Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006766.1 Hibiscus syriacus cultivar Beakdansim tig00017098_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: 208440
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1375 original size:59 final size:59
Alignment explanation
Indices: 1273--1402 Score: 188
Period size: 59 Copynumber: 2.2 Consensus size: 59
1263 CTGTAGTGCT
* * **
1273 ATCCTGAATATGACACATAAGGTCGTGCCCACCATCTGTACTAGGTATCCTTAAGTACA
1 ATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACA
* **
1332 ATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTA
1 ATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACA
*
1391 TTCCCGAATATG
1 ATCCCGAATATG
1403 CAGCCTGCTG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (59 bp):
ATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACA
Found at i:6056 original size:14 final size:14
Alignment explanation
Indices: 6034--6063 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6024 AGAAAACTTG
6034 ATAAATTTATAGCA
1 ATAAATTTATAGCA
*
6048 ATAACTTTATAGCA
1 ATAAATTTATAGCA
6062 AT
1 AT
6064 TAATGCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
ATAAATTTATAGCA
Found at i:7874 original size:59 final size:58
Alignment explanation
Indices: 7739--7875 Score: 184
Period size: 59 Copynumber: 2.3 Consensus size: 58
7729 ATAAGCACCG
* **
7739 TAGTGCTATCCCGAATATGACACATAAGGTCGTGCCCACCATCTTTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
* **
7798 AAGTACAGTCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
*
7857 TAGTGTATTCCCAAATATG
1 TAGTGTA-TCCCGAATATG
7876 CAGCATGTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
58 1 0.02
59 65 0.98
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTT
Found at i:9451 original size:15 final size:15
Alignment explanation
Indices: 9431--9464 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9421 TTAAAAGAAA
9431 AATAATGAGTAA-AAT
1 AATAAT-AGTAATAAT
9446 AATAATAGTAATAAT
1 AATAATAGTAATAAT
9461 AATA
1 AATA
9465 GAGCTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (15 bp):
AATAATAGTAATAAT
Found at i:15730 original size:10 final size:10
Alignment explanation
Indices: 15715--15745 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
15705 CAAGTTTCGC
15715 TTCGTCTCAA
1 TTCGTCTCAA
15725 TTCGTCTCAA
1 TTCGTCTCAA
15735 TTCGTCTCAA
1 TTCGTCTCAA
15745 T
1 T
15746 CACTAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.10, T:0.42
Consensus pattern (10 bp):
TTCGTCTCAA
Found at i:15834 original size:11 final size:10
Alignment explanation
Indices: 15808--15839 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
15798 CTGGTTCACT
15808 GGTTCAACCG
1 GGTTCAACCG
15818 GGTTCAACCG
1 GGTTCAACCG
15828 CGGTTCAACCG
1 -GGTTCAACCG
15839 G
1 G
15840 ATTTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.19, C:0.31, G:0.31, T:0.19
Consensus pattern (10 bp):
GGTTCAACCG
Found at i:21394 original size:18 final size:17
Alignment explanation
Indices: 21371--21416 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
21361 AATAATTAAA
**
21371 CATCGAATGCAATTAGTG
1 CATCG-ATGCAAGGAGTG
21389 CATCGATGCTAAGGAGTG
1 CATCGATGC-AAGGAGTG
21407 CATCGATGCA
1 CATCGATGCA
21417 CTCCCTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (17 bp):
CATCGATGCAAGGAGTG
Found at i:22084 original size:18 final size:18
Alignment explanation
Indices: 22061--22095 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22051 AGGGATTATC
*
22061 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGAGACAT
22079 AGTGGTCCTTCGAGACA
1 AGTGGTCCTTCGAGACA
22096 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:25316 original size:31 final size:32
Alignment explanation
Indices: 25280--25340 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
25270 AGTTAAGTTT
*
25280 TTTCGAGCTCGAGTCGAGCTT-CAATTTTTTA
1 TTTCGAGCTCGAGTCAAGCTTACAATTTTTTA
*
25311 TTTCGATCTCGAGTCAAGCTTGACAATTTT
1 TTTCGAGCTCGAGTCAAGCTT-ACAATTTT
25341 ACTTTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 19 0.73
33 7 0.27
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (32 bp):
TTTCGAGCTCGAGTCAAGCTTACAATTTTTTA
Found at i:28997 original size:2 final size:2
Alignment explanation
Indices: 28992--29025 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28982 AAAAACCATG
28992 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
29026 TCTTTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35410 original size:22 final size:22
Alignment explanation
Indices: 35382--35428 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
35372 CTTTCAGGTT
35382 GTACTAGTTGGGAATTAAACGA
1 GTACTAGTTGGGAATTAAACGA
*
35404 GTACTAGTTGGGAATTCAACGA
1 GTACTAGTTGGGAATTAAACGA
35426 GTA
1 GTA
35429 AGAGTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.28
Consensus pattern (22 bp):
GTACTAGTTGGGAATTAAACGA
Found at i:51655 original size:29 final size:29
Alignment explanation
Indices: 51612--51694 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
51602 CTCACCTAAC
51612 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
51642 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
51671 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
51695 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:56413 original size:29 final size:29
Alignment explanation
Indices: 56370--56452 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
56360 CTCACCTAAC
56370 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
56400 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
56429 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
56453 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:57806 original size:144 final size:144
Alignment explanation
Indices: 57647--57936 Score: 571
Period size: 144 Copynumber: 2.0 Consensus size: 144
57637 TCGCATTGTC
57647 ATCAAGTAGAAGACTTAATAAGTTGGTCATGTTTCCTATAGAACTTGGAATGACACCAGTAAGAT
1 ATCAAGTAGAAGACTTAATAAGTTGGTCATGTTTCCTATAGAACTTGGAATGACACCAGTAAGAT
57712 TATTTTCCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCA
66 TATTTTCCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCA
57777 GAGAGGTAATTACT
131 GAGAGGTAATTACT
57791 ATCAAGTAGAAGACTTAATAAGTTGGTCATGTTTCCTATAGAACTTGGAATGACACCAGTAAGAT
1 ATCAAGTAGAAGACTTAATAAGTTGGTCATGTTTCCTATAGAACTTGGAATGACACCAGTAAGAT
*
57856 TATTTTCCAACAACTGTAATGTGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCA
66 TATTTTCCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCA
57921 GAGAGGTAATTACT
131 GAGAGGTAATTACT
57935 AT
1 AT
57937 AAAAATAAAG
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (144 bp):
ATCAAGTAGAAGACTTAATAAGTTGGTCATGTTTCCTATAGAACTTGGAATGACACCAGTAAGAT
TATTTTCCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCA
GAGAGGTAATTACT
Found at i:57994 original size:144 final size:144
Alignment explanation
Indices: 57653--57976 Score: 508
Period size: 144 Copynumber: 2.2 Consensus size: 144
57643 TGTCATCAAG
* * * *
57653 TAGAAGACTTAATAAGTTGGTCATGTTTCCTATAGAACTTGGAATGACACCAGTAAGATTATTTT
1 TAGAAGACTTAACAAGTCGCTCAAGTTTCCTATAGAACTTGGAATGACACCAGTAAGATTATTTT
57718 CCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCAGAGAGG
66 CCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCAGAGAGG
* *
57783 TAATTACTATCAAG
131 TAATTACTATAAAA
* * * *
57797 TAGAAGACTTAATAAGTTGGTCATGTTTCCTATAGAACTTGGAATGACACCAGTAAGATTATTTT
1 TAGAAGACTTAACAAGTCGCTCAAGTTTCCTATAGAACTTGGAATGACACCAGTAAGATTATTTT
*
57862 CCAACAACTGTAATGTGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCAGAGAGG
66 CCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCAGAGAGG
57927 TAATTACTATAAAAA
131 TAATTACTAT-AAAA
*
57942 TA-AAGA-TATACCAAGTCGCTCAAGTTTCCTATAGA
1 TAGAAGACT-TAACAAGTCGCTCAAGTTTCCTATAGA
57977 TGCTGGTATA
Statistics
Matches: 170, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
143 1 0.01
144 165 0.97
145 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (144 bp):
TAGAAGACTTAACAAGTCGCTCAAGTTTCCTATAGAACTTGGAATGACACCAGTAAGATTATTTT
CCAACAACTGTAATATGGACAGCGACTTGAGCAATCCTATCTCATTGGGGATCGAACCAGAGAGG
TAATTACTATAAAA
Found at i:67272 original size:18 final size:17
Alignment explanation
Indices: 67218--67281 Score: 101
Period size: 17 Copynumber: 3.7 Consensus size: 17
67208 TATGGAATTG
67218 GATTCCAATTCCTGACA
1 GATTCCAATTCCTGACA
*
67235 GATTCTAATTCCTGACA
1 GATTCCAATTCCTGACA
*
67252 GATTCCAATTCCTTCACA
1 GATTCCAATTCC-TGACA
67270 GATTCCAATTCC
1 GATTCCAATTCC
67282 CTCAGAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
17 27 0.63
18 16 0.37
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (17 bp):
GATTCCAATTCCTGACA
Found at i:68176 original size:45 final size:44
Alignment explanation
Indices: 68079--68180 Score: 107
Period size: 45 Copynumber: 2.3 Consensus size: 44
68069 CACATTCAAT
* * *
68079 GTGTATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTA
1 GTGTATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTA
* * ** *
68123 GTGCATCGATGCACCCCCTTAAA-ATGAAAACATCGAAGGTGATTG
1 GTGTATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTA
68168 GTGTATCGATGCA
1 GTGTATCGATGCA
68181 TGGGTAGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
44 14 0.30
45 33 0.70
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (44 bp):
GTGTATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTA
Found at i:81563 original size:78 final size:78
Alignment explanation
Indices: 81324--81713 Score: 667
Period size: 78 Copynumber: 5.0 Consensus size: 78
81314 GCGAGTTTTT
* *
81324 CACGGGTATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTAATATGAATAGACATGTAAA
1 CACGGTTATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAA
81389 CTAACCGATCCAA
66 CTAACCGATCCAA
* *
81402 CACGGTTATACTTTTCTCATTAGGATATGGATAATAG-T-TGTCTCATATGATTAGACATGTAAA
1 CACGGTTATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAA
81465 CTAACCGATCCAA
66 CTAACCGATCCAA
* *
81478 CACGGTTATAATTTTCTCATTAGAATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAA
1 CACGGTTATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAA
*
81543 CTAACCGATCCAG
66 CTAACCGATCCAA
*
81556 CACGGTTATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAAACATGTAAA
1 CACGGTTATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAA
*
81621 CTAACCAATCCAA
66 CTAACCGATCCAA
* *
81634 CATGGTTATACTTTTCTCATTAGGATATGGATAATAGTTGTGTTTCATATGAATAGACATGTAAA
1 CACGGTTATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAA
81699 CTAACCGATCCAA
66 CTAACCGATCCAA
81712 CA
1 CA
81714 ATTATAGTTT
Statistics
Matches: 292, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
76 70 0.24
77 2 0.01
78 220 0.75
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (78 bp):
CACGGTTATACTTTTCTCATTAGGATATGGATAATAGTTATGTTTCATATGAATAGACATGTAAA
CTAACCGATCCAA
Found at i:88984 original size:20 final size:20
Alignment explanation
Indices: 88947--88985 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
88937 AAACTGAGTG
* * *
88947 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
88967 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
88986 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:89171 original size:21 final size:21
Alignment explanation
Indices: 89145--89205 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
89135 CAGAACCCCA
89145 GGGGGGTATCGATTCCCCTGT
1 GGGGGGTATCGATTCCCCTGT
89166 GGGGGGTATCGATTCCCCTGT
1 GGGGGGTATCGATTCCCCTGT
* *
89187 GGGGGGAATCGGTTCCCCT
1 GGGGGGTATCGATTCCCCT
89206 ACAAAGGGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.10, C:0.25, G:0.39, T:0.26
Consensus pattern (21 bp):
GGGGGGTATCGATTCCCCTGT
Found at i:89240 original size:20 final size:21
Alignment explanation
Indices: 89186--89248 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
89176 GATTCCCCTG
89186 TGGGGGGAATCGGTTCCCCTACAA
1 TGGGGGG-ATCGGTT-CCCT-CAA
* *
89210 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
89230 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
89249 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 1 0.03
22 4 0.12
23 7 0.21
24 5 0.15
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.22
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:95672 original size:32 final size:32
Alignment explanation
Indices: 95631--95692 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
95621 TTTAAACTAA
95631 AATACCTAAAACAAAAATAAAATA-TAAAAAT
1 AATACCTAAAACAAAAATAAAATACTAAAAAT
** *
95662 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACAAAAATAAAATACTAAAA
95693 CCTATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 4 0.15
32 17 0.65
33 5 0.19
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (32 bp):
AATACCTAAAACAAAAATAAAATACTAAAAAT
Found at i:97383 original size:15 final size:14
Alignment explanation
Indices: 97348--97392 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
97338 TAAGCATCTG
*
97348 ATAAAATAAAATAA
1 ATAAAATGAAATAA
*
97362 ATGAAATGAAATGAA
1 ATAAAATGAAAT-AA
97377 ATAAAATGAAAATAA
1 ATAAAATG-AAATAA
97392 A
1 A
97393 ACGAAATGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 10 0.38
15 12 0.46
16 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (14 bp):
ATAAAATGAAATAA
Found at i:97399 original size:10 final size:10
Alignment explanation
Indices: 97348--97399 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
97338 TAAGCATCTG
*
97348 ATAAAATAAA
1 ATAAAATGAA
97358 AT-AAATGAA
1 ATAAAATGAA
*
97367 ATGAAATGAA
1 ATAAAATGAA
97377 ATAAAATGAAA
1 ATAAAATG-AA
*
97388 ATAAAACGAA
1 ATAAAATGAA
97398 AT
1 AT
97400 GGGTTGCCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 8 0.22
10 20 0.54
11 9 0.24
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (10 bp):
ATAAAATGAA
Found at i:101541 original size:15 final size:16
Alignment explanation
Indices: 101507--101543 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
101497 GGTGAGTGCA
101507 ATACATGCATGACATT
1 ATACATGCATGACATT
*
101523 ATACATGGATGAC-TT
1 ATACATGCATGACATT
101538 ATACAT
1 ATACAT
101544 CATCGGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (16 bp):
ATACATGCATGACATT
Found at i:102175 original size:46 final size:46
Alignment explanation
Indices: 102083--102341 Score: 434
Period size: 46 Copynumber: 5.7 Consensus size: 46
102073 GTAAGCATGC
* *
102083 AAATAAGCTTACGATCTTATGGAA-T-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
102127 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
102173 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
* *
102219 AAATAAGCTTACGAGCTTATGGGATTAAATGGAAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
* *
102265 AAATAAGCTTACTAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
*
102311 AAATAAGCTTACGAGCTTATGGGA-TAAATGG
1 AAATAAGCTTACGAGCTTATGGAATTAAATGG
102342 ATATTATATT
Statistics
Matches: 204, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
44 23 0.11
45 8 0.04
46 173 0.85
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
Found at i:103740 original size:23 final size:24
Alignment explanation
Indices: 103714--103773 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
103704 AAGTTGTTTT
103714 TAAAATAAAATAAAA-GAATTAAA
1 TAAAATAAAATAAAATGAATTAAA
*
103737 TAAAATAAAATAAAATTAATTAAA
1 TAAAATAAAATAAAATGAATTAAA
*
103761 T-AAATAAATTAAA
1 TAAAATAAAATAAA
103774 GAGATTGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 26 0.76
24 8 0.24
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (24 bp):
TAAAATAAAATAAAATGAATTAAA
Found at i:103764 original size:28 final size:28
Alignment explanation
Indices: 103714--103773 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
103704 AAGTTGTTTT
*
103714 TAAAATAAAATAAAAGAATTAAATAAAA
1 TAAAATAAAATAAAAGAAATAAATAAAA
* ** *
103742 TAAAATAAAATTAATTAAATAAATAAAT
1 TAAAATAAAATAAAAGAAATAAATAAAA
103770 TAAA
1 TAAA
103774 GAGATTGAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (28 bp):
TAAAATAAAATAAAAGAAATAAATAAAA
Found at i:110091 original size:23 final size:23
Alignment explanation
Indices: 110038--110092 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
110028 TGACATGTTA
*
110038 TCTGCCTTTATGACACGTTTATC
1 TCTGTCTTTATGACACGTTTATC
* * * * *
110061 TTTATCTTTATGGCATGTTTTTC
1 TCTGTCTTTATGACACGTTTATC
110084 TCTGTCTTT
1 TCTGTCTTT
110093 TGGTAGCTTA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.20, G:0.13, T:0.55
Consensus pattern (23 bp):
TCTGTCTTTATGACACGTTTATC
Found at i:116630 original size:55 final size:55
Alignment explanation
Indices: 116518--117081 Score: 772
Period size: 55 Copynumber: 10.3 Consensus size: 55
116508 GATGCATGAA
* * * * * * * *
116518 ACTCGCACAATCTTCAACAAACGTCTCTGTTCTCTA-TGCTTCAAAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
*
116572 ACTCGAACAATCTTCATCAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
* * *
116627 ACTCGAACAATCTTCAACAGTCGTGTCTGCTCCTTATTTATGCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
* * * * *
116682 ACTCGAACAATTTTCATCAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
* * *
116737 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
* *
116792 ACTCGAACAATCTTCATCAATCGTGTCTGCCCCCTATTTCTGCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
* * *
116847 ACTCGAACAATCTTCAACAGTCGTGTCTGCTCCTTATTTATGCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
* * *
116902 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
* * *
116957 ACTCGAACAATCTTCATCAATCGTTTCTGCCCCCTATTTCTGCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
* * * * * *
117012 ACTCGAACAATCTTCAATAATCGGGTCCGCTCCCTCTTTCTTCAGGGAGTAT-AG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
117066 AACTCGAACAATCTTC
1 -ACTCGAACAATCTTC
117082 TGAAAATGGG
Statistics
Matches: 454, Mismatches: 54, Indels: 3
0.89 0.11 0.01
Matches are distributed among these distances:
54 32 0.07
55 422 0.93
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAG
Found at i:117107 original size:110 final size:105
Alignment explanation
Indices: 116556--117960 Score: 949
Period size: 102 Copynumber: 13.3 Consensus size: 105
116546 GTTCTCTATG
* * * * *
116556 CTTCAAAGAGTATA-AGACTCGAACAATCTTCATCAATCGTG-TCTGCTCCCTATTTCTGCAGAG
1 CTTCAGAGAGTATAGA-ACTCGAACAATCTTCAT-AATCGGGTTC-GCTCCCTCTTTCTTCAGGG
* * *
116619 AGTATA-AGACTCGAACAATCTTCAACA-GTCGTGTCTGCTCCTTATTT
63 AGTATAGA-ACTCGAAC-ATCTTCAA-ATG-GGT-TC-GCTCCCTCTTT
* * * * * *
116666 ATGCAGAGAGTATA-AGACTCGAACAATTTTCATCAATCGTG-TCTGCTCCC-CATTCCTTCAGA
1 CTTCAGAGAGTATAGA-ACTCGAACAATCTTCAT-AATCGGGTTC-GCTCCCTC-TTTCTTCAGG
* *
116728 GAGTATA-AGACTCGAACAATCTTCAACAAT-CGTGTCTGCTCCC-CATTC
62 GAGTATAGA-ACTCGAAC-ATCTTC-A-AATGGGT-TC-GCTCCCTC-TTT
* * * * *
116776 CTTCAGAGAGTATA-AGACTCGAACAATCTTCATCAATCGTG-TCTGCCCCCTATTTCTGCAGAG
1 CTTCAGAGAGTATAGA-ACTCGAACAATCTTCAT-AATCGGGTTC-GCTCCCTCTTTCTTCAGGG
* * *
116839 AGTATA-AGACTCGAACAATCTTCAACA-GTCGTGTCTGCTCCTTATTT
63 AGTATAGA-ACTCGAAC-ATCTTCAA-ATG-GGT-TC-GCTCCCTCTTT
* * * * * *
116886 ATGCAGAGAGTATA-AGACTCGAACAATCTTCAACAATCGTG-TCTGCTCCC-CATTCCTTCAGA
1 CTTCAGAGAGTATAGA-ACTCGAACAATCTTC-ATAATCGGGTTC-GCTCCCTC-TTTCTTCAGG
* * * *
116948 GAGTATA-AGACTCGAACAATCTTCATCAATCGTTTCTGCCCCCTATTT
62 GAGTATAGA-ACTCGAAC-ATCTTCA--AATGGGTTC-GCTCCCTCTTT
* *
116996 CTGCAGAGAGTATA-AGACTCGAACAATCTTCAATAATCGGGTCCGCTCCCTCTTTCTTCAGGGA
1 CTTCAGAGAGTATAGA-ACTCGAACAATCTTC-ATAATCGGGTTCGCTCCCTCTTTCTTCAGGGA
117060 GTATAGAACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTCTTT
64 GTATAGAACTCGAAC-ATCTTC---AAATGGGTTCGCTCCCTCTTT
* * *
117106 CTTCAGGGAGTATGGAACTCGAAC-ATCTTCA-ACT-GGGTTCGCTCCCTCTTTC-TCTAGGGAG
1 CTTCAGAGAGTATAGAACTCGAACAATCTTCATAATCGGGTTCGCTCCCTCTTTCTTC-AGGGAG
* * * *
117167 TATGGAACT-TAGACATCTCTTCAAACGGGTTCGCTCCTTCTTT
65 TATAGAACTCGA-ACA--TCTTCAAATGGGTTCGCTCCCTCTTT
* * * * *
117210 CTTTA-AGGAGTATGGAACTCGAAC-ATCTTCA-AA-CGGGTTCGCTCCTTCTTTCTTTAAGGAG
1 CTTCAGA-GAGTATAGAACTCGAACAATCTTCATAATCGGGTTCGCTCCCTCTTTCTTCAGGGAG
* * *
117271 TATAGAACTCGCACATCTCTTCAAACGGGTTCGCTCCTTCTTT
65 TATAGAACTCGAACA--TCTTCAAATGGGTTCGCTCCCTCTTT
* * * * * *
117314 CTTTA-AGGAGTATGGAACTCGAAC-ATCTT--TAAACGGGTTCGCTCCTTCTTTCTTTAAGGAG
1 CTTCAGA-GAGTATAGAACTCGAACAATCTTCATAATCGGGTTCGCTCCCTCTTTCTTCAGGGAG
117375 TATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTT
65 TATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTT
* * * *
117416 CTTTAGGGAGTATAGAACTCGAAC-ATC-TCTTCA-CGGGTTCGCTCCCTCTTTC-TCTAGGGAG
1 CTTCAGAGAGTATAGAACTCGAACAATCTTCATAATCGGGTTCGCTCCCTCTTTCTTC-AGGGAG
* *
117477 TATGGAACTCGAACATCTTCAAATGGGTTCGTTCCCTCTTT
65 TATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTT
* * * *
117518 CTTTAGGGAGTATAGAACTCGAAC-ATC-TCTTCA-CGGGTTCGCTCCCTCTTTC-TCTAGGGAG
1 CTTCAGAGAGTATAGAACTCGAACAATCTTCATAATCGGGTTCGCTCCCTCTTTCTTC-AGGGAG
* * *
117579 TATGGAACTCGAACATCTTCAACTGGGTTCGCTCCTTCTTT
65 TATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTT
* * * * * *
117620 CTTTA-AGGAGTATGGAACTCGAAC-ATCTT--TAAACGGGTTCGCTCCTTCTTTCTTTAAGGAG
1 CTTCAGA-GAGTATAGAACTCGAACAATCTTCATAATCGGGTTCGCTCCCTCTTTCTTCAGGGAG
* * * *
117681 TATAGAACTCGCATATCTTCACACGGGTTCGCTCCCTCTTT
65 TATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTT
* * * * * * * *
117722 C-CCTAGGGAGTATGGAACTC-AGACATCTCTTCA-AA-CGGGTTCACTCCTTCTTTCTTTAAGG
1 CTTC-AGAGAGTATAGAACTCGA-ACA-ATCTTCATAATCGGGTTCGCTCCCTCTTTCTTCAGGG
* * * *
117783 AGTATGGAACTCGAACATCTTTAAACGGGTTCGCTCCTTCTTT
63 AGTATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTT
* * *
117826 CTTTA-AGGAGTATAGAACTCG--CATATCTTCA-CA-CGGGTTCGCTCCTTCTTTC-TCTAGGG
1 CTTCAGA-GAGTATAGAACTCGAACA-ATCTTCATAATCGGGTTCGCTCCCTCTTTCTTC-AGGG
* * *
117885 AGTATGGAACTCGGACATCTTCAAACGGGTTCGCTCCCTCTTT
63 AGTATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTT
* * * *
117928 C-TCTAGGGAGTATGGAACTCAAATAATCTTCAT
1 CTTC-AGAGAGTATAGAACTCGAACAATCTTCAT
117961 TTGGTTCACC
Statistics
Matches: 1124, Mismatches: 115, Indels: 118
0.83 0.08 0.09
Matches are distributed among these distances:
101 7 0.01
102 392 0.35
103 13 0.01
104 261 0.23
105 7 0.01
106 33 0.03
107 7 0.01
108 2 0.00
109 8 0.01
110 375 0.33
111 16 0.01
112 2 0.00
113 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (105 bp):
CTTCAGAGAGTATAGAACTCGAACAATCTTCATAATCGGGTTCGCTCCCTCTTTCTTCAGGGAGT
ATAGAACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTT
Found at i:117967 original size:51 final size:51
Alignment explanation
Indices: 117012--117947 Score: 1159
Period size: 51 Copynumber: 18.1 Consensus size: 51
117002 AGAGTATAAG
* * *
117012 ACTCGAACAATCTTCAATAATCGGGTCCGCTCCCTCTTTCTTCAGGGAGTATAGA
1 ACTCGAAC-ATCTTC-A-AA-CGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* *
117067 ACTCGAACAATCTTCTGAAAATGGGTTCGCTCCCTCTTTCTTCAGGGAGTATGGA
1 ACTCGAAC-ATCTTC---AAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
*
117122 ACTCGAACATCTTC-AACTGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCAAAC-GGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * *
117173 ACT-TAGACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
1 ACTCGA-ACA--TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * *
117226 ACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGA
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * *
117277 ACTCGCACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
1 ACTCGAACA--TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * * *
117330 ACTCGAACATCTTTAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGA
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* *
117381 ACTCGAACATCTTCAAATGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGA
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
*
117432 ACTCGAACATCTCTTC--ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACA--TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * *
117483 ACTCGAACATCTTCAAATGGGTTCGTTCCCTCTTTCTTTAGGGAGTATAGA
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
*
117534 ACTCGAACATCTCTTC--ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACA--TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* *
117585 ACTCGAACATCTTC-AACTGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGA
1 ACTCGAACATCTTCAAAC-GGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * * *
117636 ACTCGAACATCTTTAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGA
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * * **
117687 ACTCGCATATCTTCACACGGGTTCGCTCCCTCTTTCCCTAGGGAGTATGGA
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * *
117738 ACTC-AGACATCTCTTCAAACGGGTTCACTCCTTCTTTCTTTAAGGAGTATGGA
1 ACTCGA-ACA--TCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * * *
117791 ACTCGAACATCTTTAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGA
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* * * * *
117842 ACTCGCATATCTTCACACGGGTTCGCTCCTTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
* *
117893 ACTCGGACATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
117944 ACTC
1 ACTC
117948 AAATAATCTT
Statistics
Matches: 790, Mismatches: 68, Indels: 50
0.87 0.07 0.06
Matches are distributed among these distances:
49 10 0.01
50 5 0.01
51 560 0.71
52 3 0.00
53 143 0.18
54 11 0.01
55 54 0.07
56 2 0.00
57 2 0.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (51 bp):
ACTCGAACATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
Found at i:118401 original size:36 final size:36
Alignment explanation
Indices: 118329--118526 Score: 238
Period size: 36 Copynumber: 5.5 Consensus size: 36
118319 ACTCTTCTGA
* * *
118329 GAAGGCTTAAAATGGATCTGCTTCACTACTT-T-TGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * * *
118365 GAAGACTTAAGATGCTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
118401 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
118437 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
118473 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
118509 GAAGGCTTAGGATGGTTT
1 GAAGGCTTAAGATGGTTT
118527 TTCTCCAATC
Statistics
Matches: 142, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
34 1 0.01
35 12 0.08
36 129 0.91
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:131063 original size:15 final size:16
Alignment explanation
Indices: 131024--131065 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
131014 AAAGATTTTA
131024 TTATTTTATATACTATT
1 TTATTTTATATA-TATT
* *
131041 TAAATTTATAT-TATT
1 TTATTTTATATATATT
131056 TTATTTTATA
1 TTATTTTATA
131066 AAAATAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 12 0.57
17 9 0.43
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTTTATATATATT
Found at i:131729 original size:3 final size:3
Alignment explanation
Indices: 131721--131747 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
131711 TTTAAAAATG
131721 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
131748 TGAAATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:132155 original size:20 final size:22
Alignment explanation
Indices: 132109--132155 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
132099 TAAATTTGGG
132109 TATTAT-ATTTTTATATTAAGA
1 TATTATAATTTTTATATTAAGA
*
132130 GA-TATAATTTTT-T-TTAAGA
1 TATTATAATTTTTATATTAAGA
132149 TATTATA
1 TATTATA
132156 TTAGAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 7 0.32
20 8 0.36
21 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (22 bp):
TATTATAATTTTTATATTAAGA
Found at i:132658 original size:21 final size:20
Alignment explanation
Indices: 132573--132729 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
132563 AATGACCAAT
** *
132573 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
132592 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
132612 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
132632 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
132653 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
132674 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
132695 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
132715 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
132730 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:132758 original size:20 final size:20
Alignment explanation
Indices: 132696--132940 Score: 246
Period size: 20 Copynumber: 12.2 Consensus size: 20
132686 CGATTTTCCA
* ** *
132696 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
132716 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
132736 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
132756 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
132776 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
132796 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
132816 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
132836 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
132856 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
132876 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
132896 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
132916 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
132936 AAATC
1 AAATC
132941 CGGTAGGGCA
Statistics
Matches: 192, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 188 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:133689 original size:24 final size:24
Alignment explanation
Indices: 133650--133696 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
133640 AAATTTGGTC
133650 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
133674 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
133697 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:133887 original size:12 final size:12
Alignment explanation
Indices: 133870--133894 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
133860 CATATATCCT
133870 GAAGAAGAAAAA
1 GAAGAAGAAAAA
133882 GAAGAAGAAAAA
1 GAAGAAGAAAAA
133894 G
1 G
133895 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:136244 original size:33 final size:34
Alignment explanation
Indices: 136193--136428 Score: 238
Period size: 33 Copynumber: 6.8 Consensus size: 34
136183 CGGAAATTAC
*
136193 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
* *
136226 AATCCCAAC-ATGAAAATCGCAATGCGGAAATAAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
136260 AATCGCAACGA-GAAAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
136293 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
136326 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
*
136364 AATCGCAACGA-GATAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
136397 AATCGCAATGCGAAATGAAAATCGCATTGCGA
1 AATCGCAA--CG--ATGAAAATCGCAATGCGA
136429 TTCTCTCGTT
Statistics
Matches: 175, Mismatches: 10, Indels: 31
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 94 0.54
34 31 0.18
35 7 0.04
36 4 0.02
37 3 0.02
38 35 0.20
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:136274 original size:19 final size:19
Alignment explanation
Indices: 136207--136428 Score: 250
Period size: 19 Copynumber: 12.7 Consensus size: 19
136197 GCAACGAGAG
136207 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
136226 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
136240 AATCGCAATGCGGAAATAAA
1 AATCGCAATGC-GAAATGAA
136260 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
136274 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
136293 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
136312 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
136326 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
136345 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
136364 AATCGCAA--CG--A-GAT
1 AATCGCAATGCGAAATGAA
136378 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
136397 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
136416 AATCGCATTGCGA
1 AATCGCAATGCGA
136429 TTCTCTCGTT
Statistics
Matches: 173, Mismatches: 9, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 42 0.24
15 3 0.02
16 7 0.04
17 6 0.03
18 4 0.02
19 99 0.57
20 12 0.07
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:136363 original size:71 final size:71
Alignment explanation
Indices: 136207--136428 Score: 237
Period size: 71 Copynumber: 3.2 Consensus size: 71
136197 GCAACGAGAG
* * * **
136207 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATAAAAATCGCAA--C
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GATAATCGAAATGC-GAAACGAAAATCGCAATGC
136269 G--A-GAA
64 GAAATGAA
* * *
136274 AATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCG-AAATGCGAAACGA-A-AATCGCAATG
136336 CGAAATGAA
63 CGAAATGAA
* *
136345 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGAAATGCGAAACGAAAATCGCAATGCGA
136410 AATGAA
66 AATGAA
*
136416 AATCGCATTGCGA
1 AATCGCAATGCGA
136429 TTCTCTCGTT
Statistics
Matches: 130, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
64 4 0.03
65 3 0.02
66 14 0.11
67 28 0.22
68 2 0.02
70 1 0.01
71 64 0.49
72 7 0.05
73 7 0.05
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGAAATGCGAAACGAAAATCGCAATGCGA
AATGAA
Found at i:136442 original size:52 final size:52
Alignment explanation
Indices: 136235--136422 Score: 340
Period size: 52 Copynumber: 3.6 Consensus size: 52
136225 AAATCCCAAC
* *
136235 ATGAAAATCGCAATGCGGAAATAAAAATCGCAACGAGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
*
136288 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
136340 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
136392 ATGAAAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCA
136423 TTGCGATTCT
Statistics
Matches: 132, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 116 0.88
53 16 0.12
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
Found at i:136531 original size:52 final size:53
Alignment explanation
Indices: 136418--136534 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
136408 GAAATGAAAA
136418 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
136471 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
136523 TCGCATTGCGAT
1 TCGCATTGCGAT
136535 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:136542 original size:19 final size:19
Alignment explanation
Indices: 136437--136534 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
136427 GATTCTCTCG
136437 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
136457 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
136476 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
136490 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
136509 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
136528 TTGCGAT
1 TTGCGAT
136535 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:136656 original size:14 final size:14
Alignment explanation
Indices: 136637--136673 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
136627 CATCAATTAC
136637 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
136651 ACAAATCATCTTTT
1 ACAAATCAACTTTT
136665 ACAAATCAA
1 ACAAATCAA
136674 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:138633 original size:19 final size:19
Alignment explanation
Indices: 138593--138727 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
138583 TAGTTTACTT
* *
138593 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
138613 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
138632 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
138651 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
138665 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
138684 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAACCAAAA
**
138698 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
138717 TCGCAATGCGA
1 TCGCAACGCGA
138728 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 18 0.19
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:138668 original size:14 final size:14
Alignment explanation
Indices: 138649--138705 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
138639 GCGAAATGAA
138649 AATCGCAACGACAG
1 AATCGCAACGACAG
*
138663 AATCGCAACGCGAAACCAA
1 AATCGCAA--CG--A-CAG
*
138682 AATCGCAACGAAAG
1 AATCGCAACGACAG
138696 AATCGCAACG
1 AATCGCAACG
138706 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.28, G:0.19, T:0.07
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:138672 original size:33 final size:33
Alignment explanation
Indices: 138630--138722 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
138620 GCGAAACCAA
*
138630 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
138663 AATCGCAACGCGAAACCAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
138696 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
138723 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:138719 original size:52 final size:54
Alignment explanation
Indices: 138593--138727 Score: 149
Period size: 52 Copynumber: 2.5 Consensus size: 54
138583 TAGTTTACTT
*
138593 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
*
138651 TCGCAA-CGACA-G--AATCGCAACGCGAAACCAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
138698 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
138728 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.07
50 6 0.09
52 39 0.57
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:138745 original size:19 final size:19
Alignment explanation
Indices: 138723--138851 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
138713 AAAATCGCAA
138723 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
138742 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
138756 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
138775 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
138789 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
138808 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
138827 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
138847 TGCGA
1 TGCGA
138852 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:138765 original size:33 final size:33
Alignment explanation
Indices: 138723--138814 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
138713 AAAATCGCAA
138723 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
138756 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
138789 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
138815 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:139035 original size:93 final size:93
Alignment explanation
Indices: 138899--139270 Score: 719
Period size: 93 Copynumber: 4.0 Consensus size: 93
138889 ATGGATTGCA
*
138899 TTAC-TTCAACCAATAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
138963 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
138991 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
139056 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
139084 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
139149 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
139177 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
139242 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
139270 T
1 T
139271 ACTAAGCAAT
Statistics
Matches: 277, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 273 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:141017 original size:19 final size:19
Alignment explanation
Indices: 140993--141076 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
140983 GCAACGAGAG
*
140993 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
141012 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
141031 AATCACAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
141045 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
141064 AATCGCAATGCGA
1 AATCGCAACGCGA
141077 TTTTGGTTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.72
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:141033 original size:52 final size:52
Alignment explanation
Indices: 140971--141076 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
140961 TCTTTGGGTT
* *
140971 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGACAATCGCAACGC
1 GAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
*
141023 GAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
141075 GA
1 GA
141077 TTTTGGTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCACAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:141126 original size:19 final size:19
Alignment explanation
Indices: 141102--141138 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
141092 GCGATTCTCT
141102 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
141121 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
141139 TCTCGTTGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:141161 original size:20 final size:20
Alignment explanation
Indices: 141095--141171 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
141085 TCGCGTTGCG
*
141095 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACTTTC
* *
141115 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACTTTC
**
141134 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGACTTTC
141155 ATTCTCTCGTTGCGACT
1 ATTCTCTCGTTGCGACT
141172 CTTCTGCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.33
20 20 0.41
21 13 0.27
ACGTcount: A:0.12, C:0.26, G:0.18, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACTTTC
Found at i:141696 original size:20 final size:20
Alignment explanation
Indices: 141669--141860 Score: 217
Period size: 20 Copynumber: 9.6 Consensus size: 20
141659 CTTTAAATAT
*
141669 CGCGTTGCGATTTACGGATT
1 CGCGTTGCGATTTACGGATA
*
141689 CTCGTTGCGATTTACGGATTA
1 CGCGTTGCGATTTACGGA-TA
*
141710 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
141729 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
141749 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
141769 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
141789 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
141809 CACGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
141829 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
141849 CGCGTTGCGATT
1 CGCGTTGCGATT
141861 GTACTATCGC
Statistics
Matches: 149, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 145 0.97
21 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:142377 original size:39 final size:38
Alignment explanation
Indices: 142266--142388 Score: 131
Period size: 39 Copynumber: 3.2 Consensus size: 38
142256 ATTTTATGAC
* * *
142266 TGCATGGCATCTTCAGGCCAAACGTAAAGACTCGAGGAG
1 TGCACGGCGTCTTCAGG-CAAACGTAAAGACTCCAGGAG
** *
142305 TGCACGGCGTCTTCAGGCCGATG-AATAGTACTCCAGGAG
1 TGCACGGCGTCTTCAGGCAAACGTAA-AG-ACTCCAGGAG
* *
142344 TGCACGGTGTCTTCAGGCTAAACGTAAAGACTCCAAGAG
1 TGCACGGCGTCTTCAGGC-AAACGTAAAGACTCCAGGAG
142383 TGCACG
1 TGCACG
142389 ACGTTTTTAG
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
37 2 0.03
38 5 0.07
39 56 0.81
40 4 0.06
41 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (38 bp):
TGCACGGCGTCTTCAGGCAAACGTAAAGACTCCAGGAG
Found at i:143776 original size:59 final size:59
Alignment explanation
Indices: 143675--143798 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 59
143665 TTTCTAAGTC
* * *
143675 CATCCCTAAACTATGAGTCATTCTAAATTGATCCTAAAAC-TTTTGAATATTTCATTTT
1 CATCCCCAAACTATGAGTCATTCTAAATTGATCCTAAAACTTTTTGAACATTTCAATTT
* *
143733 CATCCCCAAACTATGA-TCTTATTCTAAATTGGTCCCT-AAACTTTTTTAACATTTCAATTT
1 CATCCCCAAACTATGAGTC--ATTCTAAATTGAT-CCTAAAACTTTTTGAACATTTCAATTT
143793 CATCCC
1 CATCCC
143799 ACATTATACA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
57 2 0.04
58 15 0.26
59 16 0.28
60 24 0.42
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (59 bp):
CATCCCCAAACTATGAGTCATTCTAAATTGATCCTAAAACTTTTTGAACATTTCAATTT
Found at i:144032 original size:60 final size:60
Alignment explanation
Indices: 143936--144108 Score: 195
Period size: 60 Copynumber: 2.9 Consensus size: 60
143926 AAATTTGGGT
* * * * *
143936 ATGAAATTAGAAGATTAAAAAGTTTAGAGACCAATTTAGAATGAGAGTCATAGTTTAGGG
1 ATGAAAATAGAATATTTAAAAGTTTAAAGACCAATTTAGAATGAGAGTCATAGTTTAGAG
* ** * *
143996 ATGAAAATGGAATATTTAAAAGTTTAAAGAGTAATTTAGAATGATATTCATAGTTTAGAG
1 ATGAAAATAGAATATTTAAAAGTTTAAAGACCAATTTAGAATGAGAGTCATAGTTTAGAG
* * * * *
144056 ATGAAATTAGAATGTTTAAAAGTTTAAGGACCAATATAAAATGA-AGATCATAG
1 ATGAAAATAGAATATTTAAAAGTTTAAAGACCAATTTAGAATGAGAG-TCATAG
144109 AATACATTAT
Statistics
Matches: 93, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
59 1 0.01
60 92 0.99
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.31
Consensus pattern (60 bp):
ATGAAAATAGAATATTTAAAAGTTTAAAGACCAATTTAGAATGAGAGTCATAGTTTAGAG
Found at i:152570 original size:3 final size:3
Alignment explanation
Indices: 152557--152587 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
152547 TCTCCTCCTG
*
152557 CTT CTT ATT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
152588 CTTTCCTCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:163719 original size:20 final size:21
Alignment explanation
Indices: 163670--163731 Score: 81
Period size: 20 Copynumber: 2.9 Consensus size: 21
163660 ATTCCCCTGT
163670 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
*
163693 AGGGGGAATCGGTTCCCTC-A
1 GGGGGGAATCGGTTCCCTCAA
*
163713 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
163732 TACACCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.35, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:173001 original size:2 final size:2
Alignment explanation
Indices: 172994--173040 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
172984 CGCCCGGAGT
*
172994 TA TA TA TA TA TA TA TA TT TA TA TA T- TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
173034 TA TA TA T
1 TA TA TA T
173041 GCATATAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:173238 original size:36 final size:35
Alignment explanation
Indices: 173079--173507 Score: 308
Period size: 36 Copynumber: 11.9 Consensus size: 35
173069 TTTTGACAAA
*
173079 ATATAATATATAATTTTCAGAAAACGATTTTCGAAAATTT
1 ATATAATATATAGTTTT-A-AAAAC-ATTTT-GAAAA-TT
* * * *
173119 ATATATTATATAGTTTTTGAAAATATTTT-TAAA--
1 ATATAATATATAG-TTTTAAAAACATTTTGAAAATT
* *
173152 ATATAATATATAGTTTTGAAAATATTTTGAAAACATTT
1 ATATAATATATAGTTTTAAAAACATTTTG-AAA-A-TT
* * *
173190 ATATATTGTATAGTTTTTAAAACATTTTGAAAACTT
1 ATATAATATATAGTTTTAAAAACATTTTGAAAA-TT
* *
173226 ATATAGTATATAGTTTTTAAAACATTTT-AAAA--
1 ATATAATATATAGTTTTAAAAACATTTTGAAAATT
*
173258 ATAAAATATATAGTTTTAAAAA-ATTTTTTGAACAATT
1 ATATAATATATAGTTTTAAAAACA--TTTTGAA-AATT
* * *
173295 ATATAATGTATAGTTTAAAAAAATAATTTTTTTGAAAAATT
1 ATATAATATATAGTTT-TAAAAA-CA---TTTTG-AAAATT
*
173336 ATATAATATATAGTTGTAAAAACATTTTTGAAAATT
1 ATATAATATATAGTTTTAAAAACA-TTTTGAAAATT
*
173372 ATATAATATATAGTTTTAAAAACATTTTTTAAAAAACTT
1 ATATAATATATAGTTTTAAAAACA--TTTT-GAAAA-TT
*
173411 ATAT-A-ATAT--TTTTAAAAACATTTTGAAAACT
1 ATATAATATATAGTTTTAAAAACATTTTGAAAATT
* * * *
173442 ATATAACATATAGTTTTGAAAAC-TTTTTAAAA-A
1 ATATAATATATAGTTTTAAAAACATTTTGAAAATT
* * *
173475 ATATAATATATAATTTAAAAAAATATTTTGAAA
1 ATATAATATATAGTTT-TAAAAACATTTTGAAA
173508 TATATGTTAT
Statistics
Matches: 325, Mismatches: 37, Indels: 59
0.77 0.09 0.14
Matches are distributed among these distances:
31 6 0.02
32 39 0.12
33 38 0.12
34 16 0.05
35 34 0.10
36 61 0.19
37 32 0.10
38 40 0.12
39 11 0.03
40 17 0.05
41 29 0.09
42 2 0.01
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.43
Consensus pattern (35 bp):
ATATAATATATAGTTTTAAAAACATTTTGAAAATT
Found at i:173431 original size:217 final size:214
Alignment explanation
Indices: 173106--173506 Score: 513
Period size: 217 Copynumber: 1.8 Consensus size: 214
173096 CAGAAAACGA
* * * * * *
173106 TTTTCGAAAATTTATATATTATATAGTTTTTGAAAATATTTTTAAAATATAATATATAGTTTTGA
1 TTTTCGAAAAATTATATAATATATAGTTTGTAAAAACATTTTTAAAATATAATATATAGTTTTAA
* * * **
173171 AAATATTTTGAAAACATTTATATATTGTATAGTTTTTAAAACATTTTGAAAACTTATATAGTATA
66 AAACATTTTGAAAAAACTTATATA---TATAGTTTTTAAAACATTTTGAAAAC-TATATAACATA
* * * *
173236 TAGTTTTTAAAACATTTT-AAAAATAAAATATATAGTTTTAAAAAATTTTTTGAACAATTATATA
127 TAGTTTTGAAAACATTTTAAAAAATAAAATATATAATTTAAAAAAATATTTTGAACAATTATATA
173300 ATGTATAGTTTAAAAAAATAATT
192 ATGTATAGTTTAAAAAAATAATT
*
173323 TTTTTGAAAAATTATATAATATATAG-TTGTAAAAACATTTTTGAAAATTATATAATATATAGTT
1 TTTTCGAAAAATTATATAATATATAGTTTGTAAAAACATTTTT--AAA--ATATAATATATAGTT
*
173387 TTAAAAACATTTTTTAAAAAACTTATATA-ATA-TTTTTAAAAACATTTTGAAAACTATATAACA
62 TTAAAAACA-TTTTGAAAAAACTTATATATATAGTTTTT-AAAACATTTTGAAAACTATATAACA
* *
173450 TATAGTTTTGAAAACTTTTTAAAAAATATAATATATAATTTAAAAAAATATTTTGAA
125 TATAGTTTTGAAAACATTTTAAAAAATAAAATATATAATTTAAAAAAATATTTTGAA
173507 ATATATGTTA
Statistics
Matches: 158, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
216 43 0.27
217 74 0.47
218 3 0.02
220 22 0.14
221 16 0.10
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (214 bp):
TTTTCGAAAAATTATATAATATATAGTTTGTAAAAACATTTTTAAAATATAATATATAGTTTTAA
AAACATTTTGAAAAAACTTATATATATAGTTTTTAAAACATTTTGAAAACTATATAACATATAGT
TTTGAAAACATTTTAAAAAATAAAATATATAATTTAAAAAAATATTTTGAACAATTATATAATGT
ATAGTTTAAAAAAATAATT
Found at i:173488 original size:146 final size:141
Alignment explanation
Indices: 173152--173484 Score: 327
Period size: 146 Copynumber: 2.3 Consensus size: 141
173142 TATTTTTAAA
* * * * *
173152 ATATAATATATAGTTTTGAAAATATTTTGAAAACAT-TTATATATTGTATAGTTTTTAAAACATT
1 ATATAATATATAGTTTTGAAAAT-TTTT-AAAAAATATTATATAATATATAGTTGTAAAAACATT
* *
173216 TTGAAAACTTATATAGTATATAGTTTTTAAAACATTTTAAAAATAAAATATATAGTTTTAAAAAA
64 TTGAAAACTTATATAATATATAGTTTTAAAAACATTTTAAAAATAAAATATATAGTTTTAAAAAA
*
173281 TTTTTTGAACAATT
129 -TTTTTGAACAACT
* ** **
173295 ATATAATGTATAGTTTAAAAAAATAATTTTTTTGAAAA-ATTATATAATATATAGTTGTAAAAAC
1 ATATAATATATAGTTT---TGAA-AA-TTTTTAAAAAATATTATATAATATATAGTTGTAAAAAC
** *
173359 ATTTTTGAAAA-TTATATAATATATAGTTTTAAAAACATTTTTTAAAAA-ACTTATATAATATTT
61 A-TTTTGAAAACTTATATAATATATAGTTTTAAAAACA--TTTTAAAAATA-AAATAT-ATAGTT
173422 TTAAAAACA-TTTTGAA-AACT
121 TTAAAAA-ATTTTTGAACAACT
* *
173442 ATATAACATATAGTTTTGAAAACTTTTTAAAAAATATAATATA
1 ATATAATATATAGTTTTGAAAA-TTTTTAAAAAATATTATATA
173485 TAATTTAAAA
Statistics
Matches: 153, Mismatches: 24, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
143 26 0.17
144 9 0.06
146 51 0.33
147 33 0.22
148 21 0.14
149 12 0.08
150 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (141 bp):
ATATAATATATAGTTTTGAAAATTTTTAAAAAATATTATATAATATATAGTTGTAAAAACATTTT
GAAAACTTATATAATATATAGTTTTAAAAACATTTTAAAAATAAAATATATAGTTTTAAAAAATT
TTTGAACAACT
Found at i:173558 original size:9 final size:9
Alignment explanation
Indices: 173544--173595 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
173534 ATGTTATTAT
173544 TTTTTTTTA
1 TTTTTTTTA
173553 TTTTTTTTA
1 TTTTTTTTA
**
173562 TTCATTTTA
1 TTTTTTTTA
*
173571 TTTATTTTAA
1 TTT-TTTTTA
* *
173581 TTTATTTCA
1 TTTTTTTTA
173590 TTTTTT
1 TTTTTT
173596 CCAGGTACAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
9 27 0.79
10 7 0.21
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:173563 original size:22 final size:22
Alignment explanation
Indices: 173544--173593 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
173534 ATGTTATTAT
*
173544 TTTTTTTTATTTTTTTTATTCA
1 TTTTATTTATTTTTTTTATTCA
*
173566 TTTTATTTATTTTAATTTATTTCA
1 TTTTATTTATTTT-TTTTA-TTCA
173590 TTTT
1 TTTT
173594 TTCCAGGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.50
23 4 0.17
24 8 0.33
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTATTTATTTTTTTTATTCA
Found at i:173571 original size:18 final size:18
Alignment explanation
Indices: 173548--173595 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
173538 TATTATTTTT
*
173548 TTTTATTTTTTTTATTCA
1 TTTTATTTTTTTAATTCA
*
173566 TTTTATTTATTTTAATTTA
1 TTTTATTT-TTTTAATTCA
*
173585 TTTCATTTTTT
1 TTTTATTTTTT
173596 CCAGGTACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATTTTTTTAATTCA
Found at i:173583 original size:10 final size:10
Alignment explanation
Indices: 173540--173587 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
173530 TAGTATGTTA
*
173540 TTATTTTTTT
1 TTATTTATTT
173550 TTATTT-TTT
1 TTATTTATTT
*
173559 TTATTCA-TT
1 TTATTTATTT
173568 TTATTTATTT
1 TTATTTATTT
*
173578 TAATTTATTT
1 TTATTTATTT
173588 CATTTTTTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 16 0.48
10 17 0.52
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (10 bp):
TTATTTATTT
Found at i:174828 original size:18 final size:18
Alignment explanation
Indices: 174790--174828 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
174780 TATTAACTTC
* *
174790 TTTTTTTATTTGTTTTTA
1 TTTTTTTATTTGCTTTGA
174808 TTTTTTTATTTGCTTTGA
1 TTTTTTTATTTGCTTTGA
174826 TTT
1 TTT
174829 AATATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.03, G:0.08, T:0.79
Consensus pattern (18 bp):
TTTTTTTATTTGCTTTGA
Found at i:174883 original size:8 final size:8
Alignment explanation
Indices: 174825--174883 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
174815 ATTTGCTTTG
174825 ATTTAA-T
1 ATTTAATT
*
174832 ATTTTATT
1 ATTTAATT
174840 ATTCT-ATT
1 ATT-TAATT
174848 ATTTTAATT
1 A-TTTAATT
*
174857 AATTAATT
1 ATTTAATT
174865 AATTTAA-T
1 -ATTTAATT
174873 ATTTAATT
1 ATTTAATT
174881 ATT
1 ATT
174884 ATTTTACCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
7 11 0.26
8 20 0.47
9 12 0.28
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTTAATT
Found at i:178437 original size:23 final size:23
Alignment explanation
Indices: 178411--178461 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
178401 TTCTGGCGTT
178411 CATATTTCAATTTTTATTTTCAA
1 CATATTTCAATTTTTATTTTCAA
178434 CATATTTCAATTTTTATTTTCAA
1 CATATTTCAATTTTTATTTTCAA
178457 CATAT
1 CATAT
178462 CTCTTGGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (23 bp):
CATATTTCAATTTTTATTTTCAA
Found at i:179909 original size:15 final size:15
Alignment explanation
Indices: 179889--179919 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
179879 ATTATCGATG
179889 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
179904 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
179919 A
1 A
179920 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:180178 original size:2 final size:2
Alignment explanation
Indices: 180171--180200 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
180161 ACTAAAAATA
180171 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
180201 TATTTTGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:180508 original size:63 final size:64
Alignment explanation
Indices: 180412--180539 Score: 231
Period size: 63 Copynumber: 2.0 Consensus size: 64
180402 ATGGATCAAA
* *
180412 TTAATTGAATGCACAAGTGTTGATGATCAAATATGTAATTATATCAATTTTATTAATTGTCATG
1 TTAATTGAATGCACAAGTGTTGACGATCAAATATGTAATTATATCAATTTTATTAATTATCATG
180476 TTAATTGAATGCACAA-TGTTGACGATCAAATATGTAATTATATCAATTTTATTAATTATCATG
1 TTAATTGAATGCACAAGTGTTGACGATCAAATATGTAATTATATCAATTTTATTAATTATCATG
180539 T
1 T
180540 AAACACTTCT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
63 46 0.74
64 16 0.26
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (64 bp):
TTAATTGAATGCACAAGTGTTGACGATCAAATATGTAATTATATCAATTTTATTAATTATCATG
Found at i:191187 original size:4 final size:4
Alignment explanation
Indices: 191178--191216 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
191168 CAATGCATGT
191178 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
191217 CATAGTTGAA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:200474 original size:18 final size:18
Alignment explanation
Indices: 200453--200504 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
200443 GAAGCTGCAT
*
200453 AGCCCGTTGAACCTGAAG
1 AGCCCGATGAACCTGAAG
* * * *
200471 AGCCTGCTAAAGCTGAAG
1 AGCCCGATGAACCTGAAG
*
200489 AGCCCGATGACCCTGA
1 AGCCCGATGAACCTGA
200505 TCCCGTCCAT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (18 bp):
AGCCCGATGAACCTGAAG
Found at i:200493 original size:36 final size:36
Alignment explanation
Indices: 200435--200504 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
200425 GATAGTCCCC
* * * *
200435 AGCCCGCTGAAGCTGCATAGCCCGTTGAACCTGAAG
1 AGCCCGCTAAAGCTGAAGAGCCCGATGAACCTGAAG
* *
200471 AGCCTGCTAAAGCTGAAGAGCCCGATGACCCTGA
1 AGCCCGCTAAAGCTGAAGAGCCCGATGAACCTGA
200505 TCCCGTCCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (36 bp):
AGCCCGCTAAAGCTGAAGAGCCCGATGAACCTGAAG
Found at i:204045 original size:35 final size:36
Alignment explanation
Indices: 203974--204052 Score: 133
Period size: 35 Copynumber: 2.2 Consensus size: 36
203964 GACACATTAA
203974 GAGAATGATACACAGAAGTCAACGATATCAAACTAC
1 GAGAATGATACACAGAAGTCAACGATATCAAACTAC
* *
204010 GAGAATGATACACAGAATTC-ACGATATCAAGCTAC
1 GAGAATGATACACAGAAGTCAACGATATCAAACTAC
204045 GAGAATGA
1 GAGAATGA
204053 ATAAAGTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 22 0.54
36 19 0.46
ACGTcount: A:0.46, C:0.18, G:0.19, T:0.18
Consensus pattern (36 bp):
GAGAATGATACACAGAAGTCAACGATATCAAACTAC
Found at i:204995 original size:4 final size:4
Alignment explanation
Indices: 204988--207474 Score: 4394
Period size: 4 Copynumber: 635.2 Consensus size: 4
204978 TGTGTGTGTG
204988 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-A TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205035 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205083 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205131 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205179 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205225 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205273 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205321 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205369 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA --TA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205415 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205463 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205509 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205557 TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205601 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205649 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205697 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205745 TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205792 TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205838 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205886 TGTA TGTA TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205932 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
205980 TGTA TGTA TGTA TGTA TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206026 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206074 TGTA TGTA TGTA TGTA TGTA TGTA T-TA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206121 -GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206168 TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206215 TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
206262 TGTC TGTA TGTA TGTA TGTA TGTA TGTA TGGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-GTA TGTA TGTA TGTA TGTA
206311 TGTA TGTA TGTGA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGT-A TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206360 TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA T-TA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206405 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206453 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
206501 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TTTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206549 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206597 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
206645 TGTA T-TA TGTA TGTA TGTA TGTA TGTA TGTA GGTA TG-A TGTA --TA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
206689 TGTA TGTA TGTA TGTA -GTA TGTA GGTA TGTA TGTA TGTA TGT- TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206735 TGTA TGT- TGTA TGTA TGTA TGTA TGTA -GTA TGT- TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206780 TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
206826 TGTA TG-A TGTA TG-- TGTA TGTA TGTA TGTTA TGTA TGTA TGTA TGTC
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-TA TGTA TGTA TGTA TGTA
206872 TGTA --TA TGTA -GTA TGTA TGTA TGGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA T-GTA TGTA TGTA TGTA TGTA TGTA
206918 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
206966 TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
207012 TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
207058 TGTA TGTA -G-A TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-GTA
*
207103 TGTA TGTA TGTA TGTA TGGGTA TGTA TGTA TGTA TGTA TGTA TGTA GGTA
1 TGTA TGTA TGTA TGTA T--GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
207153 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
207201 TGTA TGTA TG-- TGTA TG-A TGTA TGTA TGTA TGTA TGTA GGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
207246 TGTA TGTA TGTA TGTA TGTA GGTA TGTA TGTA TGTA TGTA TGTA -GTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
207293 TGTA TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA TGTA T-TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
207339 TGTA TGTA TGTA TGTA TGTA TGTA TGT- TGTA T-TA TGTA TGTA TGT-
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
207384 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
207432 TGTA GGTA TGTA TGTA TGTA TGTA TGTA TGTA --TA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
207475 ATGTGTATTA
Statistics
Matches: 2395, Mismatches: 20, Indels: 136
0.94 0.01 0.05
Matches are distributed among these distances:
2 37 0.02
3 70 0.03
4 2264 0.95
5 20 0.01
6 4 0.00
ACGTcount: A:0.25, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
TGTA
Done.