Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012333.1 Kokia drynarioides strain JFW-HI SEQ_127335, 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: 238800
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:132 original size:29 final size:28
Alignment explanation
Indices: 76--356 Score: 183
Period size: 29 Copynumber: 9.6 Consensus size: 28
66 CCCTGGAGGT
* *
76 CCCTAAACTGTCCAAAAATTTCCATTTTAC
1 CCCTGAACT-TCCAAAAA-TACCATTTTAC
*
106 CCCTGAACTTCCAAAAATCCCATTTTTGAC
1 CCCTGAACTTCCAAAAATACCA-TTTT-AC
* * *
136 CTC-GAACCTTCTAAAAATCACTATTTTA-
1 CCCTGAA-CTTCCAAAAAT-ACCATTTTAC
* * *
164 CCCTCGATCTTCCAAAAATCCCATTTTAA
1 CCCT-GAACTTCCAAAAATACCATTTTAC
* *
193 CCTTGAAACTTCTAAAAATTACCATTTTAC
1 CCCTG-AACTTCCAAAAA-TACCATTTTAC
** * * *
223 CCCCAAACTCCCAAAAATCCCATTTTAA
1 CCCTGAACTTCCAAAAATACCATTTTAC
*
251 CCCTGAAACTTCTAAAAATTACCATTTTAC
1 CCCTG-AACTTCCAAAAA-TACCATTTTAC
**
281 CCCCAAAC-TCTCAAAAATACCATTTTTGA-
1 CCCTGAACTTC-CAAAAATACCA-TTTT-AC
* * *
310 CCCTAAAACTTCTAAAACTTACCATTTTAC
1 CCCT-GAACTTCCAAAA-ATACCATTTTAC
*
340 CCCCGAACTTCCAAAAA
1 CCCTGAACTTCCAAAAA
357 ATNCATTTTT
Statistics
Matches: 194, Mismatches: 39, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
28 33 0.17
29 85 0.44
30 67 0.35
31 9 0.05
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.30
Consensus pattern (28 bp):
CCCTGAACTTCCAAAAATACCATTTTAC
Found at i:237 original size:58 final size:59
Alignment explanation
Indices: 76--403 Score: 369
Period size: 59 Copynumber: 5.6 Consensus size: 59
66 CCCTGGAGGT
* * * *
76 CCCT-AAACTGTCCAAAAATTTCCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
1 CCCTGAAACT-TCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTGA
* * * * * * *
135 -CCTCGAACCTTCTAAAAATCACTATTTTACCCTCGATCTTCCAAAAATCCCA-TTTTAA
1 CCCT-GAAACTTCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTGA
* * *
193 CCTTGAAACTTCTAAAAATTACCATTTTACCCCCAAACTCCCAAAAATCCCA-TTTTAA
1 CCCTGAAACTTCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTGA
* * *
251 CCCTGAAACTTCTAAAAATTACCATTTTACCCCCAAACTCTCAAAAATACCATTTTTGA
1 CCCTGAAACTTCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTGA
* * * *
310 CCCTAAAACTTCTAAAACTTACCATTTTACCCCCGAACTTCCAAAAAAT-NCATTTTTGA
1 CCCTGAAACTTCTAAAAATTACCATTTTACCCCCGAAC-TCCCAAAAATCCCATTTTTGA
* * * *
369 CCCCGAAACATCTAAAAATTACTATTTTACTCCCG
1 CCCTGAAACTTCTAAAAATTACCATTTTACCCCCG
404 GATGTTCGAA
Statistics
Matches: 231, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
58 104 0.45
59 115 0.50
60 12 0.05
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (59 bp):
CCCTGAAACTTCTAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTGA
Found at i:450 original size:117 final size:113
Alignment explanation
Indices: 90--461 Score: 340
Period size: 117 Copynumber: 3.2 Consensus size: 113
80 AAACTGTCCA
* * * * *
90 AAAATTTCCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAATC
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATT
* * * *
155 ACTATTTTACCCTCGATCTTCCAAAAATCCCATTTTAACCTTGAAACTTCTA
66 ACTATTTTACCC-CGAT-TT-CAAAAATACCATTTTGACCTCGAAAC-TCTT
* * * *
207 AAAATTACCATTTTACCCCCAAACTCCCAAAAATCCCA-TTTTAACCCTGAAACTTCTAAAAATT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATT
* * * *
271 ACCATTTTACCCCCAAACTCTCAAAAATACCATTTTTGACC-CTAAAACT-TCT
66 ACTATTTTA-CCCC-GA-TTTCAAAAATACCA-TTTTGACCTC-GAAACTCT-T
* *
323 AAAACTTACCATTTTACCCCCGAACTTCCAAAAAAT-NCATTTTTGACCCCGAAACATCTAAAAA
1 AAAA-TTACCATTTTACCCCCGAACTTCC-AAAAATCCCATTTTTGACCCCGAAACTTCTAAAAA
* * * *
387 TTACTATTTTACTCCCGGATGTTCGAAGACT-CCGTTTTCGACCTCGAATCTCTT
64 TTACTATTTTAC-CCC-GAT-TTC-AAAAATACCATTTT-GACCTCGAAACTCTT
441 AAAATTACCATTTTTACCCCC
1 AAAATTACCA-TTTTACCCCC
462 CGAATGTTTT
Statistics
Matches: 207, Mismatches: 32, Indels: 31
0.77 0.12 0.11
Matches are distributed among these distances:
115 1 0.00
116 45 0.22
117 86 0.42
118 69 0.33
119 6 0.03
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.32
Consensus pattern (113 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCTAAAAATT
ACTATTTTACCCCGATTTCAAAAATACCATTTTGACCTCGAAACTCTT
Found at i:4508 original size:49 final size:49
Alignment explanation
Indices: 4452--4566 Score: 142
Period size: 49 Copynumber: 2.3 Consensus size: 49
4442 GCAACTCGGT
*
4452 AAGTAATAAAATGACCTAGTTCCCAAACT-CATAGAGGGAAGCTTATAAA
1 AAGTAATAAAATGACCTAGCTCCCAAA-TGCATAGAGGGAAGCTTATAAA
* * * * *
4501 AAGTAATAAAAAGACCTTGCTCCCAAATGCATGGGGGGAGGCTTATAAA
1 AAGTAATAAAATGACCTAGCTCCCAAATGCATAGAGGGAAGCTTATAAA
*
4550 AAATAATAATAATGACC
1 AAGTAATAA-AATGACC
4567 CTACTAGCAG
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.02
49 49 0.88
50 6 0.11
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (49 bp):
AAGTAATAAAATGACCTAGCTCCCAAATGCATAGAGGGAAGCTTATAAA
Found at i:4721 original size:45 final size:45
Alignment explanation
Indices: 4624--4726 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
4614 CCTTGCTCCC
* *
4624 ACACAT-GGAGGGAGGCGTACGAAAGGTAATAATGACCCTGCTCTT
1 ACACATGGGA-GGAGGCGTACAAAAGGTAATAATGACCCTGCTATT
* * * **
4669 ACGCATGGGAGGAGGCTTACAAAAGGTAATAATGGCTTTGCTATT
1 ACACATGGGAGGAGGCGTACAAAAGGTAATAATGACCCTGCTATT
4714 ACACATGGG-GGAG
1 ACACATGGGAGGAG
4727 TAGCGGTGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 4 0.08
45 42 0.86
46 3 0.06
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (45 bp):
ACACATGGGAGGAGGCGTACAAAAGGTAATAATGACCCTGCTATT
Found at i:5229 original size:44 final size:43
Alignment explanation
Indices: 5122--5254 Score: 142
Period size: 44 Copynumber: 3.0 Consensus size: 43
5112 TATACACAGG
* *
5122 GGAGACTTACGAAAGGTAATAATAGCCCTGCTTCCTAGCACATTGAA
1 GGAGACTTACGAAAGGTAATAATGGCCCTGC-TCCCA-CACA-T-AA
*
5169 GGAGACTTAC-AGAAGGTAATAATGGCCTTGCTCCCACACATAA
1 GGAGACTTACGA-AAGGTAATAATGGCCCTGCTCCCACACATAA
* * **
5212 GAGAGGCTTACGAAAGGTAATAATGACCCTATTCCCACACATA
1 G-GAGACTTACGAAAGGTAATAATGGCCCTGCTCCCACACATA
5255 GGGGGAAGCT
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
43 3 0.04
44 35 0.47
45 5 0.07
46 5 0.07
47 27 0.36
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (43 bp):
GGAGACTTACGAAAGGTAATAATGGCCCTGCTCCCACACATAA
Found at i:20574 original size:24 final size:24
Alignment explanation
Indices: 20547--20610 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
20537 TTTCTAAAAG
* *
20547 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
20571 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
20595 ATTTAGCATTGATTAG
1 ATTTAGCATTTATTAG
20611 AATTAGGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:20602 original size:14 final size:14
Alignment explanation
Indices: 20559--20603 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
20549 TTAGTATTTA
*
20559 TTAGTATAATATAT
1 TTAGCATAATATAT
20573 TTAGCAT--T-TA-
1 TTAGCATAATATAT
20583 TTAGCATAATATAT
1 TTAGCATAATATAT
20597 TTAGCAT
1 TTAGCAT
20604 TGATTAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
12 2 0.08
13 2 0.08
14 13 0.50
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (14 bp):
TTAGCATAATATAT
Found at i:25454 original size:25 final size:26
Alignment explanation
Indices: 25425--25487 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
25415 TATCTCATCC
*
25425 TAATTTTACCTC-AATAAAATATTGA
1 TAATTTTACCCCTAATAAAATATTGA
**
25450 TAATTTTACCCCCTTGTAAAATATTGA
1 TAATTTTA-CCCCTAATAAAATATTGA
*
25477 TGATTTTACCC
1 TAATTTTACCC
25488 TCGAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 8 0.25
26 6 0.19
27 18 0.56
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.41
Consensus pattern (26 bp):
TAATTTTACCCCTAATAAAATATTGA
Found at i:25495 original size:25 final size:25
Alignment explanation
Indices: 25425--25495 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
25415 TATCTCATCC
*
25425 TAATTTTA-CCTCAATAAAATATTGA
1 TAATTTTACCCTCGA-AAAATATTGA
* *
25450 TAATTTTACCCCCTTGTAAAATATTGA
1 TAATTTTA--CCCTCGAAAAATATTGA
*
25477 TGATTTTACCCTCGAAAAA
1 TAATTTTACCCTCGAAAAA
25496 ATTTCGAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 17 0.46
27 17 0.46
28 3 0.08
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (25 bp):
TAATTTTACCCTCGAAAAATATTGA
Found at i:29111 original size:18 final size:20
Alignment explanation
Indices: 29080--29116 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
29070 AAAAGGGGTA
29080 AAATGGTAAATTT-GTTATG
1 AAATGGTAAATTTGGTTATG
29099 AAATGGT-AATTTGGTTAT
1 AAATGGTAAATTTGGTTAT
29117 TACTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (20 bp):
AAATGGTAAATTTGGTTATG
Found at i:37543 original size:40 final size:40
Alignment explanation
Indices: 37485--37593 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
37475 TGTTCGTTAG
37485 AATTCAAGCTTCGGCTTAGCAGGCTATGAGCTAGTGATAT
1 AATTCAAGCTTCGGCTTAGCAGGCTATGAGCTAGTGATAT
** * *
37525 AATTCAAGCTTCAACTTAGCAAGCTATGAGCTGGTGATAT
1 AATTCAAGCTTCGGCTTAGCAGGCTATGAGCTAGTGATAT
37565 AATTCAAGCTTCGGCTTAGCAGGCTATGA
1 AATTCAAGCTTCGGCTTAGCAGGCTATGA
37594 ATTGATGTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (40 bp):
AATTCAAGCTTCGGCTTAGCAGGCTATGAGCTAGTGATAT
Found at i:37610 original size:40 final size:40
Alignment explanation
Indices: 37485--37628 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
37475 TGTTCGTTAG
*
37485 AATTCAAGCTTCGGCTTAGCAGGCTATGAGCT-AGTGATAT
1 AATTCAAGCTTCGACTTAGCAGGCTATGAGCTGA-TGATAT
* * *
37525 AATTCAAGCTTCAACTTAGCAAGCTATGAGCTGGTGATAT
1 AATTCAAGCTTCGACTTAGCAGGCTATGAGCTGATGATAT
* ** *
37565 AATTCAAGCTTCGGCTTAGCAGGCTATGAATTGATGTTA-
1 AATTCAAGCTTCGACTTAGCAGGCTATGAGCTGATGATAT
*
37604 AGATTCAAGCTACGACTTAGCAGGC
1 A-ATTCAAGCTTCGACTTAGCAGGC
37629 CCTAAGCCGG
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 88 0.99
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (40 bp):
AATTCAAGCTTCGACTTAGCAGGCTATGAGCTGATGATAT
Found at i:38637 original size:71 final size:71
Alignment explanation
Indices: 38485--38638 Score: 182
Period size: 71 Copynumber: 2.2 Consensus size: 71
38475 GATAGAATTC
* * * *
38485 TATGTAGTATCAGTAGTTAGGACTAATGTATCGGTAAAAACCTCCAGACCAAATAGTCTTGCTCT
1 TATGAAGTATCGGTAGTTAGGACTAATGTATCGGTAAAAACCACCAGACCAAATAGTCTTGCTCA
*
38550 CTGTCA
66 CTATCA
* * * * * **
38556 TTTGAAGTATCGGTAGTTAGGACTAATGTGTCGGTAGAAACCACCAGGCTAGTTAGTCTTGCTCA
1 TATGAAGTATCGGTAGTTAGGACTAATGTATCGGTAAAAACCACCAGACCAAATAGTCTTGCTCA
*
38621 CTATTA
66 CTATCA
*
38627 TATGAGGTATCG
1 TATGAAGTATCG
38639 ATAATGGACT
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (71 bp):
TATGAAGTATCGGTAGTTAGGACTAATGTATCGGTAAAAACCACCAGACCAAATAGTCTTGCTCA
CTATCA
Found at i:46476 original size:19 final size:19
Alignment explanation
Indices: 46452--46499 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
46442 CCCATCCCTG
*
46452 CACACCATATCCAGCCCAA
1 CACACCATATCCAACCCAA
**
46471 CACACCAATATCCAACCTTA
1 CACACC-ATATCCAACCCAA
46491 CACACCATA
1 CACACCATA
46500 GAGTGTTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.40, C:0.44, G:0.02, T:0.15
Consensus pattern (19 bp):
CACACCATATCCAACCCAA
Found at i:53782 original size:95 final size:95
Alignment explanation
Indices: 53619--53809 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
53609 ATCTTTTGCT
53619 ATTAACGAGACGAGAGAGATAACAATGCACAAAAGAAAATGATAAAATATAGAAATATATTTTTA
1 ATTAACGAGACGAGAGAGATAACAATGCACAAAAGAAAATGATAAAATATAGAAATATATTTTTA
53684 AATGGGAATGCTTGGAACTGATTTAATTAA
66 AATGGGAATGCTTGGAACTGATTTAATTAA
53714 ATTAACGAGACGAGAGAGATAACAATGCACAAAAGAAAATGATAAAATATAGAAATATATTTTTA
1 ATTAACGAGACGAGAGAGATAACAATGCACAAAAGAAAATGATAAAATATAGAAATATATTTTTA
53779 AATGGGAATGCTTGGAACTGATTTAATTAA
66 AATGGGAATGCTTGGAACTGATTTAATTAA
53809 A
1 A
53810 ACTTTCAACA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (95 bp):
ATTAACGAGACGAGAGAGATAACAATGCACAAAAGAAAATGATAAAATATAGAAATATATTTTTA
AATGGGAATGCTTGGAACTGATTTAATTAA
Found at i:60009 original size:18 final size:17
Alignment explanation
Indices: 59978--60011 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
59968 CTATACTTTT
59978 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
*
59995 CTAATCTTTTGTTGATT
1 CTAA-CTTTTATTGATT
60012 TTCTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:67375 original size:17 final size:17
Alignment explanation
Indices: 67353--67400 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
67343 TTTTCTCTAG
67353 TTGTCATTACATTTTAA
1 TTGTCATTACATTTTAA
* **
67370 TTGTCACTGTATTTTAA
1 TTGTCATTACATTTTAA
67387 TTGTTC-TTACATTT
1 TTG-TCATTACATTT
67401 GCATTGTAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 22 0.92
18 2 0.08
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.56
Consensus pattern (17 bp):
TTGTCATTACATTTTAA
Found at i:68023 original size:4 final size:4
Alignment explanation
Indices: 68014--68078 Score: 53
Period size: 4 Copynumber: 16.8 Consensus size: 4
68004 ATAAAAAGAA
* * * * * *
68014 ATAT ATAT ATAT ATAC ATAT ATAT ATGT ATGT ATGT ATCT ATAT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
68062 ATGT ATAT -TAT -TAT ATA
1 ATAT ATAT ATAT ATAT ATA
68079 ATAAATGTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
3 6 0.11
4 47 0.89
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:70050 original size:78 final size:78
Alignment explanation
Indices: 69937--70156 Score: 230
Period size: 78 Copynumber: 2.8 Consensus size: 78
69927 AGCTACATAA
* * *
69937 TGTTTACAGTGTCATTGCCAGCTCAGTACGATATTACGGTGTTTATAGTGTCACCGTCAGTTCAA
1 TGTTTACAGTGTCATTGCCAGCTCAATACGATATTACGGTGTTTACAGTGTCACCGTCAATTCAA
70002 TGTTAGAATGTAG
66 TGTTAGAATGTAG
* * *
70015 TGTTTACAGTGTTATTGCTAG-TCCAATATCG-TATTACGGTGTTTACAGTGTCACCTTCAATTC
1 TGTTTACAGTGTCATTGCCAGCT-CAATA-CGATATTACGGTGTTTACAGTGTCACCGTCAATTC
* * *
70078 ATTGTT-GTATTGCAG
64 AATGTTAG-AATGTAG
* * * * * * * * *
70093 TTTTTACAGTGTCACTACCAGTTCAGTACAAAATTATGGTGTTTACAGTGTCATCGTCAATTCA
1 TGTTTACAGTGTCATTGCCAGCTCAATACGATATTACGGTGTTTACAGTGTCACCGTCAATTCA
70157 GTATTGTATC
Statistics
Matches: 117, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
77 3 0.03
78 111 0.95
79 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (78 bp):
TGTTTACAGTGTCATTGCCAGCTCAATACGATATTACGGTGTTTACAGTGTCACCGTCAATTCAA
TGTTAGAATGTAG
Found at i:70523 original size:12 final size:12
Alignment explanation
Indices: 70506--70537 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
70496 CTGGCCATAC
70506 GCCCGTGTGCCA
1 GCCCGTGTGCCA
70518 GCCCGTGTGCCA
1 GCCCGTGTGCCA
70530 GCCCGTGT
1 GCCCGTGT
70538 ACTCTCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.06, C:0.41, G:0.34, T:0.19
Consensus pattern (12 bp):
GCCCGTGTGCCA
Found at i:76627 original size:39 final size:39
Alignment explanation
Indices: 76515--76704 Score: 118
Period size: 39 Copynumber: 4.9 Consensus size: 39
76505 GTATTACAAG
* *
76515 TGTTTACAGTGTCACCGTCAATTCAGTGTTG-A-AATGCAA
1 TGTTTACAGTGTCACCGTCAATTCAGTATTGTATTATG--A
* * * * * **
76554 TATTTACAGTGTCA-CTTCTAGTCCGATACCGTATTATGA
1 TGTTTACAGTGTCACCGTCAATTCAG-TATTGTATTATGA
* *
76593 TGTTTACAGTGTCACCGTCAATTCAGTGTTGTATTA-CA
1 TGTTTACAGTGTCACCGTCAATTCAGTATTGTATTATGA
* * * * * ** * *
76631 TTATTTACATTGTCACTGCCACTTCAGTACAGTATTACGG
1 -TGTTTACAGTGTCACCGTCAATTCAGTATTGTATTATGA
* *
76671 TGTTTACAGTGTTACCGTCAGTTCAGTATTGTAT
1 TGTTTACAGTGTCACCGTCAATTCAGTATTGTAT
76705 CACTGTCACA
Statistics
Matches: 109, Mismatches: 36, Indels: 12
0.69 0.23 0.08
Matches are distributed among these distances:
38 8 0.07
39 90 0.83
40 8 0.07
41 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (39 bp):
TGTTTACAGTGTCACCGTCAATTCAGTATTGTATTATGA
Found at i:76703 original size:78 final size:77
Alignment explanation
Indices: 76477--76704 Score: 249
Period size: 78 Copynumber: 2.9 Consensus size: 77
76467 CTACACAGTG
* * * *
76477 TTTATAGTGTCACTGCCAGCTCAATACGGTATTACAAGTGTTTACAGTGTCACCGTCAATTCAGT
1 TTTACAGTGTCACTGCCA-CTCAGTACAGTATTAC-GGTGTTTACAGTGTCACCGTCAATTCAGT
* * *
76542 GTTGAAATGCAATA
64 GTTGTATTACAATA
* * * * * * *
76556 TTTACAGTGTCACTTCTAGTCCGATACCGTATTATGATGTTTACAGTGTCACCGTCAATTCAGTG
1 TTTACAGTGTCACTGCCACTCAG-TACAGTATTACGGTGTTTACAGTGTCACCGTCAATTCAGTG
*
76621 TTGTATTACATTA
65 TTGTATTACAATA
* * * *
76634 TTTACATTGTCACTGCCACTTCAGTACAGTATTACGGTGTTTACAGTGTTACCGTCAGTTCAGTA
1 TTTACAGTGTCACTGCCAC-TCAGTACAGTATTACGGTGTTTACAGTGTCACCGTCAATTCAGTG
76699 TTGTAT
65 TTGTAT
76705 CACTGTCACA
Statistics
Matches: 122, Mismatches: 25, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
78 95 0.78
79 27 0.22
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (77 bp):
TTTACAGTGTCACTGCCACTCAGTACAGTATTACGGTGTTTACAGTGTCACCGTCAATTCAGTGT
TGTATTACAATA
Found at i:80167 original size:10 final size:10
Alignment explanation
Indices: 80152--80227 Score: 64
Period size: 10 Copynumber: 7.5 Consensus size: 10
80142 CATGAGTTTA
80152 ATGTGATTAT
1 ATGTGATTAT
* *
80162 ATGTGATGAA
1 ATGTGATTAT
* *
80172 ATGTGACTAC
1 ATGTGATTAT
80182 ATGTGATTAT
1 ATGTGATTAT
*
80192 ATGAG-TGTAT
1 ATGTGAT-TAT
* *
80202 AGGTGATTAA
1 ATGTGATTAT
80212 ATGTGATTAAT
1 ATGTGATT-AT
80223 ATGTG
1 ATGTG
80228 TTGTGTTAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
9 1 0.02
10 42 0.84
11 7 0.14
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:80176 original size:20 final size:20
Alignment explanation
Indices: 80151--80227 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
80141 ACATGAGTTT
*
80151 AATGTGATTATATGTGATGA
1 AATGTGATTATATGTGATTA
* *
80171 AATGTGACTACATGTGATTA
1 AATGTGATTATATGTGATTA
* * *
80191 TATGAG-TGTATAGGTGATTA
1 AATGTGAT-TATATGTGATTA
80211 AATGTGATTAATATGTG
1 AATGTGATT-ATATGTG
80228 TTGTGTTAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
20 36 0.84
21 7 0.16
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.39
Consensus pattern (20 bp):
AATGTGATTATATGTGATTA
Found at i:80216 original size:30 final size:30
Alignment explanation
Indices: 80151--80225 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
80141 ACATGAGTTT
* *
80151 AATGTGATTATATGTGATGAAATGTGACTA
1 AATGTGATTATATGAGATGAAAGGTGACTA
* * *
80181 CATGTGATTATATGAG-TGTATAGGTGATTA
1 AATGTGATTATATGAGATG-AAAGGTGACTA
80211 AATGTGATTAATATG
1 AATGTGATT-ATATG
80226 TGTTGTGTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 2 0.05
30 30 0.81
31 5 0.14
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.39
Consensus pattern (30 bp):
AATGTGATTATATGAGATGAAAGGTGACTA
Found at i:81425 original size:11 final size:11
Alignment explanation
Indices: 81411--81463 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 11
81401 ATTTATGATT
*
81411 TGAATATGAAA
1 TGAAAATGAAA
81422 TGAAAATGAAAA
1 TGAAAATG-AAA
81434 TGAAAATGAAAAA
1 TGAAAATG--AAA
81447 TGAAAATGGAAA
1 TGAAAAT-GAAA
81459 TGAAA
1 TGAAA
81464 TGGATGCTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
11 7 0.18
12 19 0.50
13 11 0.29
14 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (11 bp):
TGAAAATGAAA
Found at i:81448 original size:7 final size:6
Alignment explanation
Indices: 81419--81463 Score: 72
Period size: 6 Copynumber: 7.3 Consensus size: 6
81409 TTTGAATATG
*
81419 AAATGA AAATGA AAATGA AAATGAA AAATGA AAATGG AAATGA AA
1 AAATGA AAATGA AAATGA AAATG-A AAATGA AAATGA AAATGA AA
81464 TGGATGCTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.16
Consensus pattern (6 bp):
AAATGA
Found at i:81448 original size:19 final size:19
Alignment explanation
Indices: 81419--81463 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
81409 TTTGAATATG
81419 AAATG-AAAATGAAAATGA
1 AAATGAAAAATGAAAATGA
*
81437 AAATGAAAAATGAAAATGG
1 AAATGAAAAATGAAAATGA
81456 AAATGAAA
1 AAATGAAA
81464 TGGATGCTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.16
Consensus pattern (19 bp):
AAATGAAAAATGAAAATGA
Found at i:84015 original size:34 final size:32
Alignment explanation
Indices: 83968--84032 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
83958 CTATTTACTT
83968 AAAATAAATAATTTTAGTCAAAATAAAAATTAAG
1 AAAATAAATAA-TTTAGTCAAAA-AAAAATTAAG
*
84002 AAAATAACA-AATTTAGTCAAAACAAAATTAA
1 AAAATAA-ATAATTTAGTCAAAAAAAAATTAA
84033 TATTAACAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 8 0.28
33 11 0.38
34 9 0.31
35 1 0.03
ACGTcount: A:0.63, C:0.06, G:0.05, T:0.26
Consensus pattern (32 bp):
AAAATAAATAATTTAGTCAAAAAAAAATTAAG
Found at i:84736 original size:30 final size:30
Alignment explanation
Indices: 84669--84942 Score: 168
Period size: 30 Copynumber: 9.2 Consensus size: 30
84659 TTAAAACCGA
* * * *
84669 GTCAAATTTGAATTTTTGGAAGCA-TCAGGG
1 GTCAAATTTAAAATTTTGGAA-AATTTAGGG
**
84699 TGTCAAATAAAAAATTTTGGAAAATTTAGGG
1 -GTCAAATTTAAAATTTTGGAAAATTTAGGG
* *
84730 GTCAAA-TTAAAATTTTTGGAAAGTTTATGG
1 GTCAAATTTAAAA-TTTTGGAAAATTTAGGG
* * * * *
84760 GTTAAATTTTAATTTTTGAAAAATTT-TGG
1 GTCAAATTTAAAATTTTGGAAAATTTAGGG
* *
84789 GTCAAATTT-GAATATTTGGAAATTTTAGGG
1 GTCAAATTTAAAAT-TTTGGAAAATTTAGGG
* * * *
84819 GTTAAA-TTCAAATTTTTGAAAAGTTTAGGT
1 GTCAAATTTAAAATTTTGGAAAA-TTTAGGG
* * *
84849 GTTAAATTTGAATTTTTGGAAAATTTA-GG
1 GTCAAATTTAAAATTTTGGAAAATTTAGGG
* * * * *
84878 GTTATATTTGAATTTTTGG-AAATTTTGAGG
1 GTCAAATTTAAAATTTTGGAAAATTTAG-GG
* *
84908 GTCAAATTT-GAATTTTAGCAAAATTTAGGG
1 GTCAAATTTAAAATTTT-GGAAAATTTAGGG
84938 GTCAA
1 GTCAA
84943 GTTATAATTT
Statistics
Matches: 193, Mismatches: 38, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
28 8 0.04
29 58 0.30
30 81 0.42
31 46 0.24
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (30 bp):
GTCAAATTTAAAATTTTGGAAAATTTAGGG
Found at i:84794 original size:59 final size:58
Alignment explanation
Indices: 84669--84937 Score: 245
Period size: 59 Copynumber: 4.5 Consensus size: 58
84659 TTAAAACCGA
* * ** * * *
84669 GTCAAATTTGAATTTTTGGAAGCA-TCAGGGTGTCAAATAAAAAATTTTGGAAAATTTAGGG
1 GTCAAATTTGAATTTTTGGAA-AATTTAGGGT-T-AAATTTAAATTTTTGAAAAATTT-TGG
** * *
84730 GTCAAATTAAAATTTTTGGAAAGTTTATGGGTTAAATTTTAATTTTTGAAAAATTTTGG
1 GTCAAATTTGAATTTTTGGAAAATTTA-GGGTTAAATTTAAATTTTTGAAAAATTTTGG
* * * * *
84789 GTCAAATTTGAATATTTGGAAATTTTAGGGGTTAAATTCAAATTTTTGAAAAGTTTAGG
1 GTCAAATTTGAATTTTTGGAAAATTTA-GGGTTAAATTTAAATTTTTGAAAAATTTTGG
* * * *
84848 TGTTAAATTTGAATTTTTGGAAAATTTAGGGTTATATTTGAATTTTTG-GAAATTTTGAGG
1 -GTCAAATTTGAATTTTTGGAAAATTTAGGGTTAAATTTAAATTTTTGAAAAATTTT--GG
* *
84908 GTCAAATTTGAATTTTAGCAAAATTTAGGG
1 GTCAAATTTGAATTTTTGGAAAATTTAGGG
84938 GTCAAGTTAT
Statistics
Matches: 171, Mismatches: 32, Indels: 12
0.80 0.15 0.06
Matches are distributed among these distances:
58 5 0.03
59 96 0.56
60 44 0.26
61 22 0.13
62 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.41
Consensus pattern (58 bp):
GTCAAATTTGAATTTTTGGAAAATTTAGGGTTAAATTTAAATTTTTGAAAAATTTTGG
Found at i:84922 original size:89 final size:88
Alignment explanation
Indices: 84713--84937 Score: 283
Period size: 89 Copynumber: 2.5 Consensus size: 88
84703 AAATAAAAAA
* * *
84713 TTTTGGAAAATTTAGGGGTCAAATTAAAATTTTTGGAAAGTTTATGGGTTAAATTTTAATTTTTG
1 TTTTGGAAATTTTAGGGGTCAAATTAAAATTTTTGAAAAGTTTA-GGGTTAAATTTGAATTTTTG
*
84778 AAAAATTTTGGGTCAAATTTGAAT
65 AAAAATTTAGGGTCAAATTTGAAT
* * *
84802 ATTTGGAAATTTTAGGGGTTAAATTCAAATTTTTGAAAAGTTTAGGTGTTAAATTTGAATTTTTG
1 TTTTGGAAATTTTAGGGGTCAAATTAAAATTTTTGAAAAGTTTAGG-GTTAAATTTGAATTTTTG
* * *
84867 GAAAATTTAGGGTTATATTTGAAT
65 AAAAATTTAGGGTCAAATTTGAAT
** *
84891 TTTTGGAAATTTT-GAGGGTCAAATTTGAATTTTAGCAAAA-TTTAGGG
1 TTTTGGAAATTTTAG-GGGTCAAATTAAAATTTTTG-AAAAGTTTAGGG
84938 GTCAAGTTAT
Statistics
Matches: 118, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
88 4 0.03
89 110 0.93
90 4 0.03
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (88 bp):
TTTTGGAAATTTTAGGGGTCAAATTAAAATTTTTGAAAAGTTTAGGGTTAAATTTGAATTTTTGA
AAAATTTAGGGTCAAATTTGAAT
Found at i:87980 original size:4 final size:4
Alignment explanation
Indices: 87971--87996 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
87961 ACCTGTCAAA
87971 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
87997 AGGACTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:88555 original size:40 final size:39
Alignment explanation
Indices: 88489--88698 Score: 194
Period size: 39 Copynumber: 5.3 Consensus size: 39
88479 TATAGCTTTA
* *
88489 GGGGTAAAAGATTAGATTGT-TTCAATCTGCCTCATGGTT
1 GGGGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGGTT
* **
88528 GGGGTAAGAGATCTGATGGTCTTCAATCTGCCCTTTGGTT
1 GGGGTAAAAGAT-TGATGGTCTTCAATCTGCCCCATGGTT
* * *
88568 AGGGTAAAAGATTGAATTG-CTTCAATCTGCCCCATGGTC
1 GGGGTAAAAGATTG-ATGGTCTTCAATCTGCCCCATGGTT
* * * * *
88607 GGGGTAAGATATCAGATGATCTTCAATATGCCCTC-TGGTT
1 GGGGTAAAAGAT-TGATGGTCTTCAATCTGCCC-CATGGTT
* * *
88647 AGGGTAAAAGATTGGATTGT-TTCAATCTGCCCCATGGTC
1 GGGGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGGTT
88686 GGGGTAAAAGATT
1 GGGGTAAAAGATT
88699 TGGGGTCGTA
Statistics
Matches: 135, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
38 1 0.01
39 73 0.54
40 60 0.44
41 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (39 bp):
GGGGTAAAAGATTGATGGTCTTCAATCTGCCCCATGGTT
Found at i:88630 original size:79 final size:79
Alignment explanation
Indices: 88490--88697 Score: 310
Period size: 79 Copynumber: 2.6 Consensus size: 79
88480 ATAGCTTTAG
* * * *
88490 GGGTAAAAGATT-AGATTGTTTCAATCTGCCTCATGGTTGGGGTAAGAGATCTGATGGTCTTCAA
1 GGGTAAAAGATTGA-ATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGATCTTCAA
* *
88554 TCTGCCCTTTGGTTA
65 TATGCCCTCTGGTTA
* *
88569 GGGTAAAAGATTGAATTGCTTCAATCTGCCCCATGGTCGGGGTAAGATATCAGATGATCTTCAAT
1 GGGTAAAAGATTGAATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGATCTTCAAT
88634 ATGCCCTCTGGTTA
66 ATGCCCTCTGGTTA
* *
88648 GGGTAAAAGATTGGATTGTTTCAATCTGCCCCATGGTCGGGGTAAAAGAT
1 GGGTAAAAGATTGAATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGAT
88698 TTGGGGTCGT
Statistics
Matches: 116, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 115 0.99
80 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (79 bp):
GGGTAAAAGATTGAATTGTTTCAATCTGCCCCATGGTCGGGGTAAGAGATCAGATGATCTTCAAT
ATGCCCTCTGGTTA
Found at i:88873 original size:50 final size:50
Alignment explanation
Indices: 88779--88881 Score: 118
Period size: 50 Copynumber: 2.1 Consensus size: 50
88769 TTTATAGCTC
* * *
88779 TAGGTGAATGAGATTCGCCATTGCGATTTCAATCTGCCCTTCTACGACTT
1 TAGGTGAATGAGATTCGCCATTGCGACTTCAATCCGCCCTTCTACAACTT
* * * * *
88829 TAGGTGTATGAGATTTGTCATTGCGGCTTCAATCCGTTCC-TCTACAACTT
1 TAGGTGAATGAGATTCGCCATTGCGACTTCAATCCG-CCCTTCTACAACTT
88879 TAG
1 TAG
88882 AGGTATAGGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 42 0.95
51 2 0.05
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (50 bp):
TAGGTGAATGAGATTCGCCATTGCGACTTCAATCCGCCCTTCTACAACTT
Found at i:100354 original size:5 final size:5
Alignment explanation
Indices: 100337--100396 Score: 54
Period size: 5 Copynumber: 12.4 Consensus size: 5
100327 CAATATATAC
* * * *
100337 ATAAA ATACA ATAAA ATAAA ATAAT ATACAT ATAAG ATAAA AT-AA AT-AA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATA-AA ATAAA ATAAA ATAAA ATAAA
100386 AT-AA ATAAA AT
1 ATAAA ATAAA AT
100397 TACATTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
4 12 0.25
5 31 0.65
6 5 0.10
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (5 bp):
ATAAA
Found at i:100389 original size:29 final size:29
Alignment explanation
Indices: 100318--100386 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
100308 AAGTATACAT
*
100318 AATAAAA-AACAAT-ATATACATAAAATAC
1 AATAAAATAA-AATAATATACATAAAATAA
100346 AATAAAATAAAATAATATACATATAAGATAA
1 AATAAAATAAAATAATATACATA-AA-ATAA
100377 AAT-AAATAAA
1 AATAAAATAAA
100387 TAAATAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
28 10 0.28
29 11 0.31
30 9 0.25
31 6 0.17
ACGTcount: A:0.70, C:0.06, G:0.01, T:0.23
Consensus pattern (29 bp):
AATAAAATAAAATAATATACATAAAATAA
Found at i:100446 original size:30 final size:29
Alignment explanation
Indices: 100409--100624 Score: 191
Period size: 30 Copynumber: 7.2 Consensus size: 29
100399 CATTAAAATC
**
100409 GGGTCAAATTTGAATTTTTGGAATCTTTA
1 GGGTCAAATTTGAATTTTTGGAAAATTTA
***
100438 GGGATCAAATCAAAATTTTTGGAAAATTTAA
1 GGG-TCAAATTTGAATTTTTGGAAAATTT-A
* *** * * *
100469 GGCTCAAATAAAAAATTTT-GAAAGTTCAA
1 GGGTCAAATTTGAATTTTTGGAAAATT-TA
100498 GGGTCAAATTTGAATTTTTGGAAAATTTGA
1 GGGTCAAATTTGAATTTTTGGAAAATTT-A
*
100528 GGGTTAAATTTGAATTTTTGGAAAATTTA
1 GGGTCAAATTTGAATTTTTGGAAAATTTA
* * *
100557 GGGGTTAAATTTAAATTTTTAGAAAATTTGA
1 -GGGTCAAATTTGAATTTTTGGAAAATTT-A
***
100588 GGGTCAAATTTGAATTTTACAAAAATTTA
1 GGGTCAAATTTGAATTTTTGGAAAATTTA
100617 GGGGTCAA
1 -GGGTCAA
100625 GTTATAATTT
Statistics
Matches: 154, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
29 26 0.17
30 124 0.81
31 4 0.03
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTGGAAAATTTA
Found at i:100499 original size:29 final size:30
Alignment explanation
Indices: 100442--100524 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 30
100432 TCTTTAGGGA
* * *
100442 TCAAATCAAAATTTTTGGAAAATTTAAGGC
1 TCAAATAAAAAATTTTGGAAAATTCAAGGC
* *
100472 TCAAATAAAAAATTTT-GAAAGTTCAAGGG
1 TCAAATAAAAAATTTTGGAAAATTCAAGGC
*** *
100501 TCAAATTTGAATTTTTGGAAAATT
1 TCAAATAAAAAATTTTGGAAAATT
100525 TGAGGGTTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
29 22 0.52
30 20 0.48
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.35
Consensus pattern (30 bp):
TCAAATAAAAAATTTTGGAAAATTCAAGGC
Found at i:100511 original size:89 final size:90
Alignment explanation
Indices: 100409--100605 Score: 236
Period size: 89 Copynumber: 2.2 Consensus size: 90
100399 CATTAAAATC
**
100409 GGGTCAAATTTGAATTTTTGGAATCTTT-AGGGATCAAATCAAAATTTTTGGAAAATTTAAGGCT
1 GGGTCAAATTTGAATTTTTGGAAAATTTGAGGG-TCAAATCAAAATTTTTGGAAAATTTAAGGCT
*
100473 CAAATAAAAAATTTT-GAAAGTTCAA
65 CAAATAAAAAATTTTAGAAAATTCAA
* *** * * *
100498 GGGTCAAATTTGAATTTTTGGAAAATTTGAGGGTTAAATTTGAATTTTTGGAAAATTTAGGGGTT
1 GGGTCAAATTTGAATTTTTGGAAAATTTGAGGGTCAAATCAAAATTTTTGGAAAATTTAAGGCTC
** * **
100563 AAATTTAAATTTTTAGAAAATTTGA
66 AAATAAAAAATTTTAGAAAATTCAA
100588 GGGTCAAATTTGAATTTT
1 GGGTCAAATTTGAATTTT
100606 ACAAAAATTT
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
89 62 0.68
90 29 0.32
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (90 bp):
GGGTCAAATTTGAATTTTTGGAAAATTTGAGGGTCAAATCAAAATTTTTGGAAAATTTAAGGCTC
AAATAAAAAATTTTAGAAAATTCAA
Found at i:100525 original size:17 final size:17
Alignment explanation
Indices: 100503--100555 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
100493 TTCAAGGGTC
100503 AAATTTGAATTTTTGGA
1 AAATTTGAATTTTTGGA
***
100520 AAATTTG-AGGGTT---
1 AAATTTGAATTTTTGGA
100533 AAATTTGAATTTTTGGA
1 AAATTTGAATTTTTGGA
100550 AAATTT
1 AAATTT
100556 AGGGGTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
13 7 0.27
14 3 0.12
16 3 0.12
17 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.45
Consensus pattern (17 bp):
AAATTTGAATTTTTGGA
Found at i:100584 original size:60 final size:60
Alignment explanation
Indices: 100409--100624 Score: 236
Period size: 60 Copynumber: 3.6 Consensus size: 60
100399 CATTAAAATC
** * ** *
100409 GGGTCAAATTTGAATTTTTGGAATCTTTAGGGATCAAATCAAAATTTTTGGAAAATTTAA
1 GGGTCAAATTTGAATTTTTGGAAAATTTAGGGGTCAAATTTAAATTTTTGGAAAATTTGA
* *** * * * * *
100469 GGCTCAAATAAAAAATTTT-GAAAGTTCAAGGGTCAAATTTGAATTTTTGGAAAATTTGA
1 GGGTCAAATTTGAATTTTTGGAAAATTTAGGGGTCAAATTTAAATTTTTGGAAAATTTGA
* * *
100528 GGGTTAAATTTGAATTTTTGGAAAATTTAGGGGTTAAATTTAAATTTTTAGAAAATTTGA
1 GGGTCAAATTTGAATTTTTGGAAAATTTAGGGGTCAAATTTAAATTTTTGGAAAATTTGA
***
100588 GGGTCAAATTTGAATTTTACAAAAATTTAGGGGTCAA
1 GGGTCAAATTTGAATTTTTGGAAAATTTAGGGGTCAA
100625 GTTATAATTT
Statistics
Matches: 124, Mismatches: 31, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
59 44 0.35
60 80 0.65
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (60 bp):
GGGTCAAATTTGAATTTTTGGAAAATTTAGGGGTCAAATTTAAATTTTTGGAAAATTTGA
Found at i:100634 original size:30 final size:29
Alignment explanation
Indices: 100498--100639 Score: 101
Period size: 30 Copynumber: 4.8 Consensus size: 29
100488 GAAAGTTCAA
* **
100498 GGGTCAAATTTGAATTTTTGGAAAATTT-G
1 GGGTCAAATTT-AAATTTTAAAAAATTTAG
* * **
100527 AGGGTTAAATTTGAATTTTTGGAAAATTTAG
1 -GGGTCAAATTT-AAATTTTAAAAAATTTAG
* *
100558 GGGTTAAATTTAAATTTTTAGAAAATTT-G
1 GGGTCAAATTTAAA-TTTTAAAAAATTTAG
*
100587 AGGGTCAAATTTGAATTTTACAAAAATTTAG
1 -GGGTCAAATTTAAATTTTA-AAAAATTTAG
*
100618 GGGTC-AAGTTATAATTTTAAAA
1 GGGTCAAATTTA-AATTTTAAAA
100640 TAAAGTAGGG
Statistics
Matches: 98, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
29 15 0.15
30 81 0.83
31 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (29 bp):
GGGTCAAATTTAAATTTTAAAAAATTTAG
Found at i:105297 original size:7 final size:7
Alignment explanation
Indices: 105285--105310 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
105275 GTAACACCTA
105285 TAACATT
1 TAACATT
105292 TAACATT
1 TAACATT
105299 TAACATT
1 TAACATT
105306 TAACA
1 TAACA
105311 GTCTGGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (7 bp):
TAACATT
Found at i:105513 original size:21 final size:21
Alignment explanation
Indices: 105489--105529 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
105479 GTCACACGAC
*
105489 CGTGTGGCTCTCCCACATGCT
1 CGTGTGGCCCTCCCACATGCT
*
105510 CGTGTGGCCCTTCCACATGC
1 CGTGTGGCCCTCCCACATGC
105530 CCATGTGCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.39, G:0.24, T:0.27
Consensus pattern (21 bp):
CGTGTGGCCCTCCCACATGCT
Found at i:105536 original size:21 final size:21
Alignment explanation
Indices: 105491--105536 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
105481 CACACGACCG
* * *
105491 TGTGGCTCTCCCACATGCTCG
1 TGTGGCCCTCCCACATGCCCA
*
105512 TGTGGCCCTTCCACATGCCCA
1 TGTGGCCCTCCCACATGCCCA
105533 TGTG
1 TGTG
105537 CTCCCTGTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.37, G:0.24, T:0.28
Consensus pattern (21 bp):
TGTGGCCCTCCCACATGCCCA
Found at i:105580 original size:21 final size:21
Alignment explanation
Indices: 105556--105601 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
105546 TGTCAAACTG
* * *
105556 TGTGGCTCTCCCACATGCTCA
1 TGTGGCCCTCCCACACGCCCA
*
105577 TGTGGCCCTTCCACACGCCCA
1 TGTGGCCCTCCCACACGCCCA
105598 TGTG
1 TGTG
105602 CTCCCTATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.39, G:0.22, T:0.26
Consensus pattern (21 bp):
TGTGGCCCTCCCACACGCCCA
Found at i:105597 original size:65 final size:65
Alignment explanation
Indices: 105490--105613 Score: 221
Period size: 65 Copynumber: 1.9 Consensus size: 65
105480 TCACACGACC
* * *
105490 GTGTGGCTCTCCCACATGCTCGTGTGGCCCTTCCACATGCCCATGTGCTCCCTGTGTGTCAAACT
1 GTGTGGCTCTCCCACATGCTCATGTGGCCCTTCCACACGCCCATGTGCTCCCTATGTGTCAAACT
105555 GTGTGGCTCTCCCACATGCTCATGTGGCCCTTCCACACGCCCATGTGCTCCCTATGTGT
1 GTGTGGCTCTCCCACATGCTCATGTGGCCCTTCCACACGCCCATGTGCTCCCTATGTGT
105614 GAAATCGTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.12, C:0.36, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGTGGCTCTCCCACATGCTCATGTGGCCCTTCCACACGCCCATGTGCTCCCTATGTGTCAAACT
Found at i:105630 original size:65 final size:65
Alignment explanation
Indices: 105496--105630 Score: 200
Period size: 65 Copynumber: 2.1 Consensus size: 65
105486 GACCGTGTGG
* * * **
105496 CTCTCCCACATGCTCGTGTGGCCCTTCCACATGCCCATGTGCTCCCTGTGTGTCAAACTGTGTGG
1 CTCTCCCACATGCTCATGTGGCCCTTCCACACGCCCATGTGCTCCCTATGTGTCAAACTGTGTAA
*
105561 CTCTCCCACATGCTCATGTGGCCCTTCCACACGCCCATGTGCTCCCTATGTGTGAAA-TCGTGTA
1 CTCTCCCACATGCTCATGTGGCCCTTCCACACGCCCATGTGCTCCCTATGTGTCAAACT-GTGTA
105625 A
65 A
105626 CTCTC
1 CTCTC
105631 TAACTTGGGT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 1 0.02
65 62 0.98
ACGTcount: A:0.15, C:0.36, G:0.20, T:0.29
Consensus pattern (65 bp):
CTCTCCCACATGCTCATGTGGCCCTTCCACACGCCCATGTGCTCCCTATGTGTCAAACTGTGTAA
Found at i:106451 original size:32 final size:32
Alignment explanation
Indices: 106415--106760 Score: 460
Period size: 32 Copynumber: 10.8 Consensus size: 32
106405 TTCATGGTAT
* *
106415 GCTCATAAGAGCTATCAATCTATGAACAGTGA
1 GCTCGTAAGAGCTATCAATCTATGAACAGTAA
* *
106447 GCTCATAAGAGCTATCAATCTATGAACAATAA
1 GCTCGTAAGAGCTATCAATCTATGAACAGTAA
*
106479 GCTCGTAAGAG-TAATCAATCTATGAATAGTAA
1 GCTCGTAAGAGCT-ATCAATCTATGAACAGTAA
* * *
106511 GCTTGTAAGAGCTATCAATCTGTAAACAGTAA
1 GCTCGTAAGAGCTATCAATCTATGAACAGTAA
* *
106543 GCTCGTAAGAGTTATCAATTTATGAACAGTAA
1 GCTCGTAAGAGCTATCAATCTATGAACAGTAA
* * *
106575 GCTCGTAAGAGCTATCAATATGTGAAAAGTAA
1 GCTCGTAAGAGCTATCAATCTATGAACAGTAA
* *
106607 GCTCGTAAAAGCTATAAATCTATGAACAGTAA
1 GCTCGTAAGAGCTATCAATCTATGAACAGTAA
* *
106639 GCTCGTAAGAGCTATCAATCTATGAATAATAA
1 GCTCGTAAGAGCTATCAATCTATGAACAGTAA
* *
106671 GCTCGTAAGAGCTATCAATCTGTGAACAATAA
1 GCTCGTAAGAGCTATCAATCTATGAACAGTAA
* * *
106703 ACTCGTAAGAACTATCAATCTATGAACAATAA
1 GCTCGTAAGAGCTATCAATCTATGAACAGTAA
* *
106735 GCTCATAAAAGCTATCAATCTATGAA
1 GCTCGTAAGAGCTATCAATCTATGAA
106761 AATTGTCTCA
Statistics
Matches: 276, Mismatches: 36, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
31 1 0.00
32 274 0.99
33 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (32 bp):
GCTCGTAAGAGCTATCAATCTATGAACAGTAA
Found at i:110233 original size:55 final size:55
Alignment explanation
Indices: 110157--110305 Score: 226
Period size: 55 Copynumber: 2.7 Consensus size: 55
110147 GGAATAATAT
* *
110157 TTCTTTTGAATTGATTTTTTATATGTTTAAATCGATTGTCATGTTGGAATACTGC
1 TTCTTTTGAATTGATTATTTATATGTTTAAATCGATTGTCATGTTGAAATACTGC
* * *
110212 TTCTTTTGAATTGATTATTTATATGTTTAAATCGATTTTTATGTTGAAATATTGC
1 TTCTTTTGAATTGATTATTTATATGTTTAAATCGATTGTCATGTTGAAATACTGC
* * *
110267 TTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGT
1 TTCTTTTGAATTGATTATTTATATGTTTAAATCGATTGT
110306 TACATAGCAC
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 85 1.00
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.53
Consensus pattern (55 bp):
TTCTTTTGAATTGATTATTTATATGTTTAAATCGATTGTCATGTTGAAATACTGC
Found at i:110299 original size:21 final size:20
Alignment explanation
Indices: 110233--110306 Score: 52
Period size: 18 Copynumber: 4.0 Consensus size: 20
110223 TGATTATTTA
110233 TATGTTTAAATCGA-T-TTT
1 TATGTTTAAATCGATTGTTT
* *
110251 TATGTTGAAAT--ATTG-CT
1 TATGTTTAAATCGATTGTTT
* *
110268 TCT-TTTGAATCGATTGTTT
1 TATGTTTAAATCGATTGTTT
*
110287 ATATGTTTAAATCAATTGTT
1 -TATGTTTAAATCGATTGTT
110307 ACATAGCACG
Statistics
Matches: 40, Mismatches: 9, Indels: 11
0.67 0.15 0.18
Matches are distributed among these distances:
16 6 0.15
17 4 0.10
18 14 0.35
19 1 0.03
20 2 0.05
21 13 0.32
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.53
Consensus pattern (20 bp):
TATGTTTAAATCGATTGTTT
Found at i:110634 original size:27 final size:28
Alignment explanation
Indices: 110586--110639 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
110576 AAATTGAAAT
* *
110586 TTAAATCTAAAATTCAATTATTTAAATGG
1 TTAAATATAAAATT-AAGTATTTAAATGG
110615 TTAAATATAAAATT-AGTATTTAAAT
1 TTAAATATAAAATTAAGTATTTAAAT
110640 TTATTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 10 0.43
29 13 0.57
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (28 bp):
TTAAATATAAAATTAAGTATTTAAATGG
Found at i:111709 original size:7 final size:7
Alignment explanation
Indices: 111697--111737 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
111687 AATAAATGAA
111697 GAAGAAG
1 GAAGAAG
111704 GAAGAAG
1 GAAGAAG
111711 GAAGAAG
1 GAAGAAG
111718 GAAGAAG
1 GAAGAAG
111725 GAAGAAG
1 GAAGAAG
111732 G-AGAAG
1 GAAGAAG
111738 AGACGATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (7 bp):
GAAGAAG
Found at i:112279 original size:9 final size:9
Alignment explanation
Indices: 112260--112293 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
112250 TATTTCAAAC
112260 ATAACAATTA
1 ATAA-AATTA
112270 ATAAAATTA
1 ATAAAATTA
*
112279 ATAAAATAA
1 ATAAAATTA
112288 ATAAAA
1 ATAAAA
112294 ATATAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (9 bp):
ATAAAATTA
Found at i:113233 original size:18 final size:18
Alignment explanation
Indices: 113211--113261 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
113201 AAAATTACAA
* *
113211 AAAAATCAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
113230 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTTAT
113248 AAAAAATTCAAAAT
1 --AAAATTCAAAAT
113262 TTATATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 12 0.43
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:113266 original size:18 final size:20
Alignment explanation
Indices: 113209--113261 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
113199 AAAAAATTAC
*
113209 AAAAAAATCAAAATAATTT-T
1 AAAAAATTCAAAAT-ATTTAT
*
113229 -TAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
113248 AAAAAATTCAAAAT
1 AAAAAATTCAAAAT
113262 TTATATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.14
19 12 0.43
20 12 0.43
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Found at i:115812 original size:19 final size:19
Alignment explanation
Indices: 115773--115813 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
115763 ATTGCTTCTT
* *
115773 AAAAGCACTTTTGGAACAA
1 AAAAACACTTTTGAAACAA
*
115792 AAAAACACTTTTGAAATAA
1 AAAAACACTTTTGAAACAA
115811 AAA
1 AAA
115814 TATTGCTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (19 bp):
AAAAACACTTTTGAAACAA
Found at i:117982 original size:24 final size:26
Alignment explanation
Indices: 117929--117984 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
117919 AATACATTAC
*
117929 GAAATA-TGGTATATAATATTTTTAT
1 GAAATATTGGTATACAATATTTTTAT
*
117954 GAAATATTGGTTTACAAT-TTTTTAT
1 GAAATATTGGTATACAATATTTTTAT
117979 -AAATAT
1 GAAATAT
117985 CTTAAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 6 0.21
25 13 0.46
26 9 0.32
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (26 bp):
GAAATATTGGTATACAATATTTTTAT
Found at i:119303 original size:34 final size:34
Alignment explanation
Indices: 119257--119326 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
119247 GTCGACGGCA
*
119257 GTAAGAGCAACCAAGACTCCTATGGACCTTGGAT
1 GTAAGAGAAACCAAGACTCCTATGGACCTTGGAT
*
119291 GTAAGAGAAACCAAGACTCTTATGGACCTTGGAT
1 GTAAGAGAAACCAAGACTCCTATGGACCTTGGAT
119325 GT
1 GT
119327 TAGTGGAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (34 bp):
GTAAGAGAAACCAAGACTCCTATGGACCTTGGAT
Found at i:124582 original size:8 final size:8
Alignment explanation
Indices: 124569--124593 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
124559 AAAAAACATT
124569 GAGAGGGA
1 GAGAGGGA
124577 GAGAGGGA
1 GAGAGGGA
124585 GAGAGGGA
1 GAGAGGGA
124593 G
1 G
124594 GGGTGTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (8 bp):
GAGAGGGA
Found at i:125950 original size:8 final size:8
Alignment explanation
Indices: 125932--125962 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
125922 AAAATTTTCA
125932 TTTAAACAT
1 TTTAAA-AT
125941 TTTAAAAT
1 TTTAAAAT
125949 TTTAAAAT
1 TTTAAAAT
125957 TTTAAA
1 TTTAAA
125963 TTAGTAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTAAAAT
Found at i:126338 original size:31 final size:32
Alignment explanation
Indices: 126278--126354 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
126268 TCAAAAAAAA
* * *
126278 TTACCAACTTTTAAGGGGTTTAAAAATTTTTT
1 TTACTAACTTTTAAGAGATTTAAAAATTTTTT
126310 TTACTAACTTTTAAGAGATTT-AAAATTTTTT
1 TTACTAACTTTTAAGAGATTTAAAAATTTTTT
*
126341 TTATTCAACTTTTA
1 TTACT-AACTTTTA
126355 GGGAATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 14 0.35
32 26 0.65
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.51
Consensus pattern (32 bp):
TTACTAACTTTTAAGAGATTTAAAAATTTTTT
Found at i:126363 original size:32 final size:32
Alignment explanation
Indices: 126278--126366 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
126268 TCAAAAAAAA
*
126278 TTAC-CAACTTTTAAGGG-GTTTAAAAATTTTTT
1 TTACTCAACTTTT-AGGGAATTT-AAAATTTTTT
*
126310 TTACT-AACTTTTA-AGAGATTTAAAATTTTTT
1 TTACTCAACTTTTAGGGA-ATTTAAAATTTTTT
*
126341 TTATTCAACTTTTAGGGAATTTAAAA
1 TTACTCAACTTTTAGGGAATTTAAAA
126367 CTCCATTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
30 1 0.02
31 15 0.31
32 30 0.62
33 2 0.04
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (32 bp):
TTACTCAACTTTTAGGGAATTTAAAATTTTTT
Found at i:133588 original size:9 final size:9
Alignment explanation
Indices: 133574--133601 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
133564 CTCTCTCTCC
133574 TTTTCTTTT
1 TTTTCTTTT
133583 TTTTCTTTT
1 TTTTCTTTT
133592 TTTTCTTTT
1 TTTTCTTTT
133601 T
1 T
133602 CTTTTCCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:133600 original size:15 final size:14
Alignment explanation
Indices: 133573--133607 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
133563 TCTCTCTCTC
133573 CTTTTCTTTTTTTT
1 CTTTTCTTTTTTTT
*
133587 CTTTTTTTTCTTTTT
1 CTTTTCTTT-TTTTT
133602 CTTTTC
1 CTTTTC
133608 CTTAGATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
CTTTTCTTTTTTTT
Found at i:134034 original size:21 final size:21
Alignment explanation
Indices: 134010--134049 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
134000 ACAAATCCCA
* *
134010 CCACCAGCACCAGCAACACCG
1 CCACAAGCACCAACAACACCG
134031 CCACAAGCACCAACAACAC
1 CCACAAGCACCAACAACAC
134050 AGTCGCCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.50, G:0.10, T:0.00
Consensus pattern (21 bp):
CCACAAGCACCAACAACACCG
Found at i:138632 original size:16 final size:17
Alignment explanation
Indices: 138601--138639 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
138591 ATTAATTAAA
138601 TTAACTAAAGTAATTTT
1 TTAACTAAAGTAATTTT
*
138618 TTAATTAAA-TAATTTT
1 TTAACTAAAGTAATTTT
*
138634 TCAACT
1 TTAACT
138640 CAATTCTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (17 bp):
TTAACTAAAGTAATTTT
Found at i:139867 original size:30 final size:29
Alignment explanation
Indices: 139811--139867 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
139801 GTGTAATTGT
*
139811 ATATATGAACTTTGATTTTGTGCAATTTC
1 ATATATGAACTTTGATTTTGTCCAATTTC
*
139840 ATATATGAAATTTTGA-TTTGATCCAATT
1 ATATATG-AACTTTGATTTTG-TCCAATT
139868 CTTGTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (29 bp):
ATATATGAACTTTGATTTTGTCCAATTTC
Found at i:142458 original size:55 final size:55
Alignment explanation
Indices: 142365--142494 Score: 145
Period size: 55 Copynumber: 2.4 Consensus size: 55
142355 GGTGTGTATA
* * * * *
142365 TATATTGTTTTGAGGCGCACGGGCAGACACTCGTGCGTGTACCAGA-TCGTGTGTG
1 TATACTGTTTTGAGGCACACGGGCAGACACACGAGCGTGTACCAGACT-ATGTGTG
* **
142420 TATACTGTTTTGAGGCACACGGGCAGACAGACGAGCGTGTGTCAGACTATGTGTG
1 TATACTGTTTTGAGGCACACGGGCAGACACACGAGCGTGTACCAGACTATGTGTG
* * *
142475 TATACTATTTAGAGTCACAC
1 TATACTGTTTTGAGGCACAC
142495 AGGTGTGTAC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 62 0.98
56 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.28
Consensus pattern (55 bp):
TATACTGTTTTGAGGCACACGGGCAGACACACGAGCGTGTACCAGACTATGTGTG
Found at i:147111 original size:29 final size:29
Alignment explanation
Indices: 147069--147177 Score: 164
Period size: 29 Copynumber: 3.8 Consensus size: 29
147059 GCGGATAGGG
*
147069 GTATCATGTCTGCATTTGTAACTGTATCT
1 GTATCATGTCTGCATCTGTAACTGTATCT
*
147098 GTATCATGTCTGCATATGTAACTGTATCT
1 GTATCATGTCTGCATCTGTAACTGTATCT
* * *
147127 GTGTCATGTTTGTATCTGTAACTGTATCT
1 GTATCATGTCTGCATCTGTAACTGTATCT
*
147156 ATATCATGTCTGCATCTGTAAC
1 GTATCATGTCTGCATCTGTAAC
147178 GGTACCCAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (29 bp):
GTATCATGTCTGCATCTGTAACTGTATCT
Found at i:158356 original size:8 final size:8
Alignment explanation
Indices: 158343--158383 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
158333 ACCCAATTAT
158343 TTTTTTTA
1 TTTTTTTA
158351 TTTTTTTA
1 TTTTTTTA
*
158359 TTTTTCTA
1 TTTTTTTA
158367 TTTTATTTA
1 TTTT-TTTA
158376 TTTATTTT
1 TTT-TTTT
158384 TTATTTGTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 19 0.66
9 9 0.31
10 1 0.03
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTA
Found at i:158370 original size:13 final size:13
Alignment explanation
Indices: 158339--158383 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
158329 GGCAACCCAA
*
158339 TTATTTTTTTTAT
1 TTATTTTATTTAT
158352 TT-TTTTATTT-T
1 TTATTTTATTTAT
158363 TCTATTTTATTTAT
1 T-TATTTTATTTAT
158377 TTATTTT
1 TTATTTT
158384 TTATTTGTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 2 0.07
12 8 0.29
13 16 0.57
14 2 0.07
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:158370 original size:21 final size:20
Alignment explanation
Indices: 158342--158389 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
158332 AACCCAATTA
*
158342 TTTT-TTTTATTTTTTTATT
1 TTTTATTTTATTTATTTATT
158361 TTTCTATTTTATTTATTTATT
1 TTT-TATTTTATTTATTTATT
158382 TTTTATTT
1 TTTTATTT
158390 GTCCAGGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 3 0.12
20 6 0.23
21 17 0.65
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (20 bp):
TTTTATTTTATTTATTTATT
Found at i:158880 original size:27 final size:27
Alignment explanation
Indices: 158842--158896 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
158832 GGTAAAATTG
158842 ATTGAGTCTAAGTATAAGAGAACAGTT
1 ATTGAGTCTAAGTATAAGAGAACAGTT
*
158869 ATTGAGTCTAAGTATAAGAGAATAGTT
1 ATTGAGTCTAAGTATAAGAGAACAGTT
158896 A
1 A
158897 ATTCTGATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (27 bp):
ATTGAGTCTAAGTATAAGAGAACAGTT
Found at i:159936 original size:14 final size:14
Alignment explanation
Indices: 159899--159928 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
159889 TTATATTTAA
*
159899 TTTATATTTATCTT
1 TTTAGATTTATCTT
159913 TTTAGATTTATCTT
1 TTTAGATTTATCTT
159927 TT
1 TT
159929 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTAGATTTATCTT
Found at i:163497 original size:40 final size:40
Alignment explanation
Indices: 163442--163634 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 40
163432 AATAACAATC
* *
163442 CACCGGCTCGTAGCCTGCTAAGCCGTAGCTTGAGTTTTAA
1 CACCGACTCATAGCCTGCTAAGCCGTAGCTTGAGTTTTAA
* * * *
163482 CACCGACTCGTAGCCTGTTAAGCCGTAGCTTGAGCTTTAG
1 CACCGACTCATAGCCTGCTAAGCCGTAGCTTGAGTTTTAA
* * *
163522 CACCAACTCATAGCCTGCTAAGCCGTAGCTTGAATCTTAA
1 CACCGACTCATAGCCTGCTAAGCCGTAGCTTGAGTTTTAA
* * * * * * *
163562 CACC-AGGTCATAGCCTACTAAGTCATAGCTTGACTATTGA
1 CACCGA-CTCATAGCCTGCTAAGCCGTAGCTTGAGTTTTAA
* * *
163602 CACTGACTCATAGCCTGCTAATCCGTATCTTGA
1 CACCGACTCATAGCCTGCTAAGCCGTAGCTTGA
163635 ATATTTACGT
Statistics
Matches: 126, Mismatches: 25, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
39 1 0.01
40 124 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (40 bp):
CACCGACTCATAGCCTGCTAAGCCGTAGCTTGAGTTTTAA
Found at i:163674 original size:80 final size:80
Alignment explanation
Indices: 163452--163674 Score: 193
Period size: 80 Copynumber: 2.8 Consensus size: 80
163442 CACCGGCTCG
* * * * ** * *
163452 TAGCCTGCTAAGCCGTAGCTTGAGTTTTAACACC-GACTCGTAGCCTGTTAAGCCGTAGCTTGAG
1 TAGCCTGCTAAGCCGTAGCTTGAATATTAACACCAG-GTCATAGCCTACTAAGCCATAACTTGA-
**
163516 CT-TT-AGCACCAACTCA
64 CTATTGA-CACTGACTCA
* * *
163532 TAGCCTGCTAAGCCGTAGCTTGAATCTTAACACCAGGTCATAGCCTACTAAGTCATAGCTTGACT
1 TAGCCTGCTAAGCCGTAGCTTGAATATTAACACCAGGTCATAGCCTACTAAGCCATAACTTGACT
163597 ATTGACACTGACTCA
66 ATTGACACTGACTCA
* * * *** * *
163612 TAGCCTGCTAATCCGTATCTTGAATATTTAC-GTTGGCTTATAGCCTACTAAGCCGTAACTTGA
1 TAGCCTGCTAAGCCGTAGCTTGAATATTAACACCAGG-TCATAGCCTACTAAGCCATAACTTGA
163675 ATCTATTTGA
Statistics
Matches: 118, Mismatches: 21, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
79 4 0.03
80 112 0.95
81 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (80 bp):
TAGCCTGCTAAGCCGTAGCTTGAATATTAACACCAGGTCATAGCCTACTAAGCCATAACTTGACT
ATTGACACTGACTCA
Found at i:167102 original size:26 final size:26
Alignment explanation
Indices: 167066--167118 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
167056 TAGGGCGCTT
* *
167066 TCATGTTTAATAATTGTCTACAAAAC
1 TCATATTTAATAATTATCTACAAAAC
167092 TCATATTTAATAATTATCTACAAAAC
1 TCATATTTAATAATTATCTACAAAAC
167118 T
1 T
167119 TAAATTTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.40
Consensus pattern (26 bp):
TCATATTTAATAATTATCTACAAAAC
Found at i:167125 original size:26 final size:26
Alignment explanation
Indices: 167071--167125 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
167061 CGCTTTCATG
* *
167071 TTTAATAATTGTCTACAAAACTCATA
1 TTTAATAATTATCTACAAAACTCAAA
*
167097 TTTAATAATTATCTACAAAACTTAAA
1 TTTAATAATTATCTACAAAACTCAAA
167123 TTT
1 TTT
167126 CCTTTAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.42
Consensus pattern (26 bp):
TTTAATAATTATCTACAAAACTCAAA
Found at i:179435 original size:28 final size:28
Alignment explanation
Indices: 179377--179444 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
179367 ACGTGTCTAC
* *
179377 AAAAATAAATTGTAATTTTTAAGAGGTT
1 AAAAATAAATTATAATTTTTAAGAAGTT
* *
179405 AAAATTAAATTATAATTTTTATGATAG-T
1 AAAAATAAATTATAATTTTTAAGA-AGTT
179433 AAAAATATAATT
1 AAAAATA-AATT
179445 TTATTATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (28 bp):
AAAAATAAATTATAATTTTTAAGAAGTT
Found at i:179825 original size:23 final size:22
Alignment explanation
Indices: 179781--179825 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
179771 AGCATTTTGA
*
179781 TTTTTTTTAAAATATATTATTT
1 TTTTTTTTAAAATATATGATTT
179803 TTTTTTTTAATAA-ACTATGATTT
1 TTTTTTTTAA-AATA-TATGATTT
179826 AATGTGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTTTTTAAAATATATGATTT
Found at i:179870 original size:29 final size:30
Alignment explanation
Indices: 179828--179887 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
179818 TATGATTTAA
*
179828 TGTGTAATTGTATATAT-AAATTTTGATTT
1 TGTGTAATTGTATACATGAAATTTTGATTT
*
179857 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTGTATACATGAAATTTTGATTT
179887 T
1 T
179888 ATCCAATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (30 bp):
TGTGTAATTGTATACATGAAATTTTGATTT
Found at i:180113 original size:29 final size:31
Alignment explanation
Indices: 180030--180113 Score: 75
Period size: 31 Copynumber: 2.8 Consensus size: 31
180020 ATTAAAACAA
* ** *
180030 AATTAAAGTTTGAAATATACATTTGA-ACCAT
1 AATTAAAGTTTCACGTATACAATT-ACACCAT
* * *
180061 AATTAGAGTTTCACGTGTATAATTACACCA-
1 AATTAAAGTTTCACGTATACAATTACACCAT
180091 AATTAAAG-TTCACGTATACAATT
1 AATTAAAGTTTCACGTATACAATT
180114 GCACATTAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
29 13 0.31
30 8 0.19
31 21 0.50
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35
Consensus pattern (31 bp):
AATTAAAGTTTCACGTATACAATTACACCAT
Found at i:184575 original size:23 final size:24
Alignment explanation
Indices: 184531--184577 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
184521 TTAAAAATTA
* **
184531 AAAAATATTATGAAGATTATTTTT
1 AAAAATATTATAAAGAAAATTTTT
184555 AAAAA-ATTATAAAGAAAATTTTT
1 AAAAATATTATAAAGAAAATTTTT
184578 TTTTAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (24 bp):
AAAAATATTATAAAGAAAATTTTT
Found at i:184579 original size:26 final size:25
Alignment explanation
Indices: 184528--184580 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
184518 AATTTAAAAA
* * *
184528 TTAAAAAATATTATGAAGATTATTT
1 TTAAAAAATATAAAGAAAATTATTT
*
184553 TTAAAAAATTATAAAGAAAATTTTTT
1 TTAAAAAA-TATAAAGAAAATTATTT
184579 TT
1 TT
184581 TAATATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (25 bp):
TTAAAAAATATAAAGAAAATTATTT
Found at i:186503 original size:20 final size:19
Alignment explanation
Indices: 186474--186534 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
186464 TATTAAAATA
*
186474 AATTATAATATTAAATAATT
1 AATTAAAATA-TAAATAATT
*
186494 TATTAAAATAATAAATTAA-T
1 AATTAAAAT-ATAAA-TAATT
*
186514 AATTTAAATATAAATAATT
1 AATTAAAATATAAATAATT
186533 AA
1 AA
186535 ATAAGTCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 3 0.09
19 8 0.24
20 19 0.56
21 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTAAAATATAAATAATT
Found at i:190984 original size:17 final size:19
Alignment explanation
Indices: 190950--190988 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
190940 AATAATTTTT
190950 AAAAATCCAAATATTTATA
1 AAAAATCCAAATATTTATA
*
190969 AAAAATTCAAA-A-TTATA
1 AAAAATCCAAATATTTATA
190986 AAA
1 AAA
190989 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATCCAAATATTTATA
Found at i:192335 original size:24 final size:24
Alignment explanation
Indices: 192284--192335 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
192274 TTCATAAGTC
* *
192284 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
192308 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
192332 AAAT
1 AAAT
192336 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:194297 original size:24 final size:24
Alignment explanation
Indices: 194246--194291 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
194236 TTCGTAAGTC
*
194246 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATGCTAATAAATACA
*
194270 AAATATATTATGCTAATAAATA
1 AAATAAATTATGCTAATAAATA
194292 TTAAATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.33
Consensus pattern (24 bp):
AAATAAATTATGCTAATAAATACA
Found at i:194641 original size:27 final size:28
Alignment explanation
Indices: 194593--194648 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
194583 ATTATAAATA
*
194593 TTTTTATTTCCAACTTTAATAAAATCAT
1 TTTTTATTTCCAACTCTAATAAAATCAT
* *
194621 TTTTTATTTCCAAC-CTGATAAACTCAT
1 TTTTTATTTCCAACTCTAATAAAATCAT
194648 T
1 T
194649 ATACCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.48
Consensus pattern (28 bp):
TTTTTATTTCCAACTCTAATAAAATCAT
Found at i:197912 original size:3 final size:3
Alignment explanation
Indices: 197904--197932 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
197894 CACAGATTCG
197904 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
197933 GATGCAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:204109 original size:17 final size:17
Alignment explanation
Indices: 204079--204142 Score: 92
Period size: 17 Copynumber: 3.8 Consensus size: 17
204069 TGGCCCCAAC
*
204079 AAATTTAAACTTATTTT
1 AAATTTAAATTTATTTT
* *
204096 AAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTT
*
204113 AAATTTAAATTTATTAT
1 AAATTTAAATTTATTTT
204130 AAATTTAAATTTA
1 AAATTTAAATTTA
204143 AAATTCATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:204119 original size:6 final size:6
Alignment explanation
Indices: 204079--204144 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
204069 TGGCCCCAAC
* * * * *
204079 AAATTT AAACTT -ATTTT AAAATT AAGTTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
204125 --ATTAT AAATTT AAATTT AAA
1 AAATT-T AAATTT AAATTT AAA
204145 ATTCATTTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
4 3 0.07
5 8 0.17
6 32 0.70
7 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:204119 original size:23 final size:24
Alignment explanation
Indices: 204093--204156 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
204083 TTAAACTTAT
*
204093 TTTAAAATTAAGTT-T-ATTTTAAA
1 TTTAAAATTAA-TTATAAATTTAAA
*
204116 TTT-AAATTTATTATAAATTTAAA
1 TTTAAAATTAATTATAAATTTAAA
*
204139 TTTAAAATTCATT-TAAAT
1 TTTAAAATTAATTATAAAT
204157 AATGTCCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 2 0.06
22 7 0.20
23 18 0.51
24 8 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAATTAATTATAAATTTAAA
Found at i:204176 original size:14 final size:15
Alignment explanation
Indices: 204157--204188 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
204147 TCATTTAAAT
204157 AATGTCC-AATACAA
1 AATGTCCAAATACAA
204171 AATGTCCAAATACAA
1 AATGTCCAAATACAA
204186 AAT
1 AAT
204189 TACAAAGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.53, C:0.19, G:0.06, T:0.22
Consensus pattern (15 bp):
AATGTCCAAATACAA
Found at i:206019 original size:29 final size:29
Alignment explanation
Indices: 205977--206287 Score: 326
Period size: 29 Copynumber: 10.6 Consensus size: 29
205967 CCTTGGAGGT
*
205977 CCCTAAACTTCCAAAAATTACATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
206006 CCCTAAACTTCC-AAAATTCACATTTTTAC
1 CCCTAAACTTCCAAAAATTC-CATTTTTAC
*
206035 CCCAAAACTTCCAAAAATTCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* * *
206064 CCCTAAACTTCAAAAAATCCCATTTTTAA
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
206093 CCCTAAAATTTCCAAAAATTCCA-TTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* *
206122 GCCTAAACTTCCAAAAA-TCCTATTTTTAA
1 CCCTAAACTTCCAAAAATTCC-ATTTTTAC
* *
206151 CCCTAAAATTTCCAAAAAATTCCTTTTTTAC
1 CCCT-AAACTTCC-AAAAATTCCATTTTTAC
*
206182 TCCC-AAACTTCCAAAAATCCCATTTTTGAC
1 -CCCTAAACTTCCAAAAATTCCATTTTT-AC
* * *
206212 CTCGAAACTTCCAAAAATTTCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
** * *
206241 CCCCGAGCTTCCAAAAAATCCCATTTTTGA-
1 CCCTAAACTTCC-AAAAATTCCATTTTT-AC
*
206271 CCCTAAAATTCTCAAAA
1 CCCTAAACTTC-CAAAA
206288 TTACCCTTTT
Statistics
Matches: 235, Mismatches: 33, Indels: 27
0.80 0.11 0.09
Matches are distributed among these distances:
27 3 0.01
28 19 0.08
29 111 0.47
30 83 0.35
31 13 0.06
32 6 0.03
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:206071 original size:58 final size:59
Alignment explanation
Indices: 205977--206287 Score: 382
Period size: 58 Copynumber: 5.3 Consensus size: 59
205967 CCTTGGAGGT
* * *
205977 CCCT-AAACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAATTCACATTTTT-A
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAA
* *
206034 CCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCAAAAAATCCCATTTTTAA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAA
* * *
206093 CCCTAAAATTTCCAAAAATTCCA-TTTTACGCCTAAACTTCCAAAAATCCTATTTTTAA
1 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAA
* * *
206151 CCCTAAAATTTCCAAAAAATTCCTTTTTTACTCCC-AAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCC-AAAAATTCCATTTTTAC-CCCTAAACTTCCAAAAATCCCATTTTTAA
* * ** * *
206211 -CCTCGAAACTTCCAAAAATTTCATTTTTACCCCCGAGCTTCCAAAAAATCCCATTTTTGA
1 CCCT-AAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCC-AAAAATCCCATTTTTAA
206271 CCCTAAAA-TTCTCAAAA
1 CCCTAAAACTTC-CAAAA
206288 TTACCCTTTT
Statistics
Matches: 223, Mismatches: 21, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
57 3 0.01
58 96 0.43
59 58 0.26
60 61 0.27
61 5 0.02
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAAAAATCCCATTTTTAA
Found at i:206298 original size:59 final size:58
Alignment explanation
Indices: 205977--206361 Score: 343
Period size: 58 Copynumber: 6.6 Consensus size: 58
205967 CCTTGGAGGT
* * * * *
205977 CCCT-AAACTTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAATTCACATTTTT-A
1 CCCTAAAATTTCCAAAAATT-CCTTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAA
* * * *
206034 CCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCAAAAAATCCCATTTTTAA
1 CCCTAAAATTTCCAAAAATTCC-TTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAA
* * * *
206093 CCCTAAAATTTCCAAAAATTCCATTTTACGCCTAAACTTCCAAAAATCCTATTTTTAA
1 CCCTAAAATTTCCAAAAATTCCTTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAA
* *
206151 CCCTAAAATTTCCAAAAAATTCCTTTTTTACTCCCAAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAATTTCC-AAAAATTCC-TTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAA
* * * * * *
206211 -CCTCGAAACTTCCAAAAATTTCATTTTTACCCCCGAGCTTCCAAAAAATCCCATTTTTGA
1 CCCT-AAAATTTCCAAAAA-TTCCTTTTTACCCCCAAACTTCC-AAAAATCCCATTTTTAA
* * * * * *
206271 CCCTAAAA-TTCTC-AAAATTACCCTTTTACCCTCGAA-TGT-CTAAAATTCTATTTTTAA
1 CCCTAAAATTTC-CAAAAATT-CCTTTTTACCCCCAAACT-TCCAAAAATCCCATTTTTAA
* * * *
206328 CCCCAAACTTTCCCAAAATTACCATTTTACCCCC
1 CCCTAAAATTTCCAAAAATT-CCTTTTTACCCCC
206362 GTGTATCCGA
Statistics
Matches: 279, Mismatches: 35, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
57 24 0.09
58 116 0.42
59 74 0.27
60 62 0.22
61 3 0.01
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (58 bp):
CCCTAAAATTTCCAAAAATTCCTTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAA
Found at i:206346 original size:30 final size:28
Alignment explanation
Indices: 205981--206360 Score: 290
Period size: 29 Copynumber: 13.0 Consensus size: 28
205971 GGAGGTCCCT
*
205981 AAACTTCCAAAAATTACATTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
206009 TAAACTTCC-AAAATTCACATTTTTACCCC
1 -AAACTTCCAAAAATTC-CATTTTTACCCC
206038 AAAACTTCCAAAAATTCCATTTTTACCCC
1 -AAACTTCCAAAAATTCCATTTTTACCCC
* * *
206067 TAAACTTCAAAAAATCCCATTTTTAACCCTA
1 -AAACTTCCAAAAATTCCATTTTT-ACCC-C
* *
206098 AAATTTCCAAAAATTCCA-TTTTACGCCT
1 AAACTTCCAAAAATTCCATTTTTAC-CCC
*
206126 AAACTTCCAAAAA-TCCTATTTTTAACCCTA
1 AAACTTCCAAAAATTCC-ATTTTT-ACCC-C
* *
206156 AAATTTCCAAAAAATTCCTTTTTTACTCCC
1 AAACTTCC-AAAAATTCCATTTTTAC-CCC
* *
206186 AAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACC-CC
*
206216 AAACTTCCAAAAATTTCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTA-CCCC
* * * *
206245 GAGCTTCCAAAAAATCCCATTTTTGACCCT
1 AAACTTCC-AAAAATTCCATTTTT-ACCCC
* *
206275 AAAATTCTC-AAAATTACC-CTTTTACCCTC
1 AAACTTC-CAAAAATT-CCATTTTTACCC-C
* * *
206304 GAA-TGT-CTAAAATTCTATTTTTAACCCC
1 AAACT-TCCAAAAATTCCATTTTT-ACCCC
*
206332 AAACTTTCCCAAAATTACCA-TTTTACCCC
1 AAAC-TTCCAAAAATT-CCATTTTTACCCC
206361 CGTGTATCCG
Statistics
Matches: 284, Mismatches: 39, Indels: 56
0.75 0.10 0.15
Matches are distributed among these distances:
27 5 0.02
28 39 0.14
29 117 0.41
30 104 0.37
31 16 0.06
32 3 0.01
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.34
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTTACCCC
Found at i:210253 original size:19 final size:19
Alignment explanation
Indices: 210226--210268 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
210216 CGAATTAAAG
*
210226 TTATGAATTCGTAATGTAA
1 TTATAAATTCGTAATGTAA
** *
210245 TTATAAATTTTTATTGTAA
1 TTATAAATTCGTAATGTAA
210264 TTATA
1 TTATA
210269 TCTATTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (19 bp):
TTATAAATTCGTAATGTAA
Found at i:214391 original size:25 final size:25
Alignment explanation
Indices: 214304--214409 Score: 106
Period size: 25 Copynumber: 4.2 Consensus size: 25
214294 AATTTCGAAT
* * * *
214304 TCTGACTCATAAGAGCATACTTCTG
1 TCTGGCTCGTAAGAGCGTAATTCTG
* *
214329 TTTGGCTCGTAAGAGC-TAAATTTTTG
1 TCTGGCTCGTAAGAGCGT-AA-TTCTG
* *
214355 TTTGGCTCGTAAGAGTGTAATTCTG
1 TCTGGCTCGTAAGAGCGTAATTCTG
*
214380 TCTGGCTTGTAAGAGCGTAATTCTG
1 TCTGGCTCGTAAGAGCGTAATTCTG
214405 TCTGG
1 TCTGG
214410 GCTCATATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
24 1 0.01
25 45 0.66
26 21 0.31
27 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.38
Consensus pattern (25 bp):
TCTGGCTCGTAAGAGCGTAATTCTG
Found at i:214421 original size:26 final size:25
Alignment explanation
Indices: 214304--214429 Score: 94
Period size: 25 Copynumber: 5.0 Consensus size: 25
214294 AATTTCGAAT
* * *
214304 TCTGACTCATAAGAGCATACTTCTG
1 TCTGGCTCATAAGAGCGTAATTCTG
* * *
214329 TTTGGCTCGTAAGAGC-TAAATTTTTG
1 TCTGGCTCATAAGAGCGT-AA-TTCTG
* * *
214355 TTTGGCTCGTAAGAGTGTAATTCTG
1 TCTGGCTCATAAGAGCGTAATTCTG
**
214380 TCTGGCTTGTAAGAGCGTAATTCTG
1 TCTGGCTCATAAGAGCGTAATTCTG
*
214405 TCTGGGCTCATATGAGC-TAAATTCT
1 TCT-GGCTCATAAGAGCGT-AATTCT
214430 AGAAGACCTG
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.01
25 44 0.53
26 37 0.45
27 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (25 bp):
TCTGGCTCATAAGAGCGTAATTCTG
Found at i:235214 original size:20 final size:20
Alignment explanation
Indices: 235189--235236 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
235179 CTCTAGTGAG
*
235189 ACTTCTACC-AGTAGAACTCC
1 ACTTCTACCGA-TACAACTCC
235209 ACTTCTACCGATACAACTCC
1 ACTTCTACCGATACAACTCC
235229 ACTTCTAC
1 ACTTCTAC
235237 TCTATCGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.29, C:0.38, G:0.06, T:0.27
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCC
Found at i:235498 original size:20 final size:20
Alignment explanation
Indices: 235454--235511 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
235444 TAGAACCCCT
*
235454 CTTCTACTAATACAACTATA
1 CTTCTACCAATACAACTATA
* * *
235474 ATTCTACCAATACAAGTATG
1 CTTCTACCAATACAACTATA
235494 CTTCTACCGAA-ACAACTA
1 CTTCTACC-AATACAACTA
235512 AGCTGCAGAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.29
Consensus pattern (20 bp):
CTTCTACCAATACAACTATA
Found at i:238295 original size:20 final size:20
Alignment explanation
Indices: 238272--238311 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
238262 CCGATAGAAC
238272 TCCACTTCTACCAATACCTT
1 TCCACTTCTACCAATACCTT
* *
238292 TCCACTTTTACCGATACCTT
1 TCCACTTCTACCAATACCTT
238312 GAAGACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.03, T:0.38
Consensus pattern (20 bp):
TCCACTTCTACCAATACCTT
Done.