Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009032.1 Hibiscus syriacus cultivar Beakdansim tig00112433_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: 100409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:18 original size:9 final size:9
Alignment explanation
Indices: 5--62 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
1 TTTC
5 TCTTTTTTT
1 TCTTTTTTT
*
14 TCTTTTTTC
1 TCTTTTTTT
23 TCTTTTTTT
1 TCTTTTTTT
*
32 TCTTTTCTT
1 TCTTTTTTT
*
41 T-TTTTCTT
1 TCTTTTTTT
49 TC-TTTTTT
1 TCTTTTTTT
57 TCTTTT
1 TCTTTT
63 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
8 15 0.35
9 28 0.65
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:21 original size:8 final size:8
Alignment explanation
Indices: 8--62 Score: 67
Period size: 8 Copynumber: 6.5 Consensus size: 8
1 TTTCTCT
8 TTTTTTTC
1 TTTTTTTC
16 TTTTTTCTC
1 TTTTTT-TC
25 TTTTTTTTC
1 -TTTTTTTC
34 TTTTCTTT-
1 TTTT-TTTC
42 TTTTCTTTC
1 TTTT-TTTC
51 TTTTTTTC
1 TTTTTTTC
59 TTTT
1 TTTT
63 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
8 26 0.60
9 11 0.26
10 6 0.14
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTC
Found at i:24 original size:18 final size:17
Alignment explanation
Indices: 5--62 Score: 82
Period size: 17 Copynumber: 3.4 Consensus size: 17
1 TTTC
5 TCTTTTTTTTCTTTTTT
1 TCTTTTTTTTCTTTTTT
22 CTCTTTTTTTTCTTTTCTT
1 -TCTTTTTTTTCTTTT-TT
*
41 T-TTTTCTTTCTTTTTT
1 TCTTTTTTTTCTTTTTT
57 TCTTTT
1 TCTTTT
63 CTTCAAGCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 3 0.08
17 16 0.43
18 16 0.43
19 2 0.05
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TCTTTTTTTTCTTTTTT
Found at i:44 original size:25 final size:25
Alignment explanation
Indices: 7--65 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
1 TTTCTC
7 TTTT-TTTTC-TTTTTTCTCT-TTT
1 TTTTCTTTTCTTTTTTTCTCTCTTT
*
29 TTTTCTTTTCTTTTTTTCTTTCTTT
1 TTTTCTTTTCTTTTTTTCTCTCTTT
54 TTTTCTTTTCTT
1 TTTTCTTTTCTT
66 CAAGCATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 4 0.12
23 5 0.15
24 9 0.27
25 15 0.45
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (25 bp):
TTTTCTTTTCTTTTTTTCTCTCTTT
Found at i:10676 original size:29 final size:29
Alignment explanation
Indices: 10644--10707 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
10634 AAATACTTAC
*
10644 AAATAAAATAA-AACATATAAATATTATGA
1 AAATAAAATAAGAA-ATATAAAAATTATGA
*
10673 AAAT--AATAAGTAAATATAAAAATTTTGA
1 AAATAAAATAAG-AAATATAAAAATTATGA
10701 AAATAAA
1 AAATAAA
10708 GAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
27 5 0.17
28 17 0.59
29 6 0.21
30 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (29 bp):
AAATAAAATAAGAAATATAAAAATTATGA
Found at i:11143 original size:12 final size:12
Alignment explanation
Indices: 11126--11150 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11116 TCTATTATTA
11126 AAAATTCAAAAT
1 AAAATTCAAAAT
11138 AAAATTCAAAAT
1 AAAATTCAAAAT
11150 A
1 A
11151 TATTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTCAAAAT
Found at i:11397 original size:13 final size:13
Alignment explanation
Indices: 11360--11399 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
11350 TCGATATTGA
11360 AAAATAAATA-TT
1 AAAATAAATATTT
*
11372 AAAATAATTTATTT
1 AAAATAA-ATATTT
11386 AAAATAAATATTT
1 AAAATAAATATTT
11399 A
1 A
11400 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:12750 original size:3 final size:3
Alignment explanation
Indices: 12742--12858 Score: 144
Period size: 3 Copynumber: 39.0 Consensus size: 3
12732 TATATATTTT
* * * *
12742 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
12790 TTA TAG TAA TAA TAA TAA TAA TAT TTA TAG TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
12838 TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
12859 ATAAATCAAA
Statistics
Matches: 94, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:12780 original size:24 final size:24
Alignment explanation
Indices: 12744--12858 Score: 194
Period size: 24 Copynumber: 4.8 Consensus size: 24
12734 TATATTTTTA
12744 ATAATAATAATAATAATAATATTT
1 ATAATAATAATAATAATAATATTT
*
12768 ATAATAATTATAATAATAATATTT
1 ATAATAATAATAATAATAATATTT
*
12792 ATAGTAATAATAATAATAATATTT
1 ATAATAATAATAATAATAATATTT
* *
12816 ATAGTAATAATAATAATAATAATT
1 ATAATAATAATAATAATAATATTT
12840 ATAATAATAATAATAATAA
1 ATAATAATAATAATAATAA
12859 ATAAATCAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 86 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
ATAATAATAATAATAATAATATTT
Found at i:16538 original size:17 final size:18
Alignment explanation
Indices: 16506--16539 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16496 TAAATTATAA
16506 AAAAGCCCCAAAATACCT
1 AAAAGCCCCAAAATACCT
*
16524 AAAATCCCC-AAATACC
1 AAAAGCCCCAAAATACC
16540 CCCCTTTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.35, G:0.03, T:0.12
Consensus pattern (18 bp):
AAAAGCCCCAAAATACCT
Found at i:17384 original size:5 final size:5
Alignment explanation
Indices: 17329--17366 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
17319 AATCAAAATA
**
17329 ATAAT ATAAT ATAAT ATAAT ATAAT ATTCT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
17367 TACTCTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:17385 original size:2 final size:2
Alignment explanation
Indices: 17332--17506 Score: 51
Period size: 2 Copynumber: 91.5 Consensus size: 2
17322 CAAAATAATA
*
17332 AT AT A- AT AT A- AT AT A- AT AT A- AT AT -T CT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
17368 ACT CT AC AT AT A- AT AT AT ACT AT ACT AT AT A- AA AT AT AT GCT
1 A-T AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT -AT
*
17410 AT AT TT A- AT A- AT AT ACT AT AT A- AT A- AT AT -T AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
17447 AT AT AT GCT AT AT A- AT AC ACT AT AT A- AT GT AT AT ACC AT ACC
1 AT AT AT -AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT A-T
17489 AT A- AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
17507 CACACACTAT
Statistics
Matches: 127, Mismatches: 20, Indels: 52
0.64 0.10 0.26
Matches are distributed among these distances:
1 17 0.13
2 98 0.77
3 12 0.09
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:17385 original size:7 final size:7
Alignment explanation
Indices: 17375--17451 Score: 50
Period size: 7 Copynumber: 10.7 Consensus size: 7
17365 TATACTCTAC
17375 ATATAAT
1 ATATAAT
*
17382 ATATACT
1 ATATAAT
17389 ATACT-AT
1 ATA-TAAT
*
17396 ATAAAAT
1 ATATAAT
*
17403 ATATGCTAT
1 ATAT--AAT
*
17412 ATTTAAT
1 ATATAAT
*
17419 AATATACT
1 -ATATAAT
17427 ATATAAT
1 ATATAAT
*
17434 A-ATATT
1 ATATAAT
17440 ATATAAT
1 ATATAAT
17447 ATATA
1 ATATA
17452 TGCTATATAA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
6 5 0.10
7 36 0.69
8 6 0.12
9 5 0.10
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (7 bp):
ATATAAT
Found at i:17405 original size:21 final size:18
Alignment explanation
Indices: 17326--17545 Score: 80
Period size: 18 Copynumber: 11.6 Consensus size: 18
17316 TAAAATCAAA
*
17326 ATAATAATATAATATA-AT
1 ATAAT-ATATACTATACAT
*
17344 ATAATATA-A-TATTC-T
1 ATAATATATACTATACAT
*
17359 ATAATATATACTCTACAT
1 ATAATATATACTATACAT
17377 ATAATATATACTATACTAT
1 ATAATATATACTATAC-AT
*
17396 ATAAAATATATGCTAT--AT
1 AT--AATATATACTATACAT
* *
17414 TTAATAATATACTATATA-
1 ATAAT-ATATACTATACAT
*
17432 ATAATATTATA-TAATATAT
1 ATAATA-TATACT-ATACAT
** * *
17451 ATGCTATATAATACACTAT
1 ATAATATATACTATAC-AT
*
17470 ATAATGTATATACCATACCAT
1 ATAA--TATATACTATA-CAT
17491 AATATATATATA-TATACACACACT
1 -ATA-ATATATACTAT----ACA-T
17515 ATAATATAATACTATAACTAT
1 ATAATAT-ATACTAT-AC-AT
17536 ATAATATATA
1 ATAATATATA
17546 TACCATGTAG
Statistics
Matches: 155, Mismatches: 19, Indels: 54
0.68 0.08 0.24
Matches are distributed among these distances:
15 12 0.08
16 5 0.03
17 16 0.10
18 43 0.28
19 14 0.09
20 5 0.03
21 37 0.24
22 9 0.06
23 9 0.06
24 5 0.03
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.40
Consensus pattern (18 bp):
ATAATATATACTATACAT
Found at i:17470 original size:26 final size:25
Alignment explanation
Indices: 17442--17530 Score: 73
Period size: 26 Copynumber: 3.6 Consensus size: 25
17432 ATAATATTAT
17442 ATAATATATATGCTATATA-ATACAC
1 ATAATATA-ATGCTATATACATACAC
17467 -T-ATATAATG-TATATACCATAC-C
1 ATAATATAATGCTATATA-CATACAC
* *
17489 ATAATATATAT-ATATATACACACAC
1 ATAATATA-ATGCTATATACATACAC
*
17514 TATAATATAATACTATA
1 -ATAATATAATGCTATA
17531 ACTATATAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
21 6 0.11
22 4 0.08
23 10 0.19
24 10 0.19
25 11 0.21
26 12 0.23
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAATATAATGCTATATACATACAC
Found at i:18474 original size:22 final size:21
Alignment explanation
Indices: 18445--18485 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
18435 CATTGTTGTA
*
18445 TGTTTATTACTTGAGTTTACT
1 TGTTTATTACTTGACTTTACT
*
18466 TGTTCTATTATTTGACTTTA
1 TGTT-TATTACTTGACTTTA
18486 TTTATTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.59
Consensus pattern (21 bp):
TGTTTATTACTTGACTTTACT
Found at i:23160 original size:23 final size:23
Alignment explanation
Indices: 23090--23154 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
23080 AATAACATAT
*
23090 TAGGTAGCGTTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
23113 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
23136 TAGGTAGCGCTTATATAAT
1 TAGGTAGCGCTTATATAAT
23155 AAAATAAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.37
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:23674 original size:199 final size:200
Alignment explanation
Indices: 23233--23963 Score: 799
Period size: 199 Copynumber: 3.6 Consensus size: 200
23223 TAGGTAGCAC
* ** * *
23233 TTATATTGACCTATTTTCGAAGT-AAACCGGTATATTTATACCGGTAACATTGAAAATTTACCTA
1 TTATGTTGACCTATTTTCTCA-TAAAACCGGTATATTTATACTGGTTACATTGAAAATTTACCTA
* * * ** **
23297 TTATATTATTATTATCGGTTTCGAGGTTTTTTAGATCGATACAATTT-TAAATGTATCGACACTT
65 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTT
* * *
23361 TATGCTTGCACCTGGTTGAGCATTCATATTTCATTCTGGAA-AAAAGTATCGACACAAACTAACA
130 TATGGTTGCACCTGTTTGAGCATTC--A--T--TT-TGGAACAAAAGTATCGACACAAATTAACA
23425 AAGTGTCGATACA
188 AAGTGTCGATACA
* *
23438 TTAT-TTAGACCTATTCTCTCATAAAACCGATATATTTATACTGGTTACATTGAAAATTTACCTA
1 TTATGTT-GACCTATTTTCTCATAAAACCGGTATATTTATACTGGTTACATTGAAAATTTACCTA
* ** * *
23502 TTACAATATGCTTATGGGTTTCGATGTTTTCGGGATCGATACTTTTTATAAATGTATCGACACTT
65 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTT
* * *
23567 TATGGTTGCACCTTTTTG-GCATTCATTTTGGAACAAAAGTATCGACACAAATTTAGAAAGTGTC
130 TATGGTTGCACCTGTTTGAGCATTCATTTTGGAACAAAAGTATCGACACAAATTAACAAAGTGTC
*
23631 GATACT
195 GATACA
* * *
23637 TTATGCTGACCTATTTTATCATAAAACCGGTATATTTATA-TCGGTTACATTGTAAATTTACCT-
1 TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACT-GGTTACATTGAAAATTTACCTA
* *
23700 TATACATTATAATTATCGATTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACT
65 T-TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACT
* ** *
23765 TTATGCG-TGCACCTCGTTTGTGCATTCATCCTGG-ACAATAAGTATCGACACAAATTCCACAAA
129 TTATG-GTTGCACCT-GTTTGAGCATTCATTTTGGAACAA-AAGTATCGACACAAATT-AACAAA
23828 -TGTCGATACA
190 GTGTCGATACA
* * * **
23838 TTATGTTGACCTGTTTTCTAAT-TAACCGGTATATTTATACAT-GTTACATTGTTAATTTACCTA
1 TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATAC-TGGTTACATTGAAAATTTACCTA
* * *
23901 TTACATTATAATTATTGGCTTT-GATGTTTTTTGGG-TCGATAC-TTGTATAAAATGTATCAACA
65 TTACATTATAATTATCGG-TTTCGATG-TTTTTGGGATCGATACTTTTTAT-AAATGTATCGACA
23963 C
127 C
23964 ATATTTAGGT
Statistics
Matches: 455, Mismatches: 53, Indels: 41
0.83 0.10 0.07
Matches are distributed among these distances:
198 7 0.02
199 160 0.35
200 84 0.18
201 68 0.15
202 5 0.01
203 1 0.00
204 3 0.01
205 95 0.21
206 32 0.07
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (200 bp):
TTATGTTGACCTATTTTCTCATAAAACCGGTATATTTATACTGGTTACATTGAAAATTTACCTAT
TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTT
ATGGTTGCACCTGTTTGAGCATTCATTTTGGAACAAAAGTATCGACACAAATTAACAAAGTGTCG
ATACA
Found at i:27023 original size:200 final size:199
Alignment explanation
Indices: 26665--27218 Score: 797
Period size: 200 Copynumber: 2.8 Consensus size: 199
26655 TGGGGTTTAT
* * *
26665 TTAAAAAGTGTCGATACATGTTGTAGACCTATTTTCTCATAAAACCGATATATTTATACCGGTTA
1 TTAAAAAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTA
* * * *
26730 TATTACAAAAGTACCTATTACATTATAATTATCGGTTTCGATGTTTTCGGTATCGACACTTTTAA
66 TATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAA
* * * *
26795 TAAATGTATCGACACTTTGTGTGTTCATCCTTTTTGGCATCTATTCTGGAAAAAAAGTATCGACA
131 TAAATGTATC-AAACTTTATGCGTTCATCCTTTTTGGCATCCATTCTGGAAAAAAAGTATCGACA
26860 CAA-A
195 CAATA
* *
26864 CTTAACAAGTGTCGCTACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTT
1 -TTAAAAAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTT
* ** *
26929 ACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTT
65 ATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACAC-TTTT
* *
26994 AA-AAATGTATCAATACTTTATGCGTTCATCCTTTTTGGCATCCATTCTGGACAAAAATTATCGA
129 AATAAATGTATCAA-ACTTTATGCGTTCATCCTTTTTGGCATCCATTCTGGAAAAAAAGTATCGA
27058 CACAATA
193 CACAATA
* * * * *
27065 TTAAGAAGTGTTGATACATATTATAGACCTATTCTCTCATAAAACCGGTATATGTATACTGGTTA
1 TTAAAAAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTA
* * *
27130 TATTACAAAATTACCTATTACATTAAAAATATGGGTTTCGATGTTTTTGGGATTGACACTTTTAA
66 TATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAA
*
27195 TAAATATATCGAAACTTTATGCGT
131 TAAATGTATC-AAACTTTATGCGT
27219 GCAACCCTTT
Statistics
Matches: 316, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
199 7 0.02
200 300 0.95
201 9 0.03
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (199 bp):
TTAAAAAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTTTAA
TAAATGTATCAAACTTTATGCGTTCATCCTTTTTGGCATCCATTCTGGAAAAAAAGTATCGACAC
AATA
Found at i:27706 original size:33 final size:33
Alignment explanation
Indices: 27669--27734 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
27659 CATCTTAAGA
* *
27669 TCACCCCTTAACACTTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
* * *
27702 TCACCCCTCAACACCTCTATTTCTTTCATCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
27735 CCATCTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:27804 original size:21 final size:21
Alignment explanation
Indices: 27768--27809 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27758 CCCCTTATGC
*
27768 CTCTCAAGTGTATCTTTGACT
1 CTCTCAAGTGTATCTTCGACT
* *
27789 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
27810 TTTGATTGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:30083 original size:20 final size:19
Alignment explanation
Indices: 30038--30083 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
30028 CCGGTAGCTC
30038 TTTACCGATTTTATCATTT
1 TTTACCGATTTTATCATTT
* *
30057 TGATACCGGTTTTATCATATT
1 T-TTACCGATTTTATCAT-TT
30078 TTTACC
1 TTTACC
30084 TGTTATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (19 bp):
TTTACCGATTTTATCATTT
Found at i:30298 original size:180 final size:181
Alignment explanation
Indices: 30004--30477 Score: 616
Period size: 180 Copynumber: 2.6 Consensus size: 181
29994 CGTACTTATG
* *
30004 AAAGTATCAACACTTTCAATATATCCGGTAGC-TCTTTACCGATTTTATCATTTTGATACCGGTT
1 AAAGTATCAACACTTTCAATATATCCGGTAGCGT-TTTACCGGTTTTATCATTTCGATACCGG-T
*
30068 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGAAACTTTA
64 TTATCATATTTTTACCTATTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGAAACTTTA
* *
30133 TAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATAC-TTATATT
129 TAGGCACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGAT-CTTTACATT
* *
30186 AAAGTACTGAA-ACTTTAAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGATACCGG-T
1 AAAGTA-TCAACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGATACCGGTT
* * *
30249 TGTCATATTTTTACCTTTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTATTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGAAACTTTAT
* * * *
30314 TGGCATTAAAACTGTTTCTCTTTTAAATTCATAAAGTGTCGATCTTTACATT
130 AGGCACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCTTTACATT
* * * * ** * * *
30366 AAAGTATCAACACGTTCAATATATCCGATAGGGCTTTACTAGTATTGTCTTTTC-ATGACCGGTT
1 AAAGTATCAACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGAT-ACCGG-T
* * *
30430 TTATCGATATTTTTACCTATTATATTGATATGGATCGATACATTTTTA
64 TTATC-ATATTTTTACCTATTATATCGTTGTGGATCGATACATTTTTA
30478 ATTTGGATCG
Statistics
Matches: 255, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
179 6 0.02
180 151 0.59
182 56 0.22
183 42 0.16
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCAACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTCGATACCGGTTT
ATCATATTTTTACCTATTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGAAACTTTATA
GGCACTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCTTTACATT
Found at i:31664 original size:5 final size:5
Alignment explanation
Indices: 31649--31679 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
31639 AAAAATTTCG
31649 TAAAGA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAA-A TAAAA TAAAA TAAAA TAAAA TAAAA
31680 GTGAAAAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:32277 original size:30 final size:30
Alignment explanation
Indices: 32198--32338 Score: 131
Period size: 30 Copynumber: 4.7 Consensus size: 30
32188 CAATAAATAC
* *
32198 AGAAAGTTAAAGGACCAAAATAGCAAATAT
1 AGAAAGTTAAAGGACTAAAATAGCAAAAAT
*
32228 AGAAACTTAAAGGACTAAAATAG-ATAAAAT
1 AGAAAGTTAAAGGACTAAAATAGCA-AAAAT
* *
32258 AGAAAGTTAAAGGATTAAAATAACAAAAAT
1 AGAAAGTTAAAGGACTAAAATAGCAAAAAT
* * * * * * *
32288 AGATACTCAAAGGGCTAAAACAGTAAAAAC
1 AGAAAGTTAAAGGACTAAAATAGCAAAAAT
* *
32318 AGATATTTAAAAGGACTAAAA
1 AGAAAGTT-AAAGGACTAAAA
32339 CAGTAATTAC
Statistics
Matches: 90, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
29 1 0.01
30 77 0.86
31 12 0.13
ACGTcount: A:0.58, C:0.09, G:0.15, T:0.18
Consensus pattern (30 bp):
AGAAAGTTAAAGGACTAAAATAGCAAAAAT
Found at i:32328 original size:60 final size:60
Alignment explanation
Indices: 32181--32338 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
32171 AAATTTAAAA
* * * * * *
32181 GGCT-AAACAATAAATACAGAAAGTTAAAGGACCAAAATAGCAAATATAGAAACTTAAAG
1 GGCTAAAACAGTAAAAACAGAAAGTTAAAGGACTAAAATAACAAAAATAGAAACTCAAAG
* * * * *
32240 GACTAAAATAG-ATAAAATAGAAAGTTAAAGGATTAAAATAACAAAAATAGATACTCAAAG
1 GGCTAAAACAGTA-AAAACAGAAAGTTAAAGGACTAAAATAACAAAAATAGAAACTCAAAG
* *
32300 GGCTAAAACAGTAAAAACAGATATTTAAAAGGACTAAAA
1 GGCTAAAACAGTAAAAACAGAAAGTT-AAAGGACTAAAA
32339 CAGTAATTAC
Statistics
Matches: 78, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
59 4 0.05
60 62 0.79
61 12 0.15
ACGTcount: A:0.58, C:0.09, G:0.15, T:0.18
Consensus pattern (60 bp):
GGCTAAAACAGTAAAAACAGAAAGTTAAAGGACTAAAATAACAAAAATAGAAACTCAAAG
Found at i:33552 original size:3 final size:3
Alignment explanation
Indices: 33540--33612 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
33530 AAAATGTAAT
33540 TAA T-A TAA TAA 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 TAA TAA TAA TAA
33587 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
33613 TTTTTTTAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:34124 original size:30 final size:31
Alignment explanation
Indices: 34088--34192 Score: 87
Period size: 30 Copynumber: 3.5 Consensus size: 31
34078 GGAGACATAA
** *
34088 TTTGTTTCAAAG-GAAATGATCTTAAAGA-T
1 TTTGTTTCAAAGAGAAACAAACTTAAAGACT
34117 GTTTGTTTC-AAGAGAAACAAACTTAAAGACT
1 -TTTGTTTCAAAGAGAAACAAACTTAAAGACT
* * *
34148 TTTGTTTC-AAGAAAAACATACTCAAAGA-T
1 TTTGTTTCAAAGAGAAACAAACTTAAAGACT
**
34177 TTTCCTTCAAA-AGAAA
1 TTTGTTTCAAAGAGAAA
34193 ATGTCTCAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
29 14 0.22
30 48 0.76
31 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.32
Consensus pattern (31 bp):
TTTGTTTCAAAGAGAAACAAACTTAAAGACT
Found at i:34447 original size:38 final size:37
Alignment explanation
Indices: 34369--34455 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
34359 CAAATTTGGG
*
34369 GTTTTGAG-GAAAACTGTCTCAAGTGACACGAAATTT
1 GTTTTGAGAGAAAACTGTCTCAAGCGACACGAAATTT
* * *
34405 GTTTTGAGAGAAATCTGTCTTAAGCGAGAC-AACATTTT
1 GTTTTGAGAGAAAACTGTCTCAAGCGACACGAA-A-TTT
*
34443 GTTTTAAGAGAAA
1 GTTTTGAGAGAAA
34456 CAACATCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
36 10 0.23
37 18 0.42
38 15 0.35
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.32
Consensus pattern (37 bp):
GTTTTGAGAGAAAACTGTCTCAAGCGACACGAAATTT
Found at i:35673 original size:24 final size:24
Alignment explanation
Indices: 35633--35713 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
35623 GTACTTCTCA
*
35633 TCTTTTTTTTTTCATTTCTTTTG-T
1 TCTTTTTCTTTTCATTT-TTTTGTT
35657 TCGTTTTTCTTTT-ATTTTTTTGTT
1 TC-TTTTTCTTTTCATTTTTTTGTT
*
35681 TCTTTTCTCTTTTC---TCTTTGTT
1 TCTTTT-TCTTTTCATTTTTTTGTT
35703 TCTTTTTCTTT
1 TCTTTTTCTTT
35714 GATTTGATTG
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
21 5 0.10
22 13 0.25
23 9 0.18
24 15 0.29
25 9 0.18
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (24 bp):
TCTTTTTCTTTTCATTTTTTTGTT
Found at i:35699 original size:31 final size:31
Alignment explanation
Indices: 35633--35708 Score: 75
Period size: 32 Copynumber: 2.4 Consensus size: 31
35623 GTACTTCTCA
*
35633 TCTTTTTTTTTTCATTTCTTTTGTTCGTTTT
1 TCTTTTTTTTTTCATTTCTTTTGCTCGTTTT
**
35664 TCTTTTATTTTTTTGTTTCTTTT-CTC-TTTT
1 TCTTTT-TTTTTTCATTTCTTTTGCTCGTTTT
35694 CTCTTTGTTTCTTTT
1 -TCTTT-TTT-TTTT
35709 TCTTTGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
30 4 0.11
31 15 0.39
32 19 0.50
ACGTcount: A:0.03, C:0.14, G:0.05, T:0.78
Consensus pattern (31 bp):
TCTTTTTTTTTTCATTTCTTTTGCTCGTTTT
Found at i:39652 original size:30 final size:30
Alignment explanation
Indices: 39566--39654 Score: 108
Period size: 30 Copynumber: 2.9 Consensus size: 30
39556 GGCTAAACAA
*
39566 TAAATACAGAAAGTTAAAGGACCAAAATAGC
1 TAAA-ACAGAAAGTTAAAGGACTAAAATAGC
* * *
39597 -ATATATAGAAATTTAAAGGACTAAAATAGC
1 TA-AAACAGAAAGTTAAAGGACTAAAATAGC
*
39627 TAAAACAGAAAGTTAAAGGATTAAAATA
1 TAAAACAGAAAGTTAAAGGACTAAAATA
39655 ATAAAAACTA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
30 46 0.96
31 2 0.04
ACGTcount: A:0.56, C:0.08, G:0.15, T:0.21
Consensus pattern (30 bp):
TAAAACAGAAAGTTAAAGGACTAAAATAGC
Found at i:39662 original size:30 final size:30
Alignment explanation
Indices: 39520--39662 Score: 105
Period size: 30 Copynumber: 4.8 Consensus size: 30
39510 AAATAAGTAT
* * *
39520 TTAAGGGACTAAAAT-ATAATTAACAGAAAT
1 TTAAAGGACTAAAATAATAA-AAACAGAAAG
* *
39550 TTAAAAGG-CT-AAACAATAAATACAGAAAG
1 TT-AAAGGACTAAAATAATAAAAACAGAAAG
* ** * * * *
39579 TTAAAGGACCAAAATAGCATATATAGAAAT
1 TTAAAGGACTAAAATAATAAAAACAGAAAG
*
39609 TTAAAGGACTAAAATAGCT-AAAACAGAAAG
1 TTAAAGGACTAAAATA-ATAAAAACAGAAAG
*
39639 TTAAAGGATTAAAATAATAAAAAC
1 TTAAAGGACTAAAATAATAAAAAC
39663 TAATACTCAA
Statistics
Matches: 86, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
28 5 0.06
29 14 0.16
30 63 0.73
31 4 0.05
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.22
Consensus pattern (30 bp):
TTAAAGGACTAAAATAATAAAAACAGAAAG
Found at i:41149 original size:20 final size:20
Alignment explanation
Indices: 41124--41173 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
41114 GACCAACAAA
41124 TTCGCAACGCAAACTCCAAT
1 TTCGCAACGCAAACTCCAAT
* ***
41144 TTCGCAACCCAGTTTCCAAT
1 TTCGCAACGCAAACTCCAAT
41164 TTCGCAACGC
1 TTCGCAACGC
41174 GAATATGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.36, G:0.12, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCAAACTCCAAT
Found at i:41256 original size:20 final size:20
Alignment explanation
Indices: 41232--41368 Score: 195
Period size: 20 Copynumber: 6.8 Consensus size: 20
41222 CGCAACACAG
*
41232 AAGTCAAATTCCCAACGCGA
1 AAGTCAAATTCGCAACGCGA
* * *
41252 TAGTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACGCGA
*
41272 AAGTCAAATTTGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
41292 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
41312 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
*
41332 AAGTCAAATTCGCAACGTGA
1 AAGTCAAATTCGCAACGCGA
*
41352 ATAGT-AAAATCGCAACG
1 A-AGTCAAATTCGCAACG
41369 AATCTATATG
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 102 0.97
21 3 0.03
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.18
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:41676 original size:20 final size:20
Alignment explanation
Indices: 41639--41725 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
41629 TTCCTATAAA
41639 TCGCAACAC-AGAAGTCAAAT
1 TCGCAACACGA-AAGTCAAAT
* * *
41659 TCGAAATACGATAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
*
41679 TCGCAACACAAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
*
41699 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
41719 TCGCAAC
1 TCGCAAC
41726 GTGAATAGTA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 56 0.98
21 1 0.02
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAGTCAAAT
Found at i:41694 original size:40 final size:40
Alignment explanation
Indices: 41639--41725 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
41629 TTCCTATAAA
* * *
41639 TCGCAACACAGAAGTCAAATTCGAAATACGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGAAACACGAAAGTCAAAT
* *
41679 TCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGAAACACGAAAGTCAAAT
41719 TCGCAAC
1 TCGCAAC
41726 GTGAATAGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.17
Consensus pattern (40 bp):
TCGCAACACAAAAGTCAAATTCGAAACACGAAAGTCAAAT
Found at i:41726 original size:20 final size:20
Alignment explanation
Indices: 41650--41787 Score: 118
Period size: 20 Copynumber: 6.8 Consensus size: 20
41640 CGCAACACAG
* **
41650 AAGTCAAATTCGAAATACGA
1 AAGTCAAATTCGCAACGCGA
* * *
41670 TAGTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACGCGA
41690 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
*
41710 AAGTCAAATTCGCAACGTGA
1 AAGTCAAATTCGCAACGCGA
* * *
41730 ATAGTAAAAATCGCAACGTGA
1 A-AGTCAAATTCGCAACGCGA
* *
41751 ATAGTAAAATT-GCAACGTGA
1 A-AGTCAAATTCGCAACGCGA
*
41771 ATAGT-AAAATCGCAACG
1 A-AGTCAAATTCGCAACG
41788 AATCTATATG
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
19 4 0.04
20 73 0.70
21 27 0.26
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:41745 original size:21 final size:20
Alignment explanation
Indices: 41699--41787 Score: 126
Period size: 20 Copynumber: 4.4 Consensus size: 20
41689 AAAGTCAAAT
* *
41699 TCGCAACGCGAA-AGTCAAAT
1 TCGCAACGTGAATAGT-AAAA
41719 TCGCAACGTGAATAGTAAAAA
1 TCGCAACGTGAATAGT-AAAA
41740 TCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
*
41760 TTGCAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
41780 TCGCAACG
1 TCGCAACG
41788 AATCTATATG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 41 0.65
21 22 0.35
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (20 bp):
TCGCAACGTGAATAGTAAAA
Found at i:41766 original size:41 final size:40
Alignment explanation
Indices: 41699--41787 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 40
41689 AAAGTCAAAT
*
41699 TCGCAACGCGAAAGTCAAATTCGCAACGTGAATAGTAAAAA
1 TCGCAACGCGAAAGTAAAATTCGCAACGTGAATAGT-AAAA
*
41740 TCGCAACGTGAATAGTAAAATT-GCAACGTGAATAGTAAAA
1 TCGCAACGCGAA-AGTAAAATTCGCAACGTGAATAGTAAAA
41780 TCGCAACG
1 TCGCAACG
41788 AATCTATATG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
40 12 0.27
41 25 0.56
42 8 0.18
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (40 bp):
TCGCAACGCGAAAGTAAAATTCGCAACGTGAATAGTAAAA
Found at i:41996 original size:419 final size:418
Alignment explanation
Indices: 41217--42052 Score: 1431
Period size: 419 Copynumber: 2.0 Consensus size: 418
41207 GCAAAATCTG
* *
41217 TAAATCGCAACACAGAAGTCAAATTCCCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATT
1 TAAATCGCAACACAGAAGTCAAATTCCAAACACGATAGTCAAATTCGCAACACAAAAGTCAAATT
* * * *
41282 TGCAACGCGAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAA
66 CGCAACGCGAAAGTCAAATTCGCAACGCGAAAGTAAAAATCGCAACGCGAAAGTAAAATTCGCAA
41347 CGTGAATAGTAAAATCGCAACGAATCTATATGTAAATTATCTCTTATCATCCATCTATAATAATT
131 CGTGAATAGTAAAATCGCAACGAATCTATATGTAAATTATCTCTTATCATCCATCTATAATAATT
* * * * *
41412 TGTTGGAAACGTACATAAATAATTTTTATAAAAAGTATTTGTACACGTGAAAAAATTTATATGTA
196 TGTTGGAAAAGTACATAAATAACTTTTATAAAAAATATTCGTACACGTAAAAAAATTTATATGTA
* *
41477 AATGAACAACAAATCTATTTCATTTGTCAATCTTCATTACAAATTATTCTAAATTCAATTAATTA
261 AATGAACAACAAATATATTTCATTTGTCAATCTTCATTACAAATTATTCTAAATTCAACTAATTA
41542 AAGTTTGAAATTTGAAAGAATCCTTAACACAGACTAATGAAATACATTTAAAAAATTAAATTTTG
326 AAGTTTGAAATTTGAAAGAATCCTTAACACAGACTAATGAAATACATTTAAAAAATTAAATTTTG
*
41607 AATTATATTAAGAAAAACCTGATTCCTA
391 AATTATATTAAGAAAAACCTAATTCCTA
* *
41635 TAAATCGCAACACAGAAGTCAAATTCGAAATACGATAGTCAAATTCGCAACACAAAAGTCAAATT
1 TAAATCGCAACACAGAAGTCAAATTCCAAACACGATAGTCAAATTCGCAACACAAAAGTCAAATT
* *
41700 CGCAACGCGAAAGTCAAATTCGCAACGTGAATAGTAAAAATCGCAACGTGAATAGTAAAATT-GC
66 CGCAACGCGAAAGTCAAATTCGCAACGCGAA-AGTAAAAATCGCAACGCGAA-AGTAAAATTCGC
*
41764 AACGTGAATAGTAAAATCGCAACGAATCTATATGTAAATTATTTCTTATCATCCATCTATAATAA
129 AACGTGAATAGTAAAATCGCAACGAATCTATATGTAAATTATCTCTTATCATCCATCTATAATAA
41829 TTTGTTGGAAAAGTACATAAATAACTTTTATAAAAAATATTCGTACACGTAAAAAAATTTATATG
194 TTTGTTGGAAAAGTACATAAATAACTTTTATAAAAAATATTCGTACACGTAAAAAAATTTATATG
* *
41894 TAAATGAACAACAAATATATTTCATTTGTCAATCTTTATTACAAATTATTTTAAATTCAACTAAT
259 TAAATGAACAACAAATATATTTCATTTGTCAATCTTCATTACAAATTATTCTAAATTCAACTAAT
* *
41959 TAAAGTTTGAAATTTGAAAGAATCCTTAACTCAGACTAATGAAATACATTTAAAATATTAAATTT
324 TAAAGTTTGAAATTTGAAAGAATCCTTAACACAGACTAATGAAATACATTTAAAAAATTAAATTT
*
42024 TGAATTATATTAAGAAAAAGCTAATTCCT
389 TGAATTATATTAAGAAAAACCTAATTCCT
42053 GTACACATGT
Statistics
Matches: 392, Mismatches: 24, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
418 90 0.23
419 294 0.75
420 8 0.02
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (418 bp):
TAAATCGCAACACAGAAGTCAAATTCCAAACACGATAGTCAAATTCGCAACACAAAAGTCAAATT
CGCAACGCGAAAGTCAAATTCGCAACGCGAAAGTAAAAATCGCAACGCGAAAGTAAAATTCGCAA
CGTGAATAGTAAAATCGCAACGAATCTATATGTAAATTATCTCTTATCATCCATCTATAATAATT
TGTTGGAAAAGTACATAAATAACTTTTATAAAAAATATTCGTACACGTAAAAAAATTTATATGTA
AATGAACAACAAATATATTTCATTTGTCAATCTTCATTACAAATTATTCTAAATTCAACTAATTA
AAGTTTGAAATTTGAAAGAATCCTTAACACAGACTAATGAAATACATTTAAAAAATTAAATTTTG
AATTATATTAAGAAAAACCTAATTCCTA
Found at i:42175 original size:20 final size:20
Alignment explanation
Indices: 42137--42207 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
42127 CAACGCGATT
*
42137 TTGCGATTTTCTAAATTCGCG
1 TTGCGATTTTC-CAATTCGCG
42158 TTGCGATTTTCCAATTCGCG
1 TTGCGATTTTCCAATTCGCG
* * *
42178 TTGCGATTTTACTATTCACG
1 TTGCGATTTTCCAATTCGCG
*
42198 TTACGATTTT
1 TTGCGATTTT
42208 ACTATTCACG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 34 0.76
21 11 0.24
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (20 bp):
TTGCGATTTTCCAATTCGCG
Found at i:42208 original size:20 final size:20
Alignment explanation
Indices: 42151--42223 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
42141 GATTTTCTAA
* * * *
42151 ATTCGCGTTGCGATTTTCCA
1 ATTCACGTTACGATTTTACT
* *
42171 ATTCGCGTTGCGATTTTACT
1 ATTCACGTTACGATTTTACT
42191 ATTCACGTTACGATTTTACT
1 ATTCACGTTACGATTTTACT
42211 ATTCACGTTACGA
1 ATTCACGTTACGA
42224 AATTGGAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (20 bp):
ATTCACGTTACGATTTTACT
Found at i:42991 original size:22 final size:23
Alignment explanation
Indices: 42952--42997 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
42942 TGGACCCTTT
* *
42952 TTAAGCTGCGACAGCATTTTTAC
1 TTAAGCTGCGACAACATTTATAC
*
42975 TTAA-CTGCGATAACATTTATAC
1 TTAAGCTGCGACAACATTTATAC
42997 T
1 T
42998 AATGGGGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (23 bp):
TTAAGCTGCGACAACATTTATAC
Found at i:47450 original size:17 final size:18
Alignment explanation
Indices: 47411--47451 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
47401 ACGCATACCG
* *
47411 TAAAATTATTGTTTTATT
1 TAAAATTAATATTTTATT
47429 TAAAATTAATATTTTA-T
1 TAAAATTAATATTTTATT
47446 TAAAAT
1 TAAAAT
47452 GACAAATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TAAAATTAATATTTTATT
Found at i:49425 original size:17 final size:17
Alignment explanation
Indices: 49399--49431 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49389 AGGAGCAGCA
*
49399 CAAGCGTTTAGTTTTAT
1 CAAGCATTTAGTTTTAT
49416 CAAGCATTTAGTTTTA
1 CAAGCATTTAGTTTTA
49432 GTTTTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (17 bp):
CAAGCATTTAGTTTTAT
Found at i:51049 original size:20 final size:20
Alignment explanation
Indices: 51004--51051 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
50994 ATTTCAGTTA
*
51004 CAGTATCGATACCTTCCTCT
1 CAGTATCGATACCTTCCACT
**
51024 TGGTATCGATACC-TCCACAT
1 CAGTATCGATACCTTCCAC-T
51044 CAGTATCG
1 CAGTATCG
51052 TCACTGCTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (20 bp):
CAGTATCGATACCTTCCACT
Found at i:57223 original size:24 final size:24
Alignment explanation
Indices: 57196--57273 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
57186 ATAAATTGCA
57196 CCGAAGTGCCACGTAGAATTTGTC
1 CCGAAGTGCCACGTAGAATTTGTC
* *
57220 CCGAAG-GACCGCGTATAATTTGTC
1 CCGAAGTG-CCACGTAGAATTTGTC
* * * *
57244 CCGAAATACCAAGTAGAATTTATC
1 CCGAAGTGCCACGTAGAATTTGTC
57268 CCGAAG
1 CCGAAG
57274 GACCGCGTAG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 1 0.02
24 42 0.98
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (24 bp):
CCGAAGTGCCACGTAGAATTTGTC
Found at i:57283 original size:24 final size:24
Alignment explanation
Indices: 57207--57285 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 24
57197 CGAAGTGCCA
57207 CGTAGAATTTGTCCCGAAGGACCG
1 CGTAGAATTTGTCCCGAAGGACCG
* ** *
57231 CGTATAATTTGTCCCGAAATACCA
1 CGTAGAATTTGTCCCGAAGGACCG
* *
57255 AGTAGAATTTATCCCGAAGGACCG
1 CGTAGAATTTGTCCCGAAGGACCG
57279 CGTAGAA
1 CGTAGAA
57286 CCCTCGACTC
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (24 bp):
CGTAGAATTTGTCCCGAAGGACCG
Found at i:59545 original size:3 final size:3
Alignment explanation
Indices: 59516--59565 Score: 57
Period size: 3 Copynumber: 16.0 Consensus size: 3
59506 CATTTTCAAC
*
59516 TAT TAAT TAT TAT ATAT TA- TACG TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
59563 TAT
1 TAT
59566 CATAAATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
2 2 0.05
3 32 0.76
4 8 0.19
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:63294 original size:20 final size:20
Alignment explanation
Indices: 63233--63340 Score: 126
Period size: 20 Copynumber: 5.3 Consensus size: 20
63223 TTCCAATTTT
63233 GCAACGTGAATAGTAAAAATC
1 GCAACGTGAATAGT-AAAATC
*
63254 GTAACGTGAATAGTAAAAATC
1 GCAACGTGAATAGT-AAAATC
63275 GCAACGTGAATAGTAAAATC
1 GCAACGTGAATAGTAAAATC
* * *
63295 GCAACGCGAATTGGAAAATC
1 GCAACGTGAATAGTAAAATC
* * * *
63315 GCAATGCGAATTGGAAAATC
1 GCAACGTGAATAGTAAAATC
63335 GCAACG
1 GCAACG
63341 CAAATTTAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
20 47 0.59
21 33 0.41
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.19
Consensus pattern (20 bp):
GCAACGTGAATAGTAAAATC
Found at i:63352 original size:20 final size:20
Alignment explanation
Indices: 63246--63352 Score: 90
Period size: 20 Copynumber: 5.3 Consensus size: 20
63236 ACGTGAATAG
* * *
63246 TAAAAATCGTAACGTGAATAG
1 TAAAAATCGCAACGCGAAT-T
* *
63267 TAAAAATCGCAACGTGAATAG
1 TAAAAATCGCAACGCGAAT-T
63288 T-AAAATCGCAACGCGAATT
1 TAAAAATCGCAACGCGAATT
** *
63307 GGAAAATCGCAATGCGAATT
1 TAAAAATCGCAACGCGAATT
** *
63327 GGAAAATCGCAACGCAAATT
1 TAAAAATCGCAACGCGAATT
63347 TAAAAA
1 TAAAAA
63353 ATCGGAAAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
20 55 0.72
21 21 0.28
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.20
Consensus pattern (20 bp):
TAAAAATCGCAACGCGAATT
Found at i:63748 original size:21 final size:20
Alignment explanation
Indices: 63710--63798 Score: 117
Period size: 20 Copynumber: 4.4 Consensus size: 20
63700 CATATAGATT
63710 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
*
63730 CGTTGCGATTTTTATTATTCA
1 CGTTGCGA-TTTTACTATTCA
*
63751 CGTTGTGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
* *
63771 CGTTGCGAATTTGACTA-TCG
1 CGTTGCG-ATTTTACTATTCA
63791 CGTTGCGA
1 CGTTGCGA
63799 ATTTGACTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 34 0.56
21 26 0.43
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTACTATTCA
Found at i:63823 original size:40 final size:40
Alignment explanation
Indices: 63779--63854 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
63769 CACGTTGCGA
*
63779 ATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTACGG
1 ATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTACGG
63819 ATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTT
1 ATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTT
63855 GCGATTTACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.43
Consensus pattern (40 bp):
ATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTACGG
Found at i:63858 original size:20 final size:20
Alignment explanation
Indices: 63771--63846 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
63761 TTACTATTCA
63771 CGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
* *
63791 CGTTGCGAATTTGACTTTTG
1 CGTTGCGAATTTGACTATCG
* * *
63811 TGTTACGGATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
63831 CGTTGCGAATTTGACT
1 CGTTGCGAATTTGACT
63847 TCTGTGTTGC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
CGTTGCGAATTTGACTATCG
Found at i:63938 original size:40 final size:40
Alignment explanation
Indices: 63852--63927 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
63842 TGACTTCTGT
* *
63852 GTTGCGATTTACAGATTCGTGTTGTGAATTTGGAAAACGC
1 GTTGCGATTTACAGATTCGCGTTGTGAAATTGGAAAACGC
** *
63892 AATGCGATTTACATATTCGCGTTGTGAAATTGGAAA
1 GTTGCGATTTACAGATTCGCGTTGTGAAATTGGAAA
63928 CTGGGTTGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGTGAAATTGGAAAACGC
Found at i:64164 original size:16 final size:17
Alignment explanation
Indices: 64145--64178 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
64135 CAAAAATGGG
64145 AAAAGAAAAAAAT-TTC
1 AAAAGAAAAAAATATTC
*
64161 AAAAGTAAAAAATATTC
1 AAAAGAAAAAAATATTC
64178 A
1 A
64179 TTTTTAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAAGAAAAAAATATTC
Found at i:66940 original size:34 final size:34
Alignment explanation
Indices: 66891--66955 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
66881 GATTGTTGAT
* * *
66891 AAGAGCCATGGAGCAAGCGAACTGTCTAACTGAC
1 AAGAGCCAAGAAGCAAGCGAACTATCTAACTGAC
66925 AAGAGCCAAGAAGCAAGCGAACTATCTAACT
1 AAGAGCCAAGAAGCAAGCGAACTATCTAACT
66956 TTCGATGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (34 bp):
AAGAGCCAAGAAGCAAGCGAACTATCTAACTGAC
Found at i:73308 original size:117 final size:118
Alignment explanation
Indices: 73177--73402 Score: 316
Period size: 118 Copynumber: 1.9 Consensus size: 118
73167 AAATTATTAC
* *
73177 ATTTAATTCAAAATTAAATGAA-TAAATAAGAGAAATG-AGAAAAAGAAGGT-AAAACCCAAACA
1 ATTTAATTCAAAATTAAATGAACT-AATAAGAGAAATGAAAAAAAAGAAGGTCAAAAACCAAA-A
* *
73239 TTTTATGAAATTAAAAAAATTAGGGTTAC-TAATTATAAATATAAAAGTTAGTTAA
64 ATTTATGAAATTAAAAAAATTAAGGTT-CTTAATTATAAATATAAAAGTTAGTTAA
* * **
73294 ATTTAATTCAAAATTGAATGAACTAATAAGAGAAATGAAAAAAAAGAGGGTCAAAAATTAAAAAT
1 ATTTAATTCAAAATTAAATGAACTAATAAGAGAAATGAAAAAAAAGAAGGTCAAAAACCAAAAAT
*
73359 TTATGAAATTATAAAAATTAAGGTTCTTAATTATAAATATAAAA
66 TTATGAAATTAAAAAAATTAAGGTTCTTAATTATAAATATAAAA
73403 AATTGCTCCT
Statistics
Matches: 96, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
117 35 0.36
118 54 0.56
119 7 0.07
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (118 bp):
ATTTAATTCAAAATTAAATGAACTAATAAGAGAAATGAAAAAAAAGAAGGTCAAAAACCAAAAAT
TTATGAAATTAAAAAAATTAAGGTTCTTAATTATAAATATAAAAGTTAGTTAA
Found at i:76294 original size:21 final size:20
Alignment explanation
Indices: 76256--76294 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
76246 TTTAAAAATT
* *
76256 AAAATTTATTTATTTTATCA
1 AAAATTTATATATCTTATCA
76276 AAAATATTATATATCTTAT
1 AAAAT-TTATATATCTTAT
76295 TATACATTCA
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:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATTTATATATCTTATCA
Found at i:76712 original size:17 final size:17
Alignment explanation
Indices: 76690--76740 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
76680 TTACATTTTT
76690 TTATATATTTTATAATA
1 TTATATATTTTATAATA
*
76707 TTATATA-TTTA-ATTA
1 TTATATATTTTATAATA
76722 TTA-ATAATTTTAT-ATA
1 TTATAT-ATTTTATAATA
76738 TTA
1 TTA
76741 AATAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 2 0.07
15 7 0.24
16 13 0.45
17 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATATTTTATAATA
Found at i:76739 original size:16 final size:17
Alignment explanation
Indices: 76692--76741 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 17
76682 ACATTTTTTT
76692 ATATATTTTATAATATT-
1 ATATATTTTAT-ATATTA
*
76709 ATATATTTAAT-TATTA
1 ATATATTTTATATATTA
76725 ATA-ATTTTATATATTA
1 ATATATTTTATATATTA
76741 A
1 A
76742 ATAAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 10 0.34
16 9 0.31
17 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATATTTTATATATTA
Found at i:76826 original size:19 final size:22
Alignment explanation
Indices: 76802--76842 Score: 61
Period size: 19 Copynumber: 2.0 Consensus size: 22
76792 GTTTAATAAT
76802 TAATATAA-TT-T-TTTTTTAA
1 TAATATAAGTTATATTTTTTAA
76821 TAATATAAGTTATATTTTTTAA
1 TAATATAAGTTATATTTTTTAA
76843 AAAGAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 1 0.05
22 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TAATATAAGTTATATTTTTTAA
Found at i:76834 original size:26 final size:22
Alignment explanation
Indices: 76793--76840 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
76783 TATTTGTATG
76793 TTTAATAATTAATATAATTTTTT
1 TTTAATAATTAATAT-ATTTTTT
76816 TTTAATAATATAAGTTATATTTTTT
1 TTTAATAAT-TAA--TATATTTTTT
76841 AAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 9 0.41
24 3 0.14
25 7 0.32
26 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTAATAATTAATATATTTTTT
Found at i:83080 original size:4 final size:4
Alignment explanation
Indices: 83067--83109 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
83057 CTATATATAT
*
83067 ATAC ACAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
83110 GGGGCGTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
4 33 0.94
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:83092 original size:22 final size:22
Alignment explanation
Indices: 83058--83103 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
83048 TAATCTGACC
* *
83058 TATATATATATACACACATACA
1 TATACATACATACACACATACA
*
83080 TATACATACATACATACATACA
1 TATACATACATACACACATACA
83102 TA
1 TA
83104 CATACAGGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (22 bp):
TATACATACATACACACATACA
Found at i:88016 original size:20 final size:20
Alignment explanation
Indices: 87991--88051 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
87981 AGTTGAAGAA
*
87991 GTATCGATACTGAAGTAAAG
1 GTATCGATACTCAAGTAAAG
*
88011 GTATCGATAC-CAAGGATAAG
1 GTATCGATACTCAAGTA-AAG
* *
88031 GTATCAATACTTTAAGTAAAG
1 GTATCGATAC-TCAAGTAAAG
88052 AAGAAATTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
19 4 0.12
20 22 0.67
21 3 0.09
22 4 0.12
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.26
Consensus pattern (20 bp):
GTATCGATACTCAAGTAAAG
Found at i:94917 original size:21 final size:23
Alignment explanation
Indices: 94859--94914 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
94849 GTCAATGATT
94859 CTATGTGGTCATTCGAGATAAAA
1 CTATGTGGTCATTCGAGATAAAA
*
94882 CTATGTGGTCCTTCGAGAT-AAA
1 CTATGTGGTCATTCGAGATAAAA
94904 -TATGTGG-CATT
1 CTATGTGGTCATT
94915 TCGGTGCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 3 0.10
21 7 0.23
22 3 0.10
23 18 0.58
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (23 bp):
CTATGTGGTCATTCGAGATAAAA
Done.