Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 43 of 135
Found at i:11097601 original size:9 final size:9
Alignment explanation
Indices: 11097589--11097648 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
11097579 AATAAAAGAA
11097589 AAAAAAAAG
1 AAAAAAAAG
*
11097598 AAAAAAATG
1 AAAAAAAAG
11097607 AAAAAAGAA-
1 AAAAAA-AAG
*
11097616 AAAAAAAGG
1 AAAAAAAAG
*
11097625 AGAGAAAAAG
1 A-AAAAAAAG
**
11097635 AGGAAAAAG
1 AAAAAAAAG
11097644 AAAAA
1 AAAAA
11097649 GAGAGGTCGA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
8 1 0.03
9 31 0.77
10 8 0.20
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:11097601 original size:16 final size:15
Alignment explanation
Indices: 11097576--11097622 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
11097566 TTCGATGAAG
*
11097576 AAAAATAAAAGAAAAA
1 AAAAAGAAAA-AAAAA
*
11097592 AAAAAGAAAAAAATGA
1 AAAAAGAAAAAAA-AA
11097608 AAAAAGAAAAAAAAA
1 AAAAAGAAAAAAAAA
11097623 GGAGAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.87, C:0.00, G:0.09, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAAAAAAA
Found at i:11097612 original size:11 final size:10
Alignment explanation
Indices: 11097573--11097622 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
11097563 AAATTCGATG
11097573 AAGAAAAATAA
1 AAGAAAAA-AA
11097584 AAGAAAAAAA
1 AAGAAAAAAA
11097594 AA-AGAAAAAA
1 AAGA-AAAAAA
* *
11097604 ATGAAAAAAG
1 AAGAAAAAAA
11097614 AA-AAAAAAA
1 AAGAAAAAAA
11097623 GGAGAGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 7 0.21
10 17 0.52
11 9 0.27
ACGTcount: A:0.86, C:0.00, G:0.10, T:0.04
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:11097633 original size:23 final size:25
Alignment explanation
Indices: 11097592--11097653 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
11097582 AAAAGAAAAA
11097592 AAAAAGAAAAA-A-ATG-AAAA-AAG
1 AAAAAGAAAAAGAGA-GAAAAAGAAG
* *
11097614 AAAAA-AAAAGGAGAGAAAAAGAGG
1 AAAAAGAAAAAGAGAGAAAAAGAAG
11097638 AAAAAGAAAAAGAGAG
1 AAAAAGAAAAAGAGAG
11097654 GTCGAGGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.12
22 7 0.22
23 5 0.16
24 7 0.22
25 9 0.28
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.02
Consensus pattern (25 bp):
AAAAAGAAAAAGAGAGAAAAAGAAG
Found at i:11097633 original size:37 final size:38
Alignment explanation
Indices: 11097573--11097648 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
11097563 AAATTCGATG
11097573 AAGAAAAATAAAAGAAAAAAAAAAGA-AAAAAATGAAAA
1 AAGAAAAATAAAAGAAAAAAAAAAGAGAAAAAA-GAAAA
* * * *
11097611 AAGAAAAA-AAAAGGAGAGAAAAAGAGGAAAAAGAAAA
1 AAGAAAAATAAAAGAAAAAAAAAAGAGAAAAAAGAAAA
11097648 A
1 A
11097649 GAGAGGTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 20 0.61
38 13 0.39
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (38 bp):
AAGAAAAATAAAAGAAAAAAAAAAGAGAAAAAAGAAAA
Found at i:11097636 original size:8 final size:7
Alignment explanation
Indices: 11097582--11097648 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
11097572 GAAGAAAAAT
11097582 AAAAGAA
1 AAAAGAA
11097589 AAAA-AA
1 AAAAGAA
11097595 AAGAA-AA
1 AA-AAGAA
*
11097602 AAATGAA
1 AAAAGAA
11097609 AAAAGAA
1 AAAAGAA
11097616 AAAA-AA
1 AAAAGAA
*
11097622 AGGAGAGAA
1 A--AAAGAA
*
11097631 AAAGAGGA
1 AAA-AGAA
11097639 AAAAGAA
1 AAAAGAA
11097646 AAA
1 AAA
11097649 GAGAGGTCGA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
6 8 0.17
7 29 0.60
8 8 0.17
9 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (7 bp):
AAAAGAA
Found at i:11098663 original size:49 final size:49
Alignment explanation
Indices: 11098589--11098963 Score: 371
Period size: 50 Copynumber: 7.6 Consensus size: 49
11098579 TAGAGGAAAT
**
11098589 ATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACAACGAACCCGGTACC
1 ATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * *
11098638 ATGAAGATTTGGAGGGAAAGATTGAGGCCGCAACGGCGAATCCGGTACC
1 ATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* *
11098687 ATGAAGA-TTAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACC
1 ATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * *
11098735 TTAGAAGATGTGATA-GGAAAGGTTGAGGCCACAACGGCGAACTCGGTACC
1 AT-GAAGATTTGA-AGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
** * * * **
11098785 ATGAAGATACGAAGGG-AAGGTTGAGGTCGCAATGGTGAACCCAATACC
1 ATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
** ** * ** *
11098833 TAAAAAGATACGAAAGGAAAGGTTGAGGTTGCAACGGCGAACCCAGTACC
1 -ATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * * * *
11098883 TTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGTGAACCCGGTACC
1 AT-GAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
* * *
11098933 GTGAAAATTTGAAGGG-AAGGATTAAGGCCGC
1 ATGAAGATTTGAAGGGAAAGG-TTGAGGCCGC
11098964 GACGACCAAT
Statistics
Matches: 267, Mismatches: 51, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
48 67 0.25
49 98 0.37
50 101 0.38
51 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.16
Consensus pattern (49 bp):
ATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACC
Found at i:11098770 original size:98 final size:96
Alignment explanation
Indices: 11098589--11098963 Score: 335
Period size: 98 Copynumber: 3.8 Consensus size: 96
11098579 TAGAGGAAAT
* ** * * * *
11098589 ATGAAGATTTGAAGGGAAAGGTTGAGGCCGCAACAACGAACCCGGTACCAT-GAAGATTTGGAGG
1 ATGAAGA-TTAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATAT-GAAG
*
11098653 GAAAGATTGAGGCCGCAACGGCGAATCCGGTACC
64 GAAAGGTTGAGGCCGCAACGGCGAA-CCGGTACC
*
11098687 ATGAAGATTAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATGTGATAGG
1 ATGAAGATTAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATATGA-AGG
*
11098752 AAAGGTTGAGGCCACAACGGCGAACTCGGTACC
65 AAAGGTTGAGGCCGCAACGGCGAAC-CGGTACC
* * * * * * *
11098785 ATGAAGA-TACGAAGGG-AAGGTTGAGGTCGCAATGGTGAACCCAATACCTAAAAAGATACGAAA
1 ATGAAGATTA--AAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATATG-AA
** *
11098848 GGAAAGGTTGAGGTTGCAACGGCGAACCCAGTACC
63 GGAAAGGTTGAGGCCGCAACGGCGAA-CCGGTACC
* * * * * * * * *
11098883 TTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGTGAACCCGGTACCGT-GAAAATTTGAAG
1 AT-GAAGAT-TAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATATGAAG
* *
11098947 GGAAGGATTAAGGCCGC
64 GAAAGG-TTGAGGCCGC
11098964 GACGACCAAT
Statistics
Matches: 226, Mismatches: 39, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
97 43 0.19
98 127 0.56
99 28 0.12
100 27 0.12
101 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.16
Consensus pattern (96 bp):
ATGAAGATTAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTTAGAAGATATGAAGGA
AAGGTTGAGGCCGCAACGGCGAACCGGTACC
Found at i:11098902 original size:148 final size:146
Alignment explanation
Indices: 11098591--11098963 Score: 435
Period size: 148 Copynumber: 2.5 Consensus size: 146
11098581 GAGGAAATAT
* * ** *
11098591 GAAGATTTGAAGGGAAAGGTTGAGGCCGCAACAACGAACCCGGTACCATGAAGATTTGGAGGGAA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATTTGAAGGG-A
* * ** ** *
11098656 AGATTGAGGCCGCAACGGCGAATCCGGTACCATGAAGATTAAAGGGAAAGGTTGAGGCCGCAACG
65 AGGTTGAGGCCGCAACGGCGAACCCAATACCAAAAAGATTAAAAGGAAAGGTTGAGGCCGCAACG
11098721 GCGAACCCGATACCTTA
130 GCGAACCCGATACCTTA
* * * **
11098738 GAAGATGTGATAGGAAAGGTTGAGGCCACAACGGCGAACTCGGTACCATGAAGATACGAAGGGAA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATTTGAAGGGAA
* * * **
11098803 GGTTGAGGTCGCAATGGTGAACCCAATACCTAAAAAGA-TACGAAAGGAAAGGTTGAGGTTGCAA
66 GGTTGAGGCCGCAACGGCGAACCCAATACC-AAAAAGATTA--AAAGGAAAGGTTGAGGCCGCAA
11098867 CGGCGAACCC-AGTACCTTA
128 CGGCGAACCCGA-TACCTTA
* * * *
11098886 GAAGATGTGATGGGAAAGGTTGAGGCCGTAACGGTGAACCCGGTACCGTGAAAATTTGAAGGGAA
1 GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATTTGAAGGGAA
*
11098951 GGATTAAGGCCGC
66 GG-TTGAGGCCGC
11098964 GACGACCAAT
Statistics
Matches: 188, Mismatches: 33, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
146 27 0.14
147 59 0.31
148 94 0.50
149 8 0.04
ACGTcount: A:0.34, C:0.18, G:0.32, T:0.16
Consensus pattern (146 bp):
GAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATGAAGATTTGAAGGGAA
GGTTGAGGCCGCAACGGCGAACCCAATACCAAAAAGATTAAAAGGAAAGGTTGAGGCCGCAACGG
CGAACCCGATACCTTA
Found at i:11098997 original size:5 final size:5
Alignment explanation
Indices: 11098987--11099014 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
11098977 GCACCTTAAA
11098987 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
11099015 TATGAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:11099184 original size:98 final size:99
Alignment explanation
Indices: 11099068--11099290 Score: 256
Period size: 98 Copynumber: 2.3 Consensus size: 99
11099058 TGAGGATTTG
* * *
11099068 AAGGGTAAGGTTGAGGCTGTAATGACAAACCCGATATCTTAGAAGATATGAT-AGAAAGGATTGA
1 AAGGGAAAGGTTGAGGCTGTAATGACAAACCCGATACCTTAGAAGATATGATGAGAAA-CATTGA
*
11099132 GGCCGCAACGACGAATCCAGTACCAT-AAAGAT-TA
65 GGCCGAAACGACGAATCCAGTACCATGAAA-ATGTA
* * *
11099166 AAGGGAAATGTTGAGGCTGTAA-CAGCAAACCCGATACCTTAGAAGATGTGATGAGAAACATTGA
1 AAGGGAAAGGTTGAGGCTGTAATGA-CAAACCCGATACCTTAGAAGATATGATGAGAAACATTGA
** ** * *
11099230 GGTTGAAACGGTGAATCCGGTACCATGAAAATGTG
65 GGCCGAAACGACGAATCCAGTACCATGAAAATGTA
* *
11099265 ATGGGAAAGGTTGAGGCCGTAATGAC
1 AAGGGAAAGGTTGAGGCTGTAATGAC
11099291 GAACTCAATG
Statistics
Matches: 103, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
97 1 0.01
98 72 0.70
99 29 0.28
100 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (99 bp):
AAGGGAAAGGTTGAGGCTGTAATGACAAACCCGATACCTTAGAAGATATGATGAGAAACATTGAG
GCCGAAACGACGAATCCAGTACCATGAAAATGTA
Found at i:11099554 original size:39 final size:39
Alignment explanation
Indices: 11099491--11100245 Score: 285
Period size: 39 Copynumber: 19.4 Consensus size: 39
11099481 TCGACATCCG
* * * *
11099491 ATCTTTTACCCCGAGCCTGGGGCAGATCACTATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
* * * *
11099530 ATCTCTTACCCCGAGCTTGAGGCAGATTA-CAGCCATCCG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCA-TCAGCCA
* ** * ** *
11099569 ATCTTTTACCTTGAGCTTGGGGCAGATCACCATCATTCG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
** * * * * * *
11099608 ATCTCTTACCATGAG-TCTAAGACAGATTACAACCAGCCG
1 ATCTCTTACCCCGAGCT-TGAGGCAGATCACCATCAGCCA
* * * **
11099647 ATCTCTTATCTCAAGCTTG-GGACAGATCACCATCAGTTA
1 ATCTCTTACCCCGAGCTTGAGG-CAGATCACCATCAGCCA
* * *
11099686 ATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCAT---TCA
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CA-CCATCAGCCA
* * *
11099725 ATCTCTTACCCTGAGCTTGGGGCAGATTACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
* * * * **
11099764 ATCTCTTACCCCAAGCTTGAAGCAGATTGTAGC-T-ATTCA
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CACCATCAGCCA
* * *
11099803 ATCTTTTACCTCGAGCTTG-GACAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
* * *
11099841 ATCTCTTACCCTGAGCCTG-GGATAGATTGCAGCCATTC-G---
1 ATCTCTTACCCCGAGCTTGAGG-CAGA-T-CA-CCA-TCAGCCA
* * *
11099880 ATCTTTTACCCCGAGCTTGAGGCAAATCACCATCAACCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
**
11099919 ATCTCTTACCTTGAGCCTT-A-GCAGATTGCAGCCATTC-G---
1 ATCTCTTACCCCGAG-CTTGAGGCAGA-T-CA-CCA-TCAGCCA
* * * * *
11099957 ATCTTTTACCTCGAGCCT-AGGGTAAATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCATCAGCCA
* * *
11099996 ATCTCTTACCCCGAGCTTGGGGCAAATTGTAGCCATTC-G---
1 ATCTCTTACCCCGAGCTTGAGGCAGA-T-CA-CCA-TCAGCCA
* * *
11100035 ATTTTTTACCCCGAGCTTGAGGCAGATCACCATTAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
* * *
11100074 ATCTCTTACCCCGAGCTT-AGGGTAGATTGTAGCCAT---CCG
1 ATCTCTTACCCCGAGCTTGA-GGCAGA-T-CA-CCATCAGCCA
* * * * *
11100113 ATCTTTTACCTCGAGCCT-AGGGCAGATCACCATGAGCTA
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACCATCAGCCA
* * * * ** *
11100152 ATCTCTTACCCCGAGCCTGGGGTAGATTA-CAGTCATTCG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCA-TCAGCCA
* * * * *
11100191 ATCTTTTACCTCGAGCTTTAGGTAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
*
11100230 ATCTTTTACCCCGAGC
1 ATCTCTTACCCCGAGC
11100246 CTTGGGTGGA
Statistics
Matches: 533, Mismatches: 127, Indels: 112
0.69 0.16 0.15
Matches are distributed among these distances:
35 5 0.01
36 21 0.04
37 12 0.02
38 51 0.10
39 390 0.73
40 20 0.04
41 12 0.02
42 18 0.03
43 4 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGAGGCAGATCACCATCAGCCA
Found at i:11099614 original size:78 final size:78
Alignment explanation
Indices: 11099489--11100282 Score: 794
Period size: 78 Copynumber: 10.2 Consensus size: 78
11099479 TTTCGACATC
* * *
11099489 CGATCTTTTACCCCGAGCCTGGGGCAGATCACTATCAGCCAATCTCTTACCCCGAGCTTGAGGCA
1 CGATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGAGGCA
* *
11099554 GATTACAGCCATC
66 GATTGCAGCCATT
* ** * ** * *
11099567 CGATCTTTTACCTTGAGCTTGGGGCAGATCACCATCATTCGATCTCTTACCATGAG-TCTAAGAC
1 CGATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCT-TGAGGC
* * **
11099631 AGATTACAACCAGC
65 AGATTGCAGCCATT
* * * * ** * *
11099645 CGATCTCTTATCTCAAGCTTGGGACAGATCACCATCAGTTAATCTCTTACCCCGAGCCTGGGGCA
1 CGATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGAGGCA
11099710 GATTGCAGCCATT
66 GATTGCAGCCATT
* * * * *
11099723 CAATCTCTTACC-CTGAGCTTGGGGCAGATTACCATCAGCCAATCTCTTACCCCAAGCTTGAAGC
1 CGATCTTTTACCTC-GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGAGGC
* *
11099787 AGATTGTAGCTATT
65 AGATTGCAGCCATT
* * * * *
11099801 CAATCTTTTACCTCGAGCTT-GGACAGATCACCATCAGCCAATCTCTTACCCTGAGCCTG-GGAT
1 CGATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGAGG-C
11099864 AGATTGCAGCCATT
65 AGATTGCAGCCATT
* * * * **
11099878 CGATCTTTTACCCCGAGCTTGAGGCAAATCACCATCAACCAATCTCTTACCTTGAGCCTT-A-GC
1 CGATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG-CTTGAGGC
11099941 AGATTGCAGCCATT
65 AGATTGCAGCCATT
* * * * *
11099955 CGATCTTTTACCTCGAGCCTAGGGTAAATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCA
1 CGATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGAGGCA
* *
11100020 AATTGTAGCCATT
66 GATTGCAGCCATT
* * * * *
11100033 CGATTTTTTACCCCGAGCTTGAGGCAGATCACCATTAGCCAATCTCTTACCCCGAGCTT-AGGGT
1 CGATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGA-GGC
* *
11100097 AGATTGTAGCCATC
65 AGATTGCAGCCATT
* * * * * * *
11100111 CGATCTTTTACCTCGAGCCTAGGGCAGATCACCATGAGCTAATCTCTTACCCCGAGCCTGGGGTA
1 CGATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGAGGCA
* *
11100176 GATTACAGTCATT
66 GATTGCAGCCATT
** * * * *
11100189 CGATCTTTTACCTCGAGCTTTAGGTAGATCACCATCAGTCAATCTTTTACCCCGAGCCTTG-GGT
1 CGATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG-CTTGAGGC
* **
11100253 GGATTGCAGCCACC
65 AGATTGCAGCCATT
*
11100267 CGATCTCTTACCTCGA
1 CGATCTTTTACCTCGA
11100283 TCACGAGGTA
Statistics
Matches: 589, Mismatches: 114, Indels: 26
0.81 0.16 0.04
Matches are distributed among these distances:
76 4 0.01
77 128 0.22
78 451 0.77
79 6 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (78 bp):
CGATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGAGGCA
GATTGCAGCCATT
Found at i:11100724 original size:210 final size:210
Alignment explanation
Indices: 11100362--11100770 Score: 577
Period size: 210 Copynumber: 1.9 Consensus size: 210
11100352 ATAAAGCGGT
* * * * * * *
11100362 CGTCTTCTTGATGAGATACAGAGAAGTGGATTGAAATAAGTGATGCGGTCATCTTCTTGAAGAGA
1 CGTCTTCCTGATGAGATACAAAAAAGTGGATTAAAACAAATGAGGCGGTCATCTTCTTGAAGAGA
* * * *
11100427 TACAAAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACTTCGAACCTCCATCT
66 TACAAAGAAGTAAACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCTCCATCT
* *** * * *
11100492 TCTTGATGAGATACTGAGAAGTGGGTCAAAGTAAGAAAGCGGTCATCTTCTTGATGAGATACAGA
131 TCCTGATGAGATAAAAAGAAGTGGGTCAAAGCAAGAAAGCGATCATCTTCCTGATGAGATACAGA
11100557 GAAGGGGACCAAATC
196 GAAGGGGACCAAATC
*
11100572 CGTCTTCCTGATGAGATACAAAAAAGTGGATTAAAACAAATGAGGCGGTCATCTTCTTGATGAGA
1 CGTCTTCCTGATGAGATACAAAAAAGTGGATTAAAACAAATGAGGCGGTCATCTTCTTGAAGAGA
* * * *
11100637 TACAAAGAAGTAAACCAAATCAAATGAAGCAAAGTTTAATGTGAGTGAAGCTTCAAACC-CTATC
66 TACAAAGAAGTAAACCAAATC-AATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCTCCATC
* *
11100701 TTCCTGATGAGATAAAAAGAAGTGGGTCAAAGCAATAAAGTGATCATCTTCCTGATGAGATACAG
130 TTCCTGATGAGATAAAAAGAAGTGGGTCAAAGCAAGAAAGCGATCATCTTCCTGATGAGATACAG
11100766 AGAAG
195 AGAAG
11100771 TAGACCGAGA
Statistics
Matches: 173, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
210 142 0.82
211 31 0.18
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24
Consensus pattern (210 bp):
CGTCTTCCTGATGAGATACAAAAAAGTGGATTAAAACAAATGAGGCGGTCATCTTCTTGAAGAGA
TACAAAGAAGTAAACCAAATCAATGAAGCAAAGCTCAATGTGAGTGAAACTTCAAACCTCCATCT
TCCTGATGAGATAAAAAGAAGTGGGTCAAAGCAAGAAAGCGATCATCTTCCTGATGAGATACAGA
GAAGGGGACCAAATC
Found at i:11102721 original size:58 final size:59
Alignment explanation
Indices: 11102624--11102977 Score: 261
Period size: 58 Copynumber: 6.1 Consensus size: 59
11102614 GTTTTCTTTA
* * * * * *
11102624 AAAATCACATTTTAACCCTCGAAGTTCTCCAAAATTACATTTTAACCCCTAACTTTTCT
1 AAAATCACATTTTCACCCTCAAACTTTTCCAAAATTACATTTTCACCCCAAACTTTTCT
* * * * *
11102683 AAAATCACATTTTCATCCT-AAACTTTTCCAAAATTACATTTTGACCCCTAATTTTTTT
1 AAAATCACATTTTCACCCTCAAACTTTTCCAAAATTACATTTTCACCCCAAACTTTTCT
* ** *
11102741 AAAATCACATTTTTACCC-CTAAACTTTTTAAAAATCACATTTTCACCCCAAACTTTT-T
1 AAAATCACATTTTCACCCTC-AAACTTTTCCAAAATTACATTTTCACCCCAAACTTTTCT
* * * *
11102799 CAAAATTACATTTTCA-CCTCAAACTTTTTCAAAATTACATTTTCACCTCAAACTTTTCC
1 -AAAATCACATTTTCACCCTCAAACTTTTCCAAAATTACATTTTCACCCCAAACTTTTCT
* * * *
11102858 AAAATTTACCATTTTGC-CCCT-GAAC--ATCCAAAATTTACCATTTTGC-CCCCAAA--TTTCC
1 AAAA-TCA-CATTTT-CACCCTCAAACTTTTCCAAAA-TTA-CATTTT-CACCCCAAACTTTTCT
* * * *
11102916 AAAATCACATTTTTGA-CTTCAAA-TTTTCCAAAAGTT-CGATTTTAATCCCAAA-TTTTCT
1 AAAATCACA-TTTTCACCCTCAAACTTTTCCAAAA-TTAC-ATTTTCACCCCAAACTTTTCT
11102974 AAAA
1 AAAA
11102978 ATTTCAAATT
Statistics
Matches: 240, Mismatches: 35, Indels: 41
0.76 0.11 0.13
Matches are distributed among these distances:
56 5 0.02
57 19 0.08
58 122 0.51
59 68 0.28
60 21 0.09
61 5 0.02
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (59 bp):
AAAATCACATTTTCACCCTCAAACTTTTCCAAAATTACATTTTCACCCCAAACTTTTCT
Found at i:11102755 original size:88 final size:88
Alignment explanation
Indices: 11102653--11102855 Score: 268
Period size: 88 Copynumber: 2.3 Consensus size: 88
11102643 CGAAGTTCTC
* * *
11102653 CAAAATTACATTTTAACCCCT-AACTTTTCT-AAAATCACATTTTCATCCTAAACTTTTCCAAAA
1 CAAAATTACATTTTTACCCCTAAACTTTT-TAAAAATCACATTTTCACCCCAAACTTTTCCAAAA
* * *
11102716 TTACATTTTGACCCCTAATTTTTT
65 TTACATTTTCACCCCAAACTTTTT
* * *
11102740 TAAAATCACATTTTTACCCCTAAACTTTTTAAAAATCACATTTTCACCCCAAACTTTTTCAAAAT
1 CAAAATTACATTTTTACCCCTAAACTTTTTAAAAATCACATTTTCACCCCAAACTTTTCCAAAAT
*
11102805 TACATTTTCACCTCAAACTTTTT
66 TACATTTTCACCCCAAACTTTTT
* *
11102828 CAAAATTACATTTTCACCTC-AAACTTTT
1 CAAAATTACATTTTTACCCCTAAACTTTT
11102856 CCAAAATTTA
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
87 27 0.27
88 73 0.73
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.40
Consensus pattern (88 bp):
CAAAATTACATTTTTACCCCTAAACTTTTTAAAAATCACATTTTCACCCCAAACTTTTCCAAAAT
TACATTTTCACCCCAAACTTTTT
Found at i:11102863 original size:29 final size:29
Alignment explanation
Indices: 11102624--11102872 Score: 237
Period size: 29 Copynumber: 8.4 Consensus size: 29
11102614 GTTTTCTTTA
* * * * *
11102624 AAAATCACATTTTAACCCTCGAAGTTCTCC
1 AAAATTACATTTTCACCC-CAAACTTTTCC
* * *
11102654 AAAATTACATTTTAACCCCTAACTTTTCT
1 AAAATTACATTTTCACCCCAAACTTTTCC
* * *
11102683 AAAATCACATTTTCATCCTAAACTTTTCC
1 AAAATTACATTTTCACCCCAAACTTTTCC
* * * **
11102712 AAAATTACATTTTGACCCCTAATTTTTTT
1 AAAATTACATTTTCACCCCAAACTTTTCC
* * **
11102741 AAAATCACATTTTTACCCCTAAACTTTTTA
1 AAAATTACATTTTCACCCC-AAACTTTTCC
* *
11102771 AAAATCACATTTTCACCCCAAACTTTTTC
1 AAAATTACATTTTCACCCCAAACTTTTCC
* *
11102800 AAAATTACATTTTCACCTCAAACTTTTTC
1 AAAATTACATTTTCACCCCAAACTTTTCC
*
11102829 AAAATTACATTTTCACCTCAAACTTTTCC
1 AAAATTACATTTTCACCCCAAACTTTTCC
11102858 AAAATTTACCATTTT
1 AAAA-TTA-CATTTT
11102873 GCCCCTGAAC
Statistics
Matches: 187, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
29 136 0.73
30 45 0.24
31 6 0.03
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (29 bp):
AAAATTACATTTTCACCCCAAACTTTTCC
Found at i:11102916 original size:29 final size:29
Alignment explanation
Indices: 11102853--11102920 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
11102843 ACCTCAAACT
**
11102853 TTTCCAAAATTTACCATTTTGCCCCTGAA
1 TTTCCAAAATTTACCATTTTGCCCCCAAA
**
11102882 CATCCAAAATTTACCATTTTGCCCCCAAA
1 TTTCCAAAATTTACCATTTTGCCCCCAAA
11102911 TTTCCAAAAT
1 TTTCCAAAAT
11102921 CACATTTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTCCAAAATTTACCATTTTGCCCCCAAA
Found at i:11110087 original size:31 final size:30
Alignment explanation
Indices: 11110052--11110126 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
11110042 ATGAAAACTT
* * *
11110052 AATTTTTGAGGAATTTAGGGATTAAAATTGA
1 AATTTTTG-GCAAATTAGGGATTAAAATCGA
*
11110083 AATTTTTGGCAAATTCGGGATTAAAATCG-
1 AATTTTTGGCAAATTAGGGATTAAAATCGA
* *
11110112 AACTTTTGGAAAATT
1 AATTTTTGGCAAATT
11110127 TGAGGTCGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 13 0.34
30 17 0.45
31 8 0.21
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.37
Consensus pattern (30 bp):
AATTTTTGGCAAATTAGGGATTAAAATCGA
Found at i:11110126 original size:29 final size:30
Alignment explanation
Indices: 11110069--11110126 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
11110059 GAGGAATTTA
* * *
11110069 GGGATTAAAATTGAAATTTTTGGCAAATTC
1 GGGATTAAAATCGAAACTTTTGGAAAATTC
11110099 GGGATTAAAATCG-AACTTTTGGAAAATT
1 GGGATTAAAATCGAAACTTTTGGAAAATT
11110127 TGAGGTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (30 bp):
GGGATTAAAATCGAAACTTTTGGAAAATTC
Found at i:11110215 original size:57 final size:58
Alignment explanation
Indices: 11110143--11110338 Score: 261
Period size: 57 Copynumber: 3.4 Consensus size: 58
11110133 CGAAAATATG
* * *
11110143 ATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTGGATGTTAAGGGACAAAATGGTA
1 ATTTTTGGATATTTGAGGGCAAAATGGTAATTTTTGGATGTTAGGGGTCAAAATGGTA
* ** ** * *
11110201 A-TTTTGGATGTTTGAGGTTAAAATGGTAATTTTTAAATGTTTGGGGTCAAAATGATA
1 ATTTTTGGATATTTGAGGGCAAAATGGTAATTTTTGGATGTTAGGGGTCAAAATGGTA
*
11110258 ATTTTTGGATATTTGAGGGCAAAATGGTAATTTTTGGATGTTCGGGGTCAAAAT-GTA
1 ATTTTTGGATATTTGAGGGCAAAATGGTAATTTTTGGATGTTAGGGGTCAAAATGGTA
* *
11110315 ATTTTTGGATGTTTGGGGGCAAAA
1 ATTTTTGGATATTTGAGGGCAAAA
11110339 ATGCAATTTT
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
57 71 0.60
58 47 0.40
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.38
Consensus pattern (58 bp):
ATTTTTGGATATTTGAGGGCAAAATGGTAATTTTTGGATGTTAGGGGTCAAAATGGTA
Found at i:11110347 original size:86 final size:85
Alignment explanation
Indices: 11110143--11110348 Score: 245
Period size: 86 Copynumber: 2.4 Consensus size: 85
11110133 CGAAAATATG
** *
11110143 ATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTGGATGTTAAGGGACAAAATGGTAATTTTGG
1 ATTTTTGGATGTTTGGGGGCAAAAT-GTAATTTTTGGATGTTAAGGGACAAAATGGTAATTTTGG
* *
11110208 ATGTTTGAGGTTAAAATGGTA
65 ATGTTCGAGGTCAAAATGGTA
** * * *
11110229 ATTTTTAAATGTTTGGGGTCAAAATGATAATTTTTGGATATTTGAGGG-CAAAATGGTAATTTTT
1 ATTTTTGGATGTTTGGGGGCAAAATG-TAATTTTTGGAT-GTTAAGGGACAAAATGGTAA-TTTT
*
11110293 GGATGTTCGGGGTCAAAAT-GTA
63 GGATGTTCGAGGTCAAAATGGTA
*
11110315 ATTTTTGGATGTTTGGGGGCAAAAATGCAATTTT
1 ATTTTTGGATGTTTGGGGGC-AAAATGTAATTTT
11110349 GAAAAGTTTT
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
85 1 0.01
86 68 0.67
87 32 0.32
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.39
Consensus pattern (85 bp):
ATTTTTGGATGTTTGGGGGCAAAATGTAATTTTTGGATGTTAAGGGACAAAATGGTAATTTTGGA
TGTTCGAGGTCAAAATGGTA
Found at i:11110347 original size:115 final size:115
Alignment explanation
Indices: 11110115--11110357 Score: 314
Period size: 115 Copynumber: 2.1 Consensus size: 115
11110105 AAAATCGAAC
*
11110115 TTTTGGAAAA-TTTGAGGTCGAAAATATGATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTG
1 TTTT-GAAAAGTTTGAGGTCGAAAATATAATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTG
** *
11110179 GATGTTAAGGGACAAAATGGTAATTTTGGATGTTTGAGGTTAAAATGGTAA
65 GATGTTAAGGGACAAAATGGTAATTTTGGATGTTTGAGGCAAAAATGGCAA
* * * *
11110230 TTTTTAAATGTTTGGGGTC-AAAATGATAATTTTTGGATATTTGAGGGCAAAATGGTAATTTTTG
1 TTTTGAAAAGTTTGAGGTCGAAAAT-ATAATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTG
** * *
11110294 GATGTTCGGGGTCAAAAT-GTAATTTTTGGATGTTTGGGGGCAAAAAT-GCAA
65 GATGTTAAGGGACAAAATGGTAA-TTTTGGATGTTT-GAGGCAAAAATGGCAA
11110345 TTTTGAAAAGTTT
1 TTTTGAAAAGTTT
11110358 TTAAGGTGAA
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
114 12 0.11
115 90 0.82
116 8 0.07
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (115 bp):
TTTTGAAAAGTTTGAGGTCGAAAATATAATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTGG
ATGTTAAGGGACAAAATGGTAATTTTGGATGTTTGAGGCAAAAATGGCAA
Found at i:11110348 original size:29 final size:29
Alignment explanation
Indices: 11110143--11110338 Score: 225
Period size: 29 Copynumber: 6.8 Consensus size: 29
11110133 CGAAAATATG
** *
11110143 ATTTTTGGAAATTTGAGGGCAAAATGGTA
1 ATTTTTGGATGTTTGGGGGCAAAATGGTA
** *
11110172 ATTTTTGGATGTTAAGGGACAAAATGGTA
1 ATTTTTGGATGTTTGGGGGCAAAATGGTA
* **
11110201 A-TTTTGGATGTTTGAGGTTAAAATGGTA
1 ATTTTTGGATGTTTGGGGGCAAAATGGTA
** * *
11110229 ATTTTTAAATGTTTGGGGTCAAAATGATA
1 ATTTTTGGATGTTTGGGGGCAAAATGGTA
* *
11110258 ATTTTTGGATATTTGAGGGCAAAATGGTA
1 ATTTTTGGATGTTTGGGGGCAAAATGGTA
* *
11110287 ATTTTTGGATGTTCGGGGTCAAAAT-GTA
1 ATTTTTGGATGTTTGGGGGCAAAATGGTA
11110315 ATTTTTGGATGTTTGGGGGCAAAA
1 ATTTTTGGATGTTTGGGGGCAAAA
11110339 ATGCAATTTT
Statistics
Matches: 138, Mismatches: 28, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
28 48 0.35
29 90 0.65
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.38
Consensus pattern (29 bp):
ATTTTTGGATGTTTGGGGGCAAAATGGTA
Found at i:11110379 original size:115 final size:114
Alignment explanation
Indices: 11110129--11110439 Score: 306
Period size: 115 Copynumber: 2.7 Consensus size: 114
11110119 GGAAAATTTG
* * *
11110129 AGGTCGAAAATATGATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTGGATGTTAAGGGACAA
1 AGGT-GAAAATGTGATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTGGATGTTAGGGGTCAA
** * * *
11110194 AATGGTAA-TTTTGGATGTTTGAGGTTAAAATGGTAATTTTTAAATGTTTG
65 AAT-GTAATTTTTGGATGTTTGAGGCAAAAATGGCAATTTTAAAATGTTTA
* * * * *
11110244 GGGTCAAAATGATAATTTTTGGATATTTGAGGGCAAAATGGTAATTTTTGGATGTTCGGGGTCAA
1 AGGTGAAAATG-TGATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTGGATGTTAGGGGTCAA
* *
11110309 AATGTAATTTTTGGATGTTTGGGGGCAAAAAT-GCAATTTTGAAAAGTTTTTA
65 AATGTAATTTTTGGATGTTT-GAGGCAAAAATGGCAATTTT-AAAA-TGTTTA
* * * * *
11110361 AGGTGAAAATGTGA-TTTTGGAAAAGTTTAAGGGTTAAAAT-GTAATTTTGGAGAAGTTTGGGGG
1 AGGTGAAAATGTGATTTTTGG-AAA-TTTGAGGG-CAAAATGGTAATTTTTG-GATG-TTAGGGG
*
11110424 TTAAAATGTAATTTTT
61 TCAAAATGTAATTTTT
11110440 TAAACAAAAC
Statistics
Matches: 161, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
114 9 0.06
115 79 0.49
116 15 0.09
117 29 0.18
118 8 0.05
119 21 0.13
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (114 bp):
AGGTGAAAATGTGATTTTTGGAAATTTGAGGGCAAAATGGTAATTTTTGGATGTTAGGGGTCAAA
ATGTAATTTTTGGATGTTTGAGGCAAAAATGGCAATTTTAAAATGTTTA
Found at i:11110425 original size:30 final size:30
Alignment explanation
Indices: 11110301--11110438 Score: 120
Period size: 30 Copynumber: 4.6 Consensus size: 30
11110291 TTGGATGTTC
* *
11110301 GGGGTCAAAATGTAATTTTTGG--ATGTTTG
1 GGGGTTAAAATGTAA-TTTTGGAAAAGTTTG
** * *
11110330 GGGGCAAAAATGCAATTTT-GAAAAGTTTTT
1 GGGGTTAAAATGTAATTTTGGAAAAG-TTTG
** * * *
11110360 AAGGTGAAAATGTGATTTTGGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTG
* *
11110390 AGGGTTAAAATGTAATTTTGGAGAAGTTTG
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTG
11110420 GGGGTTAAAATGTAATTTT
1 GGGGTTAAAATGTAATTTT
11110439 TTAAACAAAA
Statistics
Matches: 87, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
27 1 0.01
28 4 0.05
29 14 0.16
30 62 0.71
31 6 0.07
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.37
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTGGAAAAGTTTG
Found at i:11111224 original size:27 final size:26
Alignment explanation
Indices: 11111174--11111224 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
11111164 CTTTATTTTT
* *
11111174 TATTTTTTTGTTTAAATCTGTTTTAG
1 TATTTTTTTGTTTAAATATATTTTAG
*
11111200 TATTTTTTTGTTATTAATATATTTT
1 TATTTTTTTGTT-TAAATATATTTT
11111225 TTATCTACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.69
Consensus pattern (26 bp):
TATTTTTTTGTTTAAATATATTTTAG
Found at i:11112433 original size:71 final size:71
Alignment explanation
Indices: 11112317--11112473 Score: 269
Period size: 71 Copynumber: 2.2 Consensus size: 71
11112307 AGCCTTCAAG
* *
11112317 GTATCGGTAGAAGTCCCAGGCAATAACTTCTTTACTCTCTGGAGTTTGTTCTACCGGTATAAGTC
1 GTATCGGTAGAAGTCCCAGGCAACAACTTCTTTACTCTCTGGAGTTTGTTCTACCAGTATAAGTC
11112382 ATGGTT
66 ATGGTT
* * *
11112388 GTATCGGTAGAAGTCCCAGGCCACAACTTCTTTGCTCTCTGGAGTTTGTTCTATCAGTATAAGTC
1 GTATCGGTAGAAGTCCCAGGCAACAACTTCTTTACTCTCTGGAGTTTGTTCTACCAGTATAAGTC
11112453 ATGGTT
66 ATGGTT
11112459 GTATCGGTAGAAGTC
1 GTATCGGTAGAAGTC
11112474 AGGCAGGAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 81 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (71 bp):
GTATCGGTAGAAGTCCCAGGCAACAACTTCTTTACTCTCTGGAGTTTGTTCTACCAGTATAAGTC
ATGGTT
Found at i:11114327 original size:71 final size:71
Alignment explanation
Indices: 11114252--11114398 Score: 204
Period size: 71 Copynumber: 2.1 Consensus size: 71
11114242 TGACTTGTTT
* *
11114252 CGGTAGAAGCCTTCAAGGTATTGGTAGAAGTCCCAGGCCACAACTTCTTTGCTCTCTGGAGTTTG
1 CGGTAGAAGCCATCAAGGTATTGGTAGAAGTCCCAGGCCACAACTTCTTTGCTCTCTGGAATTTG
11114317 TTCTAC
66 TTCTAC
* * **** *
11114323 CGGTATAAGTCATGGTTGTATTGGTAGAAGTCCCAGTCCACAACTTCTTTGCTCTCTGGAATTTG
1 CGGTAGAAGCCATCAAGGTATTGGTAGAAGTCCCAGGCCACAACTTCTTTGCTCTCTGGAATTTG
11114388 TTCTAC
66 TTCTAC
*
11114394 TGGTA
1 CGGTA
11114399 TAAGTCATGG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (71 bp):
CGGTAGAAGCCATCAAGGTATTGGTAGAAGTCCCAGGCCACAACTTCTTTGCTCTCTGGAATTTG
TTCTAC
Found at i:11114399 original size:71 final size:71
Alignment explanation
Indices: 11114269--11114425 Score: 269
Period size: 71 Copynumber: 2.2 Consensus size: 71
11114259 AGCCTTCAAG
*
11114269 GTATTGGTAGAAGTCCCAGGCCACAACTTCTTTGCTCTCTGGAGTTTGTTCTACCGGTATAAGTC
1 GTATTGGTAGAAGTCCCAGGCCACAACTTCTTTGCTCTCTGGAATTTGTTCTACCGGTATAAGTC
11114334 ATGGTT
66 ATGGTT
* *
11114340 GTATTGGTAGAAGTCCCAGTCCACAACTTCTTTGCTCTCTGGAATTTGTTCTACTGGTATAAGTC
1 GTATTGGTAGAAGTCCCAGGCCACAACTTCTTTGCTCTCTGGAATTTGTTCTACCGGTATAAGTC
11114405 ATGGTT
66 ATGGTT
* *
11114411 GTATCGATAGAAGTC
1 GTATTGGTAGAAGTC
11114426 AGGCAGGAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 81 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (71 bp):
GTATTGGTAGAAGTCCCAGGCCACAACTTCTTTGCTCTCTGGAATTTGTTCTACCGGTATAAGTC
ATGGTT
Found at i:11114721 original size:13 final size:12
Alignment explanation
Indices: 11114703--11114732 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
11114693 GGGCTAACAC
11114703 TTTTTTTGCTAT
1 TTTTTTTGCTAT
11114715 ATTTTTTTGCTAT
1 -TTTTTTTGCTAT
11114728 TTTTT
1 TTTTT
11114733 CTTCTTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTTTGCTAT
Found at i:11115841 original size:18 final size:18
Alignment explanation
Indices: 11115818--11115871 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
11115808 CAACTGCAGA
11115818 TTAGTTAGCTGTTAGTTG
1 TTAGTTAGCTGTTAGTTG
*
11115836 TTAGTTAACTGTTAGTTG
1 TTAGTTAGCTGTTAGTTG
*
11115854 TTGGTTAGCTGTTAGTTG
1 TTAGTTAGCTGTTAGTTG
11115872 CAAATGTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.50
Consensus pattern (18 bp):
TTAGTTAGCTGTTAGTTG
Found at i:11118375 original size:4 final size:4
Alignment explanation
Indices: 11118366--11118430 Score: 76
Period size: 4 Copynumber: 16.2 Consensus size: 4
11118356 TTTCTCCATG
* * * * * *
11118366 TATA TATA TATG TATA CATA CATA CATA CATA CATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
11118414 TATA TATA TATA TATA T
1 TATA TATA TATA TATA T
11118431 CTTGTCAAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (4 bp):
TATA
Found at i:11118610 original size:80 final size:80
Alignment explanation
Indices: 11118477--11118631 Score: 267
Period size: 80 Copynumber: 1.9 Consensus size: 80
11118467 GTTCATTATT
* * *
11118477 TCCGTCAATTCATGGCACCCGATGCCTAGTGGTTAAACCGCGATAAGTGAGCCCAGCTCTAGTTG
1 TCCGTCAATTCATGGCACCCGATGCCTAGCGGATAAACCGCGATAAGTGAGCCCAACTCTAGTTG
11118542 GATTAACCAACAAAA
66 GATTAACCAACAAAA
11118557 TCCGTCAATTCATGGCACCC-AGTGCCTAGCGGATAAACCGCGATAAGTGAGCCCAACTCTAGTT
1 TCCGTCAATTCATGGCACCCGA-TGCCTAGCGGATAAACCGCGATAAGTGAGCCCAACTCTAGTT
11118621 GGATTAACCAA
65 GGATTAACCAA
11118632 TGGTTTGCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
79 1 0.01
80 70 0.99
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (80 bp):
TCCGTCAATTCATGGCACCCGATGCCTAGCGGATAAACCGCGATAAGTGAGCCCAACTCTAGTTG
GATTAACCAACAAAA
Found at i:11135922 original size:13 final size:13
Alignment explanation
Indices: 11135906--11135941 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
11135896 ATATTTTTTG
11135906 TTTTTTATTTAAT
1 TTTTTTATTTAAT
**
11135919 TTTTACATTTAAT
1 TTTTTTATTTAAT
11135932 TTTTTTATTT
1 TTTTTTATTT
11135942 TATAGGTTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTTATTTAAT
Found at i:11138131 original size:6 final size:6
Alignment explanation
Indices: 11138122--11138184 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
11138112 TCATTTTCAT
* ** *
11138122 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAC TTCAAG TTTTA- TTTTATT
1 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTA-G
11138170 TTTTA- TTTTA- TTTTA
1 TTTTAG TTTTAG TTTTA
11138185 TTATACACTA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
5 15 0.31
6 29 0.59
7 5 0.10
ACGTcount: A:0.19, C:0.03, G:0.08, T:0.70
Consensus pattern (6 bp):
TTTTAG
Found at i:11138131 original size:13 final size:13
Alignment explanation
Indices: 11138102--11138143 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
11138092 TTTTTTTCTT
11138102 TTTTCATTTTTCA-
1 TTTTCATTTTT-AG
11138115 TTTTCATTTTTAG
1 TTTTCATTTTTAG
*
11138128 TTTT-AGTTTTAG
1 TTTTCATTTTTAG
11138140 TTTT
1 TTTT
11138144 AGTTTTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.71
Consensus pattern (13 bp):
TTTTCATTTTTAG
Found at i:11141771 original size:24 final size:23
Alignment explanation
Indices: 11141737--11141784 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
11141727 CTTTAGAGAA
11141737 TTTTGTGTTTACGTTTTGAGGGTT
1 TTTTGTGTTTACGTTTTG-GGGTT
* *
11141761 TTTTGTTTTTAGGTTTTGGGGTT
1 TTTTGTGTTTACGTTTTGGGGTT
11141784 T
1 T
11141785 AGTTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.06, C:0.02, G:0.29, T:0.62
Consensus pattern (23 bp):
TTTTGTGTTTACGTTTTGGGGTT
Found at i:11144796 original size:2 final size:2
Alignment explanation
Indices: 11144783--11144838 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
11144773 TCTATTTTTC
*
11144783 AT AT AT AC 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
11144825 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
11144839 TGTTCTGGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11150975 original size:32 final size:32
Alignment explanation
Indices: 11150937--11151217 Score: 260
Period size: 32 Copynumber: 8.7 Consensus size: 32
11150927 GTGTTGGTTG
* * * *
11150937 GATAGCTCTTACGAGCAAACTATTTATTGGTT
1 GATAGCTCTTACGAGCATACTGTTTACTGATT
*
11150969 GATAGCTCTTACGAGCATATTGTTTACTGATT
1 GATAGCTCTTACGAGCATACTGTTTACTGATT
* *
11151001 CATAGCTCTTACAAGCATACTGTTTACTGATT
1 GATAGCTCTTACGAGCATACTGTTTACTGATT
11151033 GATAGCTCTTACGAGCATACTGTTTACTGATT
1 GATAGCTCTTACGAGCATACTGTTTACTGATT
* * * *
11151065 GATAGCTCTCATGAGCATACTATATACTGATT
1 GATAGCTCTTACGAGCATACTGTTTACTGATT
* * * * *
11151097 TATCAGCTCATATGAGCTTACTG-TTACTAATT
1 GAT-AGCTCTTACGAGCATACTGTTTACTGATT
* * * * * * *
11151129 GATAACTCTCATGAGCATACTCTATAATGAAT
1 GATAGCTCTTACGAGCATACTGTTTACTGATT
* * * *
11151161 GATTAACTCATACGAGCTTACTAG-ATACTGATT
1 GA-TAGCTCTTACGAGCATACT-GTTTACTGATT
*
11151194 GATTAGCTCTTATGAGCATACTGT
1 GA-TAGCTCTTACGAGCATACTGT
11151218 GAAATTACAC
Statistics
Matches: 202, Mismatches: 42, Indels: 9
0.80 0.17 0.04
Matches are distributed among these distances:
31 14 0.07
32 133 0.66
33 55 0.27
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (32 bp):
GATAGCTCTTACGAGCATACTGTTTACTGATT
Found at i:11152244 original size:40 final size:39
Alignment explanation
Indices: 11152197--11152293 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 39
11152187 ATCCTTTTTG
*
11152197 AACAATCTTATG-T-TACTCCGACTCATAAGTCTTCCTTTCA
1 AACAATCTTATGCTCTACT--GACTCATAAGTCTTCCATT-A
*
11152237 AACAATCTTATGCTCTACTGAGTCATAAGTCTTCCATTA
1 AACAATCTTATGCTCTACTGACTCATAAGTCTTCCATTA
*
11152276 AACATAGTCTCATGCTCT
1 AACA-A-TCTTATGCTCT
11152294 TTCCAAGACA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
39 5 0.10
40 30 0.60
41 11 0.22
42 4 0.08
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (39 bp):
AACAATCTTATGCTCTACTGACTCATAAGTCTTCCATTA
Found at i:11152443 original size:41 final size:41
Alignment explanation
Indices: 11152352--11152627 Score: 293
Period size: 41 Copynumber: 6.6 Consensus size: 41
11152342 AGAACACATA
* * *** *
11152352 ATCCCAAGACATGAGTCTTCCTTTAACACATAATCTCATACTC
1 ATCCCGAGACATGAGTCTTCCTTT-A-ATATTCCCTCATGCTC
*
11152395 AACCCGAGACATGAGTCTTCCTTTAATATTCCCTCATGCTC
1 ATCCCGAGACATGAGTCTTCCTTTAATATTCCCTCATGCTC
* ***
11152436 ATCCCGAGACATGAGTCTTCCTTTAACACATAATCTCATGCTC
1 ATCCCGAGACATGAGTCTTCCTTT-A-ATATTCCCTCATGCTC
* * * *
11152479 AACCCAAGACATGAGTTTTCCTTTCATATTCCCTCATGCTC
1 ATCCCGAGACATGAGTCTTCCTTTAATATTCCCTCATGCTC
* * * *
11152520 ATCCAGAGACATAATTCTTCCTTTAATA-TCCCATCACGCTC
1 ATCCCGAGACATGAGTCTTCCTTTAATATTCCC-TCATGCTC
* * *
11152561 ATCCCGAGAGACGAGTCTTCCTTCAATATTCCCTCATGCTC
1 ATCCCGAGACATGAGTCTTCCTTTAATATTCCCTCATGCTC
11152602 ATCCCGAGACATGAGTCTTCCATTTA
1 ATCCCGAGACATGAGTCTTCC-TTTA
11152628 TACATCAAGA
Statistics
Matches: 190, Mismatches: 38, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
40 4 0.02
41 122 0.64
42 9 0.05
43 55 0.29
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (41 bp):
ATCCCGAGACATGAGTCTTCCTTTAATATTCCCTCATGCTC
Found at i:11152493 original size:84 final size:84
Alignment explanation
Indices: 11152352--11152627 Score: 369
Period size: 84 Copynumber: 3.3 Consensus size: 84
11152342 AGAACACATA
* *
11152352 ATCCCAAGACATGAGTCTTCCTTTAACACATAATCTCATACTCAACCCGAGACATGAGTCTTCCT
1 ATCCCGAGACATGAGTCTTCCTTTAACACATAATCTCATGCTCAACCCGAGACATGAGTCTTCCT
11152417 TTAATATTCCCTCATGCTC
66 TTAATATTCCCTCATGCTC
* *
11152436 ATCCCGAGACATGAGTCTTCCTTTAACACATAATCTCATGCTCAACCCAAGACATGAGTTTTCCT
1 ATCCCGAGACATGAGTCTTCCTTTAACACATAATCTCATGCTCAACCCGAGACATGAGTCTTCCT
*
11152501 TTCATATTCCCTCATGCTC
66 TTAATATTCCCTCATGCTC
* * * * ** * * * *
11152520 ATCCAGAGACATAATTCTTCCTTT-A-ATAT-CCCATCACGCTCATCCCGAGAGACGAGTCTTCC
1 ATCCCGAGACATGAGTCTTCCTTTAACACATAATC-TCATGCTCAACCCGAGACATGAGTCTTCC
*
11152582 TTCAATATTCCCTCATGCTC
65 TTTAATATTCCCTCATGCTC
11152602 ATCCCGAGACATGAGTCTTCCATTTA
1 ATCCCGAGACATGAGTCTTCC-TTTA
11152628 TACATCAAGA
Statistics
Matches: 167, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
81 1 0.01
82 62 0.37
83 4 0.02
84 100 0.60
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (84 bp):
ATCCCGAGACATGAGTCTTCCTTTAACACATAATCTCATGCTCAACCCGAGACATGAGTCTTCCT
TTAATATTCCCTCATGCTC
Found at i:11152578 original size:125 final size:126
Alignment explanation
Indices: 11152354--11152632 Score: 318
Period size: 125 Copynumber: 2.2 Consensus size: 126
11152344 AACACATAAT
* * *
11152354 CCCAAGACATGAGTCTTCCTTTAACACATAATCTCATACTCAACCCGAGACATGAGTCTTCCTTT
1 CCCAAGACATGAGTCTTCCTTT-ACACATAACCTCATACTCAACCAGAGACATAAGTCTTCCTTT
* *
11152419 AATATTCCCTCATGCTCATCCCGAGACATGAGTCTTCCTTTAACACATAATCTCATGCTCAA
65 AATATTCCCTCACGCTCATCCCGAGACACGAGTCTTCCTTTAACACATAATCTCATGCTCAA
* * ** * * *
11152481 CCCAAGACATGAGTTTTCCTTT-CATATTCCCTCATGCTCATCCAGAGACATAATTCTTCCTTTA
1 CCCAAGACATGAGTCTTCCTTTACACATAACCTCATACTCAACCAGAGACATAAGTCTTCCTTTA
* * *
11152545 ATA-TCCCATCACGCTCATCCCGAGAGACGAGTCTTCC-TT--CA-ATATTCCCTCATGCTCAT
66 ATATTCCC-TCACGCTCATCCCGAGACACGAGTCTTCCTTTAACACATAAT--CTCATGCTCAA
* *
11152604 CCCGAGACATGAGTCTTCCATTTATACAT
1 CCCAAGACATGAGTCTTCC-TTTACACAT
11152633 CAAGAGATTC
Statistics
Matches: 128, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
121 4 0.03
122 2 0.02
123 27 0.21
124 9 0.07
125 65 0.51
127 21 0.16
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (126 bp):
CCCAAGACATGAGTCTTCCTTTACACATAACCTCATACTCAACCAGAGACATAAGTCTTCCTTTA
ATATTCCCTCACGCTCATCCCGAGACACGAGTCTTCCTTTAACACATAATCTCATGCTCAA
Found at i:11157772 original size:16 final size:17
Alignment explanation
Indices: 11157753--11157786 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
11157743 TTAATTATTT
11157753 TTAAAAAAAATTA-AAA
1 TTAAAAAAAATTATAAA
*
11157769 TTAAAAAATATTATAAA
1 TTAAAAAAAATTATAAA
11157786 T
1 T
11157787 ATTAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAAAAAAATTATAAA
Found at i:11157794 original size:26 final size:24
Alignment explanation
Indices: 11157765--11157827 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 24
11157755 AAAAAAAATT
11157765 AAAATTAAAAAATATTATAAATATTA
1 AAAATTAAAAAA-ATT-TAAATATTA
*
11157791 AAAAGTATAAAAAAATTTAAATTTTA
1 AAAA-T-TAAAAAAATTTAAATATTA
**
11157817 AATTTTAAAAA
1 AAAATTAAAAA
11157828 TTAATTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
24 6 0.19
25 1 0.03
26 14 0.44
27 4 0.12
28 7 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAATTAAAAAAATTTAAATATTA
Found at i:11158805 original size:24 final size:25
Alignment explanation
Indices: 11158754--11158805 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
11158744 CTCGATTTTT
* *
11158754 TTTCTCCTAGTTAAACTCTGATTTC
1 TTTCTCCTACTTAAACTCTGATTAC
11158779 TTTC-CCTACTTAAACTCTTG-TTAC
1 TTTCTCCTACTTAAACTC-TGATTAC
11158803 TTT
1 TTT
11158806 AGGAATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.50
Consensus pattern (25 bp):
TTTCTCCTACTTAAACTCTGATTAC
Found at i:11160187 original size:59 final size:59
Alignment explanation
Indices: 11160095--11160229 Score: 207
Period size: 59 Copynumber: 2.3 Consensus size: 59
11160085 GAAAAAAAAA
* * *
11160095 TAGGTGTTAGCCATTAAATGGTTGACACCAACTTTTTAAAATAAAAAATTATTATTATT
1 TAGGTGTTGGCCATTAAATGATCGACACCAACTTTTTAAAATAAAAAATTATTATTATT
* *
11160154 TAGGTGTTGGCCATTAAATGATCGATACCAACTTTTTTAAATAAAAAATTATTATTATT
1 TAGGTGTTGGCCATTAAATGATCGACACCAACTTTTTAAAATAAAAAATTATTATTATT
* *
11160213 TAAGTGTTGGCCTTTAA
1 TAGGTGTTGGCCATTAA
11160230 TGGTCGGCAC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 69 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (59 bp):
TAGGTGTTGGCCATTAAATGATCGACACCAACTTTTTAAAATAAAAAATTATTATTATT
Found at i:11160843 original size:13 final size:13
Alignment explanation
Indices: 11160825--11160850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11160815 GACTCAAACA
11160825 AATAAACAGAGTT
1 AATAAACAGAGTT
11160838 AATAAACAGAGTT
1 AATAAACAGAGTT
11160851 TAACTGAAAG
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:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
AATAAACAGAGTT
Found at i:11164118 original size:22 final size:22
Alignment explanation
Indices: 11164092--11164141 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
11164082 TACCTTAAAA
*
11164092 CCCTAAACATTAAAACCATAAC
1 CCCTAAACACTAAAACCATAAC
*
11164114 CCCTAAACACTAAAACCCTAAC
1 CCCTAAACACTAAAACCATAAC
*
11164136 ACCTAA
1 CCCTAA
11164142 CTCATAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (22 bp):
CCCTAAACACTAAAACCATAAC
Found at i:11165009 original size:45 final size:45
Alignment explanation
Indices: 11164908--11165033 Score: 148
Period size: 45 Copynumber: 2.8 Consensus size: 45
11164898 GCAGTCCGAG
* * *
11164908 AGAGAGATAAACAACTAATATATGGGGGTAAGGTATAGATGGAAGAC
1 AGAGGGATAAACGACTAATAAAT-GGGGTAA-GTATAGATGGAAGAC
* * *
11164955 A-AGGTGATAAACGACTAATAAATGGAGTAAGTATAGATTGAAGAT
1 AGAGG-GATAAACGACTAATAAATGGGGTAAGTATAGATGGAAGAC
*
11165000 AGAGGGATAAACGAC-AATAAATGGGGTAGGTATA
1 AGAGGGATAAACGACTAATAAATGGGGTAAGTATA
11165034 AGAGAAATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
44 17 0.25
45 24 0.35
46 11 0.16
47 17 0.25
ACGTcount: A:0.45, C:0.06, G:0.29, T:0.21
Consensus pattern (45 bp):
AGAGGGATAAACGACTAATAAATGGGGTAAGTATAGATGGAAGAC
Found at i:11165808 original size:154 final size:159
Alignment explanation
Indices: 11165522--11165847 Score: 511
Period size: 154 Copynumber: 2.1 Consensus size: 159
11165512 AGAGAAATGA
* *
11165522 CTAATAAATGGGGTAGGTATTGCCAGCTTTTAAGTTACACCGAGAGAGAGAGAGAGAAGGGGGAG
1 CTAATAAATGGGATAGGTATTGCCAACTTTTAAGTTA-ACCGAGAGAGAGAGAGAGAAGGGGGAG
* * *
11165587 AGAAGCCCAAGAGAGTTTTTCTATTATTTTCTATTGAAAAAATTCATTTTGAAAACAATAAGAAT
65 AGAAACCCAAGAGAGTTTTTCTATTATTTTATATTGAAAAAAATCATTTTGAAAACAATAAGAAT
*
11165652 TTCAATGGTTTCATTTCTTGTGTAACGAAG
130 TTCAATGGTTTCATTTATTGTGTAACGAAG
* *
11165682 CTAATAAATGGGATAGGTATTGTCAACTTTTAAGTT-A-C-A-A-CGAGAGAGAGAAGGGGGAGA
1 CTAATAAATGGGATAGGTATTGCCAACTTTTAAGTTAACCGAGAGAGAGAGAGAGAAGGGGGAGA
*
11165742 GAAACCCAAGAGAGTTTTTCTATTATTTTATATTGAAAAAAATCATTTTG-AAACTAGTAAGAAT
66 GAAACCCAAGAGAGTTTTTCTATTATTTTATATTGAAAAAAATCATTTTGAAAAC-AATAAGAAT
11165806 TTCAATGGTTTCATTTATTGTGTAACGAAG
130 TTCAATGGTTTCATTTATTGTGTAACGAAG
11165836 CTAATAAATGGG
1 CTAATAAATGGG
11165848 GTAAGTACCA
Statistics
Matches: 156, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
153 4 0.03
154 115 0.74
155 1 0.01
156 1 0.01
157 1 0.01
158 1 0.01
160 33 0.21
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (159 bp):
CTAATAAATGGGATAGGTATTGCCAACTTTTAAGTTAACCGAGAGAGAGAGAGAGAAGGGGGAGA
GAAACCCAAGAGAGTTTTTCTATTATTTTATATTGAAAAAAATCATTTTGAAAACAATAAGAATT
TCAATGGTTTCATTTATTGTGTAACGAAG
Found at i:11169870 original size:28 final size:28
Alignment explanation
Indices: 11169839--11169898 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
11169829 ACTTTGGTTA
*
11169839 AAATAAAATGTATTGTCTCATAGGATTC
1 AAATAAAATGTATTCTCTCATAGGATTC
* *
11169867 AAATAAAATGTATTCTTTCGTAGGATTC
1 AAATAAAATGTATTCTCTCATAGGATTC
11169895 AAAT
1 AAAT
11169899 GATTTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (28 bp):
AAATAAAATGTATTCTCTCATAGGATTC
Found at i:11178346 original size:21 final size:21
Alignment explanation
Indices: 11178320--11178359 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
11178310 TTGTAAGCGA
11178320 CAAAAAAAATAAAAAAAATCC
1 CAAAAAAAATAAAAAAAATCC
* *
11178341 CAAAAAAAATTATAAAAAT
1 CAAAAAAAATAAAAAAAAT
11178360 GTTAAGCAAC
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:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (21 bp):
CAAAAAAAATAAAAAAAATCC
Found at i:11184442 original size:18 final size:17
Alignment explanation
Indices: 11184405--11184439 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11184395 ACCTTTCGAG
11184405 ATTTTGTTTAAGAAAAA
1 ATTTTGTTTAAGAAAAA
11184422 ATTTT-TTTGAAGAAAAA
1 ATTTTGTTT-AAGAAAAA
11184439 A
1 A
11184440 ATTGGTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (17 bp):
ATTTTGTTTAAGAAAAA
Found at i:11186621 original size:46 final size:45
Alignment explanation
Indices: 11186562--11186704 Score: 156
Period size: 45 Copynumber: 3.3 Consensus size: 45
11186552 TTGTAGCTTT
* * *
11186562 AATCTGCCTCTCTATAACTTTAAGGGTAAAATATTAGATTGTCTTC
1 AATCTGCCCCTCTATAACTTT-AGGGTAAAAGATTAGATTGTCCTC
*
11186608 AATCTGCCCCTCTATAACTTTAGGGTAAAAGATTGGATTGTCCTC
1 AATCTGCCCCTCTATAACTTTAGGGTAAAAGATTAGATTGTCCTC
* * * *
11186653 AATCTG-CCCT-T-TGA--TTAGCGTAAAAGATTGGATTG-CTTC
1 AATCTGCCCCTCTATAACTTTAGGGTAAAAGATTAGATTGTCCTC
11186692 AATCTG-CCCTCTA
1 AATCTGCCCCTCTA
11186705 GTTAGGGTAA
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
39 13 0.15
40 21 0.24
42 2 0.02
43 1 0.01
44 4 0.05
45 27 0.31
46 20 0.23
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
AATCTGCCCCTCTATAACTTTAGGGTAAAAGATTAGATTGTCCTC
Found at i:11186676 original size:40 final size:39
Alignment explanation
Indices: 11186584--11186877 Score: 297
Period size: 39 Copynumber: 7.3 Consensus size: 39
11186574 TATAACTTTA
* * *
11186584 AGGGTAAAATATTAGATTGTCTTCAATCTGCCCCTCTATAACTTT
1 AGGGTAAAAGATTGGATTG-CTTCAATCTG-CCCT-T-TGA--TT
*
11186629 AGGGTAAAAGATTGGATTGTCCTCAATCTGCCCTTTGATT
1 AGGGTAAAAGATTGGATTG-CTTCAATCTGCCCTTTGATT
* *
11186669 AGCGTAAAAGATTGGATTGCTTCAATCTGCCCTCT-AGTT
1 AGGGTAAAAGATTGGATTGCTTCAATCTGCCCTTTGA-TT
* * * * *
11186708 AGGGTAAAAGATTGGATAGTTTTCAATCAG-CCTCATGATC
1 AGGGTAAAAGATTGGATTG-CTTCAATCTGCCCT-TTGATT
*
11186748 GGGGTAAAAGATTGGATTGCTTCAATCTGCCCTTTGATT
1 AGGGTAAAAGATTGGATTGCTTCAATCTGCCCTTTGATT
* * * * *
11186787 AGGCTAAAAGATTGGATGGTCTTCAATTTGCCCTCTGGTT
1 AGGGTAAAAGATTGGATTG-CTTCAATCTGCCCTTTGATT
* *
11186827 AGGGTAAAAGACTGGATTGCTTCAATCTGCCCTTTGGTT
1 AGGGTAAAAGATTGGATTGCTTCAATCTGCCCTTTGATT
11186866 AGGGT-AAAGATT
1 AGGGTAAAAGATT
11186878 AGATGTTGTA
Statistics
Matches: 212, Mismatches: 31, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
38 7 0.03
39 87 0.41
40 83 0.39
41 1 0.00
42 2 0.01
43 1 0.00
44 4 0.02
45 27 0.13
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (39 bp):
AGGGTAAAAGATTGGATTGCTTCAATCTGCCCTTTGATT
Found at i:11186724 original size:79 final size:78
Alignment explanation
Indices: 11186627--11186877 Score: 308
Period size: 79 Copynumber: 3.2 Consensus size: 78
11186617 CTCTATAACT
* * * *
11186627 TTAGGGTAAAAGATTGGATTGTCCTCAATCTGCCCTTTGATTAGCGTAAAAGATTGGATTGCTTC
1 TTAGGGTAAAAGATTGGATAGTCTTCAATCTGCCCTATGATTAGGGTAAAAGATTGGATTGCTTC
11186692 AATCTGCCCTCTAG
66 AATCTGCCCT-TAG
* * **
11186706 TTAGGGTAAAAGATTGGATAGTTTTCAATCAG-CCTCATGATCGGGGTAAAAGATTGGATTGCTT
1 TTAGGGTAAAAGATTGGATAGTCTTCAATCTGCCCT-ATGATTAGGGTAAAAGATTGGATTGCTT
*
11186770 CAATCTGCCCTTTG
65 CAATCTGCCCTTAG
* * * * * *
11186784 ATTAGGCTAAAAGATTGGATGGTCTTCAATTTGCCCTCTGGTTAGGGTAAAAGACTGGATTGCTT
1 -TTAGGGTAAAAGATTGGATAGTCTTCAATCTGCCCTATGATTAGGGTAAAAGATTGGATTGCTT
*
11186849 CAATCTGCCCTTTGG
65 CAATCTGCCC-TTAG
11186864 TTAGGGT-AAAGATT
1 TTAGGGTAAAAGATT
11186878 AGATGTTGTA
Statistics
Matches: 147, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
78 12 0.08
79 129 0.88
80 6 0.04
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (78 bp):
TTAGGGTAAAAGATTGGATAGTCTTCAATCTGCCCTATGATTAGGGTAAAAGATTGGATTGCTTC
AATCTGCCCTTAG
Found at i:11186996 original size:50 final size:50
Alignment explanation
Indices: 11186942--11187038 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
11186932 GACTTTAATT
* *
11186942 TGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCATTGCGGCTTCATTC
1 TGCCCCTCTACAACTTTAGGTGAATGAGATTTCCCATTGCGGCTTCATTC
* * *
11186992 TGCCCTTCTACAACTTTAGGTGTATGAGATTTCCCATTGCGGTTTCA
1 TGCCCCTCTACAACTTTAGGTGAATGAGATTTCCCATTGCGGCTTCA
11187039 ATCTACACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.36
Consensus pattern (50 bp):
TGCCCCTCTACAACTTTAGGTGAATGAGATTTCCCATTGCGGCTTCATTC
Found at i:11187059 original size:50 final size:50
Alignment explanation
Indices: 11186951--11187059 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
11186941 TTGCCCCTCT
* * * *
11186951 ACAGCTTTAGGTGAATGAGATTTGCCATTGCGGCTTCATTCTGCCCTTCT
1 ACAGCTTTAGGTGAATGAGATTTCCCATTGCGGCTTCAATCTACCCTTCC
* * *
11187001 ACAACTTTAGGTGTATGAGATTTCCCATTGCGGTTTCAATCTACACC-TCC
1 ACAGCTTTAGGTGAATGAGATTTCCCATTGCGGCTTCAATCTAC-CCTTCC
*
11187051 ATAGCTTTA
1 ACAGCTTTA
11187060 AGGGTAAAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 47 0.96
51 2 0.04
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (50 bp):
ACAGCTTTAGGTGAATGAGATTTCCCATTGCGGCTTCAATCTACCCTTCC
Found at i:11197056 original size:25 final size:26
Alignment explanation
Indices: 11197010--11197060 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
11197000 GATTTGATTA
11197010 TTTCCATTAAAAAAAACCAACCCATTC
1 TTTCCATTAAAAAAAA-CAACCCATTC
* *
11197037 TTTCTATTAAAAACAA-AACCCATT
1 TTTCCATTAAAAAAAACAACCCATT
11197061 TTTTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
27 14 0.64
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.29
Consensus pattern (26 bp):
TTTCCATTAAAAAAAACAACCCATTC
Found at i:11197642 original size:11 final size:12
Alignment explanation
Indices: 11197626--11197655 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
11197616 TTTATTTATT
11197626 TAATAAAT-AAA
1 TAATAAATAAAA
11197637 TAATAAATAAAA
1 TAATAAATAAAA
11197649 TAATAAA
1 TAATAAA
11197656 ATTTGGGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAATAAATAAAA
Found at i:11198125 original size:28 final size:28
Alignment explanation
Indices: 11198093--11198186 Score: 143
Period size: 28 Copynumber: 3.4 Consensus size: 28
11198083 GTAACCTCTA
*
11198093 AAAGGAAAGTCTTTGTGGCGAATCTTTG
1 AAAGGAAAGCCTTTGTGGCGAATCTTTG
* *
11198121 AAAGGAAAGCCTTTGTGGAGAACCTTTG
1 AAAGGAAAGCCTTTGTGGCGAATCTTTG
*
11198149 AAAGGAAAGCCTTTGTGGCAAATCTTTG
1 AAAGGAAAGCCTTTGTGGCGAATCTTTG
*
11198177 AAACGAAAGC
1 AAAGGAAAGC
11198187 ATTGGAAAGC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.26
Consensus pattern (28 bp):
AAAGGAAAGCCTTTGTGGCGAATCTTTG
Found at i:11198163 original size:15 final size:15
Alignment explanation
Indices: 11198116--11198163 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
11198106 TGTGGCGAAT
11198116 CTTTGAAAGGAAAGC
1 CTTTGAAAGGAAAGC
*
11198131 CTTTG--TGGAGAA-C
1 CTTTGAAAGGA-AAGC
11198144 CTTTGAAAGGAAAGC
1 CTTTGAAAGGAAAGC
11198159 CTTTG
1 CTTTG
11198164 TGGCAAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
13 9 0.33
14 4 0.15
15 14 0.52
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (15 bp):
CTTTGAAAGGAAAGC
Found at i:11198194 original size:38 final size:38
Alignment explanation
Indices: 11198152--11198227 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
11198142 ACCTTTGAAA
11198152 GGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCATT
1 GGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCATT
11198190 GGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCATT
1 GGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCATT
11198228 TGTGGTGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (38 bp):
GGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCATT
Found at i:11198196 original size:66 final size:66
Alignment explanation
Indices: 11198124--11198252 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 66
11198114 ATCTTTGAAA
* * *
11198124 GGAAAGCCTTTGTGG-AGAACCTTTGAAAGGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCA
1 GGAAAGCCTTTGTGGCA-AACCTTTGAAACGAAAGCATTTGTGGCAAACCTTTGAAACGAAAGCA
11198188 TT
65 TT
* ** *
11198190 GGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCATTTGTGGTGAACCTTTGAAAGGAAAGC
1 GGAAAGCCTTTGTGGCAAACCTTTGAAACGAAAGCATTTGTGGCAAACCTTTGAAACGAAAGC
11198253 CTTTTTGGTG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 54 0.98
67 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (66 bp):
GGAAAGCCTTTGTGGCAAACCTTTGAAACGAAAGCATTTGTGGCAAACCTTTGAAACGAAAGCAT
T
Found at i:11198270 original size:94 final size:94
Alignment explanation
Indices: 11198096--11198273 Score: 275
Period size: 94 Copynumber: 1.9 Consensus size: 94
11198086 ACCTCTAAAA
* * * *
11198096 GGAAAGTCTTTGTGGCGAATCTTTGAAAGGAAAGCCTTTGTGGAGAACCTTTGAAAGGAAAGCCT
1 GGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCATTTGTGGAGAACCTTTGAAAGGAAAGCCT
*
11198161 TTGTGGCAAATCTTTGAAACGAAAGCATT
66 TTGTGGCAAACCTTTGAAACGAAAGCATT
*
11198190 GGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCATTTGTGGTGAACCTTTGAAAGGAAAGCCT
1 GGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCATTTGTGGAGAACCTTTGAAAGGAAAGCCT
* **
11198255 TTTTGGTGAACCTTTGAAA
66 TTGTGGCAAACCTTTGAAA
11198274 AGGGAAGCCT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 75 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (94 bp):
GGAAAGCCTTTGTGGCAAATCTTTGAAACGAAAGCATTTGTGGAGAACCTTTGAAAGGAAAGCCT
TTGTGGCAAACCTTTGAAACGAAAGCATT
Found at i:11198285 original size:29 final size:28
Alignment explanation
Indices: 11198190--11198285 Score: 120
Period size: 28 Copynumber: 3.4 Consensus size: 28
11198180 CGAAAGCATT
** *
11198190 GGAAAGCCTTTGTGGCAAATCTTTGAAA
1 GGAAAGCCTTTGTGGTGAACCTTTGAAA
* *
11198218 CGAAAGCATTTGTGGTGAACCTTTGAAA
1 GGAAAGCCTTTGTGGTGAACCTTTGAAA
*
11198246 GGAAAGCCTTTTTGGTGAACCTTTGAAAA
1 GGAAAGCCTTTGTGGTGAACCTTTG-AAA
*
11198275 GGGAAGCCTTT
1 GGAAAGCCTTT
11198286 ATGGAGAATG
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
28 45 0.78
29 13 0.22
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (28 bp):
GGAAAGCCTTTGTGGTGAACCTTTGAAA
Found at i:11206968 original size:41 final size:40
Alignment explanation
Indices: 11206873--11207033 Score: 151
Period size: 41 Copynumber: 3.9 Consensus size: 40
11206863 GCGTTTGGAC
* * * *
11206873 AGAAAACGCCGCAAAAGGTAAAGCAATAACGGCATTTATAAA
1 AGAAAACGCCGCTAAAGGTAAAGCAATAGCGACGTTTAT--A
* * *
11206915 AAAAAACGCCGCTAAAGGTCAAAGCATTAGCGACGTTTATG
1 AGAAAACGCCGCTAAAGGT-AAAGCAATAGCGACGTTTATA
* * * ** *
11206956 AGAAAACGCCGCTAAAAGTCAGAGCACTAGCGGTGTTTATT
1 AGAAAACGCCGCTAAAGGT-AAAGCAATAGCGACGTTTATA
* *
11206997 TGAAAACGCCGCTAAAGGTTAAGCAATAGCGACGTTT
1 AGAAAACGCCGCTAAAGGTAAAGCAATAGCGACGTTT
11207034 TTTCCAATAA
Statistics
Matches: 97, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
40 13 0.13
41 51 0.53
42 17 0.18
43 16 0.16
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (40 bp):
AGAAAACGCCGCTAAAGGTAAAGCAATAGCGACGTTTATA
Found at i:11208248 original size:31 final size:29
Alignment explanation
Indices: 11208180--11208240 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
11208170 TTCATTCAAT
* * * *
11208180 ATGCAATATTATATATAAATTTTGATTTT
1 ATGCAATTTTATATATAAATATTAATTTG
11208209 ATGCAATTTTATATATTAAATATTAATTTG
1 ATGCAATTTTATATA-TAAATATTAATTTG
11208239 AT
1 AT
11208241 TCAAATTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (29 bp):
ATGCAATTTTATATATAAATATTAATTTG
Found at i:11208561 original size:21 final size:22
Alignment explanation
Indices: 11208537--11208587 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
11208527 ACTAATAATT
11208537 TAATTTTAAACC-AT-TTTATCA
1 TAATTTTAAACCAATATTTAT-A
11208558 TAA-TTTAAACCAATATTTATA
1 TAATTTTAAACCAATATTTATA
*
11208579 AAATTTTAA
1 TAATTTTAA
11208588 GGATATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 8 0.31
21 8 0.31
22 10 0.38
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATTTTAAACCAATATTTATA
Found at i:11208698 original size:42 final size:43
Alignment explanation
Indices: 11208633--11208747 Score: 137
Period size: 42 Copynumber: 2.7 Consensus size: 43
11208623 AAGAAATAGT
*
11208633 GGCGTTTATGGAAAAAACGCCGCAAAAGATCCAGAG-CATTAGC
1 GGCGTTTATGGGAAAAACGCCGCAAAAGATCCAG-GTCATTAGC
* * * *
11208676 GGCTTTTATTGG-AAAACTCCGCAAAATG-TCCAGGTCATTAGT
1 GGCGTTTATGGGAAAAACGCCGCAAAA-GATCCAGGTCATTAGC
*
11208718 GGCGTTTATGGGAAAAACGCCGCTAAAGAT
1 GGCGTTTATGGGAAAAACGCCGCAAAAGAT
11208748 ATAGCAATAG
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
41 1 0.02
42 35 0.59
43 23 0.39
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (43 bp):
GGCGTTTATGGGAAAAACGCCGCAAAAGATCCAGGTCATTAGC
Found at i:11212812 original size:122 final size:121
Alignment explanation
Indices: 11212462--11213075 Score: 972
Period size: 122 Copynumber: 5.1 Consensus size: 121
11212452 AAAAACAACT
*
11212462 CAAATATTTAATTCAAAATAGTAAATTATTTAATTATATTTAAATAAATATT-AATTATTAAAAA
1 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
** *
11212526 -AAACTCA-ATT-AAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACT
66 CAAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACC
* *
11212579 AAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAAT-AATAATAAATTATTAAAAA
1 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
*
11212643 CAGAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTATTAAACTCTAAACC
66 CA-AACAAATATTAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACC
* *
11212700 CAAATATTTAATTTAAAATATTAAATAATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
1 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
*
11212765 CAGAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTATTAAATCCTAAACC
66 CA-AACAAATATTAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACC
11212822 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
1 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
**
11212887 -AAACTCA-ATTAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACC
66 CAAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACC
* * *
11212941 AAAATATTTAATTAAAAATATTTAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
1 CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
* * * *
11213006 CAACCGAATTATTTAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAATC
66 CAAAC-AAATATTAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACC
*
11213063 CAACTATTTAATT
1 CAAATATTTAATT
11213076 ATTAAAAACA
Statistics
Matches: 459, Mismatches: 29, Indels: 13
0.92 0.06 0.03
Matches are distributed among these distances:
116 5 0.01
117 55 0.12
118 1 0.00
119 112 0.24
120 10 0.02
121 84 0.18
122 192 0.42
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (121 bp):
CAAATATTTAATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA
CAAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACC
Found at i:11212960 original size:14 final size:14
Alignment explanation
Indices: 11212941--11212968 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11212931 ACCCTAAACC
11212941 AAAATATTTAATTA
1 AAAATATTTAATTA
11212955 AAAATATTTAATTA
1 AAAATATTTAATTA
11212969 TTTAATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATATTTAATTA
Found at i:11212988 original size:241 final size:241
Alignment explanation
Indices: 11212463--11213075 Score: 968
Period size: 241 Copynumber: 2.5 Consensus size: 241
11212453 AAAACAACTC
* *
11212463 AAATATTTAATTCAAAATAGTAAATTATTTAATTATATTTAAATAAATATT-AATTATTAAAAA-
1 AAATATTTAATTAAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAAC
** **
11212526 AAACTCA-ATTAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACTAAAATATTTAA
66 AAACAAATATTAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACCCAAATATTTAA
11212590 TTCAAAATATTAAATTATTTAATTATATTTAAATAATAATAAATTATTAAAAACAGAACAAATAT
131 TTCAAAATATTAAATTATTTAATTATATTTAAATAATAATAAATTATTAAAAACAGAACAAATAT
* *
11212655 TAAAATAATTAATTATTTAATTAGTTATTTATTAAACTCTAAACCC
196 TAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACCA
* *
11212701 AAATATTTAATTTAAAATATTAAATAATTTAATTATATTTAAATAAATATTAAATTATTAAAAAC
1 AAATATTTAATTAAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAAC
*
11212766 AGAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTATTAAATCCTAAACCCAAATATTT
66 A-AACAAATATT-AAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACCCAAATATTT
* **
11212831 AATTCAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAA-A-AACTCA
129 AATTCAAAATATTAAATTATTTAATTATATTTAAAT-AATAATAAATTATTAAAAACAGAACAAA
11212894 -ATTAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACCA
193 TATTAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACCA
*
11212942 AAATATTTAATTAAAAATATTTAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAAC
1 AAATATTTAATTAAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAAC
* * * *
11213007 AACCGAATTATTTAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAATCCAACTATTT
66 AAAC-AAATA-TTAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACCCAAATATTT
11213072 AATT
129 AATT
11213076 ATTAAAAACA
Statistics
Matches: 346, Mismatches: 21, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
238 48 0.14
239 12 0.03
240 3 0.01
241 170 0.49
242 9 0.03
243 86 0.25
244 18 0.05
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.42
Consensus pattern (241 bp):
AAATATTTAATTAAAAATATTAAATTATTTAATTATATTTAAATAAATATTAAATTATTAAAAAC
AAACAAATATTAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACCCAAATATTTAA
TTCAAAATATTAAATTATTTAATTATATTTAAATAATAATAAATTATTAAAAACAGAACAAATAT
TAAAATAATTAATTATTTAATTAGTTATTTATTAAACCCTAAACCA
Found at i:11219219 original size:43 final size:42
Alignment explanation
Indices: 11219139--11219314 Score: 217
Period size: 43 Copynumber: 4.1 Consensus size: 42
11219129 ATATGTTAAT
*
11219139 TTTAGCTGCGTTTGTGGAAAAGTGCCGCTAAAGACCATGTTC
1 TTTAGCTGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGTTC
* **
11219181 TGTAGCTGCGTTTGTGGTTGAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCTGCGTTTGTGG-AAAAGCGCCGCTAAAGACCATGTTC
* * * *
11219224 TTTAGCAGTGTTTTTGGAAAAAGCGCCGCAAAAGACCATGTTC
1 TTTAGCTGCGTTTGTGG-AAAAGCGCCGCTAAAGACCATGTTC
* * * *
11219267 TTTAGCGGCGTTTGTGGGAAAGCACCGCTAAATACCATGTTC
1 TTTAGCTGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGTTC
*
11219309 TATAGC
1 TTTAGC
11219315 GGTGTTTTTC
Statistics
Matches: 113, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
42 42 0.37
43 71 0.63
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (42 bp):
TTTAGCTGCGTTTGTGGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:11219309 original size:85 final size:84
Alignment explanation
Indices: 11219139--11219323 Score: 237
Period size: 85 Copynumber: 2.2 Consensus size: 84
11219129 ATATGTTAAT
* * * * * *
11219139 TTTAGCTGCGTTTGTGGAAAAGTGCCGCTAAAGACCATGTTCTGTAGCTGCGTTTGTGGTTGAAG
1 TTTAGCAGTGTTTTTGGAAAAGCGCCGCAAAAGACCATGTTCTGTAGCGGCGTTTGTGG-TGAAG
*
11219204 CGCCGCTAAAGACCATGTTC
65 CACCGCTAAAGACCATGTTC
*
11219224 TTTAGCAGTGTTTTTGGAAAAAGCGCCGCAAAAGACCATGTTCTTTAGCGGCGTTTGTGG-GAAA
1 TTTAGCAGTGTTTTTGG-AAAAGCGCCGCAAAAGACCATGTTCTGTAGCGGCGTTTGTGGTG-AA
*
11219288 GCACCGCTAAATACCATGTTC
64 GCACCGCTAAAGACCATGTTC
* *
11219309 TATAGCGGTGTTTTT
1 TTTAGCAGTGTTTTT
11219324 CCTCATAAAC
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
84 1 0.01
85 48 0.55
86 38 0.44
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (84 bp):
TTTAGCAGTGTTTTTGGAAAAGCGCCGCAAAAGACCATGTTCTGTAGCGGCGTTTGTGGTGAAGC
ACCGCTAAAGACCATGTTC
Found at i:11223557 original size:24 final size:24
Alignment explanation
Indices: 11223524--11223575 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
11223514 TTTTTAGGTC
* *
11223524 AAATAAATTATGCTAATAAATATT
1 AAATAAATTATACTAATAAATACT
*
11223548 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
11223572 AAAT
1 AAAT
11223576 CTTCTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:11243987 original size:12 final size:12
Alignment explanation
Indices: 11243970--11243998 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
11243960 TCCCGATAAA
11243970 GAGGACCTTTCC
1 GAGGACCTTTCC
11243982 GAGGACCTTTCC
1 GAGGACCTTTCC
11243994 GAGGA
1 GAGGA
11243999 ATTTTTGGGT
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:0.21, C:0.28, G:0.31, T:0.21
Consensus pattern (12 bp):
GAGGACCTTTCC
Found at i:11245651 original size:24 final size:24
Alignment explanation
Indices: 11245624--11245714 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
11245614 AGACAAAGTT
11245624 GAGGGTGAGGATGAAGATGAAGCA
1 GAGGGTGAGGATGAAGATGAAGCA
*
11245648 GAGGGTGAGGATGAAGATGAAGCC
1 GAGGGTGAGGATGAAGATGAAGCA
* ***
11245672 GAGGGTGGGGATGAAGATGAAATT
1 GAGGGTGAGGATGAAGATGAAGCA
11245696 GAGGGTG-GAGATGAAGATG
1 GAGGGTGAG-GATGAAGATG
11245715 GAGACGACAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 1 0.02
24 60 0.98
ACGTcount: A:0.34, C:0.03, G:0.47, T:0.15
Consensus pattern (24 bp):
GAGGGTGAGGATGAAGATGAAGCA
Found at i:11247923 original size:21 final size:21
Alignment explanation
Indices: 11247899--11247952 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
11247889 CTTATGATAG
11247899 TTCTACCGATACAAATGTA-AC
1 TTCTACCGATACAAAT-TATAC
* * *
11247920 TTCTACCGAAATAAATTATGC
1 TTCTACCGATACAAATTATAC
11247941 TTCTACCGATAC
1 TTCTACCGATAC
11247953 TAAAAACTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.31
Consensus pattern (21 bp):
TTCTACCGATACAAATTATAC
Found at i:11248675 original size:25 final size:25
Alignment explanation
Indices: 11248647--11248711 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
11248637 AGCTCATATG
*
11248647 AGCCTAGATAAGGTTAGCTCTTACT
1 AGCCTAGATAAAGTTAGCTCTTACT
*
11248672 AGCCCAGATAAAGTTAGCTCTTACT
1 AGCCTAGATAAAGTTAGCTCTTACT
*
11248697 AGCCTAGATAGAGTT
1 AGCCTAGATAAAGTT
11248712 TAAACAGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (25 bp):
AGCCTAGATAAAGTTAGCTCTTACT
Found at i:11253998 original size:17 final size:17
Alignment explanation
Indices: 11253976--11254009 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11253966 TTTTTATCCT
*
11253976 TTTTTACTTTAAATTTA
1 TTTTTAATTTAAATTTA
11253993 TTTTTAATTTAAATTTA
1 TTTTTAATTTAAATTTA
11254010 ATCCTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTAATTTAAATTTA
Found at i:11255641 original size:47 final size:47
Alignment explanation
Indices: 11255565--11255676 Score: 161
Period size: 47 Copynumber: 2.4 Consensus size: 47
11255555 TCCAAAAGGT
* **
11255565 TTGAACTCGTGACCGCATAACGATTGTCAACTGGCCCCCAATTATAC
1 TTGAACCCGTGACCGCATAACGACCGTCAACTGGCCCCCAATTATAC
* * *
11255612 TTGAACCCGTGATCGCATAATGACCGTCAACTGGCCCCCGATTATAC
1 TTGAACCCGTGACCGCATAACGACCGTCAACTGGCCCCCAATTATAC
*
11255659 TTGAACCCATGACCGCAT
1 TTGAACCCGTGACCGCAT
11255677 CACGTTCACC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (47 bp):
TTGAACCCGTGACCGCATAACGACCGTCAACTGGCCCCCAATTATAC
Found at i:11255957 original size:26 final size:26
Alignment explanation
Indices: 11255900--11255959 Score: 86
Period size: 25 Copynumber: 2.3 Consensus size: 26
11255890 ACTCTAATTC
11255900 TTAAAAAAACCATAACCCTAACAAAA
1 TTAAAAAAACCATAACCCTAACAAAA
* * *
11255926 TT-AAAAAACCTTAACCCTAATAGAA
1 TTAAAAAAACCATAACCCTAACAAAA
11255951 TTAAAAAAA
1 TTAAAAAAA
11255960 GATTAGGGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 22 0.73
26 8 0.27
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (26 bp):
TTAAAAAAACCATAACCCTAACAAAA
Found at i:11256251 original size:15 final size:15
Alignment explanation
Indices: 11256231--11256282 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
11256221 AAAATAGAAA
*
11256231 GAAAATTGGAAAGAT
1 GAAAATTAGAAAGAT
*
11256246 GAAAATTTGAAAGGAT
1 GAAAATTAGAAA-GAT
* *
11256262 AGAAAAATAGAAAGTT
1 -GAAAATTAGAAAGAT
11256278 GAAAA
1 GAAAA
11256283 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 16 0.52
16 5 0.16
17 10 0.32
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (15 bp):
GAAAATTAGAAAGAT
Found at i:11276692 original size:12 final size:12
Alignment explanation
Indices: 11276675--11276725 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
11276665 TAGGTTCAGT
11276675 TTCTTCCTTCTC
1 TTCTTCCTTCTC
11276687 TTCTTCCTT-TCC
1 TTCTTCCTTCT-C
* *
11276699 TTCTTCTTTTTTC
1 TTCTTC-CTTCTC
*
11276712 TTCATCCTTCTC
1 TTCTTCCTTCTC
11276724 TT
1 TT
11276726 GATCACCTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 1 0.03
12 22 0.69
13 8 0.25
14 1 0.03
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTTCCTTCTC
Found at i:11276700 original size:17 final size:17
Alignment explanation
Indices: 11276678--11276725 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
11276668 GTTCAGTTTC
11276678 TTCCTTCTCTTCTTCCT
1 TTCCTTCTCTTCTTCCT
* *
11276695 TTCCTTCTTCTTTTTTCT
1 TTCCTTC-TCTTCTTCCT
11276713 TCATCCTTCTCTT
1 T--TCCTTCTCTT
11276726 GATCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
18 9 0.35
19 4 0.15
20 6 0.23
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.62
Consensus pattern (17 bp):
TTCCTTCTCTTCTTCCT
Found at i:11297012 original size:15 final size:15
Alignment explanation
Indices: 11296992--11297024 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11296982 TTTCACTATC
11296992 ATACCAACTTGACCA
1 ATACCAACTTGACCA
11297007 ATACCAACTTGACCA
1 ATACCAACTTGACCA
11297022 ATA
1 ATA
11297025 TTCGTCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.30, G:0.06, T:0.21
Consensus pattern (15 bp):
ATACCAACTTGACCA
Found at i:11297416 original size:42 final size:41
Alignment explanation
Indices: 11297342--11297492 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 41
11297332 CCGAGTCATA
* * * * *
11297342 AGTCTTCCTTTTTAAACATAATCTCACGCTCATTCTGAGTCATG
1 AGTCTTCC--TTTAATCATATTCTCACTCTCATCCT-AGACATG
* *
11297386 GGTCTTCCTTTAATCTTATTCTCACTCTCATCCCTAGACATG
1 AGTCTTCCTTTAATCATATTCTCACTCTCAT-CCTAGACATG
* *
11297428 AGTCTTCCTTTAGTCATATTCTCATTCTCATCCTAAGACATG
1 AGTCTTCCTTTAATCATATTCTCACTCTCATCCT-AGACATG
* *
11297470 AGTCTTCCTTAAAT-ATATCCTCA
1 AGTCTTCCTTTAATCATATTCTCA
11297493 TGCTCGTTTC
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
41 11 0.12
42 71 0.78
43 2 0.02
44 7 0.08
ACGTcount: A:0.24, C:0.27, G:0.09, T:0.40
Consensus pattern (41 bp):
AGTCTTCCTTTAATCATATTCTCACTCTCATCCTAGACATG
Found at i:11306643 original size:43 final size:43
Alignment explanation
Indices: 11306582--11306685 Score: 154
Period size: 43 Copynumber: 2.4 Consensus size: 43
11306572 TGCGGATTCT
* * **
11306582 CCATAGCTCATGTAAGCAGCATCATGTAGTTTAACATCCCGAC
1 CCATAGCTCGTGTGAGCAGCATCATGTAGTCCAACATCCCGAC
*
11306625 CCATAGCTCGTGTGAGCAGCATCATGTAGTCCAGCATCCCGAC
1 CCATAGCTCGTGTGAGCAGCATCATGTAGTCCAACATCCCGAC
*
11306668 CCACAGCTCGTGTGAGCA
1 CCATAGCTCGTGTGAGCA
11306686 TTATAGGATA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.22
Consensus pattern (43 bp):
CCATAGCTCGTGTGAGCAGCATCATGTAGTCCAACATCCCGAC
Found at i:11308173 original size:55 final size:56
Alignment explanation
Indices: 11308070--11308209 Score: 162
Period size: 55 Copynumber: 2.5 Consensus size: 56
11308060 CGATGGACTA
* * *
11308070 CTTACGTCTCGGTTAGAGCGTAATGTTATGTATAGCTCGGGTTGAGCTTTGGAA-TG
1 CTTATGTCTCGGTTAGAGCGTAATGCTATGTATAGCCCGGGTTGAGCTTT-GAACTG
*
11308126 CTTATGTCTCGGGTAGAGCGTACA-GCTAT-TATAGCCCGGGTAT-AGCTTTGAACTG
1 CTTATGTCTCGGTTAGAGCGTA-ATGCTATGTATAGCCCGGGT-TGAGCTTTGAACTG
* * *
11308181 CTGATGTCTCGGTTAGAGCATAAGGCTAT
1 CTTATGTCTCGGTTAGAGCGTAATGCTAT
11308210 TTTAGCTCAT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
54 4 0.05
55 43 0.59
56 25 0.34
57 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (56 bp):
CTTATGTCTCGGTTAGAGCGTAATGCTATGTATAGCCCGGGTTGAGCTTTGAACTG
Found at i:11309564 original size:35 final size:35
Alignment explanation
Indices: 11309518--11309610 Score: 159
Period size: 35 Copynumber: 2.7 Consensus size: 35
11309508 TATTCGTTTA
11309518 CTCCCTGTTGACCCAAAGGTCATTATGCTCATTTT
1 CTCCCTGTTGACCCAAAGGTCATTATGCTCATTTT
* *
11309553 CTCCCTATTGACCCAAAGTTCATTATGCTCATTTT
1 CTCCCTGTTGACCCAAAGGTCATTATGCTCATTTT
*
11309588 CTCCCTGTTAACCCAAAGGTCAT
1 CTCCCTGTTGACCCAAAGGTCAT
11309611 GCCTTTTACC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (35 bp):
CTCCCTGTTGACCCAAAGGTCATTATGCTCATTTT
Found at i:11312451 original size:21 final size:21
Alignment explanation
Indices: 11312427--11312472 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
11312417 ACGGTTTGAG
*
11312427 ACACAAGCATGTAGAGTTGCC
1 ACACAAGCATGTAGAGTAGCC
*
11312448 ACACAAGCATGTGGAGTAGCC
1 ACACAAGCATGTAGAGTAGCC
11312469 ACAC
1 ACAC
11312473 GATCGTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (21 bp):
ACACAAGCATGTAGAGTAGCC
Found at i:11324214 original size:27 final size:27
Alignment explanation
Indices: 11324184--11324239 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
11324174 CATACCTTCC
*
11324184 ACGCTCTCAGTTCAACCATGGCGAAAT
1 ACGCTCTCAGTTCAACCACGGCGAAAT
11324211 ACGCTCTCAGTTCAACCACGGCGAAAT
1 ACGCTCTCAGTTCAACCACGGCGAAAT
11324238 AC
1 AC
11324240 TGAAGTAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (27 bp):
ACGCTCTCAGTTCAACCACGGCGAAAT
Found at i:11328737 original size:12 final size:12
Alignment explanation
Indices: 11328720--11328752 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
11328710 AAACGCATAT
11328720 AAGAAGAAGGAG
1 AAGAAGAAGGAG
11328732 AAGAAGAAGGAG
1 AAGAAGAAGGAG
*
11328744 AAGGAGAAG
1 AAGAAGAAG
11328753 CCATTTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGGAG
Found at i:11331166 original size:12 final size:12
Alignment explanation
Indices: 11331149--11331178 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
11331139 AGTATTCAAC
11331149 AATAAAATTACT
1 AATAAAATTACT
11331161 AAT-AAATTACT
1 AATAAAATTACT
11331172 AATAAAA
1 AATAAAA
11331179 AGTAATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (12 bp):
AATAAAATTACT
Found at i:11332921 original size:21 final size:21
Alignment explanation
Indices: 11332897--11332947 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
11332887 ACAGTGCAGA
* * *
11332897 CTTCTACCGATACAAGTGAAG
1 CTTCTACCGAAACAAATCAAG
*
11332918 CTTCTACCGAAACAAATCATG
1 CTTCTACCGAAACAAATCAAG
11332939 CTTCTACCG
1 CTTCTACCG
11332948 GTACTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.25
Consensus pattern (21 bp):
CTTCTACCGAAACAAATCAAG
Found at i:11334655 original size:3 final size:3
Alignment explanation
Indices: 11334647--11334671 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11334637 TCAGCTTATT
11334647 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
11334672 GAAAACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:11341184 original size:56 final size:56
Alignment explanation
Indices: 11341124--11341279 Score: 167
Period size: 56 Copynumber: 2.8 Consensus size: 56
11341114 GTCATCACTC
** *
11341124 AAAAATAATTTTTTTATCTAAAAAAGGTTGTGATGAGCATGTCTTAACAAGCACCA
1 AAAAATAATTTTTTTATCTAAAAAAGGAGGTGATGAGCATGGCTTAACAAGCACCA
* * * ** *
11341180 AAAAA-ATATTTTTTTATTTGAAAAAGGAGGTGATGATCATGGCTTGGCAATCACCA
1 AAAAATA-ATTTTTTTATCTAAAAAAGGAGGTGATGAGCATGGCTTAACAAGCACCA
*
11341236 AAAAAT-ATTTTTTTATCTGAAAAAA--AGGATGATGACCATGGCTT
1 AAAAATAATTTTTTTATCT-AAAAAAGGAGG-TGATGAGCATGGCTT
11341280 GACCATCATC
Statistics
Matches: 84, Mismatches: 12, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
54 3 0.04
55 26 0.31
56 55 0.65
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (56 bp):
AAAAATAATTTTTTTATCTAAAAAAGGAGGTGATGAGCATGGCTTAACAAGCACCA
Found at i:11341245 original size:55 final size:56
Alignment explanation
Indices: 11341124--11341282 Score: 187
Period size: 55 Copynumber: 2.8 Consensus size: 56
11341114 GTCATCACTC
* ** * * *
11341124 AAAAATAATTTTTTTATCTAAAAAAGGTTGTGATGAGCATGTCTTAACAAGCACCAA
1 AAAAAT-ATTTTTTTATCTGAAAAAGGAGGTGATGACCATGGCTTGACAAGCACCAA
* * * *
11341181 AAAAATATTTTTTTATTTGAAAAAGGAGGTGATGATCATGGCTTGGCAATCACC-A
1 AAAAATATTTTTTTATCTGAAAAAGGAGGTGATGACCATGGCTTGACAAGCACCAA
*
11341236 AAAAATATTTTTTTATCTGAAAAA-AAGGATGATGACCATGGCTTGAC
1 AAAAATATTTTTTTATCTGAAAAAGGAGG-TGATGACCATGGCTTGAC
11341283 CATCATCCAA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 3 0.03
55 40 0.45
56 39 0.44
57 6 0.07
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (56 bp):
AAAAATATTTTTTTATCTGAAAAAGGAGGTGATGACCATGGCTTGACAAGCACCAA
Found at i:11341302 original size:55 final size:54
Alignment explanation
Indices: 11341117--11341308 Score: 172
Period size: 55 Copynumber: 3.5 Consensus size: 54
11341107 TGACTTGGTC
* *** * * *
11341117 ATCACTCAAAAATAATTTTTTTATCTAAAAAAGGTTGTGATGAGCATGTCTTAACA
1 ATCAC-CAAAAAT-ATTTTTTTATCTGAAAAAGAAGGTGATGACCATGGCTTGACA
* * * * *
11341173 AGCACCAAAAAAATATTTTTTTATTTGAAAAAGGAGGTGATGATCATGGCTTGGCA
1 ATCACC--AAAAATATTTTTTTATCTGAAAAAGAAGGTGATGACCATGGCTTGACA
*
11341229 ATCACCAAAAAATATTTTTTTATCTGAAAAA-AAGGATGATGACCATGGCTTGACC
1 ATCACC-AAAAATATTTTTTTATCTGAAAAAGAAGG-TGATGACCATGGCTTGACA
* *
11341284 ATCATCC-AAATTTTTTTTTTATCTG
1 ATCA-CCAAAAATATTTTTTTATCTG
11341309 TCATCACCCA
Statistics
Matches: 115, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
54 19 0.17
55 45 0.39
56 45 0.39
57 6 0.05
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Consensus pattern (54 bp):
ATCACCAAAAATATTTTTTTATCTGAAAAAGAAGGTGATGACCATGGCTTGACA
Found at i:11341430 original size:137 final size:137
Alignment explanation
Indices: 11341181--11341430 Score: 346
Period size: 137 Copynumber: 1.8 Consensus size: 137
11341171 CAAGCACCAA
* * * * *
11341181 AAAAATATTTTTTTATTTGAAAAAGGAGGTGATGATCATGGCTTGGCAATCACCAAAAAATATTT
1 AAAAATATTTTTTTATCTGAAAAAGGAGATGATGATCATGACTTGACAAGCACCAAAAAATATTT
* * *
11341246 TTTTATCTGAAAAAAAGGATGATGACCATGGCTTGACCATCATCCAAATTTTTTTTTTATCTGTC
66 TTTTATCTGAAAAAAAGGATGATGACCATGGCTTGACAAGCACCCAAATTTTTTTTTTATCTGTC
11341311 ATCACCC
131 ATCACCC
*
11341318 AAAAATA-TTTTTTATCTGAAAAAGGAGATGAT-AGTTATGACTTGACAAGCACCAAAAAAATAT
1 AAAAATATTTTTTTATCTGAAAAAGGAGATGATGA-TCATGACTTGACAAGCACC-AAAAAATAT
*
11341381 TTTTTTATCT--AAAAAAGAGAGTGATGGCCATGGCTTGACAAGCACCCAAA
64 TTTTTTATCTGAAAAAAAG-GA-TGATGACCATGGCTTGACAAGCACCCAAA
11341431 AAATTTTTTT
Statistics
Matches: 99, Mismatches: 10, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
135 8 0.08
136 40 0.40
137 51 0.52
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (137 bp):
AAAAATATTTTTTTATCTGAAAAAGGAGATGATGATCATGACTTGACAAGCACCAAAAAATATTT
TTTTATCTGAAAAAAAGGATGATGACCATGGCTTGACAAGCACCCAAATTTTTTTTTTATCTGTC
ATCACCC
Found at i:11341432 original size:55 final size:55
Alignment explanation
Indices: 11341313--11341442 Score: 167
Period size: 56 Copynumber: 2.4 Consensus size: 55
11341303 TATCTGTCAT
* **
11341313 CACCCAAAAATA-TTTTTTATCTGAAAAAGGAGATGATAGTTATGACTTGACAAG
1 CACCCAAAAATATTTTTTTATCTAAAAAAGGAGATGATAGCCATGACTTGACAAG
* * *
11341367 CACCAAAAAAATATTTTTTTATCTAAAAAA-GAGAGTGATGGCCATGGCTTGACAAG
1 CACC-CAAAAATATTTTTTTATCTAAAAAAGGAGA-TGATAGCCATGACTTGACAAG
11341423 CACCCAAAAA-ATTTTTTTAT
1 CACCCAAAAATATTTTTTTAT
11341443 ATGATAAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
54 14 0.21
55 16 0.24
56 36 0.55
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (55 bp):
CACCCAAAAATATTTTTTTATCTAAAAAAGGAGATGATAGCCATGACTTGACAAG
Found at i:11341467 original size:54 final size:54
Alignment explanation
Indices: 11341358--11341521 Score: 136
Period size: 54 Copynumber: 3.0 Consensus size: 54
11341348 ATAGTTATGA
* * * * *
11341358 CTTGACAAGCACCAAAAAAATATTTTTTTATCTAAAAAAGAGAGTGAT-GGCCATGG
1 CTTGACAAGCACC-AAAAAA-ATTTTTTTATCTGATAAAGGGGGTG-TCGACCATGG
* *
11341414 CTTGACAAGCACCCAAAAAATTTTTTTATATGATAAAGGGGGTGTCGACCATGG
1 CTTGACAAGCACCAAAAAAATTTTTTTATCTGATAAAGGGGGTGTCGACCATGG
* * * * * * * *
11341468 AATGGGCGA-CACCTAAAATATTTTTTTATCTGATAAA-GGGGTGTCAATCATGG
1 -CTTGACAAGCACCAAAAAAATTTTTTTATCTGATAAAGGGGGTGTCGACCATGG
11341521 C
1 C
11341522 ATGGGCGACA
Statistics
Matches: 89, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
53 15 0.17
54 52 0.58
55 9 0.10
56 13 0.15
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (54 bp):
CTTGACAAGCACCAAAAAAATTTTTTTATCTGATAAAGGGGGTGTCGACCATGG
Found at i:11341520 original size:53 final size:54
Alignment explanation
Indices: 11341423--11341532 Score: 159
Period size: 53 Copynumber: 2.1 Consensus size: 54
11341413 GCTTGACAAG
*
11341423 CACCCAAAAAATTTTTTTATATGATAAAGGGGGTGTCGACCATGGAATGGGCGA
1 CACCCAAAAAATTTTTTTATATGATAAAGGGGGTGTCAACCATGGAATGGGCGA
* * * * *
11341477 CACCTAAAATATTTTTTTATCTGATAAA-GGGGTGTCAATCATGGCATGGGCGA
1 CACCCAAAAAATTTTTTTATATGATAAAGGGGGTGTCAACCATGGAATGGGCGA
11341530 CAC
1 CAC
11341533 AAAAAAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
53 25 0.50
54 25 0.50
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (54 bp):
CACCCAAAAAATTTTTTTATATGATAAAGGGGGTGTCAACCATGGAATGGGCGA
Found at i:11342606 original size:4 final size:4
Alignment explanation
Indices: 11342592--11342632 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
11342582 AACGAGTATT
*
11342592 GAAA AAAA GAAA GAAA GAAAA GAAA GAAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA G-AAA GAAA G-AAA GAAA GAAA GAA
11342633 GAAGGAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 25 0.76
5 8 0.24
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:11342614 original size:13 final size:13
Alignment explanation
Indices: 11342592--11342649 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
11342582 AACGAGTATT
11342592 GAAAA-AAAGAAA
1 GAAAAGAAAGAAA
11342604 G-AAAGAAAAGAAA
1 GAAAAG-AAAGAAA
11342617 GAAAAGAAAGAAA
1 GAAAAGAAAGAAA
* *
11342630 GAAGAAGGAAGAAG
1 GAA-AAGAAAGAAA
11342644 GAAAAG
1 GAAAAG
11342650 GAGAATGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
11 3 0.08
12 1 0.03
13 21 0.52
14 15 0.38
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAGAAA
Found at i:11342615 original size:9 final size:9
Alignment explanation
Indices: 11342592--11342629 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
11342582 AACGAGTATT
11342592 GAAAA-AAA
1 GAAAAGAAA
11342600 G-AAAGAAA
1 GAAAAGAAA
11342608 GAAAAGAAA
1 GAAAAGAAA
11342617 GAAAAGAAA
1 GAAAAGAAA
11342626 GAAA
1 GAAA
11342630 GAAGAAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 3 0.11
8 5 0.18
9 20 0.71
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
GAAAAGAAA
Found at i:11342700 original size:13 final size:12
Alignment explanation
Indices: 11342672--11342696 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11342662 AATGTAATGT
11342672 ATTTATTTTTAA
1 ATTTATTTTTAA
11342684 ATTTATTTTTAA
1 ATTTATTTTTAA
11342696 A
1 A
11342697 ATTTTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:11345154 original size:6 final size:6
Alignment explanation
Indices: 11345139--11345189 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
11345129 AACTCCTGCC
*
11345139 CCAGAT CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
11345187 CCA
1 CCA
11345190 AAGCAAGAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.33, C:0.35, G:0.29, T:0.02
Consensus pattern (6 bp):
CCAGAG
Found at i:11345363 original size:45 final size:45
Alignment explanation
Indices: 11345274--11345365 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
11345264 CCCTAGCTCA
* *
11345274 TCAAGCCAATGATATCAGCCTTCGTTTGACGAGCCATCACAATAC
1 TCAAGCCAAGGATATCAGCCTTCGTTTGACGAGCCACCACAATAC
* * *
11345319 TCAAGCCAAGGATATCATCC-TCAGTTTGACGAGCTACCATAATAC
1 TCAAGCCAAGGATATCAGCCTTC-GTTTGACGAGCCACCACAATAC
11345364 TC
1 TC
11345366 TACTCCTCCC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 2 0.05
45 39 0.95
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTTCGTTTGACGAGCCACCACAATAC
Found at i:11345400 original size:21 final size:21
Alignment explanation
Indices: 11345359--11345402 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11345349 GAGCTACCAT
*
11345359 AATACTCTACTCCTCCCGGGC
1 AATACTCTACTCCTCCAGGGC
* *
11345380 AATACTCTACTCTTCTAGGGC
1 AATACTCTACTCCTCCAGGGC
11345401 AA
1 AA
11345403 ATGGACCCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.27
Consensus pattern (21 bp):
AATACTCTACTCCTCCAGGGC
Found at i:11348013 original size:24 final size:24
Alignment explanation
Indices: 11347986--11348033 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
11347976 CCACCATACA
11347986 TGGAGTTGGATCTTCATTTTCTAC
1 TGGAGTTGGATCTTCATTTTCTAC
11348010 TGGAGTTGGATCTTCATTTTCTAC
1 TGGAGTTGGATCTTCATTTTCTAC
11348034 AGGTTCCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.46
Consensus pattern (24 bp):
TGGAGTTGGATCTTCATTTTCTAC
Found at i:11348467 original size:26 final size:28
Alignment explanation
Indices: 11348411--11348467 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
11348401 TTAAAAAAAA
* *
11348411 TAAAATACGAATTTAAAAATACATCATAC
1 TAAAATAC-AATTTAAAAATACAGCACAC
11348440 TAAAATA-AATTTAAAAATA-AGCACAC
1 TAAAATACAATTTAAAAATACAGCACAC
11348466 TA
1 TA
11348468 CCTTTCTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 12 0.46
29 7 0.27
ACGTcount: A:0.58, C:0.12, G:0.04, T:0.26
Consensus pattern (28 bp):
TAAAATACAATTTAAAAATACAGCACAC
Found at i:11348493 original size:19 final size:19
Alignment explanation
Indices: 11348469--11348509 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
11348459 AGCACACTAC
11348469 CTTTCTCTCCTTCTTCCTT
1 CTTTCTCTCCTTCTTCCTT
* * *
11348488 CTTTCTTTCTTTCTTTCTT
1 CTTTCTCTCCTTCTTCCTT
11348507 CTT
1 CTT
11348510 CTGCCCGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (19 bp):
CTTTCTCTCCTTCTTCCTT
Found at i:11352850 original size:21 final size:20
Alignment explanation
Indices: 11352801--11352893 Score: 62
Period size: 21 Copynumber: 4.5 Consensus size: 20
11352791 TAATAAAAAC
*
11352801 ACAAAAAAATAACAAAAATA
1 ACAAAAAAACAACAAAAATA
* *
11352821 TCAGAAAAAACAACAGAAATA
1 ACA-AAAAAACAACAAAAATA
* *
11352842 ACAACAAAAGCAACACCAAAACA
1 ACAA-AAAAACAACA--AAAATA
** *
11352865 GTAAAAAAAGC-ACCAAAATA
1 ACAAAAAAA-CAACAAAAATA
11352885 ACAAAAAAA
1 ACAAAAAAA
11352894 AAAACACTAG
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
20 15 0.28
21 26 0.48
22 6 0.11
23 7 0.13
ACGTcount: A:0.71, C:0.17, G:0.05, T:0.06
Consensus pattern (20 bp):
ACAAAAAAACAACAAAAATA
Found at i:11352911 original size:24 final size:23
Alignment explanation
Indices: 11352867--11352916 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
11352857 CCAAAACAGT
* *
11352867 AAAAAAAGCACCAAAATAACAAA
1 AAAAAAAACACCAAAACAACAAA
*
11352890 AAAAAAAACACTAGAAACAACAAA
1 AAAAAAAACACCA-AAACAACAAA
11352914 AAA
1 AAA
11352917 CAACAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.76, C:0.16, G:0.04, T:0.04
Consensus pattern (23 bp):
AAAAAAAACACCAAAACAACAAA
Found at i:11359055 original size:25 final size:26
Alignment explanation
Indices: 11359005--11359060 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
11358995 CATTTAAGTT
11359005 TAATTTTATAGATTTTAATAATTATA
1 TAATTTTATAGATTTTAATAATTATA
*
11359031 -AATTTTATATATTTATGAA-AA-TATA
1 TAATTTTATAGATTT-T-AATAATTATA
11359056 TAATT
1 TAATT
11359061 ATAGTATGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 17 0.65
26 7 0.27
27 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (26 bp):
TAATTTTATAGATTTTAATAATTATA
Found at i:11370416 original size:24 final size:24
Alignment explanation
Indices: 11370388--11370450 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
11370378 AGAAATAATC
11370388 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
11370412 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
11370436 TTTAAGTCAAACTCT
1 TTTCAGTTAAACTCT
11370451 TATTAGTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Done.