Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003082.1 Hibiscus syriacus cultivar Beakdansim tig00006431_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: 54884
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:335 original size:24 final size:24
Alignment explanation
Indices: 301--392 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
291 AAACGGATAT
* * *
301 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGATATCAGAACAGAATCCAG
* * *
325 ATGAGATATCAGAATAGAATCCAT
1 ATCAGATATCAGAACAGAATCCAG
* *
349 ATCAGAAATCAGAATAGAATCCAG
1 ATCAGATATCAGAACAGAATCCAG
* *
373 GTCAGGTATCAGAACAGAAT
1 ATCAGATATCAGAACAGAAT
393 TCAAATCGAA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAGATATCAGAACAGAATCCAG
Found at i:383 original size:48 final size:48
Alignment explanation
Indices: 299--409 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
289 ATAAACGGAT
* * * *
299 ATATCAGAAATCAAAACAGAATTCAGATGAGATATCAGAATAGAATCC
1 ATATCAGAAATCAGAACAGAATCCAGATCAGATATCAGAACAGAATCC
* * * *
347 ATATCAGAAATCAGAATAGAATCCAGGTCAGGTATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATCCAGATCAGATATCAGAACAGAATCC
*
395 AAATC-GAAAATCAGA
1 ATATCAG-AAATCAGA
410 TAAAATATTC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATCCAGATCAGATATCAGAACAGAATCC
Found at i:2530 original size:13 final size:14
Alignment explanation
Indices: 2511--2543 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2501 TCAAAGTCAA
2511 CGAGTTGACCCAGT
1 CGAGTTGACCCAGT
*
2525 -GAGTTGACTCAGT
1 CGAGTTGACCCAGT
2538 CGAGTT
1 CGAGTT
2544 AACTCAGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (14 bp):
CGAGTTGACCCAGT
Found at i:2551 original size:27 final size:29
Alignment explanation
Indices: 2511--2567 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
2501 TCAAAGTCAA
*
2511 CGAGTTGACCCAGTG-AG-TTGACTCAGT
1 CGAGTTAACCCAGTGCAGATTGACTCAGT
* *
2538 CGAGTTAACTCAGTGCGGATTGACTCAGT
1 CGAGTTAACCCAGTGCAGATTGACTCAGT
2567 C
1 C
2568 AAGTCAAGCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 13 0.52
28 1 0.04
29 11 0.44
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (29 bp):
CGAGTTAACCCAGTGCAGATTGACTCAGT
Found at i:2565 original size:15 final size:14
Alignment explanation
Indices: 2511--2567 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
2501 TCAAAGTCAA
*
2511 CGAGTTGACCCAGT
1 CGAGTTGACTCAGT
2525 -GAGTTGACTCAGT
1 CGAGTTGACTCAGT
*
2538 CGAGTTAACTCAGT
1 CGAGTTGACTCAGT
2552 GCG-GATTGACTCAGT
1 -CGAG-TTGACTCAGT
2567 C
1 C
2568 AAGTCAAGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 12 0.32
14 14 0.38
15 11 0.30
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (14 bp):
CGAGTTGACTCAGT
Found at i:4706 original size:19 final size:20
Alignment explanation
Indices: 4682--4724 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4672 AGCATTTATC
*
4682 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
4701 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
4721 TTCA
1 TTCA
4725 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:8383 original size:19 final size:20
Alignment explanation
Indices: 8359--8401 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
8349 AGCATTTATC
*
8359 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
8378 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
8398 TTCA
1 TTCA
8402 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:8929 original size:15 final size:15
Alignment explanation
Indices: 8906--8954 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
8896 TACTTTGATA
8906 TCATTTCTTTCCATT
1 TCATTTCTTTCCATT
*
8921 TCCTTTCTTAT-CATT
1 TCATTTCTT-TCCATT
8936 TCATTTCTTCTTCCATT
1 TCATTTC-T-TTCCATT
8953 TC
1 TC
8955 TTATTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 18 0.64
16 3 0.11
17 7 0.25
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (15 bp):
TCATTTCTTTCCATT
Found at i:11298 original size:14 final size:14
Alignment explanation
Indices: 11274--11313 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11264 AAACATAATT
*
11274 AAAATACTAAAATA
1 AAAATAATAAAATA
*
11288 ACAATAATAAAATA
1 AAAATAATAAAATA
*
11302 AAAAAAATAAAA
1 AAAATAATAAAA
11314 ACATAGAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATAATAAAATA
Found at i:19140 original size:22 final size:23
Alignment explanation
Indices: 19100--19151 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
19090 TTTTAAATCG
*
19100 TCTTC-TTAATCTTCTTTTACTTT
1 TCTTCTTTAATATTCTTTTA-TTT
19123 TC-TCTTTAATATTC-TTTATTT
1 TCTTCTTTAATATTCTTTTATTT
19144 TCTTCTTT
1 TCTTCTTT
19152 TTATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.19
22 11 0.42
23 10 0.38
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.67
Consensus pattern (23 bp):
TCTTCTTTAATATTCTTTTATTT
Found at i:23989 original size:174 final size:174
Alignment explanation
Indices: 23579--31239 Score: 10837
Period size: 174 Copynumber: 43.8 Consensus size: 174
23569 AATTTCTTAT
* *
23579 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * *
23644 GATTTATCCATTAGTACATGTTATTGAAACTTACCAACTTTCTTTGGACAGTAGAGAATAAGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
*
23709 TTGGTTTATAACATATTC-TTT--T-CA-----TGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * *
23744 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTTAAATTTGTAGCAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
23809 GATTTATCCATTAGTACATGCTATTGAAACTTACCAACTTTCTTTGGATAGTAGATAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* *
23874 TTGGTTTATAACATATTCTTTTCTTGCATTCTCTGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
*
23918 CATATTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
*
23983 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTCGGATAGTAGAAAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * * * * *
24048 TTGGTTTAGATCATATTCTTTTCATGCATTCTCCGTTTCCTGTC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
*
24092 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * * **
24157 GATTTATTCATTACTACATGTTATTCAAACTTACCAACTTTATTCGGATAGTAGAAAATTTGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
*
24222 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTAAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * *
24266 CATCTTTTTTCAAGAGAGAAAATAAAAGAAGAGAAAATAAAAGAATTATAAACCAATCAAAATTC
1 CATCTTTTTTC--------------AAG-AGAGAAAATAAAAGAATTATAGACCGATCCAAATTT
* * *
24331 AAATTTGTAACAAAAGATTTACCCATTACTACATGTTATTGAAACGTACCAACTTTCTTCGGATA
51 AAATTTGTAACAAAAGATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATA
* ** *
24396 GTAAAAAATATTAATTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTAAC
116 GTAGAAAATAGGAATTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * *
24455 CATCATTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* *
24520 GATTTATCCATTAGTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAGAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * * *
24585 TTGGTTTATAACAGATTCTTTTCATGCATTCTCCGTTTACTTAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * *
24629 CATCTTTTTTGAAAAGAGAAAATAAAAGAATTTTAGACCGATCCAAATTTAAAATTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
24694 TATTTATCCATTACTACATGTTACTCAAACTTACCAACTTTCTTTGGATAGTA-AATAATAGGAA
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAA-AATAGGAA
* ** *
24758 TTTGGTTTATAACAGATTCTTTTCCTGCATACTCCATTTCCTTAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * *
24803 CATCTTTTTTCAAGAGAAAAAAATAAAATAATTATAGACCGAACCAAATTTAAATTTGTAACAAA
1 CATCTTTTTTCAAGAG-AGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAA
* * *
24868 AGATTTATCCATTAATACTTGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAGAATAGGAA
65 AGATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAA
* * **
24933 TTTGGTTTATAACATATTCTTTTCCTGCATACTCCATTTCCTGAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
24978 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
25043 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTCGGACAGTAAAAAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
** *
25108 TTGGTTTATAACAGATTCTTTTATTGCATTCTCCGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * *
25152 CATCTTTTTTCATGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * * **
25217 GATTTATCCATTACTACAAGTTTTTGAAACGTACCAACTTTCTTCGGATAGTAGAAAATATTAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
*
25282 TTGGTTTATAACAGATTCTTTTCATGCATTCTCTGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * *
25326 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
25391 GATTTATCCATTAGTACATGTTATTGAAACTTACCAACCTTCTTTGGATAGTAGAGAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
*
25456 TTGGTTTATAACAGATTCTTTTCATGCATTCTCTGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * * *
25500 CATCTTTTTTGAAAAGAGAAAATAAAAGAATTTTAGAGCGATCCAAATTTAAAATTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
25565 GATTTATCCATTACTACATGTTACTCAAACTAACCAACTTTCTTTGGATAGTA-AAGAATAGGAA
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAA-AATAGGAA
* * *
25629 TTTGGTTTATGACATATTCTTTTCCTGCATACT-TCGTTTCCTGAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCT-GTTTCCTGAC
* * * * **
25674 AATTTTTTTTCAAGAGAAAAAATGAAAGAATTATAGACCGAAGCAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* *
25739 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTCTCTTCGGATAGTAGAAAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * *
25804 TTGGTTTATAACAGATTCTTTTCTTACATTCTCCGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
*
25848 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATGTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * * **
25913 GATTTATTCA-T--TACATGTTATTCAAACTTACCAACTTTATTCGGATAGTAGAAAATTTGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
*
25975 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTAAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * * *
26019 CATCTTTTTCAAGAGAGAAAATAAAAGAAGAGAAAATAAAAGAATTATAAACCAATCAAAATTCA
1 CATCTTTTT------------T-CAAG-AGAGAAAATAAAAGAATTATAGACCGATCCAAATTTA
* * *
26084 AATTTGTAACAAAAGATTTACCCATTACTACATGTTATTGAAACGTACCAACTTTCTTCGGATAG
52 AATTTGTAACAAAAGATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAG
** * *
26149 TAGAAAATATTAATTTGGTTTATAACAGATTTTTTTCCTGCATTCTCTGTTTCCTAAC
117 TAGAAAATAGGAATTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * *
26207 CATCATTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
26272 GATTTATCCATTAGTACATGTTATTGAAACTTAACAACTTTCTTTGGATAGTAGAGAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * *
26337 TTGGTTTATAACAGATTCTTTTCATGCATTCTCCGTTTACTTG-C
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTT-CCTGAC
* * *
26381 CATCTTTTTTCAAAAGAGAAAATAAAAGAATTTTAGACCGATCCAAATTTAAAATTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
26446 TATTTATCCATTACTACATGTTACTCAAACTTACCAACTTTCTTTGGATAGTA-AATAATAGGAA
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAA-AATAGGAA
* *
26510 TTTGGTTTATAACAGATTCTTTTCCTCCATACTCTGTTTCCTGAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* *
26555 CATCTTTTTTCAAGAGAAAAAATAAAAGAATTATAGACCGAACCAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * * *
26620 GATTTATCCATTAGTACTTGTTATTGAAACTTACCATCTTTCTTTGGATAGTAGAGAATATGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* *
26685 TTGGTTTATAACAGATTCTTTTCCTGCATACTCCGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
*
26729 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGAACGATCCAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * *
26794 GATTTATCCATTACTACATGTTATTGAAACTTACCAACATTCTTCGGACAGTAAAAAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * *
26859 TTGGTTTGTAACAGATTCTTTTCTTGCATTCTCAGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * * * *
26903 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAAATTGCAACTAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * **
26968 GATTTATCCATTACTACATGTTATTGAAACGTACCAACTTTCTTCGGATAGTAGAAAATATTAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* *
27033 TTGGTTTATAACAGATTCTTTTCATGCATTCTCTGTTTCCTGAT
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * *
27077 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGAACGATCAAAATTCAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
27142 TATTTATCCATTAGTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAGAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * *
27207 TTGGTTTATAACAGATTATTTTCATGCATTCTCAGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * *
27251 CATCTTTTTTCAAAAGAGAAAATAAAAGAATTTTAGGCCGATCCAAATTTAAAATTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
27316 GATTTATCCATTACTACATGTTACTCAAACTAACCAACTTTCTTTGGATAGTA-AAGAATAGGAA
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAA-AATAGGAA
* * * *
27380 TTTGGTTTATGACATATTCTTTTCCTGCATACTCCGTTTCCTGAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * **
27425 AATCTTTTTTCAAGAGAAAAAAATAAAAGAATTATAGACCGAAGCAAATTTAAATTTGTAACAAA
1 CATCTTTTTTCAAGAG-AGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAA
* * *
27490 AGATTTATCCATTACTACATGTTATTGAAACTTACAAACTCTCTTCGGATAGTAGAAAATAGGAA
65 AGATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAA
*
27555 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTAAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * *
27600 CATCATTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* *
27665 GATTTATCCATTAGTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAGAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * * *
27730 TTGGTTTATAACAGATTCTTTTCATGCATTCTCCGTTTACTTAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * *
27774 CATCTTTTTTGAAAAGAGAAAATAAAAGAATTTTAGACCGATCCAAATTTAAAATTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
27839 TATTTATCCATTACTACATGTTACTCAAACTTACCAACTTTCTTTGGATAGTA-AATAATAGGAA
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAA-AATAGGAA
* * *
27903 TTTGGTTTATAACAGATTCTTTTCATGCATACTCCGTTTCCTGAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * *
27948 CATCTTTTTTCAAGAGAAAAAATAAAATAATTATAGACCGAACCAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* *
28013 GATTTATCCATTTA-TACTTGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAGAATAGGAA
66 GATTTATCCA-TTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAA
* * **
28077 TTTGGTTTATAACATATTCTTTTCCTGCATACTCCATTTCCTGAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
28122 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
28187 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTCGGACAGTAAAAAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
** *
28252 TTGGTTTATAACAGATTCTTTTATTGCATTCTCCGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * *
28296 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * * **
28361 GATTTATCCATTACTACAAGTTTTTGAAACGTACCAACTTTCTTCGGATAGTAGAAAATATTAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
*
28426 TTGGTTTATAACAGATTCTTTTCATGCATTCTCTGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * *
28470 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* *
28535 GATTTATCCATTAGTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAGAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
*
28600 TTGGTTTATAACAGATTCTTTTCATGCATTCTCTGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * * *
28644 CATCTTTTTTGAAAAGAGAAAATAAAAGAATTTTAGAGCGATCCAAATTTAAAATTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
28709 GATTTATCCATTACTACATGTTACTCAAACTAACCAACTTTCTTTGGATAGTA-AAGAATAGGAA
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAA-AATAGGAA
* * *
28773 TTTGGTTTATGACATATTCTTTTCCTGCATACT-TCGTTTCCTGAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCT-GTTTCCTGAC
* * * **
28818 AATCTTTTTTCAAGAGAAAAAATGAAAGAATTATAGACCGAAGCAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* *
28883 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTCTCTTCGGATAGTAGAAAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * *
28948 TTGGTTTATAACAGATTCTTTTCTTACATTCTCCGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
*
28992 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATGTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * * **
29057 GATTTATTCATTACTACATGTTATTCAAACTTACCAACTTTATTCGGATAGTAGAAAATTTGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
*
29122 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTAAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * * *
29166 CATCTTTTTCAAGAGAGAAAATAAAAGAAGAGAAAATAAAAGAATTATAAACCAATCAAAATTCA
1 CATCTTTTT------------T-CAAG-AGAGAAAATAAAAGAATTATAGACCGATCCAAATTTA
* * *
29231 AATTTGTAACAAAAGATTTACCCATTACTACATGTTATTGAAACGTACCAACTTTCTTCGGATAG
52 AATTTGTAACAAAAGATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAG
** * *
29296 TAGAAAATATTAATTTGGTTTATAACAGATTTTTTTCCTGCATTCTCTGTTTCCTAAC
117 TAGAAAATAGGAATTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * *
29354 CATCATTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* *
29419 GATTTATCCATTAGTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAGAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * *
29484 TTGGTTTATAACAGATTCTTTTCATGCATTCTCCGTTTACTTG-C
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTT-CCTGAC
* * *
29528 CATCTTTTTTCAAAAGAGAAAATAAAAGAATTTTAGACCGATCCAAATTTAAAATTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
29593 TATTTATCCATTACTACATGTTACTCAAACTTACCAACTTTCTTTGGATAGTA-AATAATAGGAA
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAA-AATAGGAA
* *
29657 TTTGGTTTATAACAGATTCTTTTCCTCCATACTCTGTTTCCTGAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* *
29702 CATCTTTTTTCAAGAGAAAAAATAAAAGAATTATAGACCGAACCAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * * * *
29767 GATTTATCCATTAGTACTTGTTATTGAAACTTACTATCTTTCTTTGGATAGTAGAGAATATGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
*
29832 TTGGTTTATAACAGATTCTTTTCCTGCATACT-TCGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCT-GTTTCCTGAC
*
29876 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGAACGATCCAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * *
29941 GATTTATCCATTACTACATGTTATTGAAACTAACCAACTTTCTTCGGACAGTAAAAAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * *
30006 TTGGTTTGTAACAGATTCTTTTCTTGCATTCTCAGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * * *
30050 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAAATTGCAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * **
30115 GATTTATCCATTACTACATGTTATTGAAACGTACCAACTTTCTTCGGATAGTAGAAAATATTAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* *
30180 TTGGTTTATAACAGATTCTTTTCATGCATTCTCTGTTTCCTGAT
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * *
30224 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAAACCGATCAAAATTCAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
30289 TATTTATCCATTAGTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAGAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* *
30354 TTGGTTTATAACAGATTATTTTCATGCATTCTCTGTTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * *
30398 CATCTTTTTTCAAAAGAGAAAATAAAAGAATTTTAGGCCGATCCAAATTTAAAATTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * * *
30463 GATTTATCAATTACTACATGTTACTCAAACTAACCAACTTTCTTTGGATAGTA-AAGAATAGGAA
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAA-AATAGGAA
* * * *
30527 TTTGGTTTATGACATATTCTTTTCCTGCATACTCCGTTTCCTGAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * **
30572 AATCTTTTTTCAAGAGAAAAAAAATAAAAGAATTATAGACCGAAGCAAATTTAAATTTGTAACAA
1 CATCTTTTTTCAAGAG--AGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAA
* *
30637 AAGATTTATCCATTACTACATGTTATTGAAACTTACCAACTCTCTTCGGATAGTAGAAAATAGGA
64 AAGATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGA
* *
30702 ATTTGGTTTATAACAGATTCTTTTCTTGCATTCTCCGTTTCCTGAC
129 ATTTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * *
30748 CATC-TTTTTCAAGAGAGAAAATAAAATAATTATAAACCGATCAAAATTTAAATTTGTAACAAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
* * *
30812 GATTTATCCATTAGTACTTGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAGAATAGGAAT
66 GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
* * **
30877 TTGGTTTATAGCAGATTCTTTTCATGCATTCTCCATTTCCTGAC
131 TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
* * * * * *
30921 CATCTTTTTTCAAGAGAAAAAATAAAAGTATTATAAACCGGTCAAAATTTAATTTTGGT-ACAAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTT-GTAACAAA
* * * *
30985 AGATTTATCCATTAGTACATGCTATTGAAACTTACCAACTTTCTTTGGATAGTACAGAATAGGAA
65 AGATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAA
*
31050 TTTGGTTTATAACAGATTCTTTTCCTGCATACTCCT-TTTCCTGAC
130 TTTGGTTTATAACAGATTCTTTTCCTGCATTCT-CTGTTTCCTGAC
*
31095 CATCTTTTTTCAAGAGAGAAAATAAAAAAATTATAGACCGATCCAAATTTAAATTTGTATA-AAA
1 CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTA-ACAAA
* * * * * * * **
31159 AGTTTTATCCATTACTATATATCATTAAAACTTACCAACTTTCTTTGGATAATAGATAATAAAAA
65 AGATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAA
*
31224 TTTGATTTATAACAGA
130 TTTGGTTTATAACAGA
31240 CTGTTGTTTT
Statistics
Matches: 6745, Mismatches: 659, Indels: 175
0.89 0.09 0.02
Matches are distributed among these distances:
165 143 0.02
166 3 0.00
168 1 0.00
169 2 0.00
171 95 0.01
173 171 0.03
174 5355 0.79
175 349 0.05
176 147 0.02
177 2 0.00
183 1 0.00
184 3 0.00
185 54 0.01
186 2 0.00
187 3 0.00
188 255 0.04
189 159 0.02
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (174 bp):
CATCTTTTTTCAAGAGAGAAAATAAAAGAATTATAGACCGATCCAAATTTAAATTTGTAACAAAA
GATTTATCCATTACTACATGTTATTGAAACTTACCAACTTTCTTTGGATAGTAGAAAATAGGAAT
TTGGTTTATAACAGATTCTTTTCCTGCATTCTCTGTTTCCTGAC
Found at i:24300 original size:15 final size:15
Alignment explanation
Indices: 24280--24310 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
24270 TTTTTTCAAG
24280 AGAGAAAATAAAAGA
1 AGAGAAAATAAAAGA
24295 AGAGAAAATAAAAGA
1 AGAGAAAATAAAAGA
24310 A
1 A
24311 TTATAAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (15 bp):
AGAGAAAATAAAAGA
Found at i:24426 original size:189 final size:189
Alignment explanation
Indices: 24106--24484 Score: 652
Period size: 189 Copynumber: 2.0 Consensus size: 189
24096 TTTTTTCAAG
* * * **
24106 AGAGAAAATAAAAGAATTATAGACCGATCAAAATTTAAATTTGTAACAAAAGATTTATTCATTAC
1 AGAGAAAATAAAAGAATTATAAACCAATCAAAATTCAAATTTGTAACAAAAGATTTACCCATTAC
* *
24171 TACATGTTATTCAAACTTACCAACTTTATTCGGATAGTAGAAAATTTGAATTTGGTTTATAACAG
66 TACATGTTATTCAAACGTACCAACTTTATTCGGATAGTAAAAAATTTGAATTTGGTTTATAACAG
*
24236 ATTCTTTTCCTGCATTCTCTGTTTCCTAACCATCTTTTTTCAAGAGAGAAAATAAAAGA
131 ATTCTTTTCCTGCATTCTCTGTTTCCTAACCATCATTTTTCAAGAGAGAAAATAAAAGA
24295 AGAGAAAATAAAAGAATTATAAACCAATCAAAATTCAAATTTGTAACAAAAGATTTACCCATTAC
1 AGAGAAAATAAAAGAATTATAAACCAATCAAAATTCAAATTTGTAACAAAAGATTTACCCATTAC
* *
24360 TACATGTTATTGAAACGTACCAACTTTCTTCGGATAGTAAAAAATATT-AATTTGGTTTATAACA
66 TACATGTTATTCAAACGTACCAACTTTATTCGGATAGTAAAAAAT-TTGAATTTGGTTTATAACA
24424 GATTCTTTTCCTGCATTCTCTGTTTCCTAACCATCATTTTTCAAGAGAGAAAATAAAAGA
130 GATTCTTTTCCTGCATTCTCTGTTTCCTAACCATCATTTTTCAAGAGAGAAAATAAAAGA
24484 A
1 A
24485 TTATAAACCG
Statistics
Matches: 179, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
189 177 0.99
190 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (189 bp):
AGAGAAAATAAAAGAATTATAAACCAATCAAAATTCAAATTTGTAACAAAAGATTTACCCATTAC
TACATGTTATTCAAACGTACCAACTTTATTCGGATAGTAAAAAATTTGAATTTGGTTTATAACAG
ATTCTTTTCCTGCATTCTCTGTTTCCTAACCATCATTTTTCAAGAGAGAAAATAAAAGA
Found at i:26052 original size:15 final size:15
Alignment explanation
Indices: 26032--26062 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
26022 CTTTTTCAAG
26032 AGAGAAAATAAAAGA
1 AGAGAAAATAAAAGA
26047 AGAGAAAATAAAAGA
1 AGAGAAAATAAAAGA
26062 A
1 A
26063 TTATAAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (15 bp):
AGAGAAAATAAAAGA
Found at i:29199 original size:15 final size:15
Alignment explanation
Indices: 29179--29209 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29169 CTTTTTCAAG
29179 AGAGAAAATAAAAGA
1 AGAGAAAATAAAAGA
29194 AGAGAAAATAAAAGA
1 AGAGAAAATAAAAGA
29209 A
1 A
29210 TTATAAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (15 bp):
AGAGAAAATAAAAGA
Found at i:32542 original size:22 final size:22
Alignment explanation
Indices: 32498--32543 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
32488 TTAAATTAAT
**
32498 ATTTATATTCATTAATTTGTTA
1 ATTTATATTCATTAATTCATTA
**
32520 ATTTATATTTTTTAATTCATTA
1 ATTTATATTCATTAATTCATTA
32542 AT
1 AT
32544 ATAAAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTATATTCATTAATTCATTA
Found at i:33088 original size:15 final size:15
Alignment explanation
Indices: 33068--33097 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33058 AGTAACCTTT
33068 ATAAAACTCATCGTC
1 ATAAAACTCATCGTC
33083 ATAAAACTCATCGTC
1 ATAAAACTCATCGTC
33098 TCTGTCGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (15 bp):
ATAAAACTCATCGTC
Found at i:35538 original size:131 final size:131
Alignment explanation
Indices: 35303--35651 Score: 412
Period size: 131 Copynumber: 2.7 Consensus size: 131
35293 GAGAAAATAG
** *
35303 TAATATCTAATTATTTCCAATCGAGAATAAACAACCTCTCATACCTTAAAACAATCATTTAATAC
1 TAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTAATAC
* * ** * * * * *
35368 TCCAATCGAAATGAAAAGATATCATTATTCTGTCTTAAAATTCAATATCGATCCGAGTGAAAATG
66 TCCAATCGAAATGAAAAGATATCAGTATGCCATCCTAAAAATCAATATCAATCCGAGAGAAAACG
35433 A
131 A
* * * * * **
35434 TATTATCTAATAATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGTAGTCATTTACTGT
1 TAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTAATAC
* **
35499 TCCAATCGAAAT-AAAGAGATATCAGTATGCCATCCTAAAAATCAATATTAATTTGAGAGAAAAC
66 TCCAATCGAAATGAAA-AGATATCAGTATGCCATCCTAAAAATCAATATCAATCCGAGAGAAAAC
*
35563 GG
130 GA
* ** * * *
35565 TAATATCAAATTATTTCCAATCGAGAATAAATGAAATCTCATGCCTTAAAGCATTCATTTATTAC
1 TAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTAATAC
*
35630 TCCAACCGAAATGAAAAGATAT
66 TCCAATCGAAATGAAAAGATAT
35652 TATTATTCTC
Statistics
Matches: 181, Mismatches: 35, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
130 3 0.02
131 175 0.97
132 3 0.02
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (131 bp):
TAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAATCATTTAATAC
TCCAATCGAAATGAAAAGATATCAGTATGCCATCCTAAAAATCAATATCAATCCGAGAGAAAACG
A
Found at i:36274 original size:28 final size:26
Alignment explanation
Indices: 36242--36311 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 26
36232 ACAAAGAATA
36242 AAAATAAATAAAT-CATGGAGACTAAATG
1 AAAATAAATAAATGCAT-G-GAC-AAATG
*
36270 AAAATAAATTAAAATTGCATGGACAAATT
1 AAAATAAA-T-AAA-TGCATGGACAAATG
36299 AAAATAAATAAAT
1 AAAATAAATAAAT
36312 AAAACAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
26 1 0.03
27 3 0.08
28 9 0.24
29 13 0.35
30 6 0.16
31 2 0.05
32 3 0.08
ACGTcount: A:0.60, C:0.06, G:0.10, T:0.24
Consensus pattern (26 bp):
AAAATAAATAAATGCATGGACAAATG
Found at i:37503 original size:21 final size:21
Alignment explanation
Indices: 37477--37523 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
37467 TGCATAGGCC
37477 ATGGGGCTATAGTGGAACAGT
1 ATGGGGCTATAGTGGAACAGT
*
37498 ATGGGGCTATAGTGGAGCAGT
1 ATGGGGCTATAGTGGAACAGT
37519 ATGGG
1 ATGGG
37524 CGTGTAGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.43, T:0.23
Consensus pattern (21 bp):
ATGGGGCTATAGTGGAACAGT
Found at i:37763 original size:3 final size:3
Alignment explanation
Indices: 37747--37782 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
37737 ATAAAAACAA
37747 AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
37783 CAGACAGGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:38294 original size:23 final size:23
Alignment explanation
Indices: 38248--38294 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
38238 TCTAACGTTA
*
38248 GTGAACATATTCGTTTATTATTC
1 GTGAACATATTCGTTTAATATTC
* *
38271 GTGAACATTTTCGTTTAATGTTC
1 GTGAACATATTCGTTTAATATTC
38294 G
1 G
38295 GCAACCAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (23 bp):
GTGAACATATTCGTTTAATATTC
Found at i:38806 original size:21 final size:20
Alignment explanation
Indices: 38782--38820 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
38772 ATAATATCAA
*
38782 TTCTTCACATCGACGAACAAG
1 TTCTCCACATCGA-GAACAAG
*
38803 TTCTCCACATTGAGAACA
1 TTCTCCACATCGAGAACA
38821 TATTTTATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCTCCACATCGAGAACAAG
Found at i:50052 original size:9 final size:9
Alignment explanation
Indices: 50038--50071 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
50028 TTTATCATCG
50038 TCCCTCCTT
1 TCCCTCCTT
50047 TCCCTCCTCT
1 TCCCTCCT-T
*
50057 TCTCTCCTT
1 TCCCTCCTT
50066 TCCCTC
1 TCCCTC
50072 AAACCGAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (9 bp):
TCCCTCCTT
Done.