Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005031.1 Hibiscus syriacus cultivar Beakdansim tig00011290_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 257035
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2800 original size:12 final size:12
Alignment explanation
Indices: 2783--2807 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2773 CAACAACAAC
2783 AAAAATACAAAA
1 AAAAATACAAAA
2795 AAAAATACAAAA
1 AAAAATACAAAA
2807 A
1 A
2808 GAAGTGATGT
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAATACAAAA
Found at i:9086 original size:11 final size:11
Alignment explanation
Indices: 9070--9125 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
9060 ATTGGAGTGC
9070 AAAAAGAAAAG
1 AAAAAGAAAAG
9081 AAAAAGACAAA-
1 AAAAAGA-AAAG
* *
9092 AAGAAGAATCAGAA
1 AAAAAGAA--A-AG
9106 AAAAAGAAAAG
1 AAAAAGAAAAG
9117 AAAAAGAAA
1 AAAAAGAAA
9126 TTCAAAAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
10 1 0.03
11 23 0.62
12 5 0.14
13 1 0.03
14 7 0.19
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:18106 original size:23 final size:23
Alignment explanation
Indices: 18079--18127 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
18069 TTCATTATCA
18079 TATGATGCATGAGTTGTTATTAT
1 TATGATGCATGAGTTGTTATTAT
18102 TATGATGCATGAGTTGTTATTAT
1 TATGATGCATGAGTTGTTATTAT
18125 TAT
1 TAT
18128 AACCTATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.49
Consensus pattern (23 bp):
TATGATGCATGAGTTGTTATTAT
Found at i:22759 original size:19 final size:20
Alignment explanation
Indices: 22735--22783 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
22725 TATCCTTTAT
22735 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
22754 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
22774 -TATTATTATT
1 TTATT-TTATT
22784 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:23067 original size:19 final size:19
Alignment explanation
Indices: 23045--23096 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
23035 GTGCAAAAGT
23045 AAAAAGAAAAGAAAAA-CA
1 AAAAAGAAAAGAAAAAGCA
23063 CAAAAAGAAGAA-AAAAAGCA
1 -AAAAAGAA-AAGAAAAAGCA
*
23083 GAAAAGAAAAGAAA
1 AAAAAGAAAAGAAA
23097 TTCAAAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 2 0.07
19 23 0.79
20 4 0.14
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAAGCA
Found at i:24108 original size:21 final size:23
Alignment explanation
Indices: 24074--24116 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
24064 AAACACCTTG
24074 AAGAAGAACATTAAAG-CAATGA
1 AAGAAGAACATTAAAGACAATGA
*
24096 AAGAATAAC-TTAAAGACAATG
1 AAGAAGAACATTAAAGACAATG
24117 CAACTGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.58, C:0.09, G:0.16, T:0.16
Consensus pattern (23 bp):
AAGAAGAACATTAAAGACAATGA
Found at i:26474 original size:19 final size:20
Alignment explanation
Indices: 26450--26500 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
26440 CGTCCAAGAG
* *
26450 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
26469 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
26489 CATGTATTTTCA
1 CATGTATTTTCA
26501 AATGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:26937 original size:19 final size:21
Alignment explanation
Indices: 26913--26961 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 21
26903 TATCCTTTAT
26913 TTATTTTATTTT-ATT-CTTA
1 TTATTTTATTTTCATTACTTA
26932 TTA-TTTATTTTCATTACTTA
1 TTATTTTATTTTCATTACTTA
26952 -TATTATTATT
1 TTATT-TTATT
26962 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 8 0.31
19 8 0.31
20 5 0.19
21 5 0.19
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (21 bp):
TTATTTTATTTTCATTACTTA
Found at i:26940 original size:13 final size:12
Alignment explanation
Indices: 26909--26961 Score: 56
Period size: 13 Copynumber: 4.4 Consensus size: 12
26899 TCTCTATCCT
26909 TTATTTATTTTA
1 TTATTTATTTTA
26921 -T-TTTATTCTTA
1 TTATTTATT-TTA
26932 TTATTTATTTTCA
1 TTATTTATTTT-A
* *
26945 TTACTTATATTA
1 TTATTTATTTTA
26957 TTATT
1 TTATT
26962 CCCTTTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 6 0.18
11 4 0.12
12 8 0.24
13 16 0.47
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATTTATTTTA
Found at i:32412 original size:30 final size:33
Alignment explanation
Indices: 32353--32413 Score: 85
Period size: 30 Copynumber: 1.9 Consensus size: 33
32343 TTGATAACAT
32353 TTCTATCCATTTCCTTTCTTATCATTTCCATTC
1 TTCTATCCATTTCCTTTCTTATCATTTCCATTC
32386 TTCT-TCCATTT-CTTAT-TTAT-ATTTCCAT
1 TTCTATCCATTTCCTT-TCTTATCATTTCCAT
32414 CTTAATCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.30
31 7 0.26
32 8 0.30
33 4 0.15
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.57
Consensus pattern (33 bp):
TTCTATCCATTTCCTTTCTTATCATTTCCATTC
Found at i:38472 original size:13 final size:13
Alignment explanation
Indices: 38435--38472 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
38425 CTTTTTGAAC
*
38435 TTCTCTTTTTCTT
1 TTCTTTTTTTCTT
*
38448 TTCTTTTCTTCTT
1 TTCTTTTTTTCTT
38461 TTCTTTTTTTCT
1 TTCTTTTTTTCT
38473 GATTTTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:49609 original size:13 final size:13
Alignment explanation
Indices: 49586--49634 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
49576 ATTGGCTTGC
*
49586 AAAGAAAAAGAAAA
1 AAAGAAAAA-AAGA
*
49600 AAAGAAAAGAAGA
1 AAAGAAAAAAAGA
49613 ATAA-AAAAAAAGA
1 A-AAGAAAAAAAGA
49626 AAAGAAAAA
1 AAAGAAAAA
49635 GAAATTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 2 0.07
13 18 0.60
14 10 0.33
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAAGA
Found at i:49634 original size:16 final size:17
Alignment explanation
Indices: 49596--49638 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
49586 AAAGAAAAAG
49596 AAAAAAAGAAAAGAAGA
1 AAAAAAAGAAAAGAAGA
*
49613 ATAAAAA-AAAAGAA-A
1 AAAAAAAGAAAAGAAGA
*
49628 AGAAAAAGAAA
1 AAAAAAAGAAA
49639 TTCAAAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (17 bp):
AAAAAAAGAAAAGAAGA
Found at i:61537 original size:12 final size:12
Alignment explanation
Indices: 61507--61541 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
61497 TATCTTTTAT
61507 TTATCTTGTTT-
1 TTATCTTGTTTC
*
61518 TAATCTTGTTTC
1 TTATCTTGTTTC
61530 TTATCTTGTTTC
1 TTATCTTGTTTC
61542 CAGCTCCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:63159 original size:12 final size:12
Alignment explanation
Indices: 63142--63179 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
63132 GATAATTAAG
63142 AATGGAAAAGGA
1 AATGGAAAAGGA
63154 AATGGAAAAGGA
1 AATGGAAAAGGA
*
63166 AATGGAAATGGA
1 AATGGAAAAGGA
63178 AA
1 AA
63180 GAATTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.11
Consensus pattern (12 bp):
AATGGAAAAGGA
Found at i:63160 original size:6 final size:6
Alignment explanation
Indices: 63142--63179 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
63132 GATAATTAAG
* *
63142 AATGGA AAAGGA AATGGA AAAGGA AATGGA AATGGA AA
1 AATGGA AATGGA AATGGA AATGGA AATGGA AATGGA AA
63180 GAATTTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.11
Consensus pattern (6 bp):
AATGGA
Found at i:64210 original size:15 final size:15
Alignment explanation
Indices: 64190--64225 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
64180 ATTATTAGCT
*
64190 TTATAATATATGTTA
1 TTATAATATATATTA
64205 TTATAATATATATTA
1 TTATAATATATATTA
*
64220 TGATAA
1 TTATAA
64226 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:64402 original size:42 final size:42
Alignment explanation
Indices: 64343--64426 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
64333 TATACATCAA
64343 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
1 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
64385 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
1 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
64427 ATATTAACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (42 bp):
GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
Found at i:65905 original size:18 final size:19
Alignment explanation
Indices: 65866--65905 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
65856 AGCAAAGGAA
* *
65866 AAAGTACTCAAAAAGATTG
1 AAAGCACTCAAAAAGATAG
65885 AAAGCACTCAAAAAGA-AG
1 AAAGCACTCAAAAAGATAG
65903 AAA
1 AAA
65906 AAAGAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.12, G:0.15, T:0.12
Consensus pattern (19 bp):
AAAGCACTCAAAAAGATAG
Found at i:68516 original size:15 final size:15
Alignment explanation
Indices: 68496--68531 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
68486 ATTATTAGCT
*
68496 TTATAATATATGTTA
1 TTATAATATATATTA
68511 TTATAATATATATTA
1 TTATAATATATATTA
*
68526 TGATAA
1 TTATAA
68532 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:68707 original size:42 final size:42
Alignment explanation
Indices: 68648--68731 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
68638 TATACATCAA
68648 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
1 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
68690 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
1 GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
68732 ATATTAACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (42 bp):
GGCAGCATACTTATAATGCATTTCATTAGTTTATTTGCATTC
Found at i:71485 original size:24 final size:24
Alignment explanation
Indices: 71458--71509 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
71448 TCAAAATATC
71458 AAGAGACATGTCTTG-TGAATCACA
1 AAGAGACATGTCTTGTTG-ATCACA
71482 AAGAGACATGTCTTGTTGATCACA
1 AAGAGACATGTCTTGTTGATCACA
71506 AAGA
1 AAGA
71510 TTCACGCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (24 bp):
AAGAGACATGTCTTGTTGATCACA
Found at i:73510 original size:79 final size:79
Alignment explanation
Indices: 73397--73607 Score: 208
Period size: 79 Copynumber: 2.6 Consensus size: 79
73387 CATCATGTAG
* * * * *
73397 CACGTCTTGCATTCGTATTAAACAAAACAGCATGTTTATCCTTTATTTTAATTA-ACTCATGTGT
1 CACGTCTTGCA-TCTTATTCAACATAACAGCATGTTTATCATTTATTTTAATTACACTCATGTGC
* *
73461 ATTCCCATTGTTAAA
65 ATTCACATTGATAAA
* * * * *
73476 CACGTCTTGCACTCTTATTCAACATGACAACATGTTTTTCATTTAATTATAATTACCATTCATGT
1 CACGTCTTGCA-TCTTATTCAACATAACAGCATGTTTATCATTT-ATTTTAATTA-CACTCATGT
* *
73541 GCATTCATATTGATAAG
63 GCATTCACATTGATAAA
* * *
73558 CACGTTTTTGCATTTATATTCAACATAACAGCATGTTTATCATTTGTTTT
1 CACG-TCTTGCATCT-TATTCAACATAACAGCATGTTTATCATTTATTTT
73608 GTTAAATTCA
Statistics
Matches: 105, Mismatches: 22, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
79 36 0.34
80 9 0.09
82 28 0.27
83 32 0.30
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.42
Consensus pattern (79 bp):
CACGTCTTGCATCTTATTCAACATAACAGCATGTTTATCATTTATTTTAATTACACTCATGTGCA
TTCACATTGATAAA
Found at i:73674 original size:28 final size:28
Alignment explanation
Indices: 73634--73689 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
73624 CTCACATTCA
*
73634 CATAACATCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
73662 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
73690 TTAATTCACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:76599 original size:33 final size:33
Alignment explanation
Indices: 76520--76623 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
76510 ATACAATCTA
* *
76520 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
76556 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
76589 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
76622 TC
1 TC
76624 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:82134 original size:33 final size:33
Alignment explanation
Indices: 82055--82158 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
82045 ATACAATCTA
* *
82055 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
82091 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
82124 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
82157 TC
1 TC
82159 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:87666 original size:33 final size:33
Alignment explanation
Indices: 87587--87690 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
87577 ATACAATCTG
* *
87587 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
87623 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
87656 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
87689 TC
1 TC
87691 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:91080 original size:33 final size:33
Alignment explanation
Indices: 91001--91104 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
90991 ATACAATCTG
* *
91001 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
91037 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
91070 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
91103 TC
1 TC
91105 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:95115 original size:13 final size:13
Alignment explanation
Indices: 95097--95149 Score: 65
Period size: 12 Copynumber: 4.2 Consensus size: 13
95087 CCTTACATCA
95097 ATTTCATTTCTTT
1 ATTTCATTTCTTT
95110 ATTTCATTTC-TT
1 ATTTCATTTCTTT
**
95122 ATTTCAATTTAATT
1 ATTTC-ATTTCTTT
95136 ATTTC-TTTCTTT
1 ATTTCATTTCTTT
95148 AT
1 AT
95150 ATTGTGCAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 14 0.40
13 14 0.40
14 7 0.20
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTTCATTTCTTT
Found at i:100832 original size:27 final size:28
Alignment explanation
Indices: 100771--100832 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
100761 AAAGAAAATC
*
100771 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAATTGAAGCACTCAAAAAGA
* *
100799 A-AGAAAGAAATT-CAGCATTCAAAAAGA
1 AGA-AAAGAAATTGAAGCACTCAAAAAGA
100826 AGAAAAG
1 AGAAAAG
100833 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.60, C:0.11, G:0.18, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAATTGAAGCACTCAAAAAGA
Found at i:107964 original size:23 final size:24
Alignment explanation
Indices: 107922--107974 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
107912 TTTATTTCTT
107922 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
107946 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
107969 TTTCTT
1 TTTCTT
107975 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:130927 original size:27 final size:28
Alignment explanation
Indices: 130897--130958 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
130887 CGTTTGCAAT
130897 TTTTTTTGAAATTTT-GTC-TTTTTTGAC
1 TTTTTTTG-AATTTTCGTCTTTTTTTGAC
** *
130924 TTTTTTTGTTTTTTCGTCTTTTTTTGGC
1 TTTTTTTGAATTTTCGTCTTTTTTTGAC
130952 TTTTTTT
1 TTTTTTT
130959 TTGGTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 4 0.13
27 11 0.37
28 15 0.50
ACGTcount: A:0.06, C:0.08, G:0.11, T:0.74
Consensus pattern (28 bp):
TTTTTTTGAATTTTCGTCTTTTTTTGAC
Found at i:130928 original size:10 final size:9
Alignment explanation
Indices: 130915--130978 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 9
130905 AAATTTTGTC
130915 TTTTTTGACT
1 TTTTTTG-CT
130925 TTTTTTG-T
1 TTTTTTGCT
*
130933 TTTTTCGTCT
1 TTTTTTG-CT
130943 TTTTTTGGCTTT
1 TTTTTT-GC--T
*
130955 TTTTTTGGT
1 TTTTTTGCT
130964 TTTTTTG-T
1 TTTTTTGCT
130972 TTTTTTG
1 TTTTTTG
130979 AAAAAAATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
8 15 0.33
9 8 0.17
10 14 0.30
11 2 0.04
12 7 0.15
ACGTcount: A:0.02, C:0.06, G:0.14, T:0.78
Consensus pattern (9 bp):
TTTTTTGCT
Found at i:133786 original size:238 final size:238
Alignment explanation
Indices: 133368--133815 Score: 690
Period size: 238 Copynumber: 1.9 Consensus size: 238
133358 TATAGAATTG
* **
133368 GTTCTTCTTTGAGCATTCTTCAAGATACTATCCTCACAACCATCCTTTTGTTTCATCGCCATAAC
1 GTTCTTCTTTGAGCATTCTTCAAGATACTATCCTCACAACCATCCCTTTGTTTCATAACCATAAC
* * * *
133433 CATAACCATTCAATCATATTCCGCTTCCATCTCTCATTTATTAAATAGCCTACCTATTAAACCAT
66 CATAACCATTCAACCATATTCCGCTTACATCTCTCATTTATTAAACAGCCCACCTATTAAACCAT
* *
133498 ACGTTTACCACCCTTATCCATTCTATTTTGAGCCATTCACTTGTGCAGGTTGTTTTGCTTCCTTC
131 ACGTCTACCACCCTTAACCATTCTATTTTGAGCCATTCACTTGTGCAGGTTGTTTTGCTTCCTTC
133563 CTAGATCCACAATCAAACGAGAAGGTAGAATTACCTTATATCA
196 CTAGATCCACAATCAAACGAGAAGGTAGAATTACCTTATATCA
*
133606 GTTCTTCTTTGAGTC-TTCTTTAAGATACTATCCTCACAACCATCCCTTTGTTTCATAAACCATA
1 GTTCTTCTTTGAG-CATTCTTCAAGATACTATCCTCACAACCATCCCTTTGTTTCAT-AACCATA
* * *
133670 ACCATAGCCATATCAACCATCTTCCGCTTACATCTCTCA-TT-TTAAACAGCCCACCTATT-CAC
64 ACCATAACCAT-TCAACCATATTCCGCTTACATCTCTCATTTATTAAACAGCCCACCTATTAAAC
*
133732 CATACGTCTACCACCCTTAACCATTCTGTTTTTGAGCCATTCACTT-TCGCAGGTTGTTTTGCTT
128 CATACGTCTACCACCCTTAACCATTCT-ATTTTGAGCCATTCACTTGT-GCAGGTTGTTTTGCTT
133796 CCTTCCTAGATCCACAATCA
191 CCTTCCTAGATCCACAATCA
133816 TTTGTCAAGG
Statistics
Matches: 191, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
237 28 0.15
238 121 0.63
239 18 0.09
240 24 0.13
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.36
Consensus pattern (238 bp):
GTTCTTCTTTGAGCATTCTTCAAGATACTATCCTCACAACCATCCCTTTGTTTCATAACCATAAC
CATAACCATTCAACCATATTCCGCTTACATCTCTCATTTATTAAACAGCCCACCTATTAAACCAT
ACGTCTACCACCCTTAACCATTCTATTTTGAGCCATTCACTTGTGCAGGTTGTTTTGCTTCCTTC
CTAGATCCACAATCAAACGAGAAGGTAGAATTACCTTATATCA
Found at i:135181 original size:33 final size:33
Alignment explanation
Indices: 135139--135207 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
135129 GTTGATAAAT
*
135139 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
135172 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
135205 GAA
1 GAA
135208 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:139648 original size:33 final size:33
Alignment explanation
Indices: 139606--139674 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
139596 GTTGATAAAT
*
139606 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
139639 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
139672 GAA
1 GAA
139675 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:141615 original size:19 final size:19
Alignment explanation
Indices: 141562--141611 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
141552 ATAAAGGGTA
141562 AAAATATAAGTAATGAAAGG
1 AAAATATAAG-AATGAAAGG
*
141582 AAAGA-ATAAGAATGAAATG
1 AAA-ATATAAGAATGAAAGG
141601 AAAATA-AAGAA
1 AAAATATAAGAA
141612 ATGATAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 6 0.22
19 12 0.44
20 8 0.30
21 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (19 bp):
AAAATATAAGAATGAAAGG
Found at i:142063 original size:19 final size:21
Alignment explanation
Indices: 142020--142071 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
142010 GAAACCCCTT
142020 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
142041 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
142060 TGAAGATACATG
1 TGAAAATACATG
142072 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:145371 original size:19 final size:21
Alignment explanation
Indices: 145347--145398 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
145337 CGGTCAAGAG
*
145347 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
145366 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
145387 CATGTATTTTCA
1 CATGTATTTTCA
145399 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:153563 original size:330 final size:329
Alignment explanation
Indices: 152917--153576 Score: 1142
Period size: 330 Copynumber: 2.0 Consensus size: 329
152907 TTTTGAAGAC
*
152917 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCGAGTTTGAGATACAACATCAACACCATCTT
1 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGATACAACATCAACACCATCTT
152982 CATTTCATCATCAACATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGC
66 CATTTCATCATCAACATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGC
*
153047 CATCTCTATTCTTATTCTTTCATTCCATTACTTATATTATTATTCAATTCTTAAACCCATTATTA
131 CATCTCTATTCTTATTCTTTCATTCCATTACTTATATTATTATTCAATTCTTAAACCCATTACTA
* *
153112 ATCATATTTCTTTCTTATTATTTTTTTGTAGCCCAAGCTTATTAATTCAAGGGCATCAGTACTTG
196 ATCATATTTCTTTCTTATTA-TTTTTTGCAGCCCAAGCTTATTAATTCAAGGACATCAGTACTTG
* * *
153177 TCAATCTTAGATAGAGACACAATAAGGCTATCTACTCTTTTATCAAATCATGTAGATTCGCTTTA
260 TCAATCCTAGATAGAGACACAATAAGGCTATCTACTCTTTTATCAAAGCATGTAGATTCGCCTTA
153242 CATCA
325 CATCA
*
153247 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGATACAACATCACCACCATCTT
1 GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGATACAACATCAACACCATCTT
*
153312 CATTTCATCATCAACATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGT
66 CATTTCATCATCAACATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGC
*
153377 CATCTCTATTCTTATTCTTTCATTCCATTACTTATATTATTATTCATTTCTTAAACCCAATTACT
131 CATCTCTATTCTTATTCTTTCATTCCATTACTTATATTATTATTCAATTCTTAAACCC-ATTACT
*
153442 AATCATATTTCTTTCTTATTA-TTTTTGCAGCCTAAGCTTATTAATTCAAGGACATCAGTACTTG
195 AATCATATTTCTTTCTTATTATTTTTTGCAGCCCAAGCTTATTAATTCAAGGACATCAGTACTTG
* * * * *
153506 TCAATCCTAGATCGGGACACAATAAGGTTATCTACTCTTTTCATCAAAGCGTGTAGATTCTCCTT
260 TCAATCCTAGATAGAGACACAATAAGGCTATCTACTCTTTT-ATCAAAGCATGTAGATTCGCCTT
153571 ACATCA
324 ACATCA
153577 AGCGGTAATC
Statistics
Matches: 312, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
329 77 0.25
330 209 0.67
331 26 0.08
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (329 bp):
GGGATTGTGCTTCATAGCATAGTTTCCTCTTTGGCAAGTTTGAGATACAACATCAACACCATCTT
CATTTCATCATCAACATCATCAACATCCTTCATCAAGACCATCATCAATCCCATAATTCCGCAGC
CATCTCTATTCTTATTCTTTCATTCCATTACTTATATTATTATTCAATTCTTAAACCCATTACTA
ATCATATTTCTTTCTTATTATTTTTTGCAGCCCAAGCTTATTAATTCAAGGACATCAGTACTTGT
CAATCCTAGATAGAGACACAATAAGGCTATCTACTCTTTTATCAAAGCATGTAGATTCGCCTTAC
ATCA
Found at i:153688 original size:11 final size:10
Alignment explanation
Indices: 153668--153725 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
153658 ATTGGAGTGC
153668 AAAAAGAAAA
1 AAAAAGAAAA
153678 AAAAAGAAAA
1 AAAAAGAAAA
153688 AAAAA-AAAA
1 AAAAAGAAAA
* * * *
153697 CCAGAATAGAA
1 -AAAAAGAAAA
*
153708 GAAAAGAAAA
1 AAAAAGAAAA
153718 AAAAAGAA
1 AAAAAGAA
153726 TTTCAAAAAG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
9 4 0.11
10 31 0.82
11 3 0.08
ACGTcount: A:0.83, C:0.03, G:0.12, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:153702 original size:17 final size:16
Alignment explanation
Indices: 153668--153725 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 16
153658 ATTGGAGTGC
153668 AAAAAGAAAAAAAAAG
1 AAAAAGAAAAAAAAAG
153684 AAAAA-AAAAAAAACCAG
1 AAAAAGAAAAAAAA--AG
*
153701 AATAGAAGAAAAGAAAA-
1 AA-A-AAGAAAAAAAAAG
153718 AAAAAGAA
1 AAAAAGAA
153726 TTTCAAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
15 13 0.36
16 6 0.17
17 6 0.17
18 2 0.06
19 2 0.06
20 7 0.19
ACGTcount: A:0.83, C:0.03, G:0.12, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAG
Found at i:155407 original size:16 final size:16
Alignment explanation
Indices: 155386--155417 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
155376 TCTTCCACCA
*
155386 ATGTTAGAATGGAAAT
1 ATGTTAGAATGCAAAT
155402 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
155418 GAGCTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:158945 original size:16 final size:16
Alignment explanation
Indices: 158924--158955 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
158914 TCTTCCACCA
*
158924 ATGTTAGAATGGAAAT
1 ATGTTAGAATGCAAAT
158940 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
158956 GAGCTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:159369 original size:25 final size:25
Alignment explanation
Indices: 159341--159390 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
159331 ATCGTTTTCT
159341 TTGCTCAAAACGCTTCACATGTTCA
1 TTGCTCAAAACGCTTCACATGTTCA
159366 TTGCTCAAAACGCTTCACATGTTCA
1 TTGCTCAAAACGCTTCACATGTTCA
159391 AGTGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (25 bp):
TTGCTCAAAACGCTTCACATGTTCA
Found at i:162505 original size:16 final size:16
Alignment explanation
Indices: 162484--162515 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
162474 TCTTCCACCA
*
162484 ATGTTAGAATGGAAAT
1 ATGTTAGAATGCAAAT
162500 ATGTTAGAATGCAAAT
1 ATGTTAGAATGCAAAT
162516 GAGCTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGCAAAT
Found at i:165584 original size:19 final size:21
Alignment explanation
Indices: 165560--165611 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
165550 CGCCCAATAG
*
165560 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
165579 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
165600 CATGTATTTTCA
1 CATGTATTTTCA
165612 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:168271 original size:19 final size:21
Alignment explanation
Indices: 168228--168279 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
168218 AAAACCCCTT
168228 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
168249 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
168268 TGAAGATACATG
1 TGAAAATACATG
168280 CTCATGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:169786 original size:8 final size:9
Alignment explanation
Indices: 169773--169820 Score: 61
Period size: 8 Copynumber: 5.9 Consensus size: 9
169763 AAACACATTA
169773 TTTTC-TTC
1 TTTTCTTTC
169781 TTTTCTTTC
1 TTTTCTTTC
169790 -TTTCTTTC
1 TTTTCTTTC
169798 -TTTCTTTC
1 TTTTCTTTC
169806 -TTTCTTTC
1 TTTTCTTTC
169814 -TTTCTTT
1 TTTTCTTT
169821 TTGTACTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 36 0.92
9 3 0.08
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:169791 original size:4 final size:4
Alignment explanation
Indices: 169782--169820 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
169772 ATTTTCTTCT
169782 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
169821 TTGTACTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:172517 original size:15 final size:15
Alignment explanation
Indices: 172497--172526 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
172487 AACTATTATA
172497 TCCATTTCAATTCTT
1 TCCATTTCAATTCTT
*
172512 TCCATTTCATTTCTT
1 TCCATTTCAATTCTT
172527 AATTGTTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (15 bp):
TCCATTTCAATTCTT
Found at i:173675 original size:13 final size:12
Alignment explanation
Indices: 173656--173720 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
173646 TTATTGGCAT
173656 GATATGGTGATG
1 GATATGGTGATG
173668 GAATATGGTGAT-
1 G-ATATGGTGATG
*
173680 GATATAGGCG-T-
1 GATAT-GGTGATG
173691 GATAATGGTGATG
1 GAT-ATGGTGATG
173704 GACTATGGTGAT-
1 GA-TATGGTGATG
173716 GATAT
1 GATAT
173721 AGGCGCGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:173704 original size:36 final size:36
Alignment explanation
Indices: 173625--173753 Score: 156
Period size: 36 Copynumber: 3.7 Consensus size: 36
173615 ATGGTGATGA
* * * * *
173625 AATGGTAATGGAA-A-GATGATGTTATTGGCATGAT
1 AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
173659 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
* *
173694 AATGGTGATGGACTATGGTGATGATATAGGCGCGAT
1 AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
* *
173730 AATGGAGATGGATTATGGTGATGA
1 AATGGTGATGGAATATGGTGATGA
173754 AAATAGTATC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
33 11 0.13
34 1 0.01
35 16 0.19
36 55 0.66
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (36 bp):
AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
Found at i:180430 original size:2 final size:2
Alignment explanation
Indices: 180419--180455 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
180409 AAGCTGCATC
*
180419 AT AT -T AT AT AT AT TT 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
180456 TATTCTATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:181839 original size:15 final size:15
Alignment explanation
Indices: 181809--181861 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
181799 CCTTTGATAA
181809 CATTT-TTATCCATTT
1 CATTTCTTATCC-TTT
181824 CATTTCTTATCCTTT
1 CATTTCTTATCCTTT
* *
181839 CTTTTCTT-T-ATTT
1 CATTTCTTATCCTTT
181852 CATTTCTTAT
1 CATTTCTTAT
181862 TTCAATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 10 0.30
14 2 0.06
15 15 0.45
16 6 0.18
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (15 bp):
CATTTCTTATCCTTT
Found at i:182761 original size:19 final size:20
Alignment explanation
Indices: 182698--182769 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
182688 GAAACCCCTT
182698 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGA-TTTTAAA
182719 TGAAAATACATGATTTTAAA
1 TGAAAATACATGATTTTAAA
182739 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
182758 TGAAGATACATG
1 TGAAAATACATG
182770 CTCTTGGCCG
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 13 0.26
20 24 0.48
21 13 0.26
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:183698 original size:30 final size:31
Alignment explanation
Indices: 183657--183716 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
183647 ACATGTTGCC
**
183657 ATGATATCTAAATGATATGAAAACATAATAA
1 ATGATATCTAAAACATATGAAAACATAATAA
*
183688 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGAAAACATAATA
183717 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGAAAACATAATAA
Found at i:186155 original size:8 final size:8
Alignment explanation
Indices: 186144--186168 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
186134 TGTTTTTCTT
186144 TTCTTTTC
1 TTCTTTTC
186152 TTCTTTTC
1 TTCTTTTC
186160 TTCTTTTC
1 TTCTTTTC
186168 T
1 T
186169 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:186957 original size:19 final size:20
Alignment explanation
Indices: 186909--186947 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
186899 GAAACCCCTT
186909 TGAAAATACATGATTTTAAA
1 TGAAAATACATGATTTTAAA
186929 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
186948 TGGAGATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:187701 original size:30 final size:31
Alignment explanation
Indices: 187660--187719 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
187650 ACATGTTGCC
**
187660 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
187691 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
187720 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:190106 original size:17 final size:17
Alignment explanation
Indices: 190054--190125 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
190044 ATTCATGCAT
*
190054 CTAGTTCATTGAATAAAG
1 CTAGTTCATT-AATAAAA
* * *
190072 TTAGCTCATTAATTAAA
1 CTAGTTCATTAATAAAA
*
190089 CTAGTTCATTTATAAAA
1 CTAGTTCATTAATAAAA
* * *
190106 CTAATTCATTTATTAAA
1 CTAGTTCATTAATAAAA
190123 CTA
1 CTA
190126 ACTCTTAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 36 0.82
18 8 0.18
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATAAAA
Found at i:190126 original size:17 final size:17
Alignment explanation
Indices: 190077--190126 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
190067 TAAAGTTAGC
* *
190077 TCATTAATTAAACTAGT
1 TCATTTATTAAACTAAT
*
190094 TCATTTATAAAACTAAT
1 TCATTTATTAAACTAAT
190111 TCATTTATTAAACTAA
1 TCATTTATTAAACTAA
190127 CTCTTAATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (17 bp):
TCATTTATTAAACTAAT
Found at i:190547 original size:25 final size:25
Alignment explanation
Indices: 190519--190570 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
190509 AAGCATTCAA
190519 GGCTGATTTAATCATCCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
*
190544 GGCTGATTTAATCATTCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
190569 GG
1 GG
190571 TTGTTCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (25 bp):
GGCTGATTTAATCATCCAAACCAAG
Found at i:199417 original size:17 final size:17
Alignment explanation
Indices: 199376--199447 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
199366 ATTCATGCAT
199376 CTAGTTCATTCAA-TAAA
1 CTAGTTCATT-AATTAAA
*
199393 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
199411 CTAGTTCATTCATAAAA
1 CTAGTTCATTAATTAAA
*
199428 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
199445 CTA
1 CTA
199448 ACTCTTAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 34 0.72
18 13 0.28
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:199433 original size:34 final size:35
Alignment explanation
Indices: 199376--199447 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 35
199366 ATTCATGCAT
**
199376 CTAGTTCATTCAATAAAGTTAGTTCATTAATTAAA
1 CTAGTTCATTCAATAAAACTAGTTCATTAATTAAA
*
199411 CTAGTTCATTC-ATAAAACTAGTTCATTTATTAAA
1 CTAGTTCATTCAATAAAACTAGTTCATTAATTAAA
199445 CTA
1 CTA
199448 ACTCTTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 23 0.68
35 11 0.32
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (35 bp):
CTAGTTCATTCAATAAAACTAGTTCATTAATTAAA
Found at i:199878 original size:25 final size:24
Alignment explanation
Indices: 199845--199898 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
199835 TCAAAGCATT
*
199845 CAAGGCTGATTTAATCATCCAGAC
1 CAAGGCTGATTTAATCATCCAAAC
*
199869 CAAGGTCTGATTTAATCATTCAAAC
1 CAAGG-CTGATTTAATCATCCAAAC
199894 CAAGG
1 CAAGG
199899 GTTGTTCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (24 bp):
CAAGGCTGATTTAATCATCCAAAC
Found at i:204366 original size:33 final size:33
Alignment explanation
Indices: 204287--204390 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
204277 ATACAATCTG
* *
204287 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
204323 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
204356 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
204389 TC
1 TC
204391 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:204799 original size:36 final size:36
Alignment explanation
Indices: 204758--204906 Score: 190
Period size: 36 Copynumber: 4.1 Consensus size: 36
204748 ATTTATAAGT
* * * * *
204758 TGGTGATAATATGGGTGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
204794 TGGTGACGATATAAGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
204830 TGGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
204866 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
204902 TGGTG
1 TGGTG
204907 TTGGACAGAT
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.30, C:0.04, G:0.38, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:205300 original size:19 final size:20
Alignment explanation
Indices: 205253--205303 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
205243 GAAACCCCTT
**
205253 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
205273 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
205292 TGAAGATACATG
1 TGAAAATACATG
205304 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:208493 original size:22 final size:20
Alignment explanation
Indices: 208450--208494 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
208440 TGTAGGAGTC
* *
208450 TTTTTCTTTTCTTTTTGTTT
1 TTTTTCTTTTCTTGTTGCTT
208470 TTTTTCTTCTTTCTTGTTGCTT
1 TTTTTC-T-TTTCTTGTTGCTT
208492 TTT
1 TTT
208495 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 14 0.67
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTCTTGTTGCTT
Found at i:208900 original size:36 final size:36
Alignment explanation
Indices: 208859--209007 Score: 190
Period size: 36 Copynumber: 4.1 Consensus size: 36
208849 ATTTATAAGT
* * * *
208859 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
208895 TGGTGACGATATAAGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * * *
208931 TGGTGATGATAAAGGCGTGATAATTGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
208967 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
209003 TGGTG
1 TGGTG
209008 TTGGACAGAT
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 96 1.00
ACGTcount: A:0.30, C:0.05, G:0.37, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:209401 original size:19 final size:20
Alignment explanation
Indices: 209354--209404 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
209344 GAAACCCCTT
**
209354 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
209374 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
209393 TGAAGATACATG
1 TGAAAATACATG
209405 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:213397 original size:33 final size:33
Alignment explanation
Indices: 213317--213421 Score: 97
Period size: 33 Copynumber: 3.1 Consensus size: 33
213307 GATACAATCT
* *
213317 TTCCATCACCATTATCACGCCTATATCATCA-CC
1 TTCCATCACCA-TATCACGCCAATAACATCATCC
213350 ATATTCCATCACCATATCACGCCAATAACATCATCC
1 ---TTCCATCACCATATCACGCCAATAACATCATCC
* * * *
213386 TTCCATTACCATTTCATCACCATTAA-ATCATCC
1 TTCCATCACCATATCA-CGCCAATAACATCATCC
213419 TTC
1 TTC
213422 ATTTATCAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
33 24 0.39
34 7 0.11
35 17 0.28
36 13 0.21
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.31
Consensus pattern (33 bp):
TTCCATCACCATATCACGCCAATAACATCATCC
Found at i:217515 original size:33 final size:33
Alignment explanation
Indices: 217473--217541 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
217463 GTTGATAAAT
*
217473 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
217506 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
217539 GAA
1 GAA
217542 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:227070 original size:33 final size:33
Alignment explanation
Indices: 226991--227094 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
226981 ATACAATCTG
* *
226991 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
227027 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
227060 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
227093 TC
1 TC
227095 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:227503 original size:36 final size:36
Alignment explanation
Indices: 227462--227610 Score: 199
Period size: 36 Copynumber: 4.1 Consensus size: 36
227452 ATTTATAAGT
* * * *
227462 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
227498 TGGTGACGATATAAGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
227534 TGGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
227570 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
227606 TGGTG
1 TGGTG
227611 TTGGACAGAT
Statistics
Matches: 98, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 98 1.00
ACGTcount: A:0.30, C:0.05, G:0.38, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:228003 original size:19 final size:19
Alignment explanation
Indices: 227960--228006 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
227950 ACCCCTTTGA
**
227960 AAATACATGATTTTTGATG
1 AAATACATGATTTTAAATG
227979 AAATACATGA-TTTAAATG
1 AAATACATGATTTTAAATG
227997 AAGATACATG
1 AA-ATACATG
228007 CTCTTGGCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (19 bp):
AAATACATGATTTTAAATG
Found at i:231178 original size:22 final size:20
Alignment explanation
Indices: 231135--231179 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
231125 TGTAGGAGTC
* *
231135 TTTTTCTTTTCTTTTTGTTT
1 TTTTTCTTTTCTTGTTGCTT
231155 TTTTTCTTCTTTCTTGTTGCTT
1 TTTTTC-T-TTTCTTGTTGCTT
231177 TTT
1 TTT
231180 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 1 0.05
22 14 0.67
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTCTTGTTGCTT
Found at i:231585 original size:36 final size:36
Alignment explanation
Indices: 231544--231692 Score: 190
Period size: 36 Copynumber: 4.1 Consensus size: 36
231534 ATTTATAAGT
* * * *
231544 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
231580 TGGTGACGATATAAGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * * *
231616 TGGTGATGATAAAGGCGTGATAATTGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
231652 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
231688 TGGTG
1 TGGTG
231693 TTGGACAGAT
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 96 1.00
ACGTcount: A:0.30, C:0.05, G:0.37, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:232086 original size:19 final size:20
Alignment explanation
Indices: 232039--232089 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
232029 GAAACCCCTT
**
232039 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
232059 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
232078 TGAAGATACATG
1 TGAAAATACATG
232090 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:241451 original size:2 final size:2
Alignment explanation
Indices: 241444--241468 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
241434 TGGTAGCGGA
241444 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
241469 AGTTGGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:246436 original size:17 final size:17
Alignment explanation
Indices: 246395--246466 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
246385 ATTCATGCAT
246395 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
* *
246412 GTTAGTTCAATAATTAAA
1 -CTAGTTCATTAATTAAA
* *
246430 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
* *
246447 CTAGTTTATTTATTAAA
1 CTAGTTCATTAATTAAA
246464 CTA
1 CTA
246467 ACTCTTAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 32 0.73
18 12 0.27
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:246897 original size:25 final size:25
Alignment explanation
Indices: 246869--246920 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
246859 AAGCATTCAA
246869 GGCTGATTTAATCATCCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
* *
246894 GGCTTATTTAATCATTCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
246919 GG
1 GG
246921 ATGTTCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (25 bp):
GGCTGATTTAATCATCCAAACCAAG
Found at i:250885 original size:10 final size:10
Alignment explanation
Indices: 250870--250894 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
250860 TCATCCATTA
250870 ATGCATATTC
1 ATGCATATTC
250880 ATGCATATTC
1 ATGCATATTC
250890 ATGCA
1 ATGCA
250895 AGAAGCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (10 bp):
ATGCATATTC
Found at i:253051 original size:21 final size:21
Alignment explanation
Indices: 253025--253072 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
253015 TGATGGAGTT
253025 GAACATGCACAAATCAAACAA
1 GAACATGCACAAATCAAACAA
*
253046 GAACATGCACAAATCAAAGAA
1 GAACATGCACAAATCAAACAA
253067 GAACAT
1 GAACAT
253073 TGTGAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.10
Consensus pattern (21 bp):
GAACATGCACAAATCAAACAA
Done.