA
1 GATTAAAGTA
*
26557 GATTAAATTA
1 GATTAAAGTA
26567 GATTAAAGTA
1 GATTAAAGTA
26577 GAATTAAA
1 G-ATTAAA
26585 ATATATAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
10 28 0.82
11 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (10 bp):
GATTAAAGTA
Found at i:26562 original size:20 final size:20
Alignment explanation
Indices: 26537--26584 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
26527 TTTTTTTAAT
26537 GATTAAATTAGATTAAAGTA
1 GATTAAATTAGATTAAAGTA
26557 GATTAAATTAGATTAAAGTA
1 GATTAAATTAGATTAAAGTA
26577 GAATTAAA
1 G-ATTAAA
26585 ATATATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (20 bp):
GATTAAATTAGATTAAAGTA
Found at i:27097 original size:14 final size:14
Alignment explanation
Indices: 27078--27116 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
27068 TAATGGGGAG
27078 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
27092 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
27106 GAATCTCTGCA
1 TAATCCCTGCA
27117 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:28208 original size:22 final size:22
Alignment explanation
Indices: 28182--28238 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
28172 ATAATCAATT
*
28182 ATAACAAATTTATTTAGTCACA
1 ATAACAAATTTATTTAGTCAAA
* * *
28204 ATAACATATTAAATTTTGTCAAA
1 ATAACAAATT-TATTTAGTCAAA
28227 ATAA-AAATTTAT
1 ATAACAAATTTAT
28239 GTTAAATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.07
22 13 0.46
23 13 0.46
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.39
Consensus pattern (22 bp):
ATAACAAATTTATTTAGTCAAA
Found at i:28435 original size:186 final size:187
Alignment explanation
Indices: 27990--28462 Score: 529
Period size: 186 Copynumber: 2.5 Consensus size: 187
27980 AAATTATGAT
* * * * * * * * *
27990 AATTTATTTAGACAAAATAACAAATTAAATTTAGTTAAAATAAAAAATCATGTCAATTTTATTTA
1 AATTTATTTAGTCACAATAACATAGTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTT
* * * *
28055 GTCAAAATA-TTTTCTCAAAATAACAAATAATGAAAATTTTAAATAGTTACATTAACAAATTATA
66 GTCAAAATATTTTTCTCAAAATAAC---------AACTTTTGAGT-GATA-A-TAACAAATTATA
* * * * * *
28119 ATAAATATTAATTTCTCAATATAAAAATTTATGACAAATAATATTTTTTCACAATAATCAATTAT
119 ACAAATATTAATTCCTCAATATAAAAAATTACGACAAATAATATTCTTTCACAATAATCAAGTAT
28184 AACA
184 AACA
* * *
28188 AATTTATTTAGTCACAATAACATATTAAATTTTGTCAAAATAAAAATTTATGTTAAATTTATTTT
1 AATTTATTTAGTCACAATAACATAGTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTT
* *
28253 GTCAAAATA-TTTTCTCAAAATAACAACTTTTGAGTGATAATAACAATTTATAGCAAATATTAAT
66 GTCAAAATATTTTTCTCAAAATAACAACTTTTGAGTGATAATAACAAATTATAACAAATATTAAT
*
28317 TCCTCAATATAAAAAATTACGACAAATAATATTCTTTCACAATAA-CAAAGTGTAACA
131 TCCTCAATATAAAAAATTACGACAAATAATATTCTTTCACAATAATC-AAGTATAACA
** *
28374 AATTTATTTTTTTACAATAACATAGTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTT
1 AATTTATTTAGTCACAATAACATAGTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTT
* * *
28439 GTTACAATATTTTTTTCAAAATAA
66 GTCAAAATATTTTTCTCAAAATAA
28463 AAAATTATAA
Statistics
Matches: 241, Mismatches: 32, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
185 1 0.00
186 136 0.56
187 14 0.06
188 3 0.01
189 8 0.03
198 79 0.33
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (187 bp):
AATTTATTTAGTCACAATAACATAGTAAATTTAGTCAAAATAAAAATTTATGTCAAATTTATTTT
GTCAAAATATTTTTCTCAAAATAACAACTTTTGAGTGATAATAACAAATTATAACAAATATTAAT
TCCTCAATATAAAAAATTACGACAAATAATATTCTTTCACAATAATCAAGTATAACA
Found at i:28573 original size:16 final size:17
Alignment explanation
Indices: 28554--28599 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
28544 ATATTCTTTC
28554 ACAATAACAAATT-GTA
1 ACAATAACAAATTAGTA
* *
28570 ACAA-AACAATTTAGTC
1 ACAATAACAAATTAGTA
*
28586 ACAATAACACATTA
1 ACAATAACAAATTA
28600 AATTTAGCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 7 0.29
16 10 0.42
17 7 0.29
ACGTcount: A:0.54, C:0.17, G:0.04, T:0.24
Consensus pattern (17 bp):
ACAATAACAAATTAGTA
Found at i:28751 original size:198 final size:199
Alignment explanation
Indices: 28291--28784 Score: 702
Period size: 199 Copynumber: 2.5 Consensus size: 199
28281 TTTGAGTGAT
* **
28291 AATAACAATTTATAGCAAATATTAATTCCTCAATATAAAAAATTACGACAAATAATATTCTTTCA
1 AATAACAATTTATAACAAATATTAATTCCTCAATATAAAAAATTGTGACAAATAATATTCTTTCA
* * ** * * * *
28356 CAATAACAAAGTGTAACAAATTTATTTTTTTACAATAACATAGTAAATTTAGTCAAAATAAAAAT
66 CAATAACAAATTGTAACAAAATTATTTAGTCACAATAACACAGTAAATTTAGCCAAAATAAAAAG
* * *
28421 TTATGTCAAATTTATTTTGTTACAATATTTTTTTCAAAATAAAAAATTATAACAAATTTATTTAA
131 TTATGTCAAATTTATTTCGTCACAATATTTTTGTCAAAATAAAAAATTATAACAAATTTATTTAA
*
28486 TCAA
196 TAAA
* * * *
28490 AATAATACTTTATAAAAAATATTAATTCCTCAATATAAAAAATTGTGACAGATAATATTCTTTCA
1 AATAACAATTTATAACAAATATTAATTCCTCAATATAAAAAATTGTGACAAATAATATTCTTTCA
** * *
28555 CAATAACAAATTGTAACAAAACAATTTAGTCACAATAACACATTAAATTTAGCCAAAGTAAAAAG
66 CAATAACAAATTGTAACAAAATTATTTAGTCACAATAACACAGTAAATTTAGCCAAAATAAAAAG
* * * *
28620 TTATGTCAAATTTATTTCGTCATAATA-TTTTGTCAAAATAAAAAATTGTGATAAATTTATTTAA
131 TTATGTCAAATTTATTTCGTCACAATATTTTTGTCAAAATAAAAAATTATAACAAATTTATTTAA
28684 TAAA
196 TAAA
* * * *
28688 AATAACAATTTATAACAAATATTAATTTCTCATTATAAAAAATCGTGAAAAATAATATTCTTTCA
1 AATAACAATTTATAACAAATATTAATTCCTCAATATAAAAAATTGTGACAAATAATATTCTTTCA
28753 CAATAACAAATTGTAACAAAATTATTTAGTCA
66 CAATAACAAATTGTAACAAAATTATTTAGTCA
28785 AAGTAAAAAG
Statistics
Matches: 258, Mismatches: 37, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
198 123 0.48
199 135 0.52
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (199 bp):
AATAACAATTTATAACAAATATTAATTCCTCAATATAAAAAATTGTGACAAATAATATTCTTTCA
CAATAACAAATTGTAACAAAATTATTTAGTCACAATAACACAGTAAATTTAGCCAAAATAAAAAG
TTATGTCAAATTTATTTCGTCACAATATTTTTGTCAAAATAAAAAATTATAACAAATTTATTTAA
TAAA
Found at i:29633 original size:21 final size:22
Alignment explanation
Indices: 29605--29653 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
29595 GGCAATTAAA
29605 AAAT-TTAAAAGGACAATTT-G
1 AAATATTAAAAGGACAATTTAG
* *
29625 AAATATTAAATGGTCAATTTAG
1 AAATATTAAAAGGACAATTTAG
29647 AAA-ATTA
1 AAATATTA
29654 GTGAGCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (22 bp):
AAATATTAAAAGGACAATTTAG
Found at i:30370 original size:19 final size:19
Alignment explanation
Indices: 30346--30382 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30336 ATGACCAACA
*
30346 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
30365 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
30383 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:30431 original size:20 final size:20
Alignment explanation
Indices: 30408--30472 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
30398 GTTTCCAGAT
* *
30408 TCGCAACACGATTTTGACTA
1 TCGCAACGCGATTATGACTA
*
30428 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
30449 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
30469 TCGC
1 TCGC
30473 GTTGCGATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 2 0.05
20 18 0.49
21 15 0.41
22 2 0.05
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:30461 original size:41 final size:41
Alignment explanation
Indices: 30408--30504 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 41
30398 GTTTCCAGAT
* *
30408 TCGCAACACGATTTTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAA
* ***
30449 TCGCAACGCGATTCTGACTATCGCGTTGCGATAATACAAAA
1 TCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAA
*
30490 TCGCAATGCGATTTT
1 TCGCAACGCGATTTT
30505 CAAAGCACCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (41 bp):
TCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAA
Found at i:30730 original size:26 final size:22
Alignment explanation
Indices: 30647--30719 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
30637 CTATGGCGAC
*
30647 ATCCGTCCCCATCTTCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
30669 ATCCATCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
30691 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
30713 ATCCGTC
1 ATCCGTC
30720 TATCTCCATC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.22, C:0.44, G:0.14, T:0.21
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:31131 original size:19 final size:18
Alignment explanation
Indices: 31109--31152 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
31099 AAATCGCAAC
*
31109 GCGATTTTAGTTTCGCGTT
1 GCGATTTTA-TTTCGAGTT
31128 GCGATTTTTATTTCGAGTT
1 GCGA-TTTTATTTCGAGTT
31147 GCGATT
1 GCGATT
31153 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 16 0.70
20 5 0.22
ACGTcount: A:0.14, C:0.14, G:0.25, T:0.48
Consensus pattern (18 bp):
GCGATTTTATTTCGAGTT
Found at i:31191 original size:20 final size:20
Alignment explanation
Indices: 31168--31208 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
31158 GTTGCGATAG
31168 TCATTTTCGTGTTACGATTT
1 TCATTTTCGTGTTACGATTT
*
31188 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTACGATTT
31208 T
1 T
31209 AAGTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTGTTACGATTT
Found at i:31215 original size:20 final size:20
Alignment explanation
Indices: 31172--31215 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
31162 CGATAGTCAT
* *
31172 TTTCGTGTTACGATTTTCAT
1 TTTCGTGTTACGATTTTAAG
*
31192 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTACGATTTTAAG
31212 TTTC
1 TTTC
31216 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAG
Found at i:34037 original size:19 final size:20
Alignment explanation
Indices: 34000--34038 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
33990 GCAATGCGAA
* *
34000 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTACGATT
34020 TTTA-TTTCGCATTACGATT
1 TTTAGTTTCGCATTACGATT
34039 ATCTTATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTACGATT
Found at i:34070 original size:20 final size:20
Alignment explanation
Indices: 34045--34111 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
34035 GATTATCTTA
**
34045 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCATTTTCGCG
34065 TTGCGATAGTC-TTTTCCGCG
1 TTGCGATAGTCATTTT-CGCG
*
34085 TTGCAATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
*
34105 TTACGAT
1 TTGCGAT
34112 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 34 0.85
21 4 0.10
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:34121 original size:20 final size:20
Alignment explanation
Indices: 34098--34141 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
34088 CAATAGTCAT
34098 TTTCGCGTTACGATTTTAAG
1 TTTCGCGTTACGATTTTAAG
* *
34118 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTACGATTTTAAG
34138 TTTC
1 TTTC
34142 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTACGATTTTAAG
Found at i:34708 original size:21 final size:21
Alignment explanation
Indices: 34615--34722 Score: 101
Period size: 21 Copynumber: 5.1 Consensus size: 21
34605 GCCTGACTCA
*
34615 CCTGTCATCGTTCAAGTGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
34636 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
34657 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
**
34678 CCTCCCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
34699 CCTGTCATCGTTGAAGAGGTC
1 CCTGTCATCGTTCAAGAGGCC
34720 CCT
1 CCT
34723 CCCACCATTC
Statistics
Matches: 68, Mismatches: 17, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
20 1 0.01
21 66 0.97
22 1 0.01
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.26
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:34716 original size:42 final size:42
Alignment explanation
Indices: 34615--34737 Score: 140
Period size: 42 Copynumber: 2.9 Consensus size: 42
34605 GCCTGACTCA
* * * *
34615 CCTGTCATCGTTCAAGTGGCCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCATCGTTCAAGAGGCC
* **
34657 CCTATCATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCATCGTTCAAGAGGCC
* * *
34699 CCTGTCATCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGA-GTCCCCTCCCATCGTTCAAGAG
34738 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 65 0.97
43 2 0.03
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCCATCGTTCAAGAGGCC
Found at i:34736 original size:21 final size:21
Alignment explanation
Indices: 34620--34737 Score: 87
Period size: 21 Copynumber: 5.6 Consensus size: 21
34610 ACTCACCTGT
*
34620 CATCGTTCAAGTGG-CCTCTCC
1 CATCGTTCAAGAGGTCC-CTCC
* * **
34641 TATCGTTCAAGAGGCCCCTAT
1 CATCGTTCAAGAGGTCCCTCC
**
34662 CATCCCTCAAGA-GTCCCCTCC
1 CATCGTTCAAGAGGT-CCCTCC
* **
34683 CATCGTTCAAGAGGCCCCTGT
1 CATCGTTCAAGAGGTCCCTCC
*
34704 CATCGTTGAAGAGGTCCCTCC
1 CATCGTTCAAGAGGTCCCTCC
* *
34725 CACCATTCAAGAG
1 CATCGTTCAAGAG
34738 CCCGATTCAC
Statistics
Matches: 72, Mismatches: 22, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.01
21 68 0.94
22 3 0.04
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGTCCCTCC
Found at i:36282 original size:39 final size:40
Alignment explanation
Indices: 36239--36315 Score: 95
Period size: 39 Copynumber: 1.9 Consensus size: 40
36229 AGGTACACTT
* *
36239 TCGCAACGCTAAA-CTCAAAATCACAA-TCGAAAGTCAAAA
1 TCGCAACGCGAAAGC-CAAAATCACAACGCGAAAGTCAAAA
* *
36278 TCGCAATGCGAAAGCCAAAATCATAACGCGAAAGTCAA
1 TCGCAACGCGAAAGCCAAAATCACAACGCGAAAGTCAA
36316 TTCGCGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 21 0.66
40 11 0.34
ACGTcount: A:0.47, C:0.25, G:0.14, T:0.14
Consensus pattern (40 bp):
TCGCAACGCGAAAGCCAAAATCACAACGCGAAAGTCAAAA
Found at i:36291 original size:20 final size:20
Alignment explanation
Indices: 36242--36315 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
36232 TACACTTTCG
* *
36242 CAACGCTAAACTCAAAATCA
1 CAACGCGAAAGTCAAAATCA
* *
36262 CAA-TCGAAAGTCAAAATCG
1 CAACGCGAAAGTCAAAATCA
* *
36281 CAATGCGAAAGCCAAAATCA
1 CAACGCGAAAGTCAAAATCA
*
36301 TAACGCGAAAGTCAA
1 CAACGCGAAAGTCAA
36316 TTCGCGTTGC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 15 0.35
20 28 0.65
ACGTcount: A:0.49, C:0.24, G:0.14, T:0.14
Consensus pattern (20 bp):
CAACGCGAAAGTCAAAATCA
Found at i:36403 original size:20 final size:20
Alignment explanation
Indices: 36374--36553 Score: 168
Period size: 20 Copynumber: 9.6 Consensus size: 20
36364 GTCAAATTCC
* *
36374 CGATAATCAAATTCACGTTG
1 CGATAGTCAAATTCGCGTTG
*
36394 CGATAGTCAAATTCACGTTG
1 CGATAGTCAAATTCGCGTTG
36414 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
36434 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
*
36454 CGAT--T----TTTGCGTTG
1 CGATAGTCAAATTCGCGTTG
* *
36468 CGATAGTAAAATTCACGTTG
1 CGATAGTCAAATTCGCGTTG
* **
36488 CAATAGTCAAATTCATGTTG
1 CGATAGTCAAATTCGCGTTG
* *
36508 TGAT--T----TTTGCGTTG
1 CGATAGTCAAATTCGCGTTG
36522 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
*
36542 TGATAGTCAAAT
1 CGATAGTCAAAT
36554 GAATGTGTAA
Statistics
Matches: 132, Mismatches: 16, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
14 21 0.16
16 2 0.02
18 2 0.02
20 107 0.81
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:36405 original size:35 final size:37
Alignment explanation
Indices: 36354--36447 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 37
36344 GCGATTTTCT
*
36354 CGTTACGATAGTCAAATTC-C-CGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCACGCGATAATCAAATTCA
* *
36389 CGTTGCGATAGTCAAATTCACGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCAC---GCGATAATCAAATTCA
36429 CGTTGCGATAGTCAAATTC
1 CGTTGCGATAGTCAAATTC
36448 GCGTTGCGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
35 18 0.35
36 1 0.02
40 32 0.63
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (37 bp):
CGTTGCGATAGTCAAATTCACGCGATAATCAAATTCA
Found at i:36471 original size:34 final size:36
Alignment explanation
Indices: 36315--36488 Score: 130
Period size: 34 Copynumber: 4.9 Consensus size: 36
36305 GCGAAAGTCA
*
36315 ATTCGCGTTGCGATAGTCTAA-T-ACGATTTGCGAT-T
1 ATTCGCGTTGCGATAGTCAAATTCACG--TTGCGATAT
* * * * * *
36350 -TTCTCGTTACGATAGTCAAATTCCCGAT--AATCAA
1 ATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT-AT
*
36384 ATTCACGTTGCGATAGTCAAATTCACGTTGCGATAGT
1 ATTCGCGTTGCGATAGTCAAATTCACGTTGCGATA-T
*
36421 CAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT-T
1 ---ATTCGCGTTGCGATAGTCAAATTCACGTTGCGATAT
* *
36459 -TTTGCGTTGCGATAGTAAAATTCACGTTGC
1 ATTCGCGTTGCGATAGTCAAATTCACGTTGC
36489 AATAGTCAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 23
0.73 0.12 0.15
Matches are distributed among these distances:
32 2 0.02
34 45 0.41
35 25 0.23
36 3 0.03
37 2 0.02
38 1 0.01
40 32 0.29
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (36 bp):
ATTCGCGTTGCGATAGTCAAATTCACGTTGCGATAT
Found at i:36480 original size:54 final size:54
Alignment explanation
Indices: 36305--36553 Score: 237
Period size: 54 Copynumber: 4.6 Consensus size: 54
36295 AAATCATAAC
* *
36305 GCGAAAGTC-AATTCGCGTTGCGATAGTCTAA-T-ACGATTTGCGATTTTCT-CGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCACG--TTGCGATTTT-TGCGTT
* * **
36358 ACGATAGTCAAATTC-C----CGATAATCAAATTCACGTTGCGATAGTCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGAT--T----TTTGCGTT
*
36413 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGATTTTTGCGTT
* * * * *
36467 GCGATAGTAAAATTCACGTTGCAATAGTCAAATTCATGTTGTGATTTTTGCGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGATTTTTGCGTT
*
36521 GCGATAGTCAAATTCGCGTTGTGATAGTCAAAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
36554 GAATGTGTAA
Statistics
Matches: 161, Mismatches: 20, Indels: 29
0.77 0.10 0.14
Matches are distributed among these distances:
49 16 0.10
50 1 0.01
51 4 0.02
53 8 0.05
54 88 0.55
55 20 0.12
56 1 0.01
58 1 0.01
60 22 0.14
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (54 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCACGTTGCGATTTTTGCGTT
Found at i:36779 original size:139 final size:140
Alignment explanation
Indices: 36524--36805 Score: 512
Period size: 139 Copynumber: 2.0 Consensus size: 140
36514 TTGCGTTGCG
*
36524 ATAGTCAAATTCGCGTTGTGATAGTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATAGTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
36589 TAGCAATGTTCAAACTCAAGTTAATAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAACAATGTTCAAACTCAAGTTAATAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
36654 AATACAAATA
131 AATACAAATA
*
36664 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACA-ATCA
1 ATAGTCAAATTCGCGTTGCGATAGTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
36728 TAACAATGTTCAAACTCAAGTTATTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAACAATGTTCAAACTCAAGTTAATAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
*
36793 AATACACATA
131 AATACAAATA
36803 ATA
1 ATA
36806 CAATGTTTGC
Statistics
Matches: 137, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
139 79 0.58
140 58 0.42
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATAGTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAACAATGTTCAAACTCAAGTTAATAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACAAATA
Found at i:40066 original size:20 final size:20
Alignment explanation
Indices: 40017--40066 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
40007 TTGAAATTCA
*
40017 GCGTTGCGACAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
40037 GCGTTGCGATAGTCAGAATC
1 GCGTTGCGATAGTCAGAATC
*
40057 GCGTTACGAT
1 GCGTTGCGAT
40067 TTACATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (20 bp):
GCGTTGCGATAGTCAGAATC
Found at i:40185 original size:20 final size:19
Alignment explanation
Indices: 40162--40207 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40152 GGAAACTGAT
* *
40162 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
40182 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
40201 TTGCGAT
1 TTGCGAT
40208 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:40197 original size:19 final size:19
Alignment explanation
Indices: 40173--40209 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40163 TGCGATACTG
*
40173 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
40192 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
40210 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:41298 original size:17 final size:17
Alignment explanation
Indices: 41276--41311 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41266 CGTGAAGTAG
41276 ATTAGGATTAGTTTAAT
1 ATTAGGATTAGTTTAAT
*
41293 ATTAGGTTTAGTTTAAT
1 ATTAGGATTAGTTTAAT
41310 AT
1 AT
41312 ATATATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (17 bp):
ATTAGGATTAGTTTAAT
Found at i:41742 original size:14 final size:14
Alignment explanation
Indices: 41723--41753 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41713 AAAAATGAGG
*
41723 TTTTTTATTTTTAT
1 TTTTTTATTATTAT
41737 TTTTTTATTATTAT
1 TTTTTTATTATTAT
41751 TTT
1 TTT
41754 AGTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTATTATTAT
Found at i:44313 original size:6 final size:6
Alignment explanation
Indices: 44302--44337 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
44292 TAACACCTTG
*
44302 TGCATT TGCATT TGCATT TGCATT CGCATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT TGCATT
44338 CTTATTCGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (6 bp):
TGCATT
Found at i:50641 original size:42 final size:42
Alignment explanation
Indices: 50579--50671 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
50569 ACTTTGTAAG
* *
50579 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
50621 TCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
50663 TCCTTAGGG
1 TCCTTAGGG
50672 TAATTTGTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (42 bp):
TCCTTAGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:50728 original size:13 final size:13
Alignment explanation
Indices: 50710--50734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50700 TGAAGCAAAC
50710 CCATCAGTAAGTG
1 CCATCAGTAAGTG
50723 CCATCAGTAAGT
1 CCATCAGTAAGT
50735 CTTTCGAGCA
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:50762 original size:22 final size:21
Alignment explanation
Indices: 50730--50806 Score: 59
Period size: 22 Copynumber: 3.6 Consensus size: 21
50720 GTGCCATCAG
*
50730 TAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
* *
50751 TGAAGTCCTTCGGGCCAT--TAA
1 T-AAGTCCTTCGAG-CATGATGA
* *
50772 TAAGTCTTTCAAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
*
50793 TTAAATCCTTCGAG
1 -TAAGTCCTTCGAG
50807 AAATTTGTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
19 3 0.07
20 9 0.22
21 6 0.15
22 20 0.49
23 3 0.07
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (21 bp):
TAAGTCCTTCGAGCATGATGA
Found at i:50781 original size:42 final size:42
Alignment explanation
Indices: 50722--51054 Score: 176
Period size: 42 Copynumber: 8.1 Consensus size: 42
50712 ATCAGTAAGT
*
50722 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
1 GCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
* * * * *
50764 GCCATTAATAAGTCTTTCAAGCATGATGATTAAATCCTTCGA
1 GCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
** * * * * ***
50806 GAAATTTGTAAGCCTTT--ATGGAAGA-GTAGTGAAGT-AAAC--
1 GCCATTAGTAAGTCTTTCGA-GCATGATG-A-TGAAGTCCTTCGG
** *
50845 -CCACCAGTAAGTCTTTCGAACATGATGATGAAGTCCTTCGG
1 GCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
* * *
50886 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
** * * * * **
50928 GTAATTTGTAAG-CCTTC-ACCGAAGACT-AGTGAAG-CAAAT---
1 GCCATTAGTAAGTCTTTCGAGC-ATGA-TGA-TGAAGTC-CTTCGG
* * *
50967 -CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCTTTCGG
1 GCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
* * *
51008 GTCATTTGTAAGTCTTTCGAGCAAGATGAT-AAGTCCTTCGG
1 GCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
51049 GCCATT
1 GCCATT
51055 TTAAGCCTTC
Statistics
Matches: 207, Mismatches: 62, Indels: 45
0.66 0.20 0.14
Matches are distributed among these distances:
38 29 0.14
39 14 0.07
40 8 0.04
41 29 0.14
42 127 0.61
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (42 bp):
GCCATTAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
Found at i:50952 original size:122 final size:122
Alignment explanation
Indices: 50727--51074 Score: 484
Period size: 122 Copynumber: 2.9 Consensus size: 122
50717 TAAGTGCCAT
* *
50727 CAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATTAATAAGTCTTTCAAGCATGATG
1 CAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATG
* * * *
50792 ATTAAATCCTTCGAGAAATTTGTAAGCCTTTATGGAAGAGTAGTGAAGTAAACCCAC
66 ATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCAC
* *
50849 CAGTAAGTCTTTCGAACATGATGATGAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 CAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATG
* * * * *
50914 ATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGACTAGTGAAGCAAATCCAT
66 ATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCAC
* * * * *
50971 CAGTAAGTCTTTCGAGCATGATGATGAAATCTTTCGGGTCATTTGTAAGTCTTTCGAGCAAGATG
1 CAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATG
* ** *
51036 A-TAAGTCCTTCGGGCCATTT-TAAGCCTTCTCGGAAGAGT
66 ATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAGAGT
51075 GTTAGAGCAA
Statistics
Matches: 200, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
120 16 0.08
121 16 0.08
122 168 0.84
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (122 bp):
CAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATG
ATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCAC
Found at i:51574 original size:54 final size:53
Alignment explanation
Indices: 51429--51582 Score: 256
Period size: 53 Copynumber: 2.9 Consensus size: 53
51419 AGAATCACAC
*
51429 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAATGAACCCGTAGG
*
51482 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGTAAGAGGGAATGAACCCGT-GAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAATGAACCCGTAG-G
*
51535 CAGAAGATTTGATCGAGTTCTACTCCCTGAAGCAAGAGGGAATGAACC
1 CAGAAGA-TTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAATGAACC
51583 TGAAGCAAGA
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
52 1 0.01
53 56 0.59
54 38 0.40
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAATGAACCCGTAGG
Found at i:51602 original size:21 final size:21
Alignment explanation
Indices: 51560--51603 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
51550 AGTTCTACTC
*
51560 CCTGAAGCAAGAGGGAATGAA
1 CCTGAAGCAAGAGGGAACGAA
*
51581 CCTGAAGCAAGAGGGAGCGAA
1 CCTGAAGCAAGAGGGAACGAA
51602 CC
1 CC
51604 CGTAAGCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.34, T:0.07
Consensus pattern (21 bp):
CCTGAAGCAAGAGGGAACGAA
Found at i:53261 original size:13 final size:13
Alignment explanation
Indices: 53243--53272 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53233 TAAAATGAGG
*
53243 TTTTTTATTTTTA
1 TTTTTTATTATTA
53256 TTTTTTATTATTA
1 TTTTTTATTATTA
53269 TTTT
1 TTTT
53273 AGTTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTATTATTA
Found at i:62230 original size:7 final size:7
Alignment explanation
Indices: 62215--62251 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
62205 TTCCTTTTCC
62215 TTTTA-T
1 TTTTATT
62221 TTTTATT
1 TTTTATT
62228 TTTTATT
1 TTTTATT
62235 TTTTATT
1 TTTTATT
*
62242 TTTCATT
1 TTTTATT
62249 TTT
1 TTT
62252 ATTAGTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTATT
Found at i:62231 original size:13 final size:13
Alignment explanation
Indices: 62215--62254 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
62205 TTCCTTTTCC
62215 TTTTATTTTTATT
1 TTTTATTTTTATT
62228 TTTTATTTTTTATT
1 TTTTA-TTTTTATT
*
62242 TTTCATTTTTATT
1 TTTTATTTTTATT
62255 AGTCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:68600 original size:24 final size:25
Alignment explanation
Indices: 68568--68618 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
68558 AAATTTATAG
*
68568 AATTAGTAACCACAACAATAA-AAA
1 AATTAGTAACCACAACAACAACAAA
68592 AATTAGTAACCACAACAACAACAAA
1 AATTAGTAACCACAACAACAACAAA
68617 AA
1 AA
68619 CTAACACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.63, C:0.20, G:0.04, T:0.14
Consensus pattern (25 bp):
AATTAGTAACCACAACAACAACAAA
Found at i:75309 original size:2 final size:2
Alignment explanation
Indices: 75297--75337 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
75287 AGAGTTACTA
75297 AT AT GAT 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
75338 TAATGTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Done.