Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011777.1 Kokia drynarioides strain JFW-HI SEQ_126772, 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: 140136
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:4444 original size:39 final size:38
Alignment explanation
Indices: 4360--5128 Score: 281
Period size: 39 Copynumber: 19.8 Consensus size: 38
4350 TTGAAGATCC
* * **
4360 CGATCTCTTACCCCGAGCTTGCGACAGATCAT-CATCAAC
1 CGATCTCTTACCCCGAGCTTGGGGCAGAT--TGCATCATT
* * *
4399 CAATCTCTTACCACGAGCTTGGGGTAGATTGCAGTCATT
1 CGATCTCTTACCCCGAGCTTGGGGCAGATTGCA-TCATT
*** *
4438 CGATCTCTTACCCCGAGCTTGGGGCAGATCAAAATCA-G
1 CGATCTCTTACCCCGAGCTTGGGGCAGAT-TGCATCATT
* * ** * * *
4476 CAAATCTCTTACCTCGAGCCGGGGGCAGATTGTAGCCATC
1 C-GATCTCTTACCCCGAGCTTGGGGCAGATTGCA-TCATT
* ** * * *
4516 CGATCTTTTACATCGAGCCTAGGGAAGA-T-CATCATT
1 CGATCTCTTACCCCGAGCTTGGGGCAGATTGCATCATT
* * * * *
4552 AGCAAATCTCTTACCCTGAGCTTGGGGTAGATTGCAGCCATC
1 --C-GATCTCTTACCCCGAGCTTGGGGCAGATTGCA-TCATT
4594 CGATCTCTTACCCCGAGCTTGGGGCAGA-T-CATCATT
1 CGATCTCTTACCCCGAGCTTGGGGCAGATTGCATCATT
* *
4630 AGCAAATCTCTTACCCCGAGCCT-GGGCAGATTGCATCCATT
1 --C-GATCTCTTACCCCGAGCTTGGGGCAGATTGCAT-CATT
* **
4671 CGATCTCTTACCCCGAACTTGGGAAAGA-T-CATCA-T
1 CGATCTCTTACCCCGAGCTTGGGGCAGATTGCATCATT
* *
4706 CAGCAAATCTCTTACCCCGAGCTTGGGGCAGAGTGCAGCCATT
1 C-G---ATCTCTTACCCCGAGCTTGGGGCAGATTGCA-TCATT
* * * * ** **
4749 TGATCTCTTACCCCAAGCTTAGGGTAGATCACCATCAAC
1 CGATCTCTTACCCCGAGCTTGGGGCAGAT-TGCATCATT
* * * * *
4788 CAATCTCTTACCCCAAG-TCTGGGGTAGATTACAGTCATC
1 CGATCTCTTACCCCGAGCT-TGGGGCAGATTGCA-TCATT
* * ** * ** *
4827 CGATCTCTTACCCCAAGCCTAAGGTAGATCACCATCA-A
1 CGATCTCTTACCCCGAGCTTGGGGCAGAT-TGCATCATT
* * * ** * *
4865 CAAATCTCTTACCCCGAGCCTAGGGCAGATTATAGCCACT
1 C-GATCTCTTACCCCGAGCTTGGGGCAGATTGCA-TCATT
* * * * *
4905 CGATCTCTTATCTCGAGCCTGGGGCAGATTACAGTCGTT
1 CGATCTCTTACCCCGAGCTTGGGGCAGATTGCA-TCATT
* * * *
4944 CGATCTCTTACCCCGAGCCTAGGACAGATCAT-CATCAGT
1 CGATCTCTTACCCCGAGCTTGGGGCAGAT--TGCATCATT
** * * * *
4983 AAATTTCTTACCCCG-GACCTGGGGCAGATTACGACCATT
1 CGATCTCTTACCCCGAG-CTTGGGGCAGATTGC-ATCATT
* * * * * ** **
5022 CAATCTCTTACCTCAAGGC-TGAGGCAAATCACCATCAGC
1 CGATCTCTTACCCCGA-GCTTGGGGCAGAT-TGCATCATT
* * * *
5061 CAATCTCTTACCCCGAGCCTAGGGCAGATTACAGTCATT
1 CGATCTCTTACCCCGAGCTTGGGGCAGATTGCA-TCATT
* * *
5100 CGATCTCTTACCTCGAGCCTGAGGCAGAT
1 CGATCTCTTACCCCGAGCTTGGGGCAGAT
5129 CATCATCAGC
Statistics
Matches: 550, Mismatches: 135, Indels: 90
0.71 0.17 0.12
Matches are distributed among these distances:
35 2 0.00
36 9 0.02
37 8 0.01
38 43 0.08
39 454 0.83
40 17 0.03
41 10 0.02
42 6 0.01
43 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (38 bp):
CGATCTCTTACCCCGAGCTTGGGGCAGATTGCATCATT
Found at i:4494 original size:78 final size:78
Alignment explanation
Indices: 4360--4933 Score: 603
Period size: 78 Copynumber: 7.4 Consensus size: 78
4350 TTGAAGATCC
* * * * * *
4360 CGATCTCTTACCCCGAGCTTGCGACAGATCATCATCAACCAATCTCTTACCACGAGCTTGGGGTA
1 CGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCA
*
4425 GATTGCAGTCATT
66 GATTGCAGCCATT
** * **
4438 CGATCTCTTACCCCGAGCTTGGGGCAGATCAAAATCAGCAAATCTCTTACCTCGAGCCGGGGGCA
1 CGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCA
* *
4503 GATTGTAGCCATC
66 GATTGCAGCCATT
* ** * * * * * *
4516 CGATCTTTTACATCGAGCCTAGGGAAGATCATCATTAGCAAATCTCTTACCCTGAGCTTGGGGTA
1 CGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCA
*
4581 GATTGCAGCCATC
66 GATTGCAGCCATT
* *
4594 CGATCTCTTACCCCGAGCTTGGGGCAGATCATCATTAGCAAATCTCTTACCCCGAGCCT-GGGCA
1 CGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCA
*
4658 GATTGCATCCATT
66 GATTGCAGCCATT
* **
4671 CGATCTCTTACCCCGAACTTGGGAAAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCA
1 CGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCA
*
4736 GAGTGCAGCCATT
66 GATTGCAGCCATT
* * * * * * * * *
4749 TGATCTCTTACCCCAAGCTTAGGGTAGATCACCATCAACCAATCTCTTACCCCAAG-TCTGGGGT
1 CGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCT-TGGGGC
* * *
4813 AGATTACAGTCATC
65 AGATTGCAGCCATT
* * ** * * * * *
4827 CGATCTCTTACCCCAAGCCTAAGGTAGATCACCATCAACAAATCTCTTACCCCGAGCCTAGGGCA
1 CGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCA
** *
4892 GATTATAGCCACT
66 GATTGCAGCCATT
* * *
4905 CGATCTCTTATCTCGAGCCTGGGGCAGAT
1 CGATCTCTTACCCCGAGCTTGGGGCAGAT
4934 TACAGTCGTT
Statistics
Matches: 414, Mismatches: 79, Indels: 6
0.83 0.16 0.01
Matches are distributed among these distances:
77 70 0.17
78 344 0.83
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (78 bp):
CGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCTTGGGGCA
GATTGCAGCCATT
Found at i:4650 original size:117 final size:117
Alignment explanation
Indices: 4359--5134 Score: 359
Period size: 117 Copynumber: 6.6 Consensus size: 117
4349 ATTGAAGATC
* * * * * * * *
4359 CCGATCTCTTACCCCGAG-CTTGCGACAGATCATCATCAACCAATCTCTTACCACGAGCTTGGGG
1 CCGATCTCTTACCCCGAGCCTAG-GGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTAGGG
* * * * * * *
4423 TAGATTGCAGTCATT--C-GATCTCTTACCCCGAGCTTGGGGCAGATCAAAATCAG
65 CAGA-T-CA-TCATTAGCAAATCTCTTACCCCGAGCTTGGGGTAGATTACAGTCAT
** * ** * * * **
4476 CAAATCTCTTACCTCGAGCCGGGGGCAGATTGTAGCCATC--C-GATCTTTTACATCGAGCCTAG
1 CCGATCTCTTACCCCGAGCCTAGGGCAGA-T-CA-CCATCAGCAAATCTCTTACCCCGAGCCTAG
* * * *
4538 GGAAGATCATCATTAGCAAATCTCTTACCCTGAGCTTGGGGTAGATTGCAGCCAT
63 GGCAGATCATCATTAGCAAATCTCTTACCCCGAGCTTGGGGTAGATTACAGTCAT
* * * *
4593 CCGATCTCTTACCCCGAGCTTGGGGCAGATCATCATTAGCAAATCTCTTACCCCGAGCCT-GGGC
1 CCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTAGGGC
* * ** * *
4657 AGATTGCATCCATT--C-GATCTCTTACCCCGAACTTGGGAAAGATCATCA-TCAG
66 AGA-T-CAT-CATTAGCAAATCTCTTACCCCGAGCTTGGGGTAGATTA-CAGTCAT
** * * ** * *
4709 CAAATCTCTTACCCCGAGCTTGGGGCAGAGTGCAGCCATTTG---ATCTCTTACCCCAAGCTTAG
1 CCGATCTCTTACCCCGAGCCTAGGGCAGA-T-CA-CCATCAGCAAATCTCTTACCCCGAGCCTAG
* * * * * *
4771 GGTAGATCACCATCAACCAATCTCTTACCCCAAG-TCTGGGGTAGATTACAGTCAT
63 GGCAGATCATCATTAGCAAATCTCTTACCCCGAGCT-TGGGGTAGATTACAGTCAT
* * * *
4826 CCGATCTCTTACCCCAAGCCTAAGGTAGATCACCATCAACAAATCTCTTACCCCGAGCCTAGGGC
1 CCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTAGGGC
* * * * * *
4891 AGAT--T-A-TAGCCACTCGATCTCTTATCTCGAGCCTGGGGCAGATTACAGTCGT
66 AGATCATCATTAG-CA---AATCTCTTACCCCGAGCTTGGGGTAGATTACAGTCAT
* * * * * *
4943 TCGATCTCTTACCCCGAGCCTAGGACAGATCATCATCAGTAAATTTCTTACCCCG-GACCTGGGG
1 CCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCAAATCTCTTACCCCGAG-CCTAGGG
* * * * * * * *
5007 CAGATTACGACCATT--C-AATCTCTTACCTCAAGGC-TGAGGCAAATCACCA-TCAG
65 CAGA-T-C-ATCATTAGCAAATCTCTTACCCCGA-GCTTGGGGTAGATTA-CAGTCAT
* * * * *
5060 CCAATCTCTTACCCCGAGCCTAGGGCAGATTA-CAGTCATTC-GATCTCTTACCTCGAGCCT-GA
1 CCGATCTCTTACCCCGAGCCTAGGGCAGATCACCA-TCA-GCAAATCTCTTACCCCGAGCCTAG-
5122 GGCAGATCATCAT
63 GGCAGATCATCAT
5135 CAGCCAGTCT
Statistics
Matches: 499, Mismatches: 115, Indels: 93
0.71 0.16 0.13
Matches are distributed among these distances:
113 1 0.00
114 21 0.04
115 8 0.02
116 89 0.18
117 348 0.70
118 15 0.03
119 10 0.02
120 4 0.01
121 1 0.00
123 1 0.00
124 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (117 bp):
CCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGCAAATCTCTTACCCCGAGCCTAGGGC
AGATCATCATTAGCAAATCTCTTACCCCGAGCTTGGGGTAGATTACAGTCAT
Found at i:5616 original size:17 final size:17
Alignment explanation
Indices: 5594--5652 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
5584 AACTTTTGAT
*
5594 TTTAAATTTATATTAAG
1 TTTAAATTTATATTAAA
** *
5611 TTTAAATTGGTTTTAAA
1 TTTAAATTTATATTAAA
5628 TTTAAATTTAGT-TTAAA
1 TTTAAATTTA-TATTAAA
5645 TTTGAAAT
1 TTT-AAAT
5653 GGTTTCAAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 29 0.85
18 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATATTAAA
Found at i:5637 original size:34 final size:34
Alignment explanation
Indices: 5594--5670 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
5584 AACTTTTGAT
* *
5594 TTTAAATTTA-TATTAAGTTT-AAATTGGTTTTAAA
1 TTTAAATTTAGT-TTAAATTTGAAA-TGGTTTCAAA
5628 TTTAAATTTAGTTTAAATTTGAAATGGTTTCAAA
1 TTTAAATTTAGTTTAAATTTGAAATGGTTTCAAA
*
5662 CTT-AATTTA
1 TTTAAATTTA
5671 AAATTTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 6 0.16
34 28 0.74
35 4 0.11
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.51
Consensus pattern (34 bp):
TTTAAATTTAGTTTAAATTTGAAATGGTTTCAAA
Found at i:5640 original size:28 final size:28
Alignment explanation
Indices: 5593--5646 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
5583 AAACTTTTGA
*
5593 TTTTAAATTTATATTAAGTTTAAATTGG
1 TTTTAAATTTAAATTAAGTTTAAATTGG
*
5621 TTTTAAATTTAAATTTAGTTTAAATT
1 TTTTAAATTTAAATTAAGTTTAAATT
5647 TGAAATGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (28 bp):
TTTTAAATTTAAATTAAGTTTAAATTGG
Found at i:7289 original size:30 final size:30
Alignment explanation
Indices: 7232--7331 Score: 114
Period size: 30 Copynumber: 3.4 Consensus size: 30
7222 ATCCAGAGGT
* * *
7232 CCCT-AAATTTTCTAAAAATCATTATTTGA
1 CCCTCAAACTTTCCAAAAATCATAATTTGA
*
7261 CCCTCAAACTTTCCAAAAATTATAATTTGA
1 CCCTCAAACTTTCCAAAAATCATAATTTGA
* * *
7291 CTCC-CAAACTTTTCAAAAATCACATTTTGA
1 C-CCTCAAACTTTCCAAAAATCATAATTTGA
7321 CCCTCAAACTT
1 CCCTCAAACTT
7332 CAAAATAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
29 6 0.10
30 52 0.87
31 2 0.03
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
CCCTCAAACTTTCCAAAAATCATAATTTGA
Found at i:7346 original size:30 final size:29
Alignment explanation
Indices: 7256--7467 Score: 155
Period size: 30 Copynumber: 7.1 Consensus size: 29
7246 AAAATCATTA
* * *
7256 TTTGACCCTCAAACTTTCCAAAAATTATAA
1 TTTGACCCTCAAAC-TTCAAAAAATTACAT
*
7286 TTTGACTCC-CAAACTTTTC-AAAAATCACAT
1 TTTGAC-CCTCAAAC--TTCAAAAAATTACAT
7316 TTTGACCCTCAAACTTCAAAATAATTACAT
1 TTTGACCCTCAAACTTCAAAA-AATTACAT
* * * * *
7346 TTTTACCGTCGAACTTCACAATAATTATATT
1 TTTGACCCTCAAACTTCA-AAAAATTACA-T
*
7377 TTTGCCCCT-AAACTTCCAAAAAATTACAT
1 TTTGACCCTCAAACTT-CAAAAAATTACAT
* *
7406 TTT-ACCC-CTAAACTTCCAAAAAATCACTT
1 TTTGACCCTC-AAACTT-CAAAAAATTACAT
* * *
7435 TTTTACCCCCAAAATTCAAAAAATTACCAT
1 TTTGACCCTCAAACTTCAAAAAATTA-CAT
7465 TTT
1 TTT
7468 TCTCTTGAAC
Statistics
Matches: 148, Mismatches: 21, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
28 6 0.04
29 39 0.26
30 85 0.57
31 18 0.12
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTGACCCTCAAACTTCAAAAAATTACAT
Found at i:7418 original size:29 final size:29
Alignment explanation
Indices: 7305--7795 Score: 162
Period size: 29 Copynumber: 16.7 Consensus size: 29
7295 CAAACTTTTC
*
7305 AAAAATCACATTTTGA-CCCTCAAACTT-CA
1 AAAAATTACATTTT-ACCCCT-AAACTTCCA
* *
7334 AAATAATTACATTTTTA-CCGTCGAACTT-CA
1 AAA-AATTACA-TTTTACCCCT-AAACTTCCA
* * *
7364 CAATAATTATATTTTTGCCCCTAAACTTCCA
1 -AAAAATTACA-TTTTACCCCTAAACTTCCA
7395 AAAAATTACATTTTACCCCTAAACTTCCA
1 AAAAATTACATTTTACCCCTAAACTTCCA
* * * *
7424 AAAAATCACTTTTTTACCCCCAAAATT-CA
1 AAAAATTAC-ATTTTACCCCTAAACTTCCA
* * * *
7453 AAAAATTACCATTTTTCTCTTGAACTTTCCA
1 AAAAATTA-CATTTTACCCCTAAAC-TTCCA
* * *
7484 AAATA-T-CATTCTTGA--CCTTAACTTTTTC-
1 AAAAATTACATT-TT-ACCCCTAAAC--TTCCA
* * ** * *
7512 GAAAATTACCATTTT-GCTATCGAATTTCC-
1 AAAAATTA-CATTTTACCCCT-AAACTTCCA
* * *
7541 AAAATTTACCATTTTACCTCTAAATTTCC-
1 AAAAATTA-CATTTTACCCCTAAACTTCCA
* * ** * *
7570 AAAAATTCCATTTTTGACCTC-GGAGTTTCA
1 AAAAATTACA-TTTT-ACCCCTAAACTTCCA
* *
7600 AAAAATTACCATTTTACCCTTAGA-TGTCC-
1 AAAAATTA-CATTTTACCCCTAAACT-TCCA
* * *
7629 -AAAATTTCATTTTTATCCCTAAACTTTCA
1 AAAAATTACA-TTTTACCCCTAAACTTCCA
* *
7658 AAAAATTATATTTTACCCCTAAACTACCAA
1 AAAAATTACATTTTACCCCTAAACTTCC-A
* * *
7688 AAAAATCACATTTTTACCCTTAAACTT-TA
1 AAAAATTACA-TTTTACCCCTAAACTTCCA
*
7717 AAAAATTACCATTTTACCCCTGAACTTCC-
1 AAAAATTA-CATTTTACCCCTAAACTTCCA
*
7746 AAAAA-TATCATTTTTAACCCC-AAA-TTCTCT
1 AAAAATTA-CA-TTTT-ACCCCTAAACTTC-CA
7776 AAAAATTACCATTTTACCCC
1 AAAAATTA-CATTTTACCCC
7796 CAAGCTTCTA
Statistics
Matches: 351, Mismatches: 73, Indels: 76
0.70 0.15 0.15
Matches are distributed among these distances:
27 2 0.01
28 39 0.11
29 149 0.42
30 118 0.34
31 43 0.12
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAAATTACATTTTACCCCTAAACTTCCA
Found at i:7590 original size:30 final size:30
Alignment explanation
Indices: 7304--7614 Score: 98
Period size: 30 Copynumber: 10.5 Consensus size: 30
7294 CCAAACTTTT
* * *
7304 CAAAAATCA-CATTTTGACCCTC-AAACTTC
1 CAAAAATTACCATTTTTA-CCTCGAAATTTC
* *
7333 AAAATAATTA-CATTTTTACCGTCG-AACTTC
1 CAAA-AATTACCATTTTTACC-TCGAAATTTC
* * * * * *
7363 ACAATAATTA-TATTTTTGCCCCTAAACTTC
1 -CAAAAATTACCATTTTTACCTCGAAATTTC
* * *
7393 CAAAAAATTA-CA-TTTTACCCCTAAACTTC
1 C-AAAAATTACCATTTTTACCTCGAAATTTC
* * * * *
7422 CAAAAAAT-CACTTTTTTACCCCCAAAATTC
1 CAAAAATTAC-CATTTTTACCTCGAAATTTC
* * *
7452 AAAAAATTACCATTTTT-CTCTTGAACTTTC
1 CAAAAATTACCATTTTTAC-CTCGAAATTTC
* * * * *
7482 C-AAAA-TATCATTCTTGACCT-TAACTTTTT
1 CAAAAATTACCATT-TTTACCTCGAA-ATTTC
*
7511 CGAAAATTACCATTTTGCTA--TCG-AATTTC
1 CAAAAATTACCATTTT--TACCTCGAAATTTC
* *
7540 CAAAATTTACCA-TTTTACCTCTAAATTTC
1 CAAAAATTACCATTTTTACCTCGAAATTTC
* *
7569 CAAAAATT-CCATTTTTGACCTCGGAGTTTC
1 CAAAAATTACCATTTTT-ACCTCGAAATTTC
*
7599 AAAAAATTACCATTTT
1 CAAAAATTACCATTTT
7615 ACCCTTAGAT
Statistics
Matches: 214, Mismatches: 43, Indels: 48
0.70 0.14 0.16
Matches are distributed among these distances:
26 2 0.01
28 22 0.10
29 68 0.32
30 105 0.49
31 16 0.07
32 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.37
Consensus pattern (30 bp):
CAAAAATTACCATTTTTACCTCGAAATTTC
Found at i:7714 original size:60 final size:60
Alignment explanation
Indices: 7636--7795 Score: 186
Period size: 60 Copynumber: 2.7 Consensus size: 60
7626 TCCAAAATTT
*
7636 CATTTTTATCCCTAAACTTTCAAAAAATTA-TATTTTACCCCTAAACTACCAAAAAAATCA
1 CATTTTTATCCCTAAACTTT-AAAAAATTACCATTTTACCCCTAAACTACCAAAAAAATCA
* * *
7696 CATTTTTA-CCCTTAAACTTTAAAAAATTACCATTTTACCCCTGAACTTCCAAAAATAT--
1 CATTTTTATCCC-TAAACTTTAAAAAATTACCATTTTACCCCTAAACTACCAAAAAAATCA
* * *
7754 CATTTTTAACCCCAAA-TTCTCTAAAAATTACCATTTTACCCC
1 CATTTTTATCCCTAAACTT-T-AAAAAATTACCATTTTACCCC
7796 CAAGCTTCTA
Statistics
Matches: 89, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
57 2 0.02
58 12 0.13
59 35 0.39
60 40 0.45
ACGTcount: A:0.39, C:0.26, G:0.01, T:0.35
Consensus pattern (60 bp):
CATTTTTATCCCTAAACTTTAAAAAATTACCATTTTACCCCTAAACTACCAAAAAAATCA
Found at i:7791 original size:30 final size:28
Alignment explanation
Indices: 7717--7798 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 28
7707 TTAAACTTTA
*
7717 AAAAATTACCATTTT-ACCCCTGAACTTCC
1 AAAAATTACCATTTTAACCCC--AAATTCC
*
7746 AAAAA-TATCATTTTTAACCCCAAATTCTC
1 AAAAATTACCA-TTTTAACCCCAAATTC-C
*
7775 TAAAAATTACCATTTTACCCCCAA
1 -AAAAATTACCATTTTAACCCCAA
7799 GCTTCTAGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 9 0.20
29 10 0.23
30 21 0.48
31 4 0.09
ACGTcount: A:0.39, C:0.28, G:0.01, T:0.32
Consensus pattern (28 bp):
AAAAATTACCATTTTAACCCCAAATTCC
Found at i:7795 original size:59 final size:60
Alignment explanation
Indices: 7536--7795 Score: 243
Period size: 59 Copynumber: 4.4 Consensus size: 60
7526 TGCTATCGAA
* * * * * ** *
7536 TTTCCAAAATTTACCATTTTACCTCTAAATTTCCAAAAAT-TCCATTTTTGA-CCTCGGAG
1 TTTCAAAAAATTACCATTTTACCCCTAAACTTCCAAAAATATCCATTTTTAACCCT-AAAC
* * * *
7595 TTTCAAAAAATTACCATTTTACCCTTAGA-TGTCC-AAAAT-TTCATTTTTATCCCTAAAC
1 TTTCAAAAAATTACCATTTTACCCCTAAACT-TCCAAAAATATCCATTTTTAACCCTAAAC
* * *
7653 TTTCAAAAAATTA-TATTTTACCCCTAAACTACCAAAAAAATCACATTTTT-ACCCTTAAAC
1 TTTCAAAAAATTACCATTTTACCCCTAAACTTCCAAAAATATC-CATTTTTAACCC-TAAAC
* *
7713 TTT-AAAAAATTACCATTTTACCCCTGAACTTCCAAAAATAT-CATTTTTAACCCCAAA-
1 TTTCAAAAAATTACCATTTTACCCCTAAACTTCCAAAAATATCCATTTTTAACCCTAAAC
*
7770 TTCTCTAAAAATTACCATTTTACCCC
1 TT-TCAAAAAATTACCATTTTACCCC
7796 CAAGCTTCTA
Statistics
Matches: 166, Mismatches: 24, Indels: 22
0.78 0.11 0.10
Matches are distributed among these distances:
57 16 0.10
58 44 0.27
59 67 0.40
60 39 0.23
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (60 bp):
TTTCAAAAAATTACCATTTTACCCCTAAACTTCCAAAAATATCCATTTTTAACCCTAAAC
Found at i:7805 original size:29 final size:29
Alignment explanation
Indices: 7717--7869 Score: 116
Period size: 29 Copynumber: 5.2 Consensus size: 29
7707 TTAAACTTTA
*
7717 AAAAATTACCATTTTACCCCTGAA-CTTCC
1 AAAAATTACCATTTTACCCC-CAAGCTTCC
* * *
7746 AAAAA-TATCATTTTTAACCCCAA-ATTCTC
1 AAAAATTACCA-TTTTACCCCCAAGCTTC-C
*
7775 TAAAAATTACCATTTTACCCCCAAGCTTCT
1 -AAAAATTACCATTTTACCCCCAAGCTTCC
* * ** *
7805 AGAAATTGCTTTTCTTACCCCCGAG-TATCC
1 AAAAATTACCATT-TTACCCCCAAGCT-TCC
* *
7835 AAAAATTACCATTTTACCCCCGAGCATCC
1 AAAAATTACCATTTTACCCCCAAGCTTCC
7864 AAAAAT
1 AAAAAT
7870 CGTATTTTTG
Statistics
Matches: 97, Mismatches: 19, Indels: 16
0.73 0.14 0.12
Matches are distributed among these distances:
28 9 0.09
29 44 0.45
30 37 0.38
31 7 0.07
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCCAAGCTTCC
Found at i:7825 original size:59 final size:58
Alignment explanation
Indices: 7538--7869 Score: 158
Period size: 59 Copynumber: 5.6 Consensus size: 58
7528 CTATCGAATT
* ** * * * ** *
7538 TCCAAAATTTACCATTTTACCTCTAAATTTCCAAAAAT-TCCATTTTTGACCTCGGAGTT
1 TCCAAAAATTACCATTTTACC-CCCAACTTCCAAAAATAT-CATTTTTAACCCCAAAGTA
* ** * * * * *
7597 TCAAAAAATTACCATTTTACCCTTAGA-TGTCC-AAAATTTCATTTTTATCCCTAAACTT
1 TCCAAAAATTACCATTTTACCCCCA-ACT-TCCAAAAATATCATTTTTAACCCCAAAGTA
* * * * * * *
7655 TCAAAAAATTA-TATTTTACCCCTAAACTACCAAAAAAATCACATTTTT-ACCCTTAAACT-
1 TCCAAAAATTACCATTTTACCCC-CAACTTCCAAAAATAT--CATTTTTAACCC-CAAAGTA
** * * *
7714 TTAAAAAATTACCATTTTACCCCTGAACTTCCAAAAATATCATTTTTAACCCCAAATTC
1 TCCAAAAATTACCATTTTACCCC-CAACTTCCAAAAATATCATTTTTAACCCCAAAGTA
* * * * **
7773 TCTAAAAATTACCATTTTACCCCCAAGCTTCTAGAAAT-TGC-TTTTCTTACCCCCGAGTA
1 TCCAAAAATTACCATTTTACCCCCAA-CTTCCAAAAATAT-CATTTT-TAACCCCAAAGTA
* *
7832 TCCAAAAATTACCATTTTACCCCCGAGCATCCAAAAAT
1 TCCAAAAATTACCATTTTACCCCC-AACTTCCAAAAAT
7870 CGTATTTTTG
Statistics
Matches: 218, Mismatches: 39, Indels: 32
0.75 0.13 0.11
Matches are distributed among these distances:
57 12 0.06
58 57 0.26
59 111 0.51
60 38 0.17
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (58 bp):
TCCAAAAATTACCATTTTACCCCCAACTTCCAAAAATATCATTTTTAACCCCAAAGTA
Found at i:14439 original size:17 final size:17
Alignment explanation
Indices: 14412--14451 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
14402 TTTAATTTTA
14412 TATTTTGTTATTAAT-T
1 TATTTTGTTATTAATAT
*
14428 TATTTATGTTATTTATAT
1 TATTT-TGTTATTAATAT
14446 TATTTT
1 TATTTT
14452 ATTTCTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 10 0.48
18 6 0.29
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
TATTTTGTTATTAATAT
Found at i:14469 original size:23 final size:22
Alignment explanation
Indices: 14390--14469 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
14380 CAACCCATTG
*
14390 TTTTTTTTATTATTTAATTTTA
1 TTTTTTTTATTATTTTATTTTA
* *
14412 TATTTTGTTATTAATTTA-TTTA
1 T-TTTTTTTATTATTTTATTTTA
*
14434 TGTTATTTATATTATTTTATTTCTA
1 T-TT-TTTTTATTATTTTATTT-TA
14459 TTTTTTTTATT
1 TTTTTTTTATT
14470 TTTGGTATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
22 8 0.17
23 31 0.67
24 4 0.09
25 3 0.07
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.74
Consensus pattern (22 bp):
TTTTTTTTATTATTTTATTTTA
Found at i:14497 original size:16 final size:16
Alignment explanation
Indices: 14478--14508 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14468 TTTTTGGTAT
14478 TTAAAATTTTTATTTA
1 TTAAAATTTTTATTTA
*
14494 TTAATATTTTTATTT
1 TTAAAATTTTTATTT
14509 CAAACTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTAAAATTTTTATTTA
Found at i:15356 original size:12 final size:13
Alignment explanation
Indices: 15331--15357 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15321 AAGGAGTTCG
15331 AATAAAGAAAAAA
1 AATAAAGAAAAAA
15344 AATAAAGAAAAAA
1 AATAAAGAAAAAA
15357 A
1 A
15358 GAACAACAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (13 bp):
AATAAAGAAAAAA
Found at i:16212 original size:23 final size:23
Alignment explanation
Indices: 16186--16233 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
16176 TGATGTGGCA
16186 TCCAATCAGCAGCTTCTAGAAGG
1 TCCAATCAGCAGCTTCTAGAAGG
* *
16209 TCCAGTCAGCAGCTTTTAGAAGG
1 TCCAATCAGCAGCTTCTAGAAGG
16232 TC
1 TC
16234 TAGTAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (23 bp):
TCCAATCAGCAGCTTCTAGAAGG
Found at i:16242 original size:23 final size:23
Alignment explanation
Indices: 16193--16242 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
16183 GCATCCAATC
*
16193 AGCAGCTTCTAGAAGGTCCAGTC
1 AGCAGCTTCTAGAAGGTCCAGTA
* *
16216 AGCAGCTTTTAGAAGGTCTAGTA
1 AGCAGCTTCTAGAAGGTCCAGTA
16239 AGCA
1 AGCA
16243 ATGATGGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (23 bp):
AGCAGCTTCTAGAAGGTCCAGTA
Found at i:20792 original size:47 final size:47
Alignment explanation
Indices: 20709--20829 Score: 215
Period size: 47 Copynumber: 2.5 Consensus size: 47
20699 TTCGAACCCC
20709 AGCTTCCTGATGAGATACTAAGAAGCAAGGCGAAGCAATAAAAAGGTT
1 AGCTTCCTGATGAGATACT-AGAAGCAAGGCGAAGCAATAAAAAGGTT
*
20757 AGTTTCCTGATGAGATACTAGAAGCAAGGCGAAGCAATAAAAAGGTT
1 AGCTTCCTGATGAGATACTAGAAGCAAGGCGAAGCAATAAAAAGGTT
20804 AGCTTCCTGATGAGATACTTAGAAGC
1 AGCTTCCTGATGAGATAC-TAGAAGC
20830 GGACCAAATT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
47 45 0.64
48 25 0.36
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (47 bp):
AGCTTCCTGATGAGATACTAGAAGCAAGGCGAAGCAATAAAAAGGTT
Found at i:21007 original size:201 final size:200
Alignment explanation
Indices: 20760--21123 Score: 543
Period size: 201 Copynumber: 1.8 Consensus size: 200
20750 AAAGGTTAGT
* *
20760 TTCCTGATGAGATACTAGAAGCAAGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAGATACTTA
1 TTCCTGATGAGATACTAGAAGCAAGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAAATACTAA
* * *
20825 GAAGCGGACCAAATTCATCTTCCTGATGAGGAACAGAGAAGCGGATTGAAACAAGTGAGGCGGTC
66 GAAGCAGACCAAATTCATCTTCCTGATGAAGAACAGAGAAGCGGATTGAAACAAGCGAGGCGGTC
* * * *
20890 ATCTTCCTGATGAGATAC-AGAGAAGTATACCAACTCAGGGCTCGATGTGAGCAAATCTTCGAAT
131 ATCTTCATAATAAGATACTA-AGAAGTAGACCAACTCAGGGCTCGATGTGAGCAAATCTTCGAAT
20954 CCTAGC
195 CCTAGC
*
20960 TTCCTGATGAGATACTGAGAAGC-AGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAAATACT
1 TTCCTGATGAGATACT-AGAAGCAAGG-CGAAGCAATAAAAAGGTTAGCTTCCTGATGAAATACT
* * * * *
21024 AAGAAGTAGACCAAATTCGTCTTCTTGATGAAGTACAGAGAAGCGGATTGAAACAAGCGATGCGG
64 AAGAAGCAGACCAAATTCATCTTCCTGATGAAGAACAGAGAAGCGGATTGAAACAAGCGAGGCGG
*
21089 TCATTTTCATAATAAGATACTAAGAAGTAGACCAA
129 TCATCTTCATAATAAGATACTAAGAAGTAGACCAA
21124 ATCAACGACA
Statistics
Matches: 145, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
200 19 0.13
201 125 0.86
202 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (200 bp):
TTCCTGATGAGATACTAGAAGCAAGGCGAAGCAATAAAAAGGTTAGCTTCCTGATGAAATACTAA
GAAGCAGACCAAATTCATCTTCCTGATGAAGAACAGAGAAGCGGATTGAAACAAGCGAGGCGGTC
ATCTTCATAATAAGATACTAAGAAGTAGACCAACTCAGGGCTCGATGTGAGCAAATCTTCGAATC
CTAGC
Found at i:21493 original size:18 final size:18
Alignment explanation
Indices: 21470--21505 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21460 GTTTAAATTT
*
21470 ATTTAAATTTATTTTTAA
1 ATTTAAATTTAATTTTAA
21488 ATTTAAATTTAATTTTAA
1 ATTTAAATTTAATTTTAA
21506 TTTGATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTAAATTTAATTTTAA
Found at i:21513 original size:11 final size:11
Alignment explanation
Indices: 21461--21508 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 11
21451 TTAAGTTGGG
21461 TTTAAATTT-A
1 TTTAAATTTAA
*
21471 TTTAAATTTATT
1 TTTAAATTTA-A
21483 TTTAAATTTAAA
1 TTTAAATTT-AA
*
21495 TTTAATTTTAA
1 TTTAAATTTAA
21506 TTT
1 TTT
21509 GATTTAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 9 0.28
11 5 0.16
12 17 0.53
13 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:21522 original size:29 final size:29
Alignment explanation
Indices: 21462--21531 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
21452 TAAGTTGGGT
* *
21462 TTAAATTT-ATTTAAATTTATTTTTAAAT
1 TTAAATTTAATTTAAATTTATTTTAAAAC
*
21490 TTAAATTTAATTTTAATTTGA-TTTAAAAC
1 TTAAATTTAATTTAAATTT-ATTTTAAAAC
*
21519 TTAATATTAAATT
1 TTAA-ATTTAATT
21532 AAAAGTCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 8 0.23
29 19 0.54
30 8 0.23
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (29 bp):
TTAAATTTAATTTAAATTTATTTTAAAAC
Found at i:23317 original size:30 final size:30
Alignment explanation
Indices: 23282--23338 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
23272 TTAAACTATC
*
23282 CAAAATCACATTTTGACCCCTAAACTTCTA
1 CAAAATCACATTTTAACCCCTAAACTTCTA
* * *
23312 CAAAATTATATTTTAACCCTTAAACTT
1 CAAAATCACATTTTAACCCCTAAACTT
23339 TTGTGAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
CAAAATCACATTTTAACCCCTAAACTTCTA
Found at i:23386 original size:29 final size:28
Alignment explanation
Indices: 23354--23714 Score: 127
Period size: 29 Copynumber: 12.3 Consensus size: 28
23344 AAAATTATAA
23354 TTTTACCCCCTAACTTTCCAAAATTCCAT
1 TTTTA-CCCCTAACTTTCCAAAATTCCAT
* * *
23383 TTTTGA-CCTTAATTTTCCCAAAAATTACAT
1 TTTT-ACCCCTAACTTT-CC-AAAATTCCAT
** * *
23413 TTTTAGTGCCGAACTTCCCAAAATTCCAT
1 TTTTA-CCCCTAACTTTCCAAAATTCCAT
* * *
23442 TTTTAACCCTGA-TTATCCCAAAAATTGCAT
1 TTTTACCCCTAACTT-T-CC-AAAATTCCAT
*
23472 TTTTACCCTCGAACTTTCCAAAATTCCAT
1 TTTTACCC-CTAACTTTCCAAAATTCCAT
* *
23501 TTTCTA-CCC-AAATTTCACCAAAAAATACCA-
1 TTT-TACCCCTAACTTT--CC--AAAATTCCAT
*
23531 TTTTACCCCTGAACTTTCCAAAATTCTAT
1 TTTTACCCCT-AACTTTCCAAAATTCCAT
* * *
23560 TTTTA-GCCTCGA-TTTCACCAAAAAATACCA-
1 TTTTACCCCT-AACTTT--CC--AAAATTCCAT
* *
23590 TTTTACCCTCGAACTTTCCAAAATTCTAT
1 TTTTACCC-CTAACTTTCCAAAATTCCAT
23619 TTTTGACCCC-AA-TTTCACCAAAAATTACCA-
1 TTTT-ACCCCTAACTTT--CC-AAAATT-CCAT
* * *
23649 TTTTACCCTCGAA-TTGTCTAAAATTCTAT
1 TTTTACCC-CTAACTT-TCCAAAATTCCAT
* * * * *
23678 TTTTAACCTTTATTTTTCAAAATTACCA-
1 TTTTACCCCTAACTTTCCAAAATT-CCAT
23706 TTTTACCCC
1 TTTTACCCC
23715 CGGGTACCCA
Statistics
Matches: 248, Mismatches: 46, Indels: 77
0.67 0.12 0.21
Matches are distributed among these distances:
27 13 0.05
28 49 0.20
29 76 0.31
30 67 0.27
31 31 0.12
32 12 0.05
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (28 bp):
TTTTACCCCTAACTTTCCAAAATTCCAT
Found at i:23434 original size:59 final size:59
Alignment explanation
Indices: 23354--23682 Score: 327
Period size: 59 Copynumber: 5.6 Consensus size: 59
23344 AAAATTATAA
* * **
23354 TTTTACCCCCTAACTTTCCAAAATTCCATTTTTGACCTTAATTTTC-CCAAAAATTA-CAT
1 TTTTACCCTCGAACTTTCCAAAATTCCATTTTT-ACCCCAA-TTTCACCAAAAATTACCAT
** * ** *
23413 TTTTAGTGC-CGAACTTCCCAAAATTCCATTTTTAACCCTGATTATC-CCAAAAATT-GCAT
1 TTTTA-CCCTCGAACTTTCCAAAATTCCATTTTT-ACCCCAATT-TCACCAAAAATTACCAT
* *
23472 TTTTACCCTCGAACTTTCCAAAATTCCATTTTCTACCCAAATTTCACCAAAAAATACCA-
1 TTTTACCCTCGAACTTTCCAAAATTCCATTTT-TACCCCAATTTCACCAAAAATTACCAT
* * * *
23531 TTTTACCC-CTGAACTTTCCAAAATTCTATTTTTAGCCTCGATTTCACCAAAAAATACCA-
1 TTTTACCCTC-GAACTTTCCAAAATTCCATTTTTA-CCCCAATTTCACCAAAAATTACCAT
*
23590 TTTTACCCTCGAACTTTCCAAAATTCTATTTTTGACCCCAATTTCACCAAAAATTACCA-
1 TTTTACCCTCGAACTTTCCAAAATTCCATTTTT-ACCCCAATTTCACCAAAAATTACCAT
* *
23649 TTTTACCCTCGAA-TTGTCTAAAATTCTATTTTTA
1 TTTTACCCTCGAACTT-TCCAAAATTCCATTTTTA
23683 ACCTTTATTT
Statistics
Matches: 236, Mismatches: 22, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
58 11 0.05
59 219 0.93
60 6 0.03
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (59 bp):
TTTTACCCTCGAACTTTCCAAAATTCCATTTTTACCCCAATTTCACCAAAAATTACCAT
Found at i:23655 original size:177 final size:177
Alignment explanation
Indices: 23353--23680 Score: 402
Period size: 177 Copynumber: 1.9 Consensus size: 177
23343 GAAAATTATA
* *
23353 ATTTTACCCCCTAACTTTCCAAAATTCCATTTTTGACCTTAATTTTCCCAAAAATTACATTTTTA
1 ATTTTACCCCCTAACTTTCCAAAATTCCATTTTTGACCTCAATTTTCCCAAAAAATACATTTTTA
** ** *
23418 GTGCCGAACTTCCCAAAATTCCATTTTTAACCCTGATTATCCCAAAAATTGCATTTTTACCCTCG
66 GCCCCGAACTTCCCAAAATTCCATTTTTAACCCCAATTATCCCAAAAATTCCATTTTTACCCTCG
23483 AACTT-TCCAAAATTCCATTTTCTACCCAAATTTCACCAAAAAATACC
131 AA-TTGTCCAAAATTCCATTTTCTACCCAAATTTCACCAAAAAATACC
* *
23530 ATTTTA-CCCCTGAACTTTCCAAAATTCTATTTTT-AGCCTCGA-TTTCACCAAAAAATACCA-T
1 ATTTTACCCCCT-AACTTTCCAAAATTCCATTTTTGA-CCTCAATTTTC-CCAAAAAATA-CATT
* * *
23591 TTTA-CCCTCGAACTTTCCAAAATTCTATTTTTGACCCCAATT-TCACCAAAAATTACCA-TTTT
62 TTTAGCCC-CGAACTTCCCAAAATTCCATTTTTAACCCCAATTATC-CCAAAAATT-CCATTTTT
* *
23653 ACCCTCGAATTGTCTAAAATTCTATTTT
124 ACCCTCGAATTGTCCAAAATTCCATTTT
23681 TAACCTTTAT
Statistics
Matches: 129, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
176 15 0.12
177 110 0.85
178 4 0.03
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (177 bp):
ATTTTACCCCCTAACTTTCCAAAATTCCATTTTTGACCTCAATTTTCCCAAAAAATACATTTTTA
GCCCCGAACTTCCCAAAATTCCATTTTTAACCCCAATTATCCCAAAAATTCCATTTTTACCCTCG
AATTGTCCAAAATTCCATTTTCTACCCAAATTTCACCAAAAAATACC
Found at i:23672 original size:118 final size:116
Alignment explanation
Indices: 23353--23713 Score: 394
Period size: 118 Copynumber: 3.1 Consensus size: 116
23343 GAAAATTATA
* * * *
23353 ATTTTACCCCCTAACTTTCCAAAATTCCATTTTTGACCTTAATTTTC-CCAAAAATTA-CATTTT
1 ATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACC-CAAATTTCACCAAAAATTACCA-TTT
** * * **
23416 TAGTGCCGAACTTCCCAAAATTCCATTTTTAACCCTGATTATCCCAAAAATTGC
64 TA-CCCCGAACTTTCCAAAATTCTATTTTTAACCCTGATTATCCCAAAAATACC
*
23470 ATTTTTACCCTCGAACTTTCCAAAATTCCATTTTCT-ACCCAAATTTCACCAAAAAATACCATTT
1 A-TTTTACCCTCGAACTTTCCAAAATTCCATTTT-TGACCCAAATTTCACCAAAAATTACCATTT
*
23534 TACCCCTGAACTTTCCAAAATTCTATTTTT-AGCCTCGATT-TCACCAAAAAATACC
64 TACCCC-GAACTTTCCAAAATTCTATTTTTAACCCT-GATTATC-CC-AAAAATACC
* *
23589 ATTTTACCCTCGAACTTTCCAAAATTCTATTTTTGACCCCAATTTCACCAAAAATTACCATTTTA
1 ATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCCAAATTTCACCAAAAATTACCATTTTA
* * * ** *
23654 CCCTCGAA-TTGTCTAAAATTCTATTTTTAACCTTTATT-TTTCAAAATTACC
66 CCC-CGAACTT-TCCAAAATTCTATTTTTAACCCTGATTATCCCAAAAATACC
23705 ATTTTACCC
1 ATTTTACCC
23714 CCGGGTACCC
Statistics
Matches: 210, Mismatches: 22, Indels: 25
0.82 0.09 0.10
Matches are distributed among these distances:
116 17 0.08
117 19 0.09
118 159 0.76
119 15 0.07
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.38
Consensus pattern (116 bp):
ATTTTACCCTCGAACTTTCCAAAATTCCATTTTTGACCCAAATTTCACCAAAAATTACCATTTTA
CCCCGAACTTTCCAAAATTCTATTTTTAACCCTGATTATCCCAAAAATACC
Found at i:36692 original size:12 final size:12
Alignment explanation
Indices: 36675--36703 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
36665 CTTCAATAAG
36675 CAAAATGATCTA
1 CAAAATGATCTA
36687 CAAAATGATCTA
1 CAAAATGATCTA
36699 CAAAA
1 CAAAA
36704 CTACAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (12 bp):
CAAAATGATCTA
Found at i:52013 original size:21 final size:21
Alignment explanation
Indices: 51987--52040 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
51977 TCGTACTATA
51987 AACTACCGATACTTGTAATTC
1 AACTACCGATACTTGTAATTC
52008 AACTACCGATACTTGTAATTC
1 AACTACCGATACTTGTAATTC
52029 AACTACCGATAC
1 AACTACCGATAC
52041 AACCCAAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (21 bp):
AACTACCGATACTTGTAATTC
Found at i:68126 original size:6 final size:6
Alignment explanation
Indices: 68101--68139 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
68091 ACAATTCATA
* * *
68101 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
68140 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:70516 original size:94 final size:93
Alignment explanation
Indices: 70353--70542 Score: 353
Period size: 94 Copynumber: 2.0 Consensus size: 93
70343 GACCATTCAG
70353 TCGCATCTCCACGTATGGTCCTCATCTCTGATGATGACAACGAGGTGAACTCGAAGGATGTTGAA
1 TCGCATCTCCACGTATGGTCCTCATCTCTGATGATGACAACGAGGTGAACTCGAAGGATGTTGAA
70418 GACTGCTTCCGAAATTTTGCCAGCCTGT
66 GACTGCTTCCGAAATTTTGCCAGCCTGT
70446 TCNGCATCTCCACGTATGGTCCTCATCTCTGATGATGACAACGAGGTGAACTCGAAGGATGTTGA
1 TC-GCATCTCCACGTATGGTCCTCATCTCTGATGATGACAACGAGGTGAACTCGAAGGATGTTGA
* *
70511 AGACTGTTTCCGGAATTTTGCCAGCCTGT
65 AGACTGCTTCCGAAATTTTGCCAGCCTGT
70540 TCG
1 TCG
70543 AGGATTATTT
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
93 3 0.03
94 91 0.97
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.28
Consensus pattern (93 bp):
TCGCATCTCCACGTATGGTCCTCATCTCTGATGATGACAACGAGGTGAACTCGAAGGATGTTGAA
GACTGCTTCCGAAATTTTGCCAGCCTGT
Found at i:75736 original size:23 final size:22
Alignment explanation
Indices: 75710--75774 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 22
75700 TCTTCATAAT
75710 TTTTCTTACTC-TTTTC-TTTTG
1 TTTT-TTACTCATTTTCTTTTTG
75731 TGTTTTTACTCATTTTCTTTTTG
1 T-TTTTTACTCATTTTCTTTTTG
**
75754 TTCTTTTCACTTGTTTTCTTT
1 TT-TTTT-ACTCATTTTCTTT
75775 AAATCTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
21 7 0.19
22 9 0.24
23 10 0.27
24 11 0.30
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.71
Consensus pattern (22 bp):
TTTTTTACTCATTTTCTTTTTG
Found at i:75741 original size:21 final size:21
Alignment explanation
Indices: 75715--75755 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
75705 ATAATTTTTC
75715 TTACTC-TTTTCTTTTGTGTTT
1 TTACTCATTTTCTTTT-TGTTT
75736 TTACTCATTTTCTTTTTGTT
1 TTACTCATTTTCTTTTTGTT
75756 CTTTTCACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.07, C:0.15, G:0.07, T:0.71
Consensus pattern (21 bp):
TTACTCATTTTCTTTTTGTTT
Found at i:85723 original size:13 final size:14
Alignment explanation
Indices: 85705--85738 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
85695 CAAGCATTGA
*
85705 AATTTAAT-TGTTT
1 AATTTAATAAGTTT
85718 AATTTAATAAGTTT
1 AATTTAATAAGTTT
85732 AATTTAA
1 AATTTAA
85739 ATAATTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
AATTTAATAAGTTT
Found at i:88743 original size:9 final size:9
Alignment explanation
Indices: 88701--88742 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
88691 AAGATAAAAT
*
88701 AAATAAATA
1 AAATAAAGA
88710 CAAATAAAGA
1 -AAATAAAGA
88720 AAATAAAG-
1 AAATAAAGA
*
88728 AAATAATGA
1 AAATAAAGA
88737 AAATAA
1 AAATAA
88743 TATAAACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 8 0.28
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (9 bp):
AAATAAAGA
Found at i:89039 original size:17 final size:17
Alignment explanation
Indices: 89019--89077 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
89009 TAAAATAAAC
89019 AAAAATAAACT-TGAAAT
1 AAAAATAAA-TATGAAAT
89036 AAAAATAAATATGAAAT
1 AAAAATAAATATGAAAT
*
89053 --AAATAAATGATAAAAT
1 AAAAATAAAT-ATGAAAT
89069 AAAAA-AAAT
1 AAAAATAAAT
89078 GGGTAAAGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
15 8 0.22
16 7 0.19
17 19 0.51
18 3 0.08
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (17 bp):
AAAAATAAATATGAAAT
Found at i:89058 original size:15 final size:16
Alignment explanation
Indices: 89038--89071 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
89028 CTTGAAATAA
*
89038 AAATAAAT-ATGAAAT
1 AAATAAATGATAAAAT
89053 AAATAAATGATAAAAT
1 AAATAAATGATAAAAT
89069 AAA
1 AAA
89072 AAAAATGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (16 bp):
AAATAAATGATAAAAT
Found at i:89162 original size:31 final size:28
Alignment explanation
Indices: 89121--89210 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 28
89111 GAAAGAAGCC
89121 AAAAAA-AAATAGAAATGACAAGAAATAAAT
1 AAAAAATAAATA-AAATGAC-A-AAATAAAT
89151 AAAAAATAAATAAAATGACAAAATAAAT
1 AAAAAATAAATAAAATGACAAAATAAAT
89179 AATAATAAT-AATAATAAT-A-AAATATAAAT
1 AA-AA-AATAAATAA-AATGACAAA-ATAAAT
89208 AAA
1 AAA
89211 TACAAAATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
28 14 0.25
29 17 0.31
30 19 0.35
31 5 0.09
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (28 bp):
AAAAAATAAATAAAATGACAAAATAAAT
Found at i:90147 original size:13 final size:13
Alignment explanation
Indices: 90129--90153 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
90119 TTTGCTTTCG
90129 AAAATAACAAATA
1 AAAATAACAAATA
90142 AAAATAACAAAT
1 AAAATAACAAAT
90154 CTACCTTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAACAAATA
Found at i:91015 original size:51 final size:50
Alignment explanation
Indices: 90960--91158 Score: 145
Period size: 51 Copynumber: 3.9 Consensus size: 50
90950 GATTTGATGT
* *
90960 TTGTAGCTTCATCTTGCTCTATTGCAACTTTAGAGAGATAAAGATTTGCTA
1 TTGTAGCTTCATCTTGCTCTACTGCAACTTTA-AGAGATGAAGATTTGCTA
* * * * * * * * *
91011 TTGTAGCTTTGAT-TCGATCCACTGCATCTTCAA-AGATGTAGAATTTGGTGG
1 TTGTAGC-TTCATCTTGCTCTACTGCAACTTTAAGAGATGAAG-ATTTGCT-A
*** * * *
91062 TCACAGCTTCATCTTGC-CTCATTGCAACTTTAAGGAGAT-AAGGTTTGTTA
1 TTGTAGCTTCATCTTGCTCT-ACTGCAACTTTAA-GAGATGAAGATTTGCTA
*
91112 TTGTAGCTTCATCTTGCTCTACTACAACTTTAGAGAGATGAAGATTT
1 TTGTAGCTTCATCTTGCTCTACTGCAACTTTA-AGAGATGAAGATTT
91159 TAATTCAATC
Statistics
Matches: 107, Mismatches: 31, Indels: 20
0.68 0.20 0.13
Matches are distributed among these distances:
49 6 0.06
50 41 0.38
51 50 0.47
52 6 0.06
53 4 0.04
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (50 bp):
TTGTAGCTTCATCTTGCTCTACTGCAACTTTAAGAGATGAAGATTTGCTA
Found at i:92390 original size:27 final size:27
Alignment explanation
Indices: 92360--92413 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
92350 TCAAAATATC
* *
92360 AAACATTGGTTAAAAATGGCAAACATT
1 AAACAATGGCTAAAAATGGCAAACATT
* *
92387 AAACAATGGCTAACAATTGCAAACATT
1 AAACAATGGCTAAAAATGGCAAACATT
92414 GGTCAAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (27 bp):
AAACAATGGCTAAAAATGGCAAACATT
Found at i:92774 original size:21 final size:21
Alignment explanation
Indices: 92750--92789 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
92740 TCTCGGCCTC
* *
92750 TCCTTTTTTTCTTTTTCTTTT
1 TCCTTTTCTTCTTCTTCTTTT
92771 TCCTTTTCTTCTTCTTCTT
1 TCCTTTTCTTCTTCTTCTT
92790 CTTCTTCTTC
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:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (21 bp):
TCCTTTTCTTCTTCTTCTTTT
Found at i:92784 original size:3 final size:3
Alignment explanation
Indices: 92758--92801 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
92748 TCTCCTTTTT
* *
92758 TTC TTT TTC TTT TTCC TT- TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
92802 TTGGTGAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:94935 original size:4 final size:4
Alignment explanation
Indices: 94921--94957 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
94911 GTGGGGAATT
94921 TTTA TTTTA TTTA TTTA TTTA TTTA -TTA TTT- TTTA TT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
94958 GAAATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
3 6 0.20
4 20 0.67
5 4 0.13
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:96736 original size:10 final size:10
Alignment explanation
Indices: 96721--96750 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
96711 GCAAAAATAA
96721 AAATACAAAT
1 AAATACAAAT
96731 AAATACAAAT
1 AAATACAAAT
96741 AAATA-AAAT
1 AAATACAAAT
96750 A
1 A
96751 TAGAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.25
10 15 0.75
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (10 bp):
AAATACAAAT
Found at i:97025 original size:18 final size:17
Alignment explanation
Indices: 96995--97043 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
96985 GGACTAAATT
96995 AAAAAAAAGTAAAGCATG
1 AAAAAAAA-TAAAGCATG
*
97013 AATAAAAAATAAA-CATT
1 AA-AAAAAATAAAGCATG
97030 AAATAAAAATAAAG
1 AAA-AAAAATAAAG
97044 ATCAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.04
17 14 0.52
18 6 0.22
19 6 0.22
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.16
Consensus pattern (17 bp):
AAAAAAAATAAAGCATG
Found at i:97037 original size:17 final size:17
Alignment explanation
Indices: 97017--97053 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
97007 AGCATGAATA
*
97017 AAAAATAAACATTAAAT
1 AAAAATAAACATCAAAT
*
97034 AAAAATAAAGATCAAAT
1 AAAAATAAACATCAAAT
97051 AAA
1 AAA
97054 TAAATGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAAATAAACATCAAAT
Found at i:97056 original size:15 final size:16
Alignment explanation
Indices: 97036--97069 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
97026 CATTAAATAA
*
97036 AAATAAA-GATCAAAT
1 AAATAAATGATAAAAT
97051 AAATAAATGATAAAAT
1 AAATAAATGATAAAAT
97067 AAA
1 AAA
97070 AAAAAATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (16 bp):
AAATAAATGATAAAAT
Found at i:97198 original size:35 final size:37
Alignment explanation
Indices: 97121--97199 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 37
97111 AAAGAAGCAA
* *
97121 AAAAAAATATAAATAGAAATGACGAGAAATAACTAAC
1 AAAAAAATAAAAATAGAAATGACGAGAAATAAATAAC
97158 AAAAAAATAAAAAATA-AAATGAC-A-AAATAAATAA-
1 AAAAAAAT-AAAAATAGAAATGACGAGAAATAAATAAC
97192 ATAAAAAA
1 A-AAAAAA
97200 GGGCAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
34 1 0.03
35 15 0.39
36 1 0.03
37 15 0.39
38 6 0.16
ACGTcount: A:0.73, C:0.05, G:0.06, T:0.15
Consensus pattern (37 bp):
AAAAAAATAAAAATAGAAATGACGAGAAATAAATAAC
Found at i:97199 original size:37 final size:37
Alignment explanation
Indices: 97119--97199 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
97109 TGAAAGAAGC
* *
97119 AAAAAAAAATATAAATAGAAATGACGAGAAATAACTA
1 AAAAAAAAATAAAAATAGAAATGACGAGAAATAAATA
*
97156 ACAAAAAAATAAAAAATA-AAATGAC-A-AAATAAATA
1 AAAAAAAAAT-AAAAATAGAAATGACGAGAAATAAATA
*
97191 AATAAAAAA
1 AAAAAAAAA
97200 GGGCAAAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
35 15 0.39
36 1 0.03
37 16 0.42
38 6 0.16
ACGTcount: A:0.74, C:0.05, G:0.06, T:0.15
Consensus pattern (37 bp):
AAAAAAAAATAAAAATAGAAATGACGAGAAATAAATA
Found at i:97206 original size:23 final size:23
Alignment explanation
Indices: 97156--97207 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
97146 GAAATAACTA
*
97156 ACAAAAAAATAAAAAATAAAATG
1 ACAAAAAAATAAAAAATAAAAGG
*
97179 ACAAAATAAATAAATAA-AAAAGG
1 ACAAAA-AAATAAAAAATAAAAGG
*
97202 GCAAAA
1 ACAAAA
97208 GACTTATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.75, C:0.06, G:0.08, T:0.12
Consensus pattern (23 bp):
ACAAAAAAATAAAAAATAAAAGG
Found at i:99828 original size:2 final size:2
Alignment explanation
Indices: 99821--99851 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
99811 CTAATCTCCC
99821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
99852 GAGTACAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:100415 original size:31 final size:32
Alignment explanation
Indices: 100370--100434 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
100360 GCACTCAAAT
*
100370 TTGACACTTTTTTTTTAATTTGATATTTAAAC
1 TTGACACTTTTTTTTTAAGTTGATATTTAAAC
*
100402 TTGACA-TTTTTTTTTAAGTTGGTATTTAAAC
1 TTGACACTTTTTTTTTAAGTTGATATTTAAAC
100433 TT
1 TT
100435 TTTAGGGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.26, C:0.08, G:0.09, T:0.57
Consensus pattern (32 bp):
TTGACACTTTTTTTTTAAGTTGATATTTAAAC
Found at i:100415 original size:91 final size:90
Alignment explanation
Indices: 100298--100472 Score: 226
Period size: 91 Copynumber: 1.9 Consensus size: 90
100288 AATATAACAT
* * * * * *
100298 TTTGTATTTGAATTTGACATTATTTTTTAATTTAATATTTAAATTTTTTTGGGTTCAATTTGGCA
1 TTTGTATTTAAACTTGACATTATTTTTTAAGTTAATATTTAAACTTTTTAGGGTTCAATTTGACA
100363 CTCA-AATTTGACACTTTTTTTTTAA
66 C-CAGAATTTGACACTTTTTTTTTAA
* ** *
100388 TTTGATATTTAAACTTGACATTTTTTTTTAAGTTGGTATTTAAACTTTTTAGGGTTCAATTTGAT
1 TTTG-TATTTAAACTTGACATTATTTTTTAAGTTAATATTTAAACTTTTTAGGGTTCAATTTGAC
*
100453 ACCAGAATTTGACTCTTTTT
65 ACCAGAATTTGACACTTTTT
100473 CCTAATTTGG
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
90 6 0.08
91 66 0.92
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (90 bp):
TTTGTATTTAAACTTGACATTATTTTTTAAGTTAATATTTAAACTTTTTAGGGTTCAATTTGACA
CCAGAATTTGACACTTTTTTTTTAA
Found at i:101270 original size:19 final size:19
Alignment explanation
Indices: 101212--101270 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
101202 AATTTTATAA
* *
101212 TTTTAACATTTTATAACA-T
1 TTTTAATATTTT-TAAAATT
**
101231 TTTTAATAATTTTTATGATT
1 TTTTAAT-ATTTTTAAAATT
101251 TTTTAATATTTTTAAAATT
1 TTTTAATATTTTTAAAATT
101270 T
1 T
101271 AAAAGGGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTAATATTTTTAAAATT
Found at i:101510 original size:14 final size:14
Alignment explanation
Indices: 101487--101517 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
101477 TCATTTAACA
101487 TACATAAACTAATT
1 TACATAAACTAATT
*
101501 TACATGAACTAATT
1 TACATAAACTAATT
101515 TAC
1 TAC
101518 TAATAAGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.35
Consensus pattern (14 bp):
TACATAAACTAATT
Found at i:103971 original size:194 final size:193
Alignment explanation
Indices: 103625--104013 Score: 690
Period size: 194 Copynumber: 2.0 Consensus size: 193
103615 ATTTGATACT
103625 AATATTTTCCCAAGTACCCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTTTGGTC
1 AATATTTTCCCAAGTACCCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTTTGGTC
* *
103690 CCAGTTAAGTATCTATAATTTTTTTACTAGACTAGACATCAAATACTCGTTGGACCACATGATGC
66 CCAATTAAGTATCTATAATTTTTTTACTAGACTAGACATCAAATACTCATTGGACCACATGATGC
103755 CATTTGGTTTAGGTACCAAATTGAACATTGAAGTCAAACTCAGGTAGCAAATTAGGATGAATG
131 CATTTGGTTTAGGTACCAAATTGAACATTGAAGTCAAACTCAGGTAGCAAATTAGGATGAATG
* *
103818 AATATTTTTCCTAAGTATCCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTTTGGT
1 AATA-TTTTCCCAAGTACCCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTTTGGT
* *
103883 CCCAATTAA-TCATCTATATTTTTTTTACTAGATTAGACATCAAATACTCATTGGACCACATGAT
65 CCCAATTAAGT-ATCTATAATTTTTTTACTAGACTAGACATCAAATACTCATTGGACCACATGAT
*
103947 GCCATTTGGTTTAGGTACCAAATTGAACATTGAAGTCAAACTCAGGTAGCAAATTGGGATGAATG
129 GCCATTTGGTTTAGGTACCAAATTGAACATTGAAGTCAAACTCAGGTAGCAAATTAGGATGAATG
104012 AA
1 AA
104014 AACTTAGGTA
Statistics
Matches: 187, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
193 5 0.03
194 182 0.97
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (193 bp):
AATATTTTCCCAAGTACCCAAGTTTGACTTCAATGTTCTATTTAGTATCCGAGAATGTTTTGGTC
CCAATTAAGTATCTATAATTTTTTTACTAGACTAGACATCAAATACTCATTGGACCACATGATGC
CATTTGGTTTAGGTACCAAATTGAACATTGAAGTCAAACTCAGGTAGCAAATTAGGATGAATG
Found at i:109787 original size:23 final size:23
Alignment explanation
Indices: 109735--109780 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
109725 AGTATCAAAA
*
109735 CATTATTAATCAAATTGTAAATT
1 CATTAATAATCAAATTGTAAATT
109758 CATTAATAATCAAATTGTAAATT
1 CATTAATAATCAAATTGTAAATT
109781 TTTTAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (23 bp):
CATTAATAATCAAATTGTAAATT
Found at i:112792 original size:6 final size:6
Alignment explanation
Indices: 112783--112809 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
112773 AAATAAAAAG
112783 TTTAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTT
112810 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:113849 original size:6 final size:6
Alignment explanation
Indices: 113838--113869 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
113828 CTTTTTCAAC
113838 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CC
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CC
113870 TAAATCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCAAA
Found at i:114715 original size:36 final size:38
Alignment explanation
Indices: 114675--114750 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 38
114665 ATTATTTTAA
*
114675 ATGTGTTTTAAATTTAAATTATATTAATCG-TTTT-TT
1 ATGTGATTTAAATTTAAATTATATTAATCGATTTTATT
*
114711 ATGTGATTTAAATTTAAATTATGTTAATCGATTTTATT
1 ATGTGATTTAAATTTAAATTATATTAATCGATTTTATT
114749 AT
1 AT
114751 TTAGATTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 28 0.78
37 4 0.11
38 4 0.11
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (38 bp):
ATGTGATTTAAATTTAAATTATATTAATCGATTTTATT
Found at i:115407 original size:24 final size:24
Alignment explanation
Indices: 115358--115407 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
115348 GTAAAATATG
* *
115358 ATTCGGATTTTAATATTGATTGTT
1 ATTCGAATTTTAATATTGATTATT
*
115382 ATTCGAATTTTATTTATT-ATTATT
1 ATTCGAATTTTA-ATATTGATTATT
115406 AT
1 AT
115408 AATTAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.58
Consensus pattern (24 bp):
ATTCGAATTTTAATATTGATTATT
Found at i:119996 original size:20 final size:18
Alignment explanation
Indices: 119948--119996 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
119938 GAGATGGGCC
*
119948 TTTGAAATTTATTTTTCA
1 TTTGAAATATATTTTTCA
*
119966 TTTGTATATATATATTTTCA
1 TTTG-AAATATAT-TTTTCA
119986 TTTAGAAATAT
1 TTT-GAAATAT
119997 GTTTATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 4 0.16
19 6 0.24
20 14 0.56
21 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTGAAATATATTTTTCA
Found at i:120450 original size:14 final size:14
Alignment explanation
Indices: 120427--120506 Score: 65
Period size: 14 Copynumber: 5.7 Consensus size: 14
120417 AATCACTTAA
*
120427 AAACCCTAAACCCT
1 AAACCCTAAACCTT
* *
120441 AAACCATAAAATCTT
1 AAACCCT-AAACCTT
120456 AAACCCTAAACCTT
1 AAACCCTAAACCTT
* *
120470 AAA-CTTAATA-CTC
1 AAACCCTAA-ACCTT
**
120483 AAACCCTAAATATT
1 AAACCCTAAACCTT
120497 AAACCCTAAA
1 AAACCCTAAA
120507 TCTATTATCT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
13 10 0.19
14 31 0.60
15 11 0.21
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.23
Consensus pattern (14 bp):
AAACCCTAAACCTT
Found at i:120451 original size:22 final size:22
Alignment explanation
Indices: 120426--120472 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
120416 AAATCACTTA
120426 AAAACCCTAAACCCTAAACCAT
1 AAAACCCTAAACCCTAAACCAT
* * *
120448 AAAATCTTAAACCCTAAACCTT
1 AAAACCCTAAACCCTAAACCAT
120470 AAA
1 AAA
120473 CTTAATACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (22 bp):
AAAACCCTAAACCCTAAACCAT
Found at i:120552 original size:17 final size:17
Alignment explanation
Indices: 120526--120561 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
120516 TAGAAACCCT
120526 AAACCCTAAACCATTAA
1 AAACCCTAAACCATTAA
* *
120543 AAACCTTAAACCCTTAA
1 AAACCCTAAACCATTAA
120560 AA
1 AA
120562 TAATCACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (17 bp):
AAACCCTAAACCATTAA
Found at i:122869 original size:15 final size:15
Alignment explanation
Indices: 122849--122882 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
122839 GGACCACTAC
122849 TATCATATC-CATCAT
1 TATCAT-TCGCATCAT
122864 TATCATTCGCATCAT
1 TATCATTCGCATCAT
122879 TATC
1 TATC
122883 GGGTGCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.41
Consensus pattern (15 bp):
TATCATTCGCATCAT
Found at i:123468 original size:26 final size:25
Alignment explanation
Indices: 123432--123481 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
123422 AACCTTCTGT
* *
123432 TTCCTTTCCTTGTTCAAAAATTTTGC
1 TTCCTTTCCTTCTAC-AAAATTTTGC
123458 TTCCTTTCCTTCTACAAAATTTTG
1 TTCCTTTCCTTCTACAAAATTTTG
123482 TTGTTGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.50
Consensus pattern (25 bp):
TTCCTTTCCTTCTACAAAATTTTGC
Found at i:124080 original size:27 final size:27
Alignment explanation
Indices: 124049--124101 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
124039 GCAGCCTGCC
*
124049 AGGTAGGCACCTCTAGTGTCGCCTGTG
1 AGGTAGGCACCTCTAGTGCCGCCTGTG
* *
124076 AGGTAGGCACCTTTGGTGCCGCCTGT
1 AGGTAGGCACCTCTAGTGCCGCCTGT
124102 CAGATCGGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (27 bp):
AGGTAGGCACCTCTAGTGCCGCCTGTG
Found at i:124111 original size:27 final size:27
Alignment explanation
Indices: 124042--124113 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
124032 GGTTGACGCA
* * *
124042 GCCTGCCAGGTAGGCACCTCTAGTGTC
1 GCCTGTCAGATAGGCACCTCTAGTGCC
* * * *
124069 GCCTGTGAGGTAGGCACCTTTGGTGCC
1 GCCTGTCAGATAGGCACCTCTAGTGCC
*
124096 GCCTGTCAGATCGGCACC
1 GCCTGTCAGATAGGCACC
124114 ACCCCATTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.14, C:0.32, G:0.32, T:0.22
Consensus pattern (27 bp):
GCCTGTCAGATAGGCACCTCTAGTGCC
Found at i:124199 original size:18 final size:17
Alignment explanation
Indices: 124167--124214 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
124157 TTTATCGATA
124167 TATTTTTAAA-A-TTTT
1 TATTTTTAAATATTTTT
124182 TATTATTTAAATATTTTT
1 TATT-TTTAAATATTTTT
*
124200 TCATTTTTTAATATT
1 T-ATTTTTAAATATT
124215 AAAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 4 0.14
16 6 0.21
17 1 0.04
18 14 0.50
19 3 0.11
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTTTAAATATTTTT
Found at i:125324 original size:22 final size:22
Alignment explanation
Indices: 125281--125324 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
125271 TTGAAATTTA
* *
125281 TTTTTCATTTGTATATATATAT
1 TTTTTCATTTGAATATAAATAT
125303 TTTTTCATTTAGAAT-TAAATAT
1 TTTTTCATTT-GAATATAAATAT
125325 GTTTATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTTTCATTTGAATATAAATAT
Found at i:125333 original size:6 final size:6
Alignment explanation
Indices: 125322--125346 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
125312 TAGAATTAAA
125322 TATGTT TATGTT TATGTT TATGTT T
1 TATGTT TATGTT TATGTT TATGTT T
125347 TTATATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (6 bp):
TATGTT
Found at i:126047 original size:27 final size:26
Alignment explanation
Indices: 125990--126066 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
125980 CCTAAACCTC
**
125990 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
**
126016 ATTAAATAAATTCAAATTTAAAAAAGA
1 ATTAAATAAATTCAAACAT-AAAAAGA
* *
126043 ATTAATTCTAAATTCAATCATAAA
1 ATTAA--ATAAATTCAAACATAAA
126067 CTTAATTAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
26 17 0.43
27 10 0.25
28 3 0.08
29 10 0.25
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:128707 original size:25 final size:26
Alignment explanation
Indices: 128658--128709 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
128648 AACCTTCTGT
*
128658 TTCCTTTCATTCTTCAAAAAATTTGC
1 TTCCTTCCATTCTTCAAAAAATTTGC
*
128684 TTCCTTCCCTTCTT-AAAAAATTTGC
1 TTCCTTCCATTCTTCAAAAAATTTGC
128709 T
1 T
128710 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.25, C:0.25, G:0.04, T:0.46
Consensus pattern (26 bp):
TTCCTTCCATTCTTCAAAAAATTTGC
Found at i:129153 original size:2 final size:2
Alignment explanation
Indices: 129146--129195 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
129136 GAATGGATTA
129146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
129188 AT AT AT AT
1 AT AT AT AT
129196 TATTTAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:129458 original size:15 final size:16
Alignment explanation
Indices: 129440--129479 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
129430 TTTATCAGTA
*
129440 TATTTTTTAAAT-TTT
1 TATTATTTAAATATTT
129455 TATTATTTAAATATTTT
1 TATTATTTAAATA-TTT
129472 TATTATTT
1 TATTATTT
129480 TTTAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
17 11 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTTAAATATTT
Found at i:129468 original size:26 final size:27
Alignment explanation
Indices: 129439--129504 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
129429 TTTTATCAGT
* *
129439 ATATTTTTTAAATTTTTATTATTTA-A
1 ATATTTTTTAAATTTTTAATATTAATA
* *
129465 ATATTTTTATTATTTTTTAATATTAATA
1 ATATTTTT-TAAATTTTTAATATTAATA
129493 ATATTTGTTTAA
1 ATATTT-TTTAA
129505 CATTAAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
26 8 0.25
27 13 0.41
28 9 0.28
29 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
ATATTTTTTAAATTTTTAATATTAATA
Found at i:129876 original size:27 final size:28
Alignment explanation
Indices: 129846--129902 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
129836 TATTATTGGG
* *
129846 TGGTGTCTACCTGACAGGCGGCACC-AA
1 TGGTGCCTACCTAACAGGCGGCACCTAA
* *
129873 TGGTGCCTATCTAACAGGCTGCACCTAA
1 TGGTGCCTACCTAACAGGCGGCACCTAA
129901 TG
1 TG
129903 CTGTTTCCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (28 bp):
TGGTGCCTACCTAACAGGCGGCACCTAA
Found at i:133846 original size:7 final size:7
Alignment explanation
Indices: 133813--133949 Score: 68
Period size: 7 Copynumber: 19.6 Consensus size: 7
133803 CACCATATCC
*
133813 TAAACTT
1 TAAACCT
*
133820 TAAACCC
1 TAAACCT
* *
133827 TAACCCA
1 TAAACCT
133834 TAAACCT
1 TAAACCT
133841 TAAACCAT
1 TAAACC-T
*
133849 AAAACCT
1 TAAACCT
133856 TAAA-CT
1 TAAACCT
* *
133862 CATACC-
1 TAAACCT
133868 TAAACCT
1 TAAACCT
*
133875 TAAACAT
1 TAAACCT
133882 TAAACCT
1 TAAACCT
*
133889 TAAATC-
1 TAAACCT
*
133895 TACTACCT
1 TA-AACCT
* *
133903 AAAACCC
1 TAAACCT
133910 T-AACCT
1 TAAACCT
*
133916 CATAACCT
1 TA-AACCT
*
133924 TCAACAC-
1 TAAAC-CT
133931 TAAACCT
1 TAAACCT
133938 TAAACCAT
1 TAAACC-T
133946 TAAA
1 TAAA
133950 AACCCTAAAC
Statistics
Matches: 94, Mismatches: 26, Indels: 19
0.68 0.19 0.14
Matches are distributed among these distances:
6 15 0.16
7 61 0.65
8 18 0.19
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAACCT
Found at i:133873 original size:34 final size:34
Alignment explanation
Indices: 133834--133905 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
133824 CCCTAACCCA
133834 TAAACCTTAAACCATAAAACCTTAAA-CT-CATACC
1 TAAACCTTAAA-CATAAAACCTTAAATCTAC-TACC
*
133868 TAAACCTTAAACATTAAACCTTAAATCTACTACC
1 TAAACCTTAAACATAAAACCTTAAATCTACTACC
133902 TAAA
1 TAAA
133906 ACCCTAACCT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
33 13 0.37
34 21 0.60
35 1 0.03
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (34 bp):
TAAACCTTAAACATAAAACCTTAAATCTACTACC
Found at i:133958 original size:17 final size:17
Alignment explanation
Indices: 133932--133967 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
133922 CTTCAACACT
*
133932 AAACCTTAAACCATTAA
1 AAACCCTAAACCATTAA
*
133949 AAACCCTAAACCCTTAA
1 AAACCCTAAACCATTAA
133966 AA
1 AA
133968 TAATCACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (17 bp):
AAACCCTAAACCATTAA
Found at i:133996 original size:15 final size:15
Alignment explanation
Indices: 133948--133998 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
133938 TAAACCATTA
*
133948 AAAACCCTAAACCCTT
1 AAAA-CCTAAACACTT
*
133964 AAAA--TAATCACTT
1 AAAACCTAAACACTT
*
133977 TAAACCTAAACACTT
1 AAAACCTAAACACTT
133992 AAAACCT
1 AAAACCT
133999 TAAAAATCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 10 0.36
15 14 0.50
16 4 0.14
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAACCTAAACACTT
Found at i:134002 original size:53 final size:53
Alignment explanation
Indices: 133930--134056 Score: 161
Period size: 54 Copynumber: 2.4 Consensus size: 53
133920 ACCTTCAACA
*
133930 CTAAACCTT-AAACCATTAAAAA-CCCTAAACCCTTAAAATAATCACTTTAA-AC
1 CTAAACCTTAAAACC-TTAAAAATCACTAAA-CCTTAAAATAATCACTTTAAGAC
* * *
133982 CTAAACACTTAAAACCTTAAAAATCACTAAACCTTAAACTCATCACTTTAAGCC
1 CTAAAC-CTTAAAACCTTAAAAATCACTAAACCTTAAAATAATCACTTTAAGAC
134036 CTAAATCCTTAAAACCTTAAA
1 CTAAA-CCTTAAAACCTTAAA
134057 CCTTAAGCTA
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
52 6 0.09
53 28 0.42
54 31 0.47
55 1 0.02
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (53 bp):
CTAAACCTTAAAACCTTAAAAATCACTAAACCTTAAAATAATCACTTTAAGAC
Found at i:136962 original size:25 final size:26
Alignment explanation
Indices: 136918--136969 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
136908 AACTTTCTGT
* *
136918 TTCCTTTTCTTCTTCAAAAATTTTGC
1 TTCCTTTCCTTCTTCAAAAAATTTGC
136944 TTCCTTTCCTTCTTC-AAAAATTTGC
1 TTCCTTTCCTTCTTCAAAAAATTTGC
136969 T
1 T
136970 GTTAAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.19, C:0.25, G:0.04, T:0.52
Consensus pattern (26 bp):
TTCCTTTCCTTCTTCAAAAAATTTGC
Found at i:137672 original size:15 final size:17
Alignment explanation
Indices: 137654--137700 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
137644 TTTATCGATA
137654 TATTTTTTAA-A-TTTT
1 TATTTTTTAATATTTTT
*
137669 TATTATTTAAATATTTTT
1 TATT-TTTTAATATTTTT
137687 TATTTTTTAATATT
1 TATTTTTTAATATT
137701 AATAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 5 0.19
17 10 0.37
18 8 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTTTAATATTTTT
Found at i:137710 original size:26 final size:25
Alignment explanation
Indices: 137653--137717 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
137643 TTTTATCGAT
*
137653 ATATTTTTTAAATTTTTATTATTTAA
1 ATATTTTTT-AATTTTTAATATTTAA
*
137679 ATATTTTTTATTTTTTAATATTAATAA
1 ATATTTTTTAATTTTTAATATT--TAA
137706 A-ATTTATTTAAT
1 ATATTT-TTTAAT
137718 ATTAATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 11 0.33
26 13 0.39
27 9 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATATTTTTTAATTTTTAATATTTAA
Found at i:137717 original size:20 final size:19
Alignment explanation
Indices: 137688--137728 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
137678 AATATTTTTT
137688 ATTTTTTAATATTAATAAA
1 ATTTTTTAATATTAATAAA
*
137707 ATTTATTTAATATTAATTAA
1 ATTT-TTTAATATTAATAAA
137727 AT
1 AT
137729 AAAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTTTAATATTAATAAA
Found at i:140114 original size:2 final size:2
Alignment explanation
Indices: 140107--140136 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
140097 CCCCTATTTA
140107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.