Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold16
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: 5287347
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 8769 characters in sequence are not A, C, G, or T
File 33 of 35
Found at i:4861765 original size:28 final size:28
Alignment explanation
Indices: 4861729--4861805 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
4861719 TTTTTTCACA
* *
4861729 ATCGAGGATACTCCAACCTCGTTA-TCTC
1 ATCGGGGATACTCCAACCCCGTTACT-TC
4861757 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
4861785 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
4861806 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 42 0.98
29 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:4861909 original size:79 final size:78
Alignment explanation
Indices: 4861759--4861963 Score: 207
Period size: 79 Copynumber: 2.6 Consensus size: 78
4861749 GTTATCTCAT
* * *
4861759 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCT-AAATAT
** * *
4861824 TGATTTCTCATAAT
65 CAATTTCTCACAAC
* * ** * * *
4861838 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTCT-GATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCG-GCTTTATTCCTAAAT-A
4861902 TCAATTTCTCACAAC
64 TCAATTTCTCACAAC
* * *
4861917 CGGGGATACTCCAGCCCCGCTATTTTC-AAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCCCG
4861964 TTATTATCTC
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
78 7 0.07
79 90 0.87
80 7 0.07
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCTAAATATC
AATTTCTCACAAC
Found at i:4868149 original size:61 final size:60
Alignment explanation
Indices: 4868071--4869428 Score: 1498
Period size: 55 Copynumber: 23.3 Consensus size: 60
4868061 TTAGCCCTTC
*
4868071 CCAGTCCTCAAAAAGCAGGACGCCTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* *
4868132 CCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCATTTT
* * * **
4868193 TCAGTCCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * **
4868253 -CAGTCCTCAAAGAGCAGGACACTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * *
4868312 -CAGTCCTTAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCA-TTTT
* **
4868373 -CAGTCCCCAAAGAGCAGGA--CC---TCTTTCGAAGCCCACACAAGTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * * *
4868427 CTAGTCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACTTC
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * ** *
4868482 CCAGTCCTCAGAGAGCAGGATGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * * ** *
4868543 CCAATCCTCAAAAAGCAGGATGATTTTTCTTTTCAAAGCCCACACAAGTTGGGGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCATTTT
* * **
4868604 CCAGTCCCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* *
4868664 -CAGTCCTCAAAGAGTAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* *
4868724 CCAATCCTCAAAGAGCAGGATGCC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * *
4868779 CCAATCCTCAAAGAGCAGGATGCC-TTTC----AAAGCCCACACAACTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * * *
4868834 CCAATCCTCAAAGAGCAGGATGCC-TTTC----GAAGCCCGCACAAGTTGGTGGCATTTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTT
* * *
4868890 TCAGTCCTCAAAGAGCAGGATGCC-TTTC----AAATCCCACACAAGTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * * * *
4868945 CCAATCCTCAAAGAGTAGGATGCTTTTTCTTTTCAAAGCCCATACAAGTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCATTTT
* *
4869006 CCAGTCCCCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* *
4869067 CCAATCCTCAAAGAGCAGGATGCC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * * *
4869122 CCAATCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCACTTC
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * * *
4869177 CCAGTCCTCAAAGAGCAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTC
1 CCAGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* * * *
4869238 CCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGGCCACACAAGTTGGTGGCA-CTT
1 CCAGTCCTCAAAGAGCAGGACGCCTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
* *
4869298 CCTAGTCCTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTT
1 CC-AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTT
*
4869355 -CAGTCCTCAAAGAGCAGGACGCC-TTTC----AAAGCCCACACGAGTTGGTGGCACTTTT
1 CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTT
*
4869410 -TAGTCCTCAAAGAGCAGGA
1 CCAGTCCTCAAAGAGCAGGA
4869429 TACACTTTAT
Statistics
Matches: 1152, Mismatches: 111, Indels: 74
0.86 0.08 0.06
Matches are distributed among these distances:
54 4 0.00
55 427 0.37
56 61 0.05
57 11 0.01
59 115 0.10
60 116 0.10
61 412 0.36
62 6 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (60 bp):
CCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT
Found at i:4868611 original size:232 final size:233
Alignment explanation
Indices: 4868071--4869429 Score: 1594
Period size: 232 Copynumber: 5.8 Consensus size: 233
4868061 TTAGCCCTTC
* *
4868071 CCAGTCCTCAAAAAGCAGGACGCCTTCTTCTTTT-AAAGCCCACACAAGTTGGTGGCATTTTCCA
1 CCAGTCCTCAAAGAGCAGGATGCCTTCTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
*
4868135 GTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTT-TCAGTC
66 GTCCTCAAAGAGCAGGAT-C-----CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCT-AGTC
* * *
4868199 CCCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTT-CAGTCCTCAA
124 CTCAAAGAGCAGGACGCC-TTTC----AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAA
* * * **
4868263 AGAGCAGGA--CACTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
184 AGAGCAGGATGC-CTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
* *
4868312 -CAGTCCTTAAAGAGCAGGATG-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-C
1 CCAGTCCTCAAAGAGCAGGATGCCTTCTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
4868374 AGTCCCCAAAGAGCAGGA-CCTCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAA
65 AGTCCTCAAAGAGCAGGATCC-CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAA
* * *
4868438 AGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAGAGAGCAGGA
129 AGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGA
*
4868502 TGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
193 TGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
* * * * *
4868543 CCAATCCTCAAAAAGCAGGATG-ATTTTTCTTTTCAAAGCCCACACAAGTTGGGGGCATTTTCCA
1 CCAGTCCTCAAAGAGCAGGATGCCTTCTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
* * **
4868607 GTCCCCAAAGAGCAGGA-CGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC-AGTCC
66 GTCCTCAAAGAGCAGGATC-CC-TTTC----AAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
* * *
4868670 TCAAAGAGTAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAA
125 TCAAAGAGCAGGACG----C--CTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAA
4868735 AGAGCAGGATG------CCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
184 AGAGCAGGATGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
* *
4868779 CCAATCCTCAAAGAGCAGGATG----C--C-TTTCAAAGCCCACACAACTTGGTGGCATTTTCCA
1 CCAGTCCTCAAAGAGCAGGATGCCTTCTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
* * * * *
4868837 ATCCTCAAAGAGCAGGATGCCTTTCGAAGCCCGCACAAGTTGGTGGCATTTTTTCAGTCCTCAAA
66 GTCCTCAAAGAGCAGGATCCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCT-AGTCCTCAAA
* * * * *
4868902 GAGCAGGATGCCTTTCAAATCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGTAGGATG
130 GAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGATG
* * * *
4868967 CTTTTTCTTTTCAAAGCCCATACAAGTTGGTGGCATTTT
195 CCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
* *
4869006 CCAGTCCCCAAAGAGCAGGACGCCTTCTTC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
1 CCAGTCCTCAAAGAGCAGGATGCCTTCTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
* * * *
4869070 ATCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAG
66 GTCCTCAAAGAGCAGGATCCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAG
* * **
4869135 AGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACAC
131 AGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGATGC
* * *
4869200 CTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTC
196 CTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
* * *
4869238 CCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTT-AAAGGCCACACAAGTTGGTGGCA-CTTCCT
1 CCAGTCCTCAAAGAGCAGGATGCCTTCTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC-
*
4869301 AGTCCTCAAAGAGCAGGA-CACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTC
65 AGTCCTCAAAGAGCAGGATC-CCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTC
* **
4869363 AAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGG
127 AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGG
4869428 AT
192 AT
4869430 ACACTTTATT
Statistics
Matches: 982, Mismatches: 93, Indels: 95
0.84 0.08 0.08
Matches are distributed among these distances:
221 52 0.05
223 1 0.00
225 22 0.02
227 68 0.07
229 28 0.03
230 67 0.07
231 42 0.04
232 329 0.34
233 100 0.10
234 52 0.05
235 1 0.00
236 72 0.07
237 24 0.02
238 1 0.00
239 10 0.01
240 60 0.06
241 6 0.01
242 47 0.05
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (233 bp):
CCAGTCCTCAAAGAGCAGGATGCCTTCTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
GTCCTCAAAGAGCAGGATCCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAG
AGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGATGC
CTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
Found at i:4868751 original size:27 final size:27
Alignment explanation
Indices: 4868721--4868861 Score: 76
Period size: 27 Copynumber: 5.1 Consensus size: 27
4868711 TTGGTGGCAT
4868721 TTTCCAATCCTCAAAGAGCAGGATGCC
1 TTTCCAATCCTCAAAGAGCAGGATGCC
* * ** *
4868748 TTTCAAAGCC-CACACA-AGTTGG-TGGCAT
1 TTTCCAATCCTCA-A-AGAGCAGGAT-GC-C
4868776 TTTCCAATCCTCAAAGAGCAGGATGCC
1 TTTCCAATCCTCAAAGAGCAGGATGCC
* * * * * * *
4868803 TTTCAAAGCC-CACACAACTTGG-TGGCAT
1 TTTCCAATCCTCAAAGAGC-AGGAT-GC-C
4868831 TTTCCAATCCTCAAAGAGCAGGATGCC
1 TTTCCAATCCTCAAAGAGCAGGATGCC
4868858 TTTC
1 TTTC
4868862 GAAGCCCGCA
Statistics
Matches: 78, Mismatches: 24, Indels: 24
0.62 0.19 0.19
Matches are distributed among these distances:
26 9 0.12
27 32 0.41
28 28 0.36
29 9 0.12
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.25
Consensus pattern (27 bp):
TTTCCAATCCTCAAAGAGCAGGATGCC
Found at i:4870156 original size:21 final size:21
Alignment explanation
Indices: 4870109--4870166 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
4870099 AAAATTTATC
*
4870109 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
4870130 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
4870151 CAAATGTATCGATACA
1 CAAATGTATCGATACA
4870167 GGGTCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:4870226 original size:19 final size:20
Alignment explanation
Indices: 4870202--4870255 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
4870192 AATTCAACAA
4870202 TTTGTATCGATACATA-AGT-
1 TTTGTATCGATACATAGA-TC
* *
4870221 TTTGTATCGATAGATGGATC
1 TTTGTATCGATACATAGATC
4870241 TTTGTATCGATACAT
1 TTTGTATCGATACAT
4870256 TTGGAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.43
Consensus pattern (20 bp):
TTTGTATCGATACATAGATC
Found at i:4872689 original size:51 final size:52
Alignment explanation
Indices: 4872613--4872712 Score: 157
Period size: 51 Copynumber: 1.9 Consensus size: 52
4872603 CAATTCTCCG
* * * *
4872613 TAATCGGGGATATTCCATCTCCGATTTTATTTTC-AAAACACTAATTTTCTA
1 TAATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTCTA
4872664 TAATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTT
1 TAATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTT
4872713 TTTCACAATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 31 0.70
52 13 0.30
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (52 bp):
TAATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTCTA
Found at i:4872756 original size:28 final size:28
Alignment explanation
Indices: 4872720--4872796 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
4872710 TTTTTTCACA
* *
4872720 ATCGAGGATACTCCAACCTCGTTA-TCTC
1 ATCGGGGATACTCCAACCCCGTTACT-TC
4872748 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
4872776 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
4872797 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 42 0.98
29 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:4883196 original size:174 final size:174
Alignment explanation
Indices: 4882906--4883239 Score: 490
Period size: 174 Copynumber: 1.9 Consensus size: 174
4882896 TGGATTACCA
* * *
4882906 TTTGAGAGGTATTAAGCACCAAATAAACTTCATTCCCGATTCATCAATCCTTAATAGACCAGCAT
1 TTTGAGAGGTATTAAGAACCAAATAAACTTCATTCCAGATTCATCAATCCTTAATAGACCAACAT
* * * * *
4882971 ATAGAGCAAATCTTGAGGAGACAAAGGAAATTTAAAAGTAAGTGGATGAATTAGTGCAAAGGGGA
66 ATAGAGCAAATCCTGAGGAGACAAAAGAAATTCAAAAGCAAGTGGATGAATTAGTGCAAAAGGGA
* * *
4883036 TTCGTAAGAGAGAGTCTTGGTCCATGTTCTATTTCTATACCTCT
131 TCCGTAAGAAAGAGTCTTAGTCCATGTTCTATTTCTATACCTCT
* * * * *
4883080 TTTGAGAGGTATTGAGAACCAAGTAGACTTCATTCTCAG-TTCATTAATCCTTAATAGACTAACA
1 TTTGAGAGGTATTAAGAACCAAATAAACTTCATTC-CAGATTCATCAATCCTTAATAGACCAACA
* *
4883144 TATAGAGCAAATCCTGAGGAGACAAAAGAGATTCAAAGGCAAGTGGATGAATTAGTGCAAAAGGG
65 TATAGAGCAAATCCTGAGGAGACAAAAGAAATTCAAAAGCAAGTGGATGAATTAGTGCAAAAGGG
4883209 ATCCGTAAGAAAGAGTCTTAGTCCATGTTCT
130 ATCCGTAAGAAAGAGTCTTAGTCCATGTTCT
4883240 GTTCTTGTGA
Statistics
Matches: 141, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
174 139 0.99
175 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (174 bp):
TTTGAGAGGTATTAAGAACCAAATAAACTTCATTCCAGATTCATCAATCCTTAATAGACCAACAT
ATAGAGCAAATCCTGAGGAGACAAAAGAAATTCAAAAGCAAGTGGATGAATTAGTGCAAAAGGGA
TCCGTAAGAAAGAGTCTTAGTCCATGTTCTATTTCTATACCTCT
Found at i:4887236 original size:20 final size:21
Alignment explanation
Indices: 4887204--4887244 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4887194 GGAGGTGCTG
4887204 AACATGCTAT-AAATGCATGA
1 AACATGCTATAAAATGCATGA
4887224 AACATAGCT-TAAAATGCATGA
1 AACAT-GCTATAAAATGCATGA
4887245 TTCATGGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (21 bp):
AACATGCTATAAAATGCATGA
Found at i:4888248 original size:52 final size:52
Alignment explanation
Indices: 4888098--4888228 Score: 235
Period size: 52 Copynumber: 2.5 Consensus size: 52
4888088 CCCGAAATAT
4888098 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
* *
4888150 GAAAATTTGCCTGTATGTATCAATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
*
4888202 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
4888229 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
Found at i:4888255 original size:13 final size:13
Alignment explanation
Indices: 4888237--4888261 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4888227 CAAAGATCAG
4888237 TGTATCGATACAA
1 TGTATCGATACAA
4888250 TGTATCGATACA
1 TGTATCGATACA
4888262 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4888324 original size:13 final size:13
Alignment explanation
Indices: 4888306--4888357 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
4888296 AGCTTCATAG
4888306 CGATACATTGTAT
1 CGATACATTGTAT
4888319 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
4888338 CGATACATTGTAT
1 CGATACATTGTAT
4888351 CGATACA
1 CGATACA
4888358 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:4897108 original size:167 final size:167
Alignment explanation
Indices: 4896793--4897096 Score: 434
Period size: 167 Copynumber: 1.8 Consensus size: 167
4896783 TACTAGAAGA
* * *
4896793 AATTTATTTTCCATTCTTTTGCTATACTCTATGAAGGCATACTTTAACATCTAAAATGTTGGAGG
1 AATTTATTTTCCATTCTTTTGCTATACTCTATGAAGGCATACTTTAACATCTAAAATATTGAAGA
4896858 GTGATTTCTAAATATGTTAAAACAATTGTTTTAGTGTGCCTAAAAACCTCTCTCTATAAGGTGAC
66 GTGATTTCTAAATATGTTAAAACAATTGTTTTAGTGTGCCTAAAAACCTCTCTCTATAAGGTGAC
4896923 TTTTAAACTAAAAATTCAATTTTTTTTTGCGAGGGAG
131 TTTTAAACTAAAAATTCAATTTTTTTTTGCGAGGGAG
* * * * * * *
4896960 AATTTGTTTTTCATTCTTTTGCTATACTTTATGAAGGTGAT-TTTTAATATTTAAAATATTGAAG
1 AATTTATTTTCCATTCTTTTGCTATACTCTATGAAGG-CATACTTTAACATCTAAAATATTGAAG
* * *
4897024 AGTGATTTCTAAGTATGTTAAAAC-ATTTTTTTAGTGTGCCTAAAAACCTC-CTTCTATAAATGT
65 AGTGATTTCTAAATATGTTAAAACAATTGTTTTAGTGTGCCTAAAAACCTCTC-TCTAT-AAGGT
*
4897087 GATTTTTAAA
128 GACTTTTAAA
4897097 TTGGAAATTC
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
165 1 0.01
166 30 0.25
167 87 0.73
168 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (167 bp):
AATTTATTTTCCATTCTTTTGCTATACTCTATGAAGGCATACTTTAACATCTAAAATATTGAAGA
GTGATTTCTAAATATGTTAAAACAATTGTTTTAGTGTGCCTAAAAACCTCTCTCTATAAGGTGAC
TTTTAAACTAAAAATTCAATTTTTTTTTGCGAGGGAG
Found at i:4898076 original size:34 final size:34
Alignment explanation
Indices: 4898038--4898103 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
4898028 ATGAACATGC
*
4898038 ATAAATCCATCCAAGCATA-CATACATACATATAT
1 ATAAATCCATCCAACCA-AGCATACATACATATAT
*
4898072 ATAAATCCATCCATCCAAGCATACATACATAT
1 ATAAATCCATCCAACCAAGCATACATACATAT
4898104 GTATGTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.26
Consensus pattern (34 bp):
ATAAATCCATCCAACCAAGCATACATACATATAT
Found at i:4902415 original size:16 final size:15
Alignment explanation
Indices: 4902370--4902442 Score: 76
Period size: 16 Copynumber: 4.6 Consensus size: 15
4902360 TGATTTTGAA
4902370 TTAAATTAATTTAAAT
1 TTAAATTAA-TTAAAT
*
4902386 ATTAAAATT-TTTAAAT
1 -TT-AAATTAATTAAAT
*
4902402 TTAAATTATATTAATT
1 TTAAATTA-ATTAAAT
4902418 TTAAATTAATTAAAT
1 TTAAATTAATTAAAT
4902433 TTAAAATTAA
1 TT-AAATTAA
4902443 ATTATTTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
14 5 0.10
15 10 0.21
16 26 0.54
17 2 0.04
18 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAAATTAATTAAAT
Found at i:4902417 original size:15 final size:14
Alignment explanation
Indices: 4902399--4902456 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 14
4902389 AAAATTTTTA
4902399 AATTTAAATTATATT
1 AATTTAAATTA-ATT
4902414 AATTTTAAATTAATT
1 AA-TTTAAATTAATT
4902429 AAATTTAAAATTAAATT
1 -AATTT-AAATT-AATT
*
4902446 -ATTTCAATTAA
1 AATTTAAATTAA
4902457 AATTGATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 2 0.05
14 4 0.11
15 12 0.32
16 16 0.42
17 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTAAATTAATT
Found at i:4902454 original size:21 final size:20
Alignment explanation
Indices: 4902368--4902460 Score: 60
Period size: 21 Copynumber: 4.2 Consensus size: 20
4902358 ATTGATTTTG
4902368 AATTAAATTAATTTAAATATTAA
1 AATTAAATTAA-TT-AA-ATTAA
*
4902391 AATTTTTAAATTTAAATTATATTAA
1 AA---TTAAA-TT-AATTAAATTAA
**
4902416 TTTTAAATTAATTAAATTTAA
1 AATTAAATTAATTAAA-TTAA
* *
4902437 AATTAAATTATTTCAATTAA
1 AATTAAATTAATTAAATTAA
4902457 AATT
1 AATT
4902461 GATCAAGTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
20 14 0.25
21 18 0.32
22 5 0.09
23 2 0.04
25 5 0.09
26 6 0.11
27 4 0.07
28 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTAAATTAATTAAATTAA
Found at i:4902543 original size:31 final size:33
Alignment explanation
Indices: 4902502--4902570 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
4902492 AAAAATATTT
* *
4902502 AGATTTAATTTAT-T-AATTTTAAAATCAAATC
1 AGATTAAATTTATATAAATTATAAAATCAAATC
**
4902533 AGATTAAATTTATATAAATTATCTAATCAAATC
1 AGATTAAATTTATATAAATTATAAAATCAAATC
4902566 AGATT
1 AGATT
4902571 TTATTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 12 0.38
32 1 0.03
33 19 0.59
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (33 bp):
AGATTAAATTTATATAAATTATAAAATCAAATC
Found at i:4902992 original size:15 final size:15
Alignment explanation
Indices: 4902974--4903004 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4902964 CCATGGATTG
4902974 ATAGGAGAGACCCAC
1 ATAGGAGAGACCCAC
4902989 ATAGGAGAGACCCAC
1 ATAGGAGAGACCCAC
4903004 A
1 A
4903005 CCTGAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.26, T:0.06
Consensus pattern (15 bp):
ATAGGAGAGACCCAC
Found at i:4903394 original size:30 final size:27
Alignment explanation
Indices: 4903321--4903380 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
4903311 TTGGGTCGTG
4903321 GTAGGATATGATGGGTATAGAGGTTGA
1 GTAGGATATGATGGGTATAGAGGTTGA
*
4903348 GTAGGATATGATGGGTATGGAGGTTGA
1 GTAGGATATGATGGGTATAGAGGTTGA
4903375 GTAGGA
1 GTAGGA
4903381 AAATATGGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.43, T:0.28
Consensus pattern (27 bp):
GTAGGATATGATGGGTATAGAGGTTGA
Found at i:4903502 original size:15 final size:15
Alignment explanation
Indices: 4903480--4903520 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
4903470 TGGATAAACA
4903480 GGTGGTGGATGCA-T
1 GGTGGTGGATGCACT
*
4903494 GGGTTGTGGATGCACT
1 -GGTGGTGGATGCACT
4903510 GGTGGTGGATG
1 GGTGGTGGATG
4903521 GACAGGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 22 0.96
16 1 0.04
ACGTcount: A:0.12, C:0.07, G:0.51, T:0.29
Consensus pattern (15 bp):
GGTGGTGGATGCACT
Found at i:4908408 original size:15 final size:15
Alignment explanation
Indices: 4908388--4908424 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4908378 TTTTGTACTA
4908388 TAAACTAATTACCCT
1 TAAACTAATTACCCT
*
4908403 TAAACTTATTACCCT
1 TAAACTAATTACCCT
*
4908418 AAAACTA
1 TAAACTA
4908425 TTTCAACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAACTAATTACCCT
Found at i:4908683 original size:21 final size:21
Alignment explanation
Indices: 4908657--4908699 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
4908647 TTAGAGAGAT
4908657 AAGAGAA-TTGAGAAAATTTTA
1 AAGAGAAGTT-AGAAAATTTTA
4908678 AAGAGAAGTTAGAAAATTTTA
1 AAGAGAAGTTAGAAAATTTTA
4908699 A
1 A
4908700 GAGTAGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (21 bp):
AAGAGAAGTTAGAAAATTTTA
Found at i:4909773 original size:15 final size:17
Alignment explanation
Indices: 4909735--4909769 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4909725 CTTTTAGAAG
*
4909735 TATTTTGATAATTTTTA
1 TATTATGATAATTTTTA
4909752 TATTATGATAATTTTTA
1 TATTATGATAATTTTTA
4909769 T
1 T
4909770 TATGTTAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (17 bp):
TATTATGATAATTTTTA
Found at i:4911541 original size:15 final size:16
Alignment explanation
Indices: 4911521--4911551 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4911511 AATTATATTG
4911521 TATTTA-AAATTATCA
1 TATTTATAAATTATCA
4911536 TATTTATAAATTATCA
1 TATTTATAAATTATCA
4911552 ATTATCTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTATAAATTATCA
Found at i:4917867 original size:20 final size:19
Alignment explanation
Indices: 4917828--4917868 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
4917818 AAAGATCCTT
*
4917828 AATATGTTAAAAGGCCTAA
1 AATATGTTAAAAGGCATAA
*
4917847 AATATGTTTAAAATGCATAA
1 AATATG-TTAAAAGGCATAA
4917867 AA
1 AA
4917869 CAATTCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (19 bp):
AATATGTTAAAAGGCATAA
Found at i:4919385 original size:1 final size:1
Alignment explanation
Indices: 4919381--4919416 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
4919371 TTTTTTTTTT
* *
4919381 AAAAAAAAAATAAAATAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4919417 TTCCAAATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.94, C:0.00, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:4919468 original size:20 final size:20
Alignment explanation
Indices: 4919416--4919497 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 20
4919406 AAAAAAAAAA
4919416 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
4919435 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
4919456 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
4919476 ATTCTACAAATGTATCGATAC
1 ATTC-ACAAATGTATCGATAC
4919497 A
1 A
4919498 GGGTCCCAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.05
20 18 0.33
21 34 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:4919477 original size:41 final size:40
Alignment explanation
Indices: 4919416--4919497 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
4919406 AAAAAAAAAA
* *
4919416 ATTCCAAATGTATCGATACATTTGTA-GAATGTATCGATAC
1 ATTCCAAATGTATCGATACA-TTCTACAAATGTATCGATAC
4919456 ATTCACAAATGTATCGATACATTCTACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATTCTACAAATGTATCGATAC
4919497 A
1 A
4919498 GGGTCCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTCTACAAATGTATCGATAC
Found at i:4919557 original size:19 final size:19
Alignment explanation
Indices: 4919533--4919600 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
4919523 AATTCAACAA
4919533 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
4919552 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
4919567 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
4919584 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
4919601 TTGGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:4919572 original size:13 final size:13
Alignment explanation
Indices: 4919554--4919578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4919544 ACATAAGTTT
4919554 TGTATCGATACAA
1 TGTATCGATACAA
4919567 TGTATCGATACA
1 TGTATCGATACA
4919579 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4919576 original size:32 final size:32
Alignment explanation
Indices: 4919535--4919597 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4919525 TTCAACAATT
*
4919535 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
4919567 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
4919598 TAATTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:4919658 original size:13 final size:13
Alignment explanation
Indices: 4919640--4919665 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4919630 CATTTTTCTG
4919640 TGTATCGATACAT
1 TGTATCGATACAT
4919653 TGTATCGATACAT
1 TGTATCGATACAT
4919666 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4919662 original size:33 final size:33
Alignment explanation
Indices: 4919620--4919686 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4919610 GCCAAGGAAA
***
4919620 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
4919653 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
4919686 T
1 T
4919687 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:4922132 original size:52 final size:54
Alignment explanation
Indices: 4922023--4922154 Score: 155
Period size: 52 Copynumber: 2.5 Consensus size: 54
4922013 AGTTGCTCAA
* * * **
4922023 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTACTTTCAAAAACATTAATT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTACTTTCAAAAACACCAATT
*
4922077 TTC-T-ATAATCGGGGATACTCCAACTCCGATTTTA-TTTCCAAAAAACACCAA-T
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTACTTT-C-AAAAACACCAATT
*
4922129 TTCTTCACAATCGGGGACACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
4922155 CCCGTTAATC
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
51 3 0.05
52 32 0.48
53 10 0.15
54 21 0.32
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.31
Consensus pattern (54 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTACTTTCAAAAACACCAATT
Found at i:4922208 original size:28 final size:27
Alignment explanation
Indices: 4922141--4922213 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
4922131 CTTCACAATC
*
4922141 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGACACTCCAACCCCGTTAATCATA
*
4922168 GGGGACACTCCAACCCCGTTATTTC-TGA
1 GGGGACACTCCAACCCCGTTA-ATCAT-A
*
4922196 GGGGATACTCCAACCCCG
1 GGGGACACTCCAACCCCG
4922214 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.23, C:0.36, G:0.22, T:0.19
Consensus pattern (27 bp):
GGGGACACTCCAACCCCGTTAATCATA
Found at i:4922258 original size:51 final size:51
Alignment explanation
Indices: 4922196--4922366 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
4922186 TTATTTCTGA
* * *
4922196 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
4922247 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
4922300 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
4922352 GAGGATACTCCAACC
1 GGGGATACTCCAACC
4922367 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:4922385 original size:28 final size:28
Alignment explanation
Indices: 4922349--4922430 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
4922339 ATTTTTCACA
*
4922349 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
4922377 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
4922405 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
4922431 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:4922474 original size:213 final size:212
Alignment explanation
Indices: 4922031--4922459 Score: 519
Period size: 212 Copynumber: 2.0 Consensus size: 212
4922021 AATTCTCCAC
* * **
4922031 AATCGAGGATATTCCAACTCCGATTTTACTTTCAAAAACATTAATTTTCTATAATCGGGGATACT
1 AATCGGGGATATTCCAACCCCGATTTTACTTTCAAAAACACCAATTTTCTATAATCGGGGATACT
*
4922096 CCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTT
66 CCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTT
* * * * * *
4922161 AATCATCGGGGACACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTTTCA
131 AATCATCGGGGACACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATCTCCA
* **
4922226 AAATATCGATTTTTCAT
196 AAACATCGAAATTTCAT
* * * * *
4922243 AATCGGGGATACTCCAACCCCGGTTTTATTTTC-ACAACACCAATTTCTCCTTTAATCGGGGATA
1 AATCGGGGATATTCCAACCCCGATTTTACTTTCAAAAACACCAATTT-T-CTATAATCGGGGATA
* * * *
4922307 CTCCAATTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCG
64 CTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCG
* * * *
4922370 TTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCTCG-TTATTATC
129 TTA-ATCATCGGGGACACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACT-TTATC
*
4922434 TCCAAAACAT-TAAATTTC-T
192 TCCAAAACATCGAAATTTCAT
*
4922453 CATCGGG
1 AATCGGG
4922460 AAATATATTC
Statistics
Matches: 184, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
210 7 0.04
211 43 0.23
212 99 0.54
213 35 0.19
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
AATCGGGGATATTCCAACCCCGATTTTACTTTCAAAAACACCAATTTTCTATAATCGGGGATACT
CCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGACACTCCAACCCCGTT
AATCATCGGGGACACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATCTCCA
AAACATCGAAATTTCAT
Found at i:4925395 original size:41 final size:41
Alignment explanation
Indices: 4925350--4925431 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
4925340 CTTCAAGGAA
4925350 TAACAATAAAGAATACAAAAGCTCTTTGAAAAGTAGAAAAT
1 TAACAATAAAGAATACAAAAGCTCTTTGAAAAGTAGAAAAT
4925391 TAACAATAAAGAATACAAAAGCTCTTTGAAAAGTAGAAAAT
1 TAACAATAAAGAATACAAAAGCTCTTTGAAAAGTAGAAAAT
4925432 GATAGAACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (41 bp):
TAACAATAAAGAATACAAAAGCTCTTTGAAAAGTAGAAAAT
Found at i:4925781 original size:20 final size:19
Alignment explanation
Indices: 4925756--4925808 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
4925746 TGCCAGTTTC
* *
4925756 ATGTATCGATACAATTCACT
1 ATGTATCGATACAA-GCAAT
4925776 ATGTATCGATACTAAGCAAT
1 ATGTATCGATAC-AAGCAAT
4925796 ATGTATCGATACA
1 ATGTATCGATACA
4925809 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 27 0.90
21 2 0.07
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACAAGCAAT
Found at i:4930263 original size:3 final size:3
Alignment explanation
Indices: 4930255--4930306 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
4930245 TTCATCTGAG
* *
4930255 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA CCA TTA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
4930303 TCA T
1 TCA T
4930307 ATTTGATGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:4931931 original size:32 final size:33
Alignment explanation
Indices: 4931888--4931950 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
4931878 ACAATTCACT
*
4931888 ATGTATCGATACCAAG-AACATGTATCGATATA
1 ATGTATAGATACCAAGCAACATGTATCGATATA
* *
4931920 ATGTATAGATACTAAGCAATATGTATCGATA
1 ATGTATAGATACCAAGCAACATGTATCGATA
4931951 CATTTAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATAGATACCAAGCAACATGTATCGATATA
Found at i:4932073 original size:20 final size:21
Alignment explanation
Indices: 4932048--4932087 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
4932038 GATACTTTGG
4932048 ATTATTTTTA-ACTTGAAAAC
1 ATTATTTTTATACTTGAAAAC
*
4932068 ATTATTTTTATGCTTGAAAA
1 ATTATTTTTATACTTGAAAA
4932088 ATATTTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
ATTATTTTTATACTTGAAAAC
Found at i:4934420 original size:66 final size:66
Alignment explanation
Indices: 4934256--4934408 Score: 189
Period size: 66 Copynumber: 2.3 Consensus size: 66
4934246 ATTCTAAATG
** * *
4934256 ATTTAAAATTTTAAATTTAAATTATATATTATTTTGATTTAATCTCATTAAATCTAAAATATTCA
1 ATTTAAAA-TTTAAATTTAAATTATATATTATCATGATTAAATCTCATTAAATCTAAAATATCCA
4934321 AA
65 AA
* * * ** * * *
4934323 ACTCAAAATTTAAATCTAAATTGGATATTATCATGATTAAATCTTATTGAATCTTAAATATCCAA
1 ATTTAAAATTTAAATTTAAATTATATATTATCATGATTAAATCTCATTAAATCTAAAATATCCAA
4934388 A
66 A
4934389 ATTTAAAATTTAAATTTAAA
1 ATTTAAAATTTAAATTTAAA
4934409 GTTTATCTTA
Statistics
Matches: 71, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
66 65 0.92
67 6 0.08
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (66 bp):
ATTTAAAATTTAAATTTAAATTATATATTATCATGATTAAATCTCATTAAATCTAAAATATCCAA
A
Found at i:4939265 original size:22 final size:22
Alignment explanation
Indices: 4939237--4939291 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
4939227 TGGACATGTT
4939237 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
4939259 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
4939281 AAAAATGCATG
1 AAAAATGCATG
4939292 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:4940251 original size:20 final size:20
Alignment explanation
Indices: 4940204--4940278 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
4940194 AAAAAGACAT
*
4940204 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
4940223 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
4940244 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
4940264 AATGTATCGATACAT
1 AATGTATCGATACAT
4940279 CAGGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:4940272 original size:40 final size:39
Alignment explanation
Indices: 4940201--4940278 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
4940191 GGTAAAAAGA
* *
4940201 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
4940240 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
4940279 CAGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:4942009 original size:13 final size:13
Alignment explanation
Indices: 4941991--4942018 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4941981 GCTAAACCTC
4941991 ACTTTGTATCGAT
1 ACTTTGTATCGAT
4942004 ACTTTGTATCGAT
1 ACTTTGTATCGAT
4942017 AC
1 AC
4942019 ATACTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (13 bp):
ACTTTGTATCGAT
Found at i:4943623 original size:3 final size:3
Alignment explanation
Indices: 4943615--4943648 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
4943605 TCAACCATCA
**
4943615 ATG ATG ATG AAA ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
4943649 AGAAGAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:4958645 original size:13 final size:13
Alignment explanation
Indices: 4958627--4958652 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4958617 TGCTAGTTTC
4958627 ATGTATCGATACA
1 ATGTATCGATACA
4958640 ATGTATCGATACA
1 ATGTATCGATACA
4958653 TCTGAAAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4966490 original size:32 final size:32
Alignment explanation
Indices: 4966447--4966529 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
4966437 CAAGTTAATT
* *
4966447 GTTTGGGTCATTTC-GAGTTTGGATCATTTTGG
1 GTTTAGGTCATTTCAG-GTTTGGATCATTTTAG
*
4966479 GTTTAGGTCATTTCAGGTTTGGGTCATTTTAG
1 GTTTAGGTCATTTCAGGTTTGGATCATTTTAG
** *
4966511 GTTCGGGTTATTTCAGGTT
1 GTTTAGGTCATTTCAGGTT
4966530 CAGCTTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
32 43 0.98
33 1 0.02
ACGTcount: A:0.13, C:0.10, G:0.30, T:0.47
Consensus pattern (32 bp):
GTTTAGGTCATTTCAGGTTTGGATCATTTTAG
Found at i:4966512 original size:16 final size:16
Alignment explanation
Indices: 4966447--4966529 Score: 78
Period size: 16 Copynumber: 5.2 Consensus size: 16
4966437 CAAGTTAATT
*
4966447 GTTTGGGTCA-TTTCG
1 GTTTGGGTCATTTTAG
* *
4966462 AGTTTGGATCATTTTGG
1 -GTTTGGGTCATTTTAG
* *
4966479 GTTTAGGTCATTTCAG
1 GTTTGGGTCATTTTAG
4966495 GTTTGGGTCATTTTAG
1 GTTTGGGTCATTTTAG
* * *
4966511 GTTCGGGTTATTTCAG
1 GTTTGGGTCATTTTAG
4966527 GTT
1 GTT
4966530 CAGCTTATTT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
16 51 0.93
17 4 0.07
ACGTcount: A:0.13, C:0.10, G:0.30, T:0.47
Consensus pattern (16 bp):
GTTTGGGTCATTTTAG
Found at i:4969359 original size:74 final size:73
Alignment explanation
Indices: 4969262--4969401 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 73
4969252 AAATAATCCG
* * *
4969262 AAAGGTTCAATATTAATGTAAAAATATTAAAATAA-CCTAAAAGCTCGATTTTAGCATGAAAGTG
1 AAAGGTTCAATATTAACGTAAAAATACTAAAATAATCCTAAAAGCT-GACTTTA-CATGAAAGTG
4969326 CTAGCACGAT
64 CTAGCACGAT
* * * *
4969336 AAAGGTTCAATTTTAACGTAAAAATACTAAAATAATCCTAGAGGCTTACTTTACATGAAAGTGCT
1 AAAGGTTCAATATTAACGTAAAAATACTAAAATAATCCTAAAAGCTGACTTTACATGAAAGTGCT
4969401 A
66 A
4969402 AAAATAACCC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
73 13 0.22
74 37 0.64
75 8 0.14
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (73 bp):
AAAGGTTCAATATTAACGTAAAAATACTAAAATAATCCTAAAAGCTGACTTTACATGAAAGTGCT
AGCACGAT
Found at i:4972670 original size:19 final size:19
Alignment explanation
Indices: 4972644--4972680 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4972634 AATAAATAAT
4972644 TTTAAAATA-CAAAATTTA
1 TTTAAAATACCAAAATTTA
4972662 TTTATAAATACCAAAATTT
1 TTTA-AAATACCAAAATTT
4972681 TAAATAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAAAATACCAAAATTTA
Found at i:4973843 original size:27 final size:27
Alignment explanation
Indices: 4973822--4973924 Score: 111
Period size: 27 Copynumber: 3.8 Consensus size: 27
4973812 AATTAGTAAT
* *
4973822 TTTATGTGT-AAAGTTTTAATTAAAAA
1 TTTATATGTAAAAATTTTAATTAAAAA
4973848 TTTATATGTAAAAATTTTAATTAAAAAA
1 TTTATATGTAAAAATTTTAATT-AAAAA
* * *
4973876 TTTATGTATAAAAAGTTTAATTAAAAA
1 TTTATATGTAAAAATTTTAATTAAAAA
* *
4973903 TTT-TATATATAAAAGTTTAATT
1 TTTATATGTA-AAAATTTTAATT
4973925 TTTTTTTTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 13 0.19
27 31 0.46
28 24 0.35
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (27 bp):
TTTATATGTAAAAATTTTAATTAAAAA
Found at i:4973861 original size:14 final size:13
Alignment explanation
Indices: 4973836--4973921 Score: 70
Period size: 14 Copynumber: 6.3 Consensus size: 13
4973826 TGTGTAAAGT
4973836 TTTA-ATTAAAAA
1 TTTATATTAAAAA
4973848 TTTATATGTAAAAA
1 TTTATAT-TAAAAA
4973862 TTT-TAATTAAAAAA
1 TTTAT-ATT-AAAAA
*
4973876 TTTATGTATAAAAA
1 TTTATAT-TAAAAA
4973890 GTTTA-ATTAAAAA
1 -TTTATATTAAAAA
*
4973903 TTTTATATATAAAAG
1 -TTTATAT-TAAAAA
4973918 TTTA
1 TTTA
4973922 ATTTTTTTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
12 4 0.07
13 14 0.23
14 32 0.52
15 11 0.18
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (13 bp):
TTTATATTAAAAA
Found at i:4973872 original size:13 final size:13
Alignment explanation
Indices: 4973835--4973907 Score: 76
Period size: 13 Copynumber: 5.4 Consensus size: 13
4973825 ATGTGTAAAG
4973835 TTTTAATTAAAAA
1 TTTTAATTAAAAA
4973848 -TTTATATGTAAAAA
1 TTTTA-AT-TAAAAA
4973862 TTTTAATTAAAAA
1 TTTTAATTAAAAA
* *
4973875 ATTTATGTATAAAAA
1 TTTTA-AT-TAAAAA
*
4973890 GTTTAATTAAAAA
1 TTTTAATTAAAAA
4973903 TTTTA
1 TTTTA
4973908 TATATAAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
12 4 0.08
13 22 0.44
14 10 0.20
15 14 0.28
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (13 bp):
TTTTAATTAAAAA
Found at i:4973874 original size:28 final size:27
Alignment explanation
Indices: 4973831--4973924 Score: 118
Period size: 28 Copynumber: 3.4 Consensus size: 27
4973821 TTTTATGTGT
*
4973831 AAAGTTTTAATT-AAAAATTTATATGTAA
1 AAAG-TTTAATTAAAAAATTTATATAT-A
* *
4973859 AAATTTTAATTAAAAAATTTATGTATAA
1 AAAGTTTAATTAAAAAATTTATATAT-A
*
4973887 AAAGTTTAATTAAAAATTTTATATATA
1 AAAGTTTAATTAAAAAATTTATATATA
4973914 AAAGTTTAATT
1 AAAGTTTAATT
4973925 TTTTTTTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
27 19 0.32
28 40 0.68
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (27 bp):
AAAGTTTAATTAAAAAATTTATATATA
Found at i:4974078 original size:27 final size:27
Alignment explanation
Indices: 4974040--4974104 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
4974030 AAGTAAAAGG
*
4974040 TTTAATTAAAAATTCGAT-ATGTGAAAA
1 TTTAATTAAAAATT-GATCATATGAAAA
**
4974067 TTTAATTAAAAATTTTTCATATGAAAA
1 TTTAATTAAAAATTGATCATATGAAAA
4974094 TTTAATTAAAA
1 TTTAATTAAAA
4974105 GCTAAATTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (27 bp):
TTTAATTAAAAATTGATCATATGAAAA
Found at i:4976184 original size:6 final size:6
Alignment explanation
Indices: 4976173--4976197 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4976163 TATAAATTAA
4976173 TTAAAT TTAAAT TTAAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT T
4976198 GGATATAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:4979001 original size:204 final size:203
Alignment explanation
Indices: 4978643--4979017 Score: 682
Period size: 204 Copynumber: 1.8 Consensus size: 203
4978633 GTCAAATCCT
4978643 TTTACTTGGCACTGTTAACATGATATTTATAAAAATTATAACTAAAATAAATTTAAATATACCAT
1 TTTACTTGGCACTGTTAACATGATATTTATAAAAATTATAACTAAAATAAATTTAAATATACCAT
4978708 CCTTTTCTGTTTGCTAAGATATTTATTATTTTTTACATTCTGTTTGCAATTTTTTTAATACAATT
66 CCTTTTCTGTTTGCTAAGATATTTATTATTTTTTACATTCTGTTTGCAATTTTTTTAATACAATT
4978773 GTCTCTCTTTCTGTATTTTGGTGGTTAACTAGTATATGAAATTTATCTTAATTTTATATTATTTA
131 GTCTCTCTTTCTGTATTTTGGTGGTTAACTAGTATATGAAATTTATCTTAATTTTATATTATTTA
4978838 TGAATTGA
196 TGAATTGA
*
4978846 TTTA-TTGGCCACTGTTAATATGATATTTATAAAAATTATAACTAAAA-AAATTTAAATATACCA
1 TTTACTTGG-CACTGTTAACATGATATTTATAAAAATTATAACTAAAATAAATTTAAATATACCA
*
4978909 TCCTTTTCTGTTTTTGCTAAGATATTTATTATTTTTTACATTCTGTTTGCAATTTTTTTAATGCA
65 TCCTTTTCTG--TTTGCTAAGATATTTATTATTTTTTACATTCTGTTTGCAATTTTTTTAATACA
*
4978974 TTTGTCTCTCTTTCTGTATTTTGGTGGTTAACTAGTATATGAAA
128 ATTGTCTCTCTTTCTGTATTTTGGTGGTTAACTAGTATATGAAA
4979018 CCATTGTCAT
Statistics
Matches: 166, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
202 30 0.18
203 41 0.25
204 95 0.57
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (203 bp):
TTTACTTGGCACTGTTAACATGATATTTATAAAAATTATAACTAAAATAAATTTAAATATACCAT
CCTTTTCTGTTTGCTAAGATATTTATTATTTTTTACATTCTGTTTGCAATTTTTTTAATACAATT
GTCTCTCTTTCTGTATTTTGGTGGTTAACTAGTATATGAAATTTATCTTAATTTTATATTATTTA
TGAATTGA
Found at i:4979295 original size:17 final size:17
Alignment explanation
Indices: 4979214--4979296 Score: 53
Period size: 17 Copynumber: 4.7 Consensus size: 17
4979204 ATACAAGTGC
*
4979214 TTTAATTATGATTTAAAGTT
1 TTTAATTAT--TTTAAA-AT
* * *
4979234 TTTTATTATTATAATAT
1 TTTAATTATTTTAAAAT
*
4979251 TTGAATTA--TTAAAAT
1 TTTAATTATTTTAAAAT
*
4979266 AATTAATATATTTTAAAAT
1 -TTTAAT-TATTTTAAAAT
4979285 TTTAATTATTTT
1 TTTAATTATTTT
4979297 CAACAATTTG
Statistics
Matches: 48, Mismatches: 11, Indels: 11
0.69 0.16 0.16
Matches are distributed among these distances:
15 5 0.10
16 4 0.08
17 15 0.31
18 9 0.19
19 7 0.15
20 8 0.17
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (17 bp):
TTTAATTATTTTAAAAT
Found at i:4981341 original size:13 final size:13
Alignment explanation
Indices: 4981323--4981349 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4981313 ACATTATGCT
4981323 TTGTATCGATACA
1 TTGTATCGATACA
4981336 TTGTATCGATACA
1 TTGTATCGATACA
4981349 T
1 T
4981350 GTTTATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4981359 original size:19 final size:19
Alignment explanation
Indices: 4981335--4981395 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
4981325 GTATCGATAC
***
4981335 ATTGTATCGATACATGTTT
1 ATTGTATCGATACATGACA
*
4981354 ATTGTATCAATACATGGACA
1 ATTGTATCGATACAT-GACA
4981374 ATTGTATCGATACATGA-A
1 ATTGTATCGATACATGACA
4981392 ATTG
1 ATTG
4981396 GTAGTAGCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 5 0.14
19 16 0.44
20 15 0.42
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:4983071 original size:86 final size:86
Alignment explanation
Indices: 4982926--4983100 Score: 350
Period size: 86 Copynumber: 2.0 Consensus size: 86
4982916 AATCGGAGGT
4982926 AAATTCAAATTCTTATACTTTTGAAAAATTACAAGATGCCTTTGATGAATTAGTATTGGAATTTG
1 AAATTCAAATTCTTATACTTTTGAAAAATTACAAGATGCCTTTGATGAATTAGTATTGGAATTTG
4982991 AATCGATGAACCTAAAGCATA
66 AATCGATGAACCTAAAGCATA
4983012 AAATTCAAATTCTTATACTTTTGAAAAATTACAAGATGCCTTTGATGAATTAGTATTGGAATTTG
1 AAATTCAAATTCTTATACTTTTGAAAAATTACAAGATGCCTTTGATGAATTAGTATTGGAATTTG
4983077 AATCGATGAACCTAAAGCATA
66 AATCGATGAACCTAAAGCATA
4983098 AAA
1 AAA
4983101 AGACAATCTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 89 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (86 bp):
AAATTCAAATTCTTATACTTTTGAAAAATTACAAGATGCCTTTGATGAATTAGTATTGGAATTTG
AATCGATGAACCTAAAGCATA
Found at i:4987266 original size:13 final size:13
Alignment explanation
Indices: 4987248--4987272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4987238 TAATATTCCT
4987248 TGTATCGATACAA
1 TGTATCGATACAA
4987261 TGTATCGATACA
1 TGTATCGATACA
4987273 TGGGTTACTA
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4989203 original size:23 final size:23
Alignment explanation
Indices: 4989150--4989204 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
4989140 TTTGACAAAA
* *
4989150 GGGAGAGAAATGCTTTGATTAAGG
1 GGGAGA-AAATGCTTTAAATAAGG
*
4989174 GGG-GAAAATTCTTTAAATAAGG
1 GGGAGAAAATGCTTTAAATAAGG
4989196 GGGAGAAAA
1 GGGAGAAAA
4989205 ACCAAAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.63
23 7 0.26
24 3 0.11
ACGTcount: A:0.40, C:0.04, G:0.35, T:0.22
Consensus pattern (23 bp):
GGGAGAAAATGCTTTAAATAAGG
Found at i:4989796 original size:19 final size:19
Alignment explanation
Indices: 4989771--4989827 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
4989761 TTGTATCGAT
* *
4989771 ACATTGTATCGTTACATGT
1 ACATTGTATCGATACATGG
* *
4989790 TCATTGTATCAATACATGG
1 ACATTGTATCGATACATGG
4989809 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
4989828 AAATTGGCAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:4995199 original size:11 final size:11
Alignment explanation
Indices: 4995183--4995207 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4995173 AAAGAAAAAG
4995183 AGAAAAAATAA
1 AGAAAAAATAA
4995194 AGAAAAAATAA
1 AGAAAAAATAA
4995205 AGA
1 AGA
4995208 GATGTTAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (11 bp):
AGAAAAAATAA
Found at i:4995420 original size:14 final size:15
Alignment explanation
Indices: 4995393--4995422 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4995383 AACTCAAAAA
4995393 AAAAATATAGAATTG
1 AAAAATATAGAATTG
4995408 AAAAATATA-AATTG
1 AAAAATATAGAATTG
4995422 A
1 A
4995423 CCTATATTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (15 bp):
AAAAATATAGAATTG
Found at i:4997321 original size:13 final size:13
Alignment explanation
Indices: 4997303--4997328 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4997293 CAATTTTTTG
4997303 TGTATCGATACAT
1 TGTATCGATACAT
4997316 TGTATCGATACAT
1 TGTATCGATACAT
4997329 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4998061 original size:16 final size:17
Alignment explanation
Indices: 4998040--4998083 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 17
4998030 CCCCCGTTTA
4998040 TTAATCAA-TCTCCCCC
1 TTAATCAATTCTCCCCC
4998056 TTAATCAAGTATTCTCCCCC
1 TTAATC-A--ATTCTCCCCC
4998076 TTAATCAA
1 TTAATCAA
4998084 GTAATTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 6 0.25
17 2 0.08
19 2 0.08
20 14 0.58
ACGTcount: A:0.30, C:0.34, G:0.02, T:0.34
Consensus pattern (17 bp):
TTAATCAATTCTCCCCC
Found at i:4998090 original size:21 final size:20
Alignment explanation
Indices: 4998048--4998086 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
4998038 TATTAATCAA
4998048 TCTCCCCCTTAATCAAGTAT
1 TCTCCCCCTTAATCAAGTAT
4998068 TCTCCCCCTTAATCAAGTA
1 TCTCCCCCTTAATCAAGTA
4998087 ATTCATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.36, G:0.05, T:0.33
Consensus pattern (20 bp):
TCTCCCCCTTAATCAAGTAT
Found at i:4999916 original size:13 final size:13
Alignment explanation
Indices: 4999898--4999923 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4999888 ATAATCACCC
4999898 TGTATCGATACAA
1 TGTATCGATACAA
4999911 TGTATCGATACAA
1 TGTATCGATACAA
4999924 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5002024 original size:15 final size:15
Alignment explanation
Indices: 5002004--5002034 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5001994 ATTTCGTTTG
*
5002004 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5002019 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5002034 G
1 G
5002035 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:5003867 original size:21 final size:21
Alignment explanation
Indices: 5003838--5003882 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5003828 AAGTTTTTAT
*
5003838 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
5003858 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
5003880 TTT
1 TTT
5003883 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:5006121 original size:13 final size:13
Alignment explanation
Indices: 5006103--5006128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5006093 CAATTTTTTG
5006103 TGTATCGATACAT
1 TGTATCGATACAT
5006116 TGTATCGATACAT
1 TGTATCGATACAT
5006129 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5010785 original size:17 final size:19
Alignment explanation
Indices: 5010763--5010800 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5010753 TCAATCTTAA
5010763 TAAATTT-GAT-AGTTTTT
1 TAAATTTAGATAAGTTTTT
5010780 TAAATTTAGGATAAGTTTTT
1 TAAATTTA-GATAAGTTTTT
5010800 T
1 T
5010801 GTTTTGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TAAATTTAGATAAGTTTTT
Found at i:5011309 original size:15 final size:14
Alignment explanation
Indices: 5011266--5011308 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
5011256 GTAAGGTGAT
5011266 AAATAATT-AAATA
1 AAATAATTAAAATA
* *
5011279 ATAT-ATAAAAATA
1 AAATAATTAAAATA
5011292 AAATAATTAAAATA
1 AAATAATTAAAATA
5011306 AAA
1 AAA
5011309 AGTGGTGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 2 0.08
13 11 0.46
14 11 0.46
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATAATTAAAATA
Found at i:5013850 original size:58 final size:57
Alignment explanation
Indices: 5013771--5013908 Score: 138
Period size: 58 Copynumber: 2.4 Consensus size: 57
5013761 AAAATGGGCC
* ** * * * *
5013771 TAAAATGCATGAAATTACATAATAATTTCTAAGTCAT-TAAATATTACTAAAATG-CTAA
1 TAAAATGTATGAAATGGCATAAGAATCTCTAAATCATGCAAA-ATTACTAAAATGAC--A
*
5013829 TAAAATGTATGAAATGGCATAAGAATCTCTAAATCATGCGAAATTACTAAAATGACA
1 TAAAATGTATGAAATGGCATAAGAATCTCTAAATCATGCAAAATTACTAAAATGACA
5013886 TGAAAATGCT-TGAAATGGCATAA
1 T-AAAATG-TATGAAATGGCATAA
5013909 AGGTCCTTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
57 2 0.03
58 62 0.91
59 4 0.06
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (57 bp):
TAAAATGTATGAAATGGCATAAGAATCTCTAAATCATGCAAAATTACTAAAATGACA
Found at i:5014719 original size:17 final size:17
Alignment explanation
Indices: 5014697--5014731 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5014687 ATCTACTTTC
*
5014697 CTTTTTTTCTTTCTTTTT
1 CTTTTTTT-TCTCTTTTT
5014715 CTTTTTTTTCTCTTTTT
1 CTTTTTTTTCTCTTTTT
5014732 TTGCTCTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
CTTTTTTTTCTCTTTTT
Found at i:5014730 original size:9 final size:9
Alignment explanation
Indices: 5014693--5014733 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
5014683 GAAAATCTAC
*
5014693 TTTCCTTTT
1 TTTCTTTTT
5014702 TTTCTTTCTT
1 TTTCTTT-TT
5014712 TTTCTTTTT
1 TTTCTTTTT
5014721 TTTCTCTTTT
1 TTTCT-TTTT
5014731 TTT
1 TTT
5014734 GCTCTCATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 13 0.45
10 16 0.55
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:5014739 original size:13 final size:11
Alignment explanation
Indices: 5014698--5014738 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
5014688 TCTACTTTCC
5014698 TTTTTT-TCTT
1 TTTTTTCTCTT
*
5014708 TCTTTT-TCTT
1 TTTTTTCTCTT
5014718 TTTTTTCTCTT
1 TTTTTTCTCTT
*
5014729 TTTTTGCTCT
1 TTTTTTCTCT
5014739 CATTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 14 0.52
11 13 0.48
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:5015990 original size:25 final size:25
Alignment explanation
Indices: 5015925--5015990 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
5015915 TTTTTTTTAA
*** *
5015925 AAGTTGAGCTTGCCTTTAACTAGCT
1 AAGTTGAGCTTATTTTTAACTAGAT
* *
5015950 AAGTTAAGCTTTTTTTTAACTAGAT
1 AAGTTGAGCTTATTTTTAACTAGAT
5015975 AAGTTGAGCTTATTTT
1 AAGTTGAGCTTATTTT
5015991 CACTAATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (25 bp):
AAGTTGAGCTTATTTTTAACTAGAT
Found at i:5016782 original size:56 final size:57
Alignment explanation
Indices: 5016567--5016861 Score: 245
Period size: 56 Copynumber: 5.3 Consensus size: 57
5016557 ACTGACCAGT
* ** * *
5016567 TACTCTTAGG-CTTTTTCATTTTGATGCTAAAATCAATTGAAACAAAACTTACTAGC
1 TACTCTTAGGACTTTTTCATTTTGATGCCAATTTCAATTGAGACAAAACCTACTAGC
* * * * * * * *
5016623 TACTCTTAAG-C-TTTTCATTTTGGTGCCACTTTTAACT-AGAAAAAAACCTACCAAC
1 TACTCTTAGGACTTTTTCATTTTGATGCCAATTTCAATTGAG-ACAAAACCTACTAGC
* * * * *
5016678 TACTCTTAGG-CTTTGTCATTCTAATGCCAATTTCAATTG-GGCTGAAACCTACTAGC
1 TACTCTTAGGACTTTTTCATTTTGATGCCAATTTCAATTGAGAC-AAAACCTACTAGC
* *
5016734 TACTATT-GGACTTTTTCATTTTTATGCCAATTTCAATTGAGACAAAACCTACTAGC
1 TACTCTTAGGACTTTTTCATTTTGATGCCAATTTCAATTGAGACAAAACCTACTAGC
* * *
5016790 TACT-TTGGGGCTTTTTCATTTTTG-TGCCAATTTCAACTTG-GACAAAAACTAGC-AGC
1 TACTCTTAGGACTTTTTCA-TTTTGATGCCAATTTCAA-TTGAGACAAAACCTA-CTAGC
*
5016846 TACTTTTAGG-CTTTTT
1 TACTCTTAGGACTTTTT
5016862 TAATTGAAGT
Statistics
Matches: 192, Mismatches: 36, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
54 1 0.01
55 44 0.23
56 133 0.69
57 14 0.07
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.38
Consensus pattern (57 bp):
TACTCTTAGGACTTTTTCATTTTGATGCCAATTTCAATTGAGACAAAACCTACTAGC
Found at i:5026006 original size:3 final size:3
Alignment explanation
Indices: 5025992--5026035 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
5025982 GGAGTCAACT
* *
5025992 TCA TCA TTA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
5026036 TTTGATAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.39
Consensus pattern (3 bp):
TCA
Found at i:5027030 original size:21 final size:21
Alignment explanation
Indices: 5027004--5027080 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
5026994 AAATTATCCA
5027004 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* *
5027025 AATGTATCGATAAATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
5027046 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
5027067 AATGTATCGATACA
1 AATGTATCGATACA
5027081 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:5027141 original size:19 final size:18
Alignment explanation
Indices: 5027116--5027183 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
5027106 AATTCAACAA
5027116 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5027134 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
5027150 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5027166 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
5027184 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 27 0.63
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:5027155 original size:13 final size:13
Alignment explanation
Indices: 5027137--5027161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5027127 ACATAAGTGT
5027137 TGTATCGATACAA
1 TGTATCGATACAA
5027150 TGTATCGATACA
1 TGTATCGATACA
5027162 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5027155 original size:32 final size:32
Alignment explanation
Indices: 5027118--5027180 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
5027108 TTCAACAATT
*
5027118 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
5027150 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
5027181 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:5027241 original size:13 final size:13
Alignment explanation
Indices: 5027223--5027248 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5027213 CATTTTTCTG
5027223 TGTATCGATACAT
1 TGTATCGATACAT
5027236 TGTATCGATACAT
1 TGTATCGATACAT
5027249 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5027245 original size:33 final size:33
Alignment explanation
Indices: 5027203--5027269 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5027193 GCCAAGGAAA
***
5027203 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
5027236 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
5027269 T
1 T
5027270 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:5027797 original size:10 final size:10
Alignment explanation
Indices: 5027781--5027810 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5027771 AATCCTTTAG
5027781 CAAAAAAAC-
1 CAAAAAAACA
5027790 CAAAAAAACA
1 CAAAAAAACA
5027800 CAAAAAAACA
1 CAAAAAAACA
5027810 C
1 C
5027811 TATTCTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAAAACA
Found at i:5029689 original size:51 final size:51
Alignment explanation
Indices: 5029612--5029999 Score: 233
Period size: 52 Copynumber: 7.4 Consensus size: 51
5029602 CAATTCTCCT
* * *
5029612 CAATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTA
* * *
5029663 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAAAACACAAAATTTTC-A
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTC---AAAACAC-TAATTTTCTA
** * * * *
5029717 CAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAACCCCGTTA-TTTC--
1 CAATCGGGGATACTCCAACCCCGATT--T--T-----ATTTTCAAAACAC-TAATTTTCTA
* * * *
5029774 CAA--GGGGATACTCCAACCCCTG-CTTTATTCTT-AAAATATTGA-TTTCTCA
1 CAATCGGGGATACTCCAACCCC-GATTTTATT-TTCAAAACACTAATTTTCT-A
* * * *
5029823 TAATCGGGGATACTCGAACCCCGATTTTA-TTGCTAAAACACTAATTTTTCCA
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACTAA-TTTTCTA
* *
5029875 CAATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACTAATTTTCCTT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTT-CTA
* * * * *
5029927 TAATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAA-ACATCAATTTTTTCA
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACAC-T-AATTTTCT-A
*
5029980 CAATCGAGGATACTCCAACC
1 CAATCGGGGATACTCCAACC
5030000 TCGTTATTTC
Statistics
Matches: 259, Mismatches: 48, Indels: 58
0.71 0.13 0.16
Matches are distributed among these distances:
46 6 0.02
47 4 0.02
48 1 0.00
49 3 0.01
50 2 0.01
51 64 0.25
52 75 0.29
53 30 0.12
54 30 0.12
55 25 0.10
56 2 0.01
57 4 0.02
58 4 0.02
59 5 0.02
62 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTA
Found at i:5029753 original size:27 final size:29
Alignment explanation
Indices: 5029719--5029793 Score: 111
Period size: 27 Copynumber: 2.7 Consensus size: 29
5029709 AATTTTCACA
5029719 ATCGGGGATACTCCAACCCCGTTA-AT-C
1 ATCGGGGATACTCCAACCCCGTTATATCC
*
5029746 ATCGGGGATACTCCAACCCCGTTATTTCC
1 ATCGGGGATACTCCAACCCCGTTATATCC
*
5029775 A-AGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
5029794 TGCTTTATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 24 0.55
28 18 0.41
29 2 0.05
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTATATCC
Found at i:5030010 original size:31 final size:28
Alignment explanation
Indices: 5029982--5030058 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
5029972 TTTTTTCACA
*
5029982 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
* **
5030010 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
5030038 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
5030059 ACTTTATTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:5030081 original size:264 final size:263
Alignment explanation
Indices: 5029612--5030108 Score: 766
Period size: 264 Copynumber: 1.9 Consensus size: 263
5029602 CAATTCTCCT
* * *
5029612 CAATCGGGGATATTCCATCTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
*
5029677 CCAACTCCGATTTTATTTTCAAAAAAACACAAAATTTTCACAATCGGGGATACTCCAACCCCGTT
66 CCAACTCCGATTTTATTTTCAAAAAAACACAAAATTTTCACAATCGAGGATACTCCAACCCCGTT
** **
5029742 AATCATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCTGCTTTATTCTTA
131 AATCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCTGCTTTATTCCCA
*
5029807 AAATATTGATTTCTCATAATCGGGGATACTCGAACCCCGATTTTATTGCTAAAACACTAATTTTT
196 AAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTT
5029872 CCA
261 CCA
* *
5029875 CAATCGGGGATACTCCAACCCCGATTTTATTTTTAAAACACTAATTTTCCTTTAATCGGGGATAC
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGATAC
* * ** *
5029940 TCCAGCTCCGATTTTA-TTTC-CAAAAACATCAATTTTTTCACAATCGAGGATACTCCAACCTCG
65 TCCAACTCCGATTTTATTTTCAAAAAAACA-CAAAATTTTCACAATCGAGGATACTCCAACCCCG
* *
5030003 TTATTTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCC-GACTTTATT
129 TTA-ATCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCTG-CTTTATT
*
5030067 CCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCC
192 CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCC
5030109 ATTATTTTCG
Statistics
Matches: 211, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
262 7 0.03
263 82 0.39
264 122 0.58
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (263 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACT
CCAACTCCGATTTTATTTTCAAAAAAACACAAAATTTTCACAATCGAGGATACTCCAACCCCGTT
AATCATCGGGGATACTCCAACCCCGTTACCTCCAAGGGGATACTCCAACCCCTGCTTTATTCCCA
AAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTT
CCA
Found at i:5030161 original size:79 final size:79
Alignment explanation
Indices: 5030012--5030203 Score: 215
Period size: 79 Copynumber: 2.4 Consensus size: 79
5030002 GTTATTTCAT
** * *
5030012 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGACTTTATTCCCAAAATAT
* * *
5030077 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * * * *
5030091 TGGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCAAATCCCGATTTTTTTTCC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGACTTTATTCCCAAAAT-A
5030155 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * *
5030170 CGGGGATACTCCAGCCCCGTCATTTTCAAGGGGA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGA
5030204 CACCCCAACC
Statistics
Matches: 93, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
78 3 0.03
79 90 0.97
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCAAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:5042051 original size:51 final size:51
Alignment explanation
Indices: 5041891--5042062 Score: 191
Period size: 51 Copynumber: 3.3 Consensus size: 51
5041881 GAAATAACGA
* * *
5041891 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
5041943 AATTGGAGTATCCCCGATTTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGA-TT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
5041997 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
5042048 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
5042063 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
51 39 0.40
52 14 0.14
53 4 0.04
54 30 0.31
55 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:5042108 original size:27 final size:28
Alignment explanation
Indices: 5042045--5042120 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
5042035 AAAATAAAGT
*
5042045 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
5042073 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
5042100 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
5042121 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:5056979 original size:51 final size:51
Alignment explanation
Indices: 5056819--5056990 Score: 191
Period size: 51 Copynumber: 3.3 Consensus size: 51
5056809 GAAATAACGA
* * *
5056819 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
5056871 AATTGGAGTATCCCCGATTTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGA-TT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
5056925 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
5056976 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
5056991 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
51 39 0.40
52 14 0.14
53 4 0.04
54 30 0.31
55 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:5057036 original size:27 final size:28
Alignment explanation
Indices: 5056973--5057048 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
5056963 AAAATAAAGT
*
5056973 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
5057001 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
5057028 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
5057049 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:5059532 original size:13 final size:13
Alignment explanation
Indices: 5059514--5059539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5059504 ACAAAGATCC
5059514 ATGTATCGATACA
1 ATGTATCGATACA
5059527 ATGTATCGATACA
1 ATGTATCGATACA
5059540 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5059535 original size:33 final size:33
Alignment explanation
Indices: 5059493--5059559 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5059483 AAAATTTCCA
***
5059493 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
5059526 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
5059559 A
1 A
5059560 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:5059603 original size:19 final size:18
Alignment explanation
Indices: 5059579--5059646 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
5059569 CAGTAGCTAA
5059579 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
5059598 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
5059613 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
5059630 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
5059647 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:5059619 original size:13 final size:13
Alignment explanation
Indices: 5059601--5059625 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5059591 ACAATACTTA
5059601 TGTATCGATACAT
1 TGTATCGATACAT
5059614 TGTATCGATACA
1 TGTATCGATACA
5059626 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5059623 original size:32 final size:32
Alignment explanation
Indices: 5059582--5059644 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
5059572 TAGCTAATTA
*
5059582 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
5059614 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
5059645 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:5059726 original size:21 final size:21
Alignment explanation
Indices: 5059702--5059758 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
5059692 CATTTGTAGG
5059702 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
5059723 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
5059744 ATGTATCGATACATT
1 ATGTATCGATACATT
5059759 AAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:5059769 original size:1 final size:1
Alignment explanation
Indices: 5059763--5059834 Score: 117
Period size: 1 Copynumber: 72.0 Consensus size: 1
5059753 TACATTAAAA
***
5059763 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5059828 TTTTTTT
1 TTTTTTT
5059835 CAAACACTTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.03, C:0.01, G:0.00, T:0.96
Consensus pattern (1 bp):
T
Found at i:5063303 original size:235 final size:235
Alignment explanation
Indices: 5062815--5064764 Score: 3161
Period size: 235 Copynumber: 8.3 Consensus size: 235
5062805 TCTGCTTTTT
* * * * *
5062815 AGTCCTTAAAGAGCGGGACGCCTT-TTCCTTTTAAAAGCCCCCATAAGTTGGTGGCATTCTT-CA
1 AGTCCTCAAAGAGCAGGACGCCTTCTT-C-TTTCAAAGCCCACACAAGTTGGTGGCATT-TTCCA
* * * *
5062878 GTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC
63 ATCCTCAAAGAGCAGGATG-C----CTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTC
* * * * * ** *
5062943 AAAGAGCGGGACGCCTTTTCTTTT-AAAGCCCACCCAAGTTAGTGGCAGCTT-CAGTCCTCAAAG
123 AAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAG
* * *
5063006 AGCAGGATGCTTTTTCTTTCCAAAGCCCACACAAGTTAGTGGCACCTTC
188 AGCAGGACGCCTTTTCTTT-TAAAGCCCACACAAGTTAGTGGCACCTTC
5063055 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
1 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
*
5063120 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAACTTGGTGGCACCTTCAGTCCTCAAAGAGCA
66 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
5063185 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
131 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
*
5063250 GTCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
196 GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
5063290 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
1 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
5063355 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
66 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
5063420 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
131 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
*
5063485 GTCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
196 GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
5063525 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
1 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
5063590 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
66 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
*
5063655 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGTAGGAC
131 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
5063720 GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
196 GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
5063760 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
1 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
* * *
5063825 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTTAGTCCTCAAAAAGTA
66 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
* * *
5063890 GGATGCTTTTTCTTTTCAAAACCCACACAAGTTGGTGGCATTTTTCAGTCCCCAAAGAGCACGAC
131 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
5063955 GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
196 GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
*
5063995 AGTCCTCAAAGAGCAGGACGCCTTCTTTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
1 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
5064060 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
66 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
5064125 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
131 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
5064190 GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
196 GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
*
5064230 AGTCCTCAAAGAGCAGGACGCCTTCTTTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
1 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
5064295 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
66 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
5064360 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
131 GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
5064425 GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
196 GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
*
5064465 AGTCCTCAAAGAGCAGGACGCCTTCTTTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
1 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
** * * ** * *
5064530 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGT
66 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGC
* * * *
5064595 AGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGA
130 AGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGA
* * *
5064654 CACC-TTTC----AAAGCCCACACAAGTTGGTGGCACCTTTT
195 CGCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACC-TTC
* * * *
5064691 AGTCCTCAAAGAGCAGGA---C-AC--CTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGT
1 AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAAT
*
5064749 CCTCAATGAGCAGGAT
65 CCTCAAAGAGCAGGAT
5064765 ACACTTATTT
Statistics
Matches: 1642, Mismatches: 61, Indels: 34
0.95 0.04 0.02
Matches are distributed among these distances:
220 42 0.03
221 4 0.00
222 1 0.00
223 1 0.00
225 24 0.01
226 20 0.01
229 4 0.00
230 53 0.03
234 60 0.04
235 1317 0.80
236 44 0.03
238 3 0.00
239 44 0.03
240 23 0.01
241 2 0.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (235 bp):
AGTCCTCAAAGAGCAGGACGCCTTCTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATC
CTCAAAGAGCAGGATGCCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCA
GGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCCCAAAGAGCAGGAC
GCCTTTTCTTTTAAAGCCCACACAAGTTAGTGGCACCTTC
Found at i:5064661 original size:27 final size:27
Alignment explanation
Indices: 5064631--5064716 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 27
5064621 TTGGTGGCAT
5064631 TTTCTAGTCCTCAAAGAGCAGGACACC
1 TTTCTAGTCCTCAAAGAGCAGGACACC
* * * * **
5064658 TTTCAAAGCCCACACAAGTTGGTGG-CACC
1 TTTC-TAGTCCTCA-AAG-AGCAGGACACC
5064687 TTT-TAGTCCTCAAAGAGCAGGACACC
1 TTTCTAGTCCTCAAAGAGCAGGACACC
5064713 TTTC
1 TTTC
5064717 AAAGCCCACA
Statistics
Matches: 42, Mismatches: 12, Indels: 10
0.66 0.19 0.16
Matches are distributed among these distances:
25 3 0.07
26 10 0.24
27 10 0.24
28 6 0.14
29 10 0.24
30 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (27 bp):
TTTCTAGTCCTCAAAGAGCAGGACACC
Found at i:5065515 original size:21 final size:21
Alignment explanation
Indices: 5065490--5065547 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
5065480 AAAAATTATC
5065490 CAAATGTATCGATACATTCCA
1 CAAATGTATCGATACATTCCA
* *
5065511 TAAATGTATCGATACATTCTA
1 CAAATGTATCGATACATTCCA
5065532 CAAATGTATCGATACA
1 CAAATGTATCGATACA
5065548 GGGTCCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (21 bp):
CAAATGTATCGATACATTCCA
Found at i:5065608 original size:19 final size:18
Alignment explanation
Indices: 5065583--5065650 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
5065573 AATTCAACAA
5065583 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5065601 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
5065617 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5065633 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
5065651 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 27 0.63
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:5065622 original size:13 final size:13
Alignment explanation
Indices: 5065604--5065628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5065594 ACATAAGTGT
5065604 TGTATCGATACAA
1 TGTATCGATACAA
5065617 TGTATCGATACA
1 TGTATCGATACA
5065629 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5065622 original size:32 final size:32
Alignment explanation
Indices: 5065585--5065647 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
5065575 TTCAACAATT
*
5065585 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
5065617 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
5065648 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:5065708 original size:13 final size:13
Alignment explanation
Indices: 5065690--5065715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5065680 CATTTTTCTG
5065690 TGTATCGATACAT
1 TGTATCGATACAT
5065703 TGTATCGATACAT
1 TGTATCGATACAT
5065716 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5065712 original size:33 final size:33
Alignment explanation
Indices: 5065670--5065736 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5065660 GCCAAGGAAA
***
5065670 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
5065703 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
5065736 T
1 T
5065737 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Done.