Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 60 of 130
Found at i:12700270 original size:14 final size:13
Alignment explanation
Indices: 12700241--12700280 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
12700231 AAAAAATACG
12700241 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
*
12700254 AAAAAATAGACA-A
1 AAAAAA-AGAAAGA
12700267 AAAAAAAGAAAGA
1 AAAAAAAGAAAGA
12700280 A
1 A
12700281 GCAATTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.17
13 15 0.65
14 4 0.17
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAAAAAGAAAGA
Found at i:12703615 original size:44 final size:44
Alignment explanation
Indices: 12703566--12703753 Score: 137
Period size: 44 Copynumber: 4.2 Consensus size: 44
12703556 TATTTGATTT
* *
12703566 TTTTGAAAATTTAAAAAGGCTCCTCTCAA-TATAAGCTCAATGAC
1 TTTTGAAAATTTAAAAAGGCTCCTCT-AAGTAGAAGCTCAATAAC
* * * * *
12703610 TTTTGAAAATTTAAAAAAGTTCTTCTAAGTAGAGGTTCAATAAC
1 TTTTGAAAATTTAAAAAGGCTCCTCTAAGTAGAAGCTCAATAAC
* * * * * *
12703654 TTTTGAAAATATAAAATGGCTCATCTAAGCAGAGGCTCAACAAC
1 TTTTGAAAATTTAAAAAGGCTCCTCTAAGTAGAAGCTCAATAAC
** * * * * *
12703698 TTTAAAAATCATCTTGAAAAA-GCTTCTCTATGTAGAGGCTTAACAAC
1 TTTTGAAA--AT-TT-AAAAAGGCTCCTCTAAGTAGAAGCTCAATAAC
12703745 TTTTGAAAA
1 TTTTGAAAA
12703754 ATAAAATGGC
Statistics
Matches: 113, Mismatches: 26, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
43 2 0.02
44 76 0.67
45 1 0.01
46 2 0.02
47 28 0.25
48 4 0.04
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (44 bp):
TTTTGAAAATTTAAAAAGGCTCCTCTAAGTAGAAGCTCAATAAC
Found at i:12703736 original size:47 final size:48
Alignment explanation
Indices: 12703677--12704234 Score: 429
Period size: 47 Copynumber: 11.7 Consensus size: 48
12703667 AAATGGCTCA
12703677 TCTAAGCAGAGGCTCAACAACTTTAAAAA-TCATCTTGAAAAAGCTTC
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTTC
* * * ** *
12703724 TCTATGTAGAGGCTTAACAACTTTTGAAAAA-T-A-----AAATGGCTTA
1 TCTAAGCAGAGGCTCAACAAC-TTT-AAAAATTCATCTTGAAAAAGCTTC
* *
12703767 TCTAAGCAAAGGCTCAACAACTTTAAAAATT-ATCTTGAAAAAGC-AC
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTTC
* * * *
12703813 TTCTAAGCAGAGGCTCCACAACTTTTAAAAATTTATTTTGAGAAAGCTAT-
1 -TCTAAGCAGAGGCTCAACAAC-TTTAAAAATTCATCTTGAAAAAGCT-TC
* * * *
12703863 TATAAGCAAAGGCTCCACAACTTTAAAAATTCATCTTGAGAAAAAGCTCC
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTT--GAAAAAGCTTC
* * * * * *
12703913 TCTAAGTAAAGGCTCCACAACTTT--GAATTCAT-TCT-ACAAAGCTCC
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCT-TGAAAAAGCTTC
* *
12703958 TCTAAGCAGAGGCTCAACAACTTTAGAAA-TCATCTTGAAAAAAC-TC
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTTC
* *** *
12704004 TTCTAAGTAGAGGCTTTGCAACTTTAAAAATTCATCTTGAGAAAAAGTTTC
1 -TCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTT--GAAAAAGCTTC
* * *
12704055 TCTAAGCAGAGG-TTAACAATTTTAAAAATTTATCTTCAGAAAAAG-TTCC
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTT--GAAAAAGCTT-C
* * * *
12704104 TCTAAGTAGAGGCTCTACAACTTTAAAAATTCATCTT-AAAAAACTCC
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTTC
* * * * *
12704151 TTTAAGTAGAAGCTCAACAACCTTAAAAATTCATCTTGAGAAAAAGCTCC
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTT--GAAAAAGCTTC
* *
12704201 TCTAAGCAGAGGTTTC-ATAACTTTAAAAATTCAT
1 TCTAAGCAGAGG-CTCAACAACTTTAAAAATTCAT
12704235 TTGTTCTCGA
Statistics
Matches: 411, Mismatches: 67, Indels: 63
0.76 0.12 0.12
Matches are distributed among these distances:
41 5 0.01
42 5 0.01
43 24 0.06
45 30 0.07
46 6 0.01
47 114 0.28
48 46 0.11
49 76 0.18
50 101 0.25
51 4 0.01
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.29
Consensus pattern (48 bp):
TCTAAGCAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTTC
Found at i:12703780 original size:90 final size:91
Alignment explanation
Indices: 12703623--12704028 Score: 339
Period size: 90 Copynumber: 4.4 Consensus size: 91
12703613 TGAAAATTTA
*
12703623 AAAAAG-TTCTTCTAAGTAGAGG-TTCAATAACTTTTG-AAAATATAAAATGGCTCATCTAAGCA
1 AAAAAGCTTCTTCTAAGTAGAGGCTT-AACAACTTTTGAAAAATAT-AAA-GGCTCATCTAAGCA
*
12703685 GAGGCTCAACAACTTTAAAAATCATCTTG
63 AAGGCTCAACAACTTTAAAAATCATCTTG
* *
12703714 AAAAAGCTTC-TCTATGTAGAGGCTTAACAACTTTTGAAAAATA-AAATGGCTTATCTAAGCAAA
1 AAAAAGCTTCTTCTAAGTAGAGGCTTAACAACTTTTGAAAAATATAAA-GGCTCATCTAAGCAAA
*
12703777 GGCTCAACAACTTTAAAAATTATCTTG
65 GGCTCAACAACTTTAAAAATCATCTTG
* * ** * *
12703804 AAAAAGC-ACTTCTAAGCAGAGGCTCCACAACTTTT-AAAAATTTATTTTGAGAAAGCT-ATTAT
1 AAAAAGCTTCTTCTAAGTAGAGGCTTAACAACTTTTGAAAAA--TA---T-A-AAGGCTCA-TCT
*
12703866 AAGCAAAGGCTCCACAACTTTAAAAATTCATCTTGAG
58 AAGCAAAGGCTCAACAACTTTAAAAA-TCATCTT--G
* * ** * * * * *
12703903 AAAAAGC-TCCTCTAAGTAAAGGCTCCACAAC-TTTGAATTCATTCTACAAAGCTCCTCTAAGCA
1 AAAAAGCTTCTTCTAAGTAGAGGCTTAACAACTTTTGAA--AAATATA-AAGGCTCATCTAAGCA
* *
12703966 GAGGCTCAACAACTTTAGAAATCATCTTG
63 AAGGCTCAACAACTTTAAAAATCATCTTG
* **
12703995 AAAAAAC-TCTTCTAAGTAGAGGCTTTGCAACTTT
1 AAAAAGCTTCTTCTAAGTAGAGGCTTAACAACTTT
12704029 AAAAATTCAT
Statistics
Matches: 261, Mismatches: 33, Indels: 40
0.78 0.10 0.12
Matches are distributed among these distances:
89 6 0.02
90 72 0.28
91 29 0.11
92 37 0.14
93 2 0.01
94 7 0.03
95 33 0.13
96 32 0.12
97 8 0.03
98 3 0.01
99 31 0.12
101 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (91 bp):
AAAAAGCTTCTTCTAAGTAGAGGCTTAACAACTTTTGAAAAATATAAAGGCTCATCTAAGCAAAG
GCTCAACAACTTTAAAAATCATCTTG
Found at i:12703786 original size:43 final size:43
Alignment explanation
Indices: 12703633--12703790 Score: 140
Period size: 43 Copynumber: 3.6 Consensus size: 43
12703623 AAAAAGTTCT
* * * *
12703633 TCTAAGTAGAGGTTCAATAACTTTTGAAAATATAAAATGGCTCA
1 TCTAAGCAGAGGCTCAACAACTTTTGAAAA-ATAAAATGGCTTA
** *
12703677 TCTAAGCAGAGGCTCAACAAC-TTT-AAAAATCATCTTGAAAAAGCTTC
1 TCTAAGCAGAGGCTCAACAACTTTTGAAAAAT-A-----AAATGGCTTA
* * *
12703724 TCTATGTAGAGGCTTAACAACTTTTGAAAAATAAAATGGCTTA
1 TCTAAGCAGAGGCTCAACAACTTTTGAAAAATAAAATGGCTTA
*
12703767 TCTAAGCAAAGGCTCAACAACTTT
1 TCTAAGCAGAGGCTCAACAACTTT
12703791 AAAAATTATC
Statistics
Matches: 89, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
41 2 0.02
42 5 0.06
43 30 0.34
44 18 0.20
47 24 0.27
48 4 0.04
49 6 0.07
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (43 bp):
TCTAAGCAGAGGCTCAACAACTTTTGAAAAATAAAATGGCTTA
Found at i:12703982 original size:191 final size:191
Alignment explanation
Indices: 12703767--12704236 Score: 543
Period size: 191 Copynumber: 2.4 Consensus size: 191
12703757 AAATGGCTTA
* * *
12703767 TCTAAGCAAAGGCTCAACAACTTTAAAAATTATCTTGAAAAAGCACTTCTAAGCAGAGGCTCCAC
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATTATCTTGAAAAAGCTCTTCTAAGCAGAGGCTTCAC
* *
12703832 AACTTTTAAAAATTTATTTTGAG-AAAGCTAT-TATAAGCAAAGGCTCCACAACTTTAAAAATTC
66 AAC-TTTAAAAATTCATTTTGAGAAAAG-TATCTATAAGCAAAGG-TCAACAACTTTAAAAATTC
* * * *
12703895 ATCTTGAGAAAAAGCTCCTCTAAGTAAAGGCTCCACAACTTT-GAATTCAT-TCTACAAAGCTCC
128 ATCTTCAGAAAAAGCTCCTCTAAGTAAAGGCTCCACAACTTTAAAATTCATCT-TAAAAAACTCC
* * * * **
12703958 TCTAAGCAGAGGCTCAACAACTTTAGAAATCATCTTGAAAAAACTCTTCTAAGTAGAGGCTTTGC
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATTATCTTGAAAAAGCTCTTCTAAGCAGAGGCTTCAC
* * * * * * *
12704023 AACTTTAAAAATTCATCTTGAGAAAAAGTTTCTCTAAGCAGAGGTTAACAATTTTAAAAATTTAT
66 AACTTTAAAAATTCATTTTGAG-AAAAGTATCTATAAGCAAAGGTCAACAACTTTAAAAATTCAT
* * *
12704088 CTTCAGAAAAAGTTCCTCTAAGTAGAGGCTCTACAACTTTAAAAATTCATCTTAAAAAACTCC
130 CTTCAGAAAAAGCTCCTCTAAGTAAAGGCTCCACAACTTT-AAAATTCATCTTAAAAAACTCC
* * * * * *
12704151 TTTAAGTAGAAGCTCAACAACCTTAAAAATTCATCTTGAGAAAAAGCTCCTCTAAGCAGAGGTTT
1 TCTAAGCAGAGGCTCAACAACTTTAAAAATT-ATCTT--GAAAAAGCTCTTCTAAGCAGAGGCTT
*
12704216 CATAACTTTAAAAATTCATTT
63 CACAACTTTAAAAATTCATTT
12704237 GTTCTCGAAA
Statistics
Matches: 231, Mismatches: 39, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
190 17 0.07
191 114 0.49
192 14 0.06
193 41 0.18
194 6 0.03
196 39 0.17
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (191 bp):
TCTAAGCAGAGGCTCAACAACTTTAAAAATTATCTTGAAAAAGCTCTTCTAAGCAGAGGCTTCAC
AACTTTAAAAATTCATTTTGAGAAAAGTATCTATAAGCAAAGGTCAACAACTTTAAAAATTCATC
TTCAGAAAAAGCTCCTCTAAGTAAAGGCTCCACAACTTTAAAATTCATCTTAAAAAACTCC
Found at i:12704158 original size:146 final size:146
Alignment explanation
Indices: 12703767--12704214 Score: 441
Period size: 146 Copynumber: 3.1 Consensus size: 146
12703757 AAATGGCTTA
* * * * *
12703767 TCTAAGCAAAGGCTCAACAACTTTAAAAA-TTATCTT--GAAAAAGCACTTCTAAGCAGAGGCTC
1 TCTAAGCAGAGG-TTAACAATTTTAAAAATTTATCTTCAGAAAAAGCTCCTCTAAGCAGAGGCTC
* * * * * * * * * *
12703829 CACAACTTTTAAAAATTTATTTTGAGAAAGCTATTATAAGCA-AAGGCTCCACAACTTTAAAAAT
65 AACAAC-TTTAAAAA-TCATCTTGAAAAAACTCTTCTAAGTAGAA-GCTCAACAACCTTAAAAAT
12703893 TCATCTTGAGAAAAAGCTCC
127 TCATCTTGAGAAAAAGCTCC
* * ** * * * * *
12703913 TCTAAGTAAAGGCTCCACAACTTT--GAATTCA--TTC-TACAAAGCTCCTCTAAGCAGAGGCTC
1 TCTAAGCAGAGG-TTAACAATTTTAAAAATTTATCTTCAGAAAAAGCTCCTCTAAGCAGAGGCTC
* * *** *
12703973 AACAACTTTAGAAATCATCTTGAAAAAACTCTTCTAAGTAGAGGCTTTGCAACTTTAAAAATTCA
65 AACAACTTTAAAAATCATCTTGAAAAAACTCTTCTAAGTAGAAGCTCAACAACCTTAAAAATTCA
* *
12704038 TCTTGAGAAAAAGTTTC
130 TCTTGAGAAAAAGCTCC
* * *
12704055 TCTAAGCAGAGGTTAACAATTTTAAAAATTTATCTTCAGAAAAAGTTCCTCTAAGTAGAGGCTCT
1 TCTAAGCAGAGGTTAACAATTTTAAAAATTTATCTTCAGAAAAAGCTCCTCTAAGCAGAGGCTCA
12704120 ACAACTTTAAAAATTCATCTT-AAAAAACTCCTT-TAAGTAGAAGCTCAACAACCTTAAAAATTC
66 ACAACTTTAAAAA-TCATCTTGAAAAAACT-CTTCTAAGTAGAAGCTCAACAACCTTAAAAATTC
12704183 ATCTTGAGAAAAAGCTCC
129 ATCTTGAGAAAAAGCTCC
12704201 TCTAAGCAGAGGTT
1 TCTAAGCAGAGGTT
12704215 TCATAACTTT
Statistics
Matches: 249, Mismatches: 43, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
141 8 0.03
142 63 0.25
143 15 0.06
144 29 0.12
145 5 0.02
146 119 0.48
147 10 0.04
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (146 bp):
TCTAAGCAGAGGTTAACAATTTTAAAAATTTATCTTCAGAAAAAGCTCCTCTAAGCAGAGGCTCA
ACAACTTTAAAAATCATCTTGAAAAAACTCTTCTAAGTAGAAGCTCAACAACCTTAAAAATTCAT
CTTGAGAAAAAGCTCC
Found at i:12705080 original size:13 final size:13
Alignment explanation
Indices: 12705062--12705091 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12705052 TTATTTTTTC
*
12705062 TTTTTTTTTACTT
1 TTTTTTTTTAATT
12705075 TTTTTTTTTAATT
1 TTTTTTTTTAATT
12705088 TTTT
1 TTTT
12705092 GAGCAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTAATT
Found at i:12717809 original size:5 final size:5
Alignment explanation
Indices: 12717801--12717829 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12717791 AGAAAAAGAA
12717801 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
12717830 ATTAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:12721311 original size:24 final size:25
Alignment explanation
Indices: 12721249--12721301 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
12721239 ATATTTTTAA
*
12721249 AAATAAATAAATAATTTAATATGTT
1 AAATGAATAAATAATTTAATATGTT
12721274 AAATGAATAAATAATTT-ATATGTT
1 AAATGAATAAATAATTTAATATGTT
12721298 AAAT
1 AAAT
12721302 TCTTAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
AAATGAATAAATAATTTAATATGTT
Found at i:12726266 original size:15 final size:15
Alignment explanation
Indices: 12726246--12726278 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
12726236 TAATCCTACC
12726246 ATCTACTTTCACTAA
1 ATCTACTTTCACTAA
12726261 ATCTACTTTCACTAA
1 ATCTACTTTCACTAA
12726276 ATC
1 ATC
12726279 CATGTCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.39
Consensus pattern (15 bp):
ATCTACTTTCACTAA
Found at i:12729738 original size:10 final size:10
Alignment explanation
Indices: 12729725--12729758 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
12729715 TTTAAAAACC
*
12729725 TTTCTTTTCT
1 TTTCTTTTCA
12729735 TTTCTTTTCA
1 TTTCTTTTCA
*
12729745 TTTCCTTTCA
1 TTTCTTTTCA
12729755 TTTC
1 TTTC
12729759 CTTTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTCTTTTCA
Found at i:12732606 original size:23 final size:23
Alignment explanation
Indices: 12732571--12732619 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
12732561 TTTGGTATAC
* *
12732571 TTCATTTTGTTATCATACATTGA
1 TTCACTTTATTATCATACATTGA
12732594 TTCACTTTATTATCATACATTGA
1 TTCACTTTATTATCATACATTGA
12732617 TTC
1 TTC
12732620 TCATAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (23 bp):
TTCACTTTATTATCATACATTGA
Found at i:12732992 original size:2 final size:2
Alignment explanation
Indices: 12732987--12733013 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12732977 TCTCTCTCTC
12732987 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
12733014 CATGCGCACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12737512 original size:94 final size:96
Alignment explanation
Indices: 12737344--12737532 Score: 226
Period size: 93 Copynumber: 2.0 Consensus size: 96
12737334 CTGATAATTT
* * *
12737344 TGTTAATGTAATAATATTCTATATATTATGTAACTATGTAATCAAACGTAATATCTGTGATTATG
1 TGTTAATGTAATAATATTCTATATATTATGTAACTATGTAATCAAACATAATATCTATGATTATA
* *
12737409 ATACATAATTAAAATAATATTTAAGATTATTG
66 ATACATAATTAAAA-AAAATCTAAGATTATTG
* * *
12737441 TGTTAATGTAAT-AT-TT-TGTATATTATGTAATTAT-TAATCAAACATGATAT-TAATGATTAT
1 TGTTAATGTAATAATATTCTATATATTATGTAACTATGTAATCAAACATAATATCT-ATGATTAT
**
12737501 AATATTGTAATTAAAAAAAATCTAAGATTATT
65 AATA-CATAATTAAAAAAAATCTAAGATTATT
12737533 AAATAATTAA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
92 1 0.01
93 38 0.47
94 25 0.31
95 2 0.03
96 2 0.03
97 12 0.15
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (96 bp):
TGTTAATGTAATAATATTCTATATATTATGTAACTATGTAATCAAACATAATATCTATGATTATA
ATACATAATTAAAAAAAATCTAAGATTATTG
Found at i:12737542 original size:49 final size:50
Alignment explanation
Indices: 12737489--12737595 Score: 155
Period size: 49 Copynumber: 2.2 Consensus size: 50
12737479 CAAACATGAT
* * *
12737489 ATTAATGATTATAATATTGTAATTAAAA-AAAATCTAAGATTATTAAATA
1 ATTAATGATTATAATACTATAATTAAAATAAAATCTAAAATTATTAAATA
* *
12737538 ATTAATGATTATAATACTATAATTAAAATAATATTTAAAATTATTAAATA
1 ATTAATGATTATAATACTATAATTAAAATAAAATCTAAAATTATTAAATA
12737588 ATT-ATGAT
1 ATTAATGAT
12737596 ATCGCATATA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
49 31 0.60
50 21 0.40
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (50 bp):
ATTAATGATTATAATACTATAATTAAAATAAAATCTAAAATTATTAAATA
Found at i:12737912 original size:12 final size:12
Alignment explanation
Indices: 12737895--12737919 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12737885 CTCCTGCAGC
12737895 TTTCTCAAATTT
1 TTTCTCAAATTT
12737907 TTTCTCAAATTT
1 TTTCTCAAATTT
12737919 T
1 T
12737920 GTTAAATATT
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:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTCTCAAATTT
Found at i:12741948 original size:18 final size:17
Alignment explanation
Indices: 12741917--12741966 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
12741907 TAAGTCTATT
*
12741917 TTTTTTTTTGTATTTTACA
1 TTTTTATTT-TATTTT-CA
*
12741936 TTTTTATTTTATTTTTA
1 TTTTTATTTTATTTTCA
12741953 TTTTTATTATTATT
1 TTTTTATT-TTATT
12741967 ATTTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 9 0.32
18 11 0.39
19 8 0.29
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTATTTTCA
Found at i:12741950 original size:26 final size:25
Alignment explanation
Indices: 12741935--12742023 Score: 62
Period size: 26 Copynumber: 3.6 Consensus size: 25
12741925 TGTATTTTAC
**
12741935 ATTTTTATTTTATTTTTATTTTTATT
1 ATTTTT-TTTTATTTTTATCATTATT
*
12741961 ATTATTATTTT-TTTTTAT-A-TATT
1 ATT-TTTTTTTATTTTTATCATTATT
12741984 -TTTTTCTTTTATTTTTATC-TTATGT
1 ATTTTT-TTTTATTTTTATCATTAT-T
*
12742009 ATTTATTATTTATTT
1 ATTT-TTTTTTATTT
12742024 ATTTATTACT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
21 2 0.04
22 6 0.12
23 11 0.22
24 3 0.06
25 8 0.16
26 17 0.33
27 4 0.08
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.76
Consensus pattern (25 bp):
ATTTTTTTTTATTTTTATCATTATT
Found at i:12741957 original size:25 final size:25
Alignment explanation
Indices: 12741913--12741978 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
12741903 TAGGTAAGTC
*
12741913 TATT-TTTTTTTTTGTATTTTA-CAT
1 TATTATTTTTTTTTAT-TTTTATCAT
* *
12741937 TTTTATTTTATTTTTATTTTTATTAT
1 TATTATTTT-TTTTTATTTTTATCAT
12741963 TATTATTTTTTTTTAT
1 TATTATTTTTTTTTAT
12741979 ATATTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 3 0.09
25 16 0.46
26 16 0.46
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (25 bp):
TATTATTTTTTTTTATTTTTATCAT
Found at i:12741996 original size:13 final size:14
Alignment explanation
Indices: 12741950--12742012 Score: 67
Period size: 13 Copynumber: 4.4 Consensus size: 14
12741940 TATTTTATTT
*
12741950 TTATTTTTATTATTA
1 TTATTTTT-TTCTTA
12741965 TTATTTTTTT-TTA
1 TTATTTTTTTCTTA
12741978 TATATTTTTTTCTT-
1 T-TATTTTTTTCTTA
*
12741992 TTATTTTTATCTTA
1 TTATTTTTTTCTTA
12742006 TGTATTT
1 T-TATTT
12742013 ATTATTTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
13 15 0.35
14 13 0.30
15 15 0.35
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (14 bp):
TTATTTTTTTCTTA
Found at i:12742193 original size:22 final size:22
Alignment explanation
Indices: 12742168--12742221 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
12742158 TTTGTTTATC
12742168 TTATTTATTTTTATTAATATTT
1 TTATTTATTTTTATTAATATTT
* * *
12742190 TTATTTGATTTTTTTTATTTTTT
1 TTATTT-ATTTTTATTAATATTT
12742213 TTATTTATT
1 TTATTTATT
12742222 CGGCTAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TTATTTATTTTTATTAATATTT
Found at i:12742211 original size:9 final size:10
Alignment explanation
Indices: 12742128--12742218 Score: 64
Period size: 9 Copynumber: 9.0 Consensus size: 10
12742118 AATTTATCTA
12742128 TTATTTAATTT
1 TTATTT-ATTT
* *
12742139 TAATTTATCTG
1 TTATTTAT-TT
*
12742150 TTAATT-TTT
1 TTATTTATTT
* *
12742159 TTGTTTA-TC
1 TTATTTATTT
12742168 TTATTTATTT
1 TTATTTATTT
12742178 TTATTAATATTT
1 TTATT--TATTT
12742190 TTATTTGATTT
1 TTATTT-ATTT
12742201 TT-TTTATTT
1 TTATTTATTT
12742210 TT-TTTATTT
1 TTATTTATTT
12742219 ATTCGGCTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
9 25 0.39
10 13 0.20
11 16 0.25
12 10 0.16
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (10 bp):
TTATTTATTT
Found at i:12742752 original size:21 final size:22
Alignment explanation
Indices: 12742723--12742766 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
12742713 ATTCTAGAGA
*
12742723 GAAGGGAGAGAAG-AAAGAAGG
1 GAAGAGAGAGAAGAAAAGAAGG
12742744 GAAGAGAGAGAAGAAAAGAAGG
1 GAAGAGAGAGAAGAAAAGAAGG
12742766 G
1 G
12742767 TTCTGCTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (22 bp):
GAAGAGAGAGAAGAAAAGAAGG
Found at i:12743026 original size:4 final size:4
Alignment explanation
Indices: 12743014--12743106 Score: 52
Period size: 4 Copynumber: 22.8 Consensus size: 4
12743004 TTTTATTATT
* *
12743014 TTTA TTTTA TTTA TTTA TTTA -TTA -TTA TTAGA TTAGGA TTT- TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TT--TA TTTA TTTA
* *
12743059 TTTA TTTTCA TTTT TTTA -TTA TTATT TTTA TTTA TTTA -TTA TTTA TTT
1 TTTA -TTT-A TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTT
12743107 TCTTTAAATA
Statistics
Matches: 72, Mismatches: 7, Indels: 19
0.73 0.07 0.19
Matches are distributed among these distances:
3 15 0.21
4 36 0.50
5 16 0.22
6 5 0.07
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:12743083 original size:20 final size:20
Alignment explanation
Indices: 12743052--12743108 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
12743042 TAGATTAGGA
12743052 TTTTTTA-T-TTATTTTCAT
1 TTTTTTATTATTATTTTCAT
*
12743070 TTTTTTATTATTATTTTTAT
1 TTTTTTATTATTATTTTCAT
*
12743090 TTATTTATTATTTATTTTC
1 TTTTTTATTA-TTATTTTC
12743109 TTTAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.21
19 1 0.03
20 18 0.55
21 7 0.21
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTATTATTATTTTCAT
Found at i:12743104 original size:45 final size:46
Alignment explanation
Indices: 12743005--12743106 Score: 106
Period size: 45 Copynumber: 2.3 Consensus size: 46
12742995 TTCGTTTTTT
12743005 TTTATTA-TT-TTTATTTTATTTATTTATTTATTATTATTAGATTA
1 TTTATTATTTATTTATTTTATTTATTTATTTATTATTATTAGATTA
** * * * *
12743049 -GGATTTTTTATTTATTTTCATTTTTTTA-TTATTATTTTTA-TTTA
1 TTTATTATTTATTTATTTT-ATTTATTTATTTATTATTATTAGATTA
12743093 TTTATTATTTATTT
1 TTTATTATTTATTT
12743107 TCTTTAAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
43 3 0.07
44 5 0.11
45 29 0.64
46 8 0.18
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.73
Consensus pattern (46 bp):
TTTATTATTTATTTATTTTATTTATTTATTTATTATTATTAGATTA
Found at i:12743284 original size:59 final size:59
Alignment explanation
Indices: 12743125--12743578 Score: 502
Period size: 59 Copynumber: 7.7 Consensus size: 59
12743115 TAAAATAAAA
* * * * *
12743125 AAAAAACA-TTTTAGGGAAAATGTTGAAAATATCAATTTTCCT-TAAGAAT-AAA-TTTTC
1 AAAAAATATTTTTA-GGAAAAAGTTGAAAGTATCAATTTTCCTCGAA-ATTAAAAGTTTTC
* * *
12743182 AAAAAAAGATTTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAAGTTTTC
1 -AAAAAATA-TTTTTAG-GAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
*
12743244 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAG-TTTC
1 AAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
12743302 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
1 -AAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
* *
12743362 AAAAAATATTTTTAGGAAAAAGTTGAAAATATCAATTTTTCTCGAAATTAAAAG-TTTC
1 AAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
* * ** *
12743420 CAAGAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAAA-TTTTC
1 AAAAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
* * *
12743478 AAAAAAAAAAGGGTTTTGAGCG--AAAGTTGAAAGTATCAATTTTTCTCGAAATT-AAAG-TTTC
1 --AAAAAATA---TTTTTAG-GAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
*
12743539 AAAAGAATATTTTT-GGAAAAAAATTGAAAGTATCAATTTT
1 AAAA-AATATTTTTAGG-AAAAAGTTGAAAGTATCAATTTT
12743579 TTCTTGTACA
Statistics
Matches: 344, Mismatches: 31, Indels: 42
0.82 0.07 0.10
Matches are distributed among these distances:
55 1 0.00
56 1 0.00
57 4 0.01
58 81 0.24
59 150 0.44
60 49 0.14
61 19 0.06
62 34 0.10
63 5 0.01
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (59 bp):
AAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
Found at i:12743339 original size:118 final size:117
Alignment explanation
Indices: 12743125--12743578 Score: 553
Period size: 118 Copynumber: 3.8 Consensus size: 117
12743115 TAAAATAAAA
* * * *
12743125 AAAAAACA-TTTTAGGGAAAATGTTGAAAATATCAATTTTCCT-TAAGAATAAATTTTCAAAAAA
1 AAAAAATATTTTTAGGGAAAA-GTTGAAAATATCAATTTTCCTCGAA-ATTAAAGTTTCAAAAAA
* *
12743188 AGATTTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAAGTTTTC
64 ATA-TTTTTAG-GAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAAGTTTTC
*
12743244 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTCAAAAAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAATATCAATTTTCCTCGAAATT-AAAGTTTCAAAAAAA
*
12743309 TATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAAGTTTTC
65 TATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAAGTTTTC
* * * *
12743362 AAAAAATATTTTTAGGAAAAAGTTGAAAATATCAATTTTTCTCGAAATTAAAAGTTTC-CAAGAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAATATCAATTTTCCTCGAAATT-AAAGTTTCAAAAAAA
* *
12743426 TATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAAA-TTTTC
65 TATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAAGTTTTC
* * * * *
12743478 AAAAAAAAAAGGGTTTTGAGCG-AAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCAAA
1 --AAAAAATA---TTTTTAGGGAAAAGTTGAAAATATCAATTTTCCTCGAAATTAAAGTTTCAAA
* *
12743542 AGAATATTTTT-GGAAAAAAATTGAAAGTATCAATTTT
61 AAAATATTTTTAGG-AAAAAGTTGAAAGTATCAATTTT
12743579 TTCTTGTACA
Statistics
Matches: 300, Mismatches: 23, Indels: 23
0.87 0.07 0.07
Matches are distributed among these distances:
116 5 0.02
117 44 0.15
118 110 0.37
119 43 0.14
120 92 0.31
121 6 0.02
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (117 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAATATCAATTTTCCTCGAAATTAAAGTTTCAAAAAAAT
ATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAAGTTTTC
Found at i:12755070 original size:41 final size:39
Alignment explanation
Indices: 12755027--12755326 Score: 301
Period size: 41 Copynumber: 7.6 Consensus size: 39
12755017 GATTGTCAAA
* * *
12755027 GAGCAATTTACTTTTCAAAGTTTCGTTGTCTCTGTTTAGAA
1 GAGCAATTTACTTTTCAAAG-TT-GGTGCCTCTGTTTAGAG
*
12755068 GAGCAATTTAATTTTCAAAGTCGTGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGT--TGGTGCCTCTGTTTAGAG
12755109 GAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGT--TGGTGCCTCTGTTTAGAG
* *
12755150 GAGCAATCTACTTTTC-AAGTCGTGGTGCCTCTGTTTATAG
1 GAGCAATTTACTTTTCAAAGT--TGGTGCCTCTGTTTAGAG
**
12755190 GAATAATTTACTTTTCCAAA----GT---TCTGTTTAGAG
1 GAGCAATTTACTTTT-CAAAGTTGGTGCCTCTGTTTAGAG
*
12755223 GAGCAATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAG
1 GAGCAATTTACTTTTCAAAGT--TGGTGCCTCTGTTTAGAG
* * *
12755264 GAGCAATTTACTTTCCAAAGTCATGGTGCCTCTATTTAGAT
1 GAGCAATTTACTTTTCAAAGT--TGGTGCCTCTGTTTAGAG
* *
12755305 GAGCCATTTATTTTTCAAAGTT
1 GAGCAATTTACTTTTCAAAGTT
12755327 ATTGAGCCTC
Statistics
Matches: 225, Mismatches: 21, Indels: 28
0.82 0.08 0.10
Matches are distributed among these distances:
32 4 0.02
33 22 0.10
36 2 0.01
38 2 0.01
39 1 0.00
40 35 0.16
41 156 0.69
42 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.39
Consensus pattern (39 bp):
GAGCAATTTACTTTTCAAAGTTGGTGCCTCTGTTTAGAG
Found at i:12755231 original size:33 final size:32
Alignment explanation
Indices: 12755179--12755243 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
12755169 TCGTGGTGCC
* *
12755179 TCTGTTTATAGGAATAATTTACTTTTCCAAAGT
1 TCTGTTTAGAGGAACAATTTAC-TTTCCAAAGT
*
12755212 TCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
1 TCTGTTTAGAGGAACAATTTACTTTCCAAAGT
12755244 CATGGTGCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 10 0.34
33 19 0.66
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (32 bp):
TCTGTTTAGAGGAACAATTTACTTTCCAAAGT
Found at i:12755279 original size:73 final size:73
Alignment explanation
Indices: 12755139--12755284 Score: 222
Period size: 73 Copynumber: 2.0 Consensus size: 73
12755129 TCATGGTGCC
* * * *
12755139 TCTGTTTAGAGGAGCAATCTACTTTTCAAGTCGTGGTGCCTCTGTTTATAGGAATAATTTACTTT
1 TCTGTTTAGAGGAGCAATCTACTTTCCAAGTCATGGTGCCTCTGTTTAGAGGAACAATTTACTTT
12755204 TCCAAAGT
66 TCCAAAGT
* *
12755212 TCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTAC-T
1 TCTGTTTAGAGGAGCAATCTACTTTCC-AAGTCATGGTGCCTCTGTTTAGAGGAACAATTTACTT
12755276 TTCCAAAGT
65 TTCCAAAGT
12755285 CATGGTGCCT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 35 0.53
74 31 0.47
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (73 bp):
TCTGTTTAGAGGAGCAATCTACTTTCCAAGTCATGGTGCCTCTGTTTAGAGGAACAATTTACTTT
TCCAAAGT
Found at i:12755324 original size:114 final size:114
Alignment explanation
Indices: 12755098--12755326 Score: 343
Period size: 114 Copynumber: 2.0 Consensus size: 114
12755088 TCGTGGTGCC
*
12755098 TCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATCTACTT
1 TCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATCTACTT
* * * * *
12755163 TTCAAGTCGTGGTGCCTCTGTTTATAGGAATAATTTACTTTTCCAAAGT
66 TCCAAGTCATGGTGCCTCTATTTAGAGGAACAATTTACTTTTCCAAAGT
*
12755212 TCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTT
1 TCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATCTACTT
* * * *
12755277 TCCAAAGTCATGGTGCCTCTATTTAGATGAGCCATTTA-TTTTTCAAAGT
66 TCC-AAGTCATGGTGCCTCTATTTAGAGGAACAATTTACTTTTCCAAAGT
12755326 T
1 T
12755327 ATTGAGCCTC
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 76 0.74
115 27 0.26
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (114 bp):
TCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATCTACTT
TCCAAGTCATGGTGCCTCTATTTAGAGGAACAATTTACTTTTCCAAAGT
Found at i:12755336 original size:41 final size:41
Alignment explanation
Indices: 12755216--12755349 Score: 187
Period size: 41 Copynumber: 3.3 Consensus size: 41
12755206 CAAAGTTCTG
*
12755216 TTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTG
1 TTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTA
12755257 TTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTA
1 TTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTA
* * * * * * *
12755298 TTTAGATGAGCCATTTATTTTTCAAAGTTATTGAGCCTCTA
1 TTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTA
*
12755339 CTTAGAGGAGC
1 TTTAGAGGAGC
12755350 TTTGATCAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 83 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (41 bp):
TTTAGAGGAGCAATTTACTTTCCAAAGTCATGGTGCCTCTA
Found at i:12755379 original size:5 final size:5
Alignment explanation
Indices: 12755369--12755399 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
12755359 ATTTAAAAGC
12755369 CAAAA CAAAA CAAAA CAAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA C-AAAA CAAAA CAAAA
12755400 AAATTACCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:12755391 original size:11 final size:11
Alignment explanation
Indices: 12755369--12755400 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
12755359 ATTTAAAAGC
12755369 CAAAAC-AAAA
1 CAAAACAAAAA
12755379 CAAAACAAAAA
1 CAAAACAAAAA
12755390 CAAAACAAAAA
1 CAAAACAAAAA
12755401 AATTACCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAACAAAAA
Found at i:12755522 original size:44 final size:44
Alignment explanation
Indices: 12755406--12755597 Score: 282
Period size: 43 Copynumber: 4.4 Consensus size: 44
12755396 AAAAAAATTA
* *
12755406 CCTCTGTTTAGAGGAGCTTTGTTTA-TTTTCAAAAGTCGTTGAG
1 CCTCTGATTAGAGGAGCTTTATTTATTTTTCAAAAGTCGTTGAG
*
12755449 CCTCTGATTAGAGGAGCTTTATTTATTTTTC-AAAGTCGTTGTG
1 CCTCTGATTAGAGGAGCTTTATTTATTTTTCAAAAGTCGTTGAG
12755492 CCTCTGATTAGAGGAGCTTTATTTATTTTTTC-AAAGTCGTTGAG
1 CCTCTGATTAGAGGAGCTTTATTTA-TTTTTCAAAAGTCGTTGAG
* *
12755536 CCTCTGATTAGAGGAGCATTGTTTATGTTTTTCAAAAGTCGTTGAG
1 CCTCTGATTAGAGGAGCTTTATTTA--TTTTTCAAAAGTCGTTGAG
*
12755582 CCTCTGCTTAGAGGAG
1 CCTCTGATTAGAGGAG
12755598 TTTTGATCAA
Statistics
Matches: 137, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
43 59 0.43
44 45 0.33
45 6 0.04
46 27 0.20
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.41
Consensus pattern (44 bp):
CCTCTGATTAGAGGAGCTTTATTTATTTTTCAAAAGTCGTTGAG
Found at i:12755551 original size:87 final size:88
Alignment explanation
Indices: 12755406--12755597 Score: 282
Period size: 87 Copynumber: 2.2 Consensus size: 88
12755396 AAAAAAATTA
* * *
12755406 CCTCTGTTTAGAGGAGCTTTGTTTATTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTTAT
1 CCTCTGATTAGAGGAGCTTTATTTATTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCATTAT
*
12755471 TTA-TTTTTC-AAAGTCGTTGTG
66 TTAGTTTTTCAAAAGTCGTTGAG
12755492 CCTCTGATTAGAGGAGCTTTATTTATTTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCATT
1 CCTCTGATTAGAGGAGCTTTATTTA--TTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCATT
*
12755556 GTTTATGTTTTTCAAAAGTCGTTGAG
64 ATTTA-GTTTTTCAAAAGTCGTTGAG
*
12755582 CCTCTGCTTAGAGGAG
1 CCTCTGATTAGAGGAG
12755598 TTTTGATCAA
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
86 23 0.24
87 35 0.37
88 5 0.05
89 6 0.06
90 26 0.27
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.41
Consensus pattern (88 bp):
CCTCTGATTAGAGGAGCTTTATTTATTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCATTAT
TTAGTTTTTCAAAAGTCGTTGAG
Found at i:12755770 original size:7 final size:6
Alignment explanation
Indices: 12755747--12755851 Score: 65
Period size: 6 Copynumber: 16.8 Consensus size: 6
12755737 TAGGTAAGTC
* *
12755747 TATTTT T-TTTT TTTTTT GTATTTT ATATTTT TATTTT TATTTT TATTATCG
1 TATTTT TATTTT TATTTT -TATTTT -TATTTT TATTTT TATTTT TATT-T-T
* * *
12755798 T-TTTT TATATA TATTTT T-TCTTT TATTTT TA-TCT TATGTATT TATTATT
1 TATTTT TATTTT TATTTT TAT-TTT TATTTT TATTTT TAT-T-TT TATT-TT
12755847 TATTT
1 TATTT
12755852 ATTTATTACT
Statistics
Matches: 79, Mismatches: 10, Indels: 20
0.72 0.09 0.18
Matches are distributed among these distances:
5 11 0.14
6 39 0.49
7 24 0.30
8 5 0.06
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (6 bp):
TATTTT
Found at i:12755783 original size:20 final size:18
Alignment explanation
Indices: 12755747--12755851 Score: 65
Period size: 19 Copynumber: 5.6 Consensus size: 18
12755737 TAGGTAAGTC
*
12755747 TATTTTT-TTTTTTTTTT
1 TATTTTTATTTTTATTTT
12755764 GTATTTTATATTTTTATTTT
1 -TATTTT-TATTTTTATTTT
*
12755784 TATTTTTATTATCGT-TTTT
1 TATTTTTATT-T-TTATTTT
* *
12755803 TATATATATTTTT-TCTTT
1 TATTTTTATTTTTAT-TTT
*
12755821 TATTTTTA-TCTTATGTATT
1 TATTTTTATTTTTAT-T-TT
12755840 TATTATTTATTT
1 TATT-TTTATTT
12755852 ATTTATTACT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
17 5 0.07
18 22 0.32
19 26 0.38
20 14 0.21
21 1 0.01
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (18 bp):
TATTTTTATTTTTATTTT
Found at i:12755790 original size:31 final size:31
Alignment explanation
Indices: 12755747--12755851 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 31
12755737 TAGGTAAGTC
* *
12755747 TATTTTTTTTTTTTTTTGTATTTTATATTTT
1 TATTTTTATTTTTTTTTGTATTTTATATATT
* * *
12755778 TATTTTTATTTTTATTATCGTTTTTTATATATA
1 TATTTTTATTTTT-TT-TTGTATTTTATATATT
* * * *
12755811 T-TTTTTCTTTTATTTT-TATCTTATGTATT
1 TATTTTTATTTTTTTTTGTATTTTATATATT
12755840 TATTATTTATTT
1 TATT-TTTATTT
12755852 ATTTATTACT
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
29 10 0.18
30 3 0.05
31 20 0.35
32 11 0.19
33 13 0.23
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (31 bp):
TATTTTTATTTTTTTTTGTATTTTATATATT
Found at i:12755842 original size:37 final size:34
Alignment explanation
Indices: 12755747--12755855 Score: 91
Period size: 37 Copynumber: 3.1 Consensus size: 34
12755737 TAGGTAAGTC
* *
12755747 TATTTTT-TTTTTTTTTTGTATTT-TATAT-TTT
1 TATTTTTATTTTTATTATGTATTTATATATATTT
*
12755778 TATTTTTATTTTTATTATCGTTTTTTATATATATTT
1 TATTTTTATTTTTATTAT-G-TATTTATATATATTT
* *
12755814 TTTCTTTTATTTTTATCTTATGTATTTAT-TATTTATT
1 TAT-TTTTATTTTTA--TTATGTATTTATATATAT-TT
12755851 TATTT
1 TATTT
12755856 ATTACTACTA
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
31 7 0.11
32 8 0.13
33 1 0.02
34 4 0.06
35 5 0.08
36 11 0.18
37 21 0.34
38 1 0.02
39 4 0.06
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (34 bp):
TATTTTTATTTTTATTATGTATTTATATATATTT
Found at i:12755849 original size:15 final size:16
Alignment explanation
Indices: 12755821--12755859 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
12755811 TTTTTTCTTT
12755821 TATTT-TTATCTTATG
1 TATTTATTATCTTATG
*
12755836 TATTTATTAT-TTATT
1 TATTTATTATCTTATG
12755851 TATTTATTA
1 TATTTATTA
12755860 CTACTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (16 bp):
TATTTATTATCTTATG
Found at i:12755927 original size:21 final size:22
Alignment explanation
Indices: 12755902--12755965 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
12755892 TTTTTTATTA
12755902 ATATTTATATGTAT-ATTTATC
1 ATATTTATATGTATAATTTATC
12755923 ATA-TTATATGTATAATTTATC
1 ATATTTATATGTATAATTTATC
*
12755944 TATTATTTA-AT-TTTAATTTATC
1 -A-TATTTATATGTATAATTTATC
12755966 TGTTAATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
20 10 0.26
21 10 0.26
22 11 0.29
23 4 0.11
24 3 0.08
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (22 bp):
ATATTTATATGTATAATTTATC
Found at i:12755931 original size:20 final size:20
Alignment explanation
Indices: 12755906--12755949 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
12755896 TTATTAATAT
12755906 TTATATGTAT-ATTTATCATA
1 TTATATGTATAATTTATC-TA
12755926 TTATATGTATAATTTATCTA
1 TTATATGTATAATTTATCTA
12755946 TTAT
1 TTAT
12755950 TTAATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (20 bp):
TTATATGTATAATTTATCTA
Found at i:12756849 original size:9 final size:8
Alignment explanation
Indices: 12756835--12756933 Score: 71
Period size: 9 Copynumber: 11.9 Consensus size: 8
12756825 TTCCCAGGTT
12756835 TTTTTTTCA
1 TTTTTTT-A
12756844 TTTTTTTTA
1 -TTTTTTTA
12756853 TTATTTTTA
1 TT-TTTTTA
12756862 --TTTTTA
1 TTTTTTTA
12756868 TTTTCTTTA
1 TTTT-TTTA
*
12756877 TTTATTTA
1 TTTTTTTA
*
12756885 TTTATTTA
1 TTTTTTTA
*
12756893 -TATTTTA
1 TTTTTTTA
12756900 TTTATTATTA
1 TTT-TT-TTA
12756910 TTTTATTTA
1 TTTT-TTTA
12756919 -TTTTTTA
1 TTTTTTTA
12756926 TTTATTTT
1 TTT-TTTT
12756934 CTTTAAATAA
Statistics
Matches: 75, Mismatches: 4, Indels: 21
0.75 0.04 0.21
Matches are distributed among these distances:
6 6 0.08
7 9 0.12
8 22 0.29
9 24 0.32
10 14 0.19
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTTA
Found at i:12756850 original size:12 final size:11
Alignment explanation
Indices: 12756833--12756938 Score: 86
Period size: 11 Copynumber: 9.0 Consensus size: 11
12756823 CGTTCCCAGG
*
12756833 TTTTTTTTTCA
1 TTTTTTTTTTA
12756844 TTTTTTTTATTA
1 TTTTTTTT-TTA
12756856 TTTTTATTTTTA
1 TTTTT-TTTTTA
12756868 TTTTCTTTATTTA
1 TTTT-TTT-TTTA
*
12756881 TTTATTTATTTA
1 TTT-TTTTTTTA
* *
12756893 TATTTTATTTA
1 TTTTTTTTTTA
* *
12756904 TTATTATTTTA
1 TTTTTTTTTTA
*
12756915 TTTATTTTTTA
1 TTTTTTTTTTA
12756926 TTTATTTTCTTTA
1 TTT-TTTT-TTTA
12756939 AATAAAATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
11 34 0.44
12 25 0.32
13 17 0.22
14 1 0.01
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTTTTA
Found at i:12756882 original size:4 final size:4
Alignment explanation
Indices: 12756873--12756932 Score: 74
Period size: 4 Copynumber: 15.8 Consensus size: 4
12756863 TTTTATTTTC
*
12756873 TTTA TTTA TTTA TTTA TTTA TAT- TTTA TTTA -TTA -TTA TTTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
12756919 TTT- TTTA TTTA TTT
1 TTTA TTTA TTTA TTT
12756933 TCTTTAAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
3 11 0.22
4 36 0.72
5 3 0.06
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:12756914 original size:26 final size:26
Alignment explanation
Indices: 12756850--12756931 Score: 103
Period size: 26 Copynumber: 3.1 Consensus size: 26
12756840 TTCATTTTTT
* *
12756850 TTATTATTTTTATTTTTATTTTCTTTA
1 TTATTA-TTTTATTTATATTTTATTTA
12756877 TTTATT-TATTTATTTATATTTTATTTA
1 -TTATTAT-TTTATTTATATTTTATTTA
*
12756904 TTATTATTTTATTTATTTTTTATTTA
1 TTATTATTTTATTTATATTTTATTTA
12756930 TT
1 TT
12756932 TTCTTTAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
26 26 0.53
27 18 0.37
28 5 0.10
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (26 bp):
TTATTATTTTATTTATATTTTATTTA
Found at i:12756929 original size:15 final size:15
Alignment explanation
Indices: 12756846--12756932 Score: 81
Period size: 15 Copynumber: 5.7 Consensus size: 15
12756836 TTTTTTCATT
*
12756846 TTTTTTA-TTATTTT
1 TTTTTTATTTATTTA
*
12756860 TATTTTTATTTTCTTTA
1 T-TTTTTA-TTTATTTA
12756877 TTTATTTATTTATTTA
1 TTT-TTTATTTATTTA
*
12756893 TATTTTATTTA-TTA
1 TTTTTTATTTATTTA
12756907 TTATTTTATTTATTT-
1 TT-TTTTATTTATTTA
12756922 TTTATTTATTT
1 TTT-TTTATTT
12756933 TCTTTAAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
14 6 0.10
15 32 0.52
16 13 0.21
17 10 0.16
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTATTTATTTA
Found at i:12756931 original size:11 final size:11
Alignment explanation
Indices: 12756846--12756933 Score: 79
Period size: 12 Copynumber: 7.4 Consensus size: 11
12756836 TTTTTTCATT
12756846 TTTTTTA-TTA
1 TTTTTTATTTA
*
12756856 TTTTTATTTTTA
1 TTTTT-TATTTA
12756868 TTTTCTTTATTTA
1 -TTT-TTTATTTA
12756881 TTTATTTATTTA
1 TTT-TTTATTTA
*
12756893 TATTTTATTTATTA
1 T-TTTT-TAT-TTA
12756907 TTATTTTATTTA
1 TT-TTTTATTTA
12756919 TTTTTTATTTA
1 TTTTTTATTTA
12756930 TTTT
1 TTTT
12756934 CTTTAAATAA
Statistics
Matches: 65, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
10 5 0.08
11 14 0.22
12 22 0.34
13 15 0.23
14 9 0.14
ACGTcount: A:0.20, C:0.01, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:12757106 original size:62 final size:60
Alignment explanation
Indices: 12756969--12757172 Score: 338
Period size: 62 Copynumber: 3.4 Consensus size: 60
12756959 ATTTTAGGGA
12756969 AAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAAAGATTTTTTTGAGG
1 AAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAAAGATTTTTTTGAGG
* * *
12757029 AAAACTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTTGAAAAAAAGATTTTTTTTTAGG
1 AAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAA-TTTTCAAAAAAAGA-TTTTTTTGAGG
* *
12757091 AAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATTTTCAAAAAAAG-GTTTTTTGAGG
1 AAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAAAGATTTTTTTGAGG
12757150 AAAAGTTGAAAGTATCAATTTTC
1 AAAAGTTGAAAGTATCAATTTTC
12757173 TTTCAACTTT
Statistics
Matches: 133, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
59 31 0.23
60 34 0.26
61 25 0.19
62 43 0.32
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (60 bp):
AAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAAAGATTTTTTTGAGG
Found at i:12757245 original size:58 final size:58
Alignment explanation
Indices: 12757175--12757299 Score: 191
Period size: 58 Copynumber: 2.1 Consensus size: 58
12757165 CAATTTTCTT
* *
12757175 TCAACTTTTCCTCGAAATTAAAAGTTTC-CAAGAATATTTTT-GAGGAAAAGTTGAAAGTA
1 TCAA-TTTTCCTCGAAATT-AAAGTTTCAAAAGAATATTTTTGGA-AAAAAGTTGAAAGTA
12757234 TCAATTTTCCTCGAAATTAAAGTTTCAAAAGAATATTTTTGGAAAAAAGTTGAAAGTA
1 TCAATTTTCCTCGAAATTAAAGTTTCAAAAGAATATTTTTGGAAAAAAGTTGAAAGTA
12757292 TCAATTTT
1 TCAATTTT
12757300 TTCTTGTACA
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
57 8 0.13
58 48 0.77
59 6 0.10
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (58 bp):
TCAATTTTCCTCGAAATTAAAGTTTCAAAAGAATATTTTTGGAAAAAAGTTGAAAGTA
Found at i:12757298 original size:27 final size:27
Alignment explanation
Indices: 12757220--12757300 Score: 67
Period size: 27 Copynumber: 2.9 Consensus size: 27
12757210 ATTTTTGAGG
12757220 AAAAGTTGAAAGTATCAATTTTCCTCGAA
1 AAAAGTTGAAAGTATCAATTTT--TCGAA
* * *
12757249 ATTAAAGTTTCAAAAGAAT--ATTTTTGGAA
1 A--AAAG-TT-GAAAGTATCAATTTTTCGAA
12757278 AAAAGTTGAAAGTATCAATTTTT
1 AAAAGTTGAAAGTATCAATTTTT
12757301 TCTTGTACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
25 6 0.15
26 2 0.05
27 10 0.24
29 6 0.15
31 9 0.22
32 2 0.05
33 6 0.15
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (27 bp):
AAAAGTTGAAAGTATCAATTTTTCGAA
Found at i:12762607 original size:13 final size:12
Alignment explanation
Indices: 12762589--12762640 Score: 59
Period size: 13 Copynumber: 4.1 Consensus size: 12
12762579 TAATTAAATT
12762589 AATTAAAAAAAGA
1 AATTAAAAAAA-A
*
12762602 ATTTAAACAAAAA
1 AATTAAA-AAAAA
12762615 AATTAAAAATAAA
1 AATTAAAAA-AAA
*
12762628 AGTTAAAAAAAA
1 AATTAAAAAAAA
12762640 A
1 A
12762641 GGGTAGAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 6 0.18
13 24 0.71
14 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (12 bp):
AATTAAAAAAAA
Found at i:12762618 original size:26 final size:25
Alignment explanation
Indices: 12762589--12762640 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
12762579 TAATTAAATT
*
12762589 AATTAAAAA-AAGAATTTAAACAAAAA
1 AATTAAAAATAA-AAGTTAAA-AAAAA
12762615 AATTAAAAATAAAAGTTAAAAAAAA
1 AATTAAAAATAAAAGTTAAAAAAAA
12762640 A
1 A
12762641 GGGTAGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 16 0.67
27 2 0.08
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (25 bp):
AATTAAAAATAAAAGTTAAAAAAAA
Found at i:12763851 original size:18 final size:18
Alignment explanation
Indices: 12763828--12763865 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12763818 TTAGGATAAA
12763828 AAAAAG-TGAAAGTTTTTT
1 AAAAAGATG-AAGTTTTTT
*
12763846 AAAAAGATGAATTTTTTT
1 AAAAAGATGAAGTTTTTT
12763864 AA
1 AA
12763866 GAATGAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AAAAAGATGAAGTTTTTT
Found at i:12766014 original size:23 final size:24
Alignment explanation
Indices: 12765968--12766022 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
12765958 AATATTTAAC
12765968 AAAACAAACAAAAAACAAAAAAAT
1 AAAACAAACAAAAAACAAAAAAAT
* *
12765992 -AAACAAACAAAAGAA-ACAGAAAT
1 AAAACAAACAAAA-AACAAAAAAAT
12766015 AAAACAAA
1 AAAACAAA
12766023 AGTCAAGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.80, C:0.13, G:0.04, T:0.04
Consensus pattern (24 bp):
AAAACAAACAAAAAACAAAAAAAT
Found at i:12766785 original size:20 final size:19
Alignment explanation
Indices: 12766739--12766785 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
12766729 ATCCGCGCGT
12766739 CAACCCGCGACCCGACCCG
1 CAACCCGCGACCCGACCCG
** *
12766758 GGATCCGCGCACCCGACCCG
1 CAACCCGCG-ACCCGACCCG
12766778 CAACCCGC
1 CAACCCGC
12766786 TCCTTTATCA
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.19, C:0.55, G:0.23, T:0.02
Consensus pattern (19 bp):
CAACCCGCGACCCGACCCG
Found at i:12766851 original size:13 final size:13
Alignment explanation
Indices: 12766835--12766879 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
12766825 AACCGTCGGA
12766835 CCGAATCGAACCG
1 CCGAATCGAACCG
*
12766848 CCGAATCGAACAG
1 CCGAATCGAACCG
* *
12766861 ACCGAACCGAACCT
1 -CCGAATCGAACCG
12766875 CCGAA
1 CCGAA
12766880 CCCGGAACCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.36, C:0.38, G:0.20, T:0.07
Consensus pattern (13 bp):
CCGAATCGAACCG
Found at i:12767718 original size:21 final size:23
Alignment explanation
Indices: 12767692--12767741 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
12767682 TTTTTTCTTC
*
12767692 AAAATTTTAAT-TAA-AATTAAT
1 AAAATTTTAATAAAATAATTAAT
12767713 AAAA--TTAATAAAATAATTAAT
1 AAAATTTTAATAAAATAATTAAT
12767734 AAAATTTT
1 AAAATTTT
12767742 TGAATGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 5 0.21
20 2 0.08
21 15 0.62
23 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATTTTAATAAAATAATTAAT
Found at i:12768444 original size:13 final size:13
Alignment explanation
Indices: 12768426--12768450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12768416 CAATTTCTTA
12768426 GTAAAAAAAAAAG
1 GTAAAAAAAAAAG
12768439 GTAAAAAAAAAA
1 GTAAAAAAAAAA
12768451 AAACCAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (13 bp):
GTAAAAAAAAAAG
Found at i:12774137 original size:109 final size:108
Alignment explanation
Indices: 12773990--12774255 Score: 322
Period size: 109 Copynumber: 2.5 Consensus size: 108
12773980 TTTTTGACTC
* *
12773990 GTGGTTTAATCTCGATCATTCTTATAGCTTCTCAACTTACTG-TTTAATCCTAATCGCTTTTATT
1 GTGGTTTAATCCCGATCATTCTTATAGCTTATCAACTTAC-GATTTAATCCTAATCGCTTTTATT
* * * *
12774054 TCTTTGACTTGCGATTCAGTCTCAGTTATCTTTAATCTTTAACTT
65 GCTCTGACTTACGATTCAATC-CAGTTATCTTTAATCTTTAACTT
* * *
12774099 GTGGTTTAATCCCGATTATTCTTATAGCTTATCGACTTACGATTTAATCCTAGTCGCTTTTATTG
1 GTGGTTTAATCCCGATCATTCTTATAGCTTATCAACTTACGATTTAATCCTAATCGCTTTTATTG
*
12774164 CTCTGACTTACGATTCAATCCAGTTATCTTTAATCTTTGA-TT
66 CTCTGACTTACGATTCAATCCAGTTATCTTTAATCTTTAACTT
* * * * ** * *
12774206 CGTAGTTTAATTCTGATCATTTTTATAATTTTTGAA-TTACGATTTAATCC
1 -GTGGTTTAATCCCGATCATTCTTATAGCTTATCAACTTACGATTTAATCC
12774256 CAGTCTCCTT
Statistics
Matches: 135, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
107 16 0.12
108 45 0.33
109 74 0.55
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (108 bp):
GTGGTTTAATCCCGATCATTCTTATAGCTTATCAACTTACGATTTAATCCTAATCGCTTTTATTG
CTCTGACTTACGATTCAATCCAGTTATCTTTAATCTTTAACTT
Found at i:12774626 original size:44 final size:45
Alignment explanation
Indices: 12774532--12774666 Score: 182
Period size: 45 Copynumber: 3.0 Consensus size: 45
12774522 AAATCTTAGT
* * **
12774532 TTAATCTCAATTGTTGTTATTTTCTGACTCATGGTTTAATTTCGA
1 TTAATCTCAATTGTTGTTATTTTTTGACTCGTGGTTTAATCCCGA
* *
12774577 TTAATCTCAATTGTTGTTATTTTTTTA-TCGTGGTTTAATCCCGG
1 TTAATCTCAATTGTTGTTATTTTTTGACTCGTGGTTTAATCCCGA
* * *
12774621 TTAATCTCGATTGTTGTTATTTTTTGAGTAGTGGTTTAATCCCGA
1 TTAATCTCAATTGTTGTTATTTTTTGACTCGTGGTTTAATCCCGA
12774666 T
1 T
12774667 CTCTTTATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 38 0.48
45 41 0.52
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (45 bp):
TTAATCTCAATTGTTGTTATTTTTTGACTCGTGGTTTAATCCCGA
Found at i:12774687 original size:224 final size:225
Alignment explanation
Indices: 12774352--12774795 Score: 631
Period size: 224 Copynumber: 2.0 Consensus size: 225
12774342 AAATTATAGT
* *
12774352 TTAATCTCAATTGTTGTTATTTTCTAACTCGTGATTTATTCCCGGTTAATCTTGATTATTGTTAT
1 TTAATCTCAATTGTTGTTATTTTCTAACTCGTGATTTAATCCCGGTTAATCTCGATTATTGTTAT
* * * *
12774417 TTTTTGACTCGTGGTTTAATCCTGGTCTCTTTATTTTCTAACTTGTGATTCAATCCAAGTTGATG
66 TTTTTGACTAGTGGTTTAATCCCGATCTCTTTATTTTCTAACTTGTGATTCAATCCAAGTTGACG
* **
12774482 TTATTCTGACTCGCGGTTCAATCCCTACTT-CTCTAATCTAAAATCTTAGTTTAATCTCAATTGT
131 TTATTCTGACTCGCGGTTCAATCCCGA-TTCCTCTAATCTAAAATCACAGTTTAATCTCAATTGT
*
12774546 TGTTATTTTCTGACTCATGGTTTAATTTCGA
195 TATTATTTTCTGACTCATGGTTTAATTTCGA
* * * *
12774577 TTAATCTCAATTGTTGTTATTTTTTTA-TCGTGGTTTAATCCCGGTTAATCTCGATTGTTGTTAT
1 TTAATCTCAATTGTTGTTATTTTCTAACTCGTGATTTAATCCCGGTTAATCTCGATTATTGTTAT
* * *
12774641 TTTTTGAGTAGTGGTTTAATCCCGATCTCTTTATTTTTTGACTTGTGATTCAATCCAAGTTGACG
66 TTTTTGACTAGTGGTTTAATCCCGATCTCTTTATTTTCTAACTTGTGATTCAATCCAAGTTGACG
* * * * ** * *
12774706 TTATTTTGGCTTGCGTTTCAATTTCGATTCCTTTAATCTAAAATCACAGTTTAATCTCGATTGTT
131 TTATTCTGACTCGCGGTTCAATCCCGATTCCTCTAATCTAAAATCACAGTTTAATCTCAATTGTT
*
12774771 ATTTTTTTCTGACTCATGGTTTAAT
196 ATTATTTTCTGACTCATGGTTTAAT
12774796 CCCGGTCTCT
Statistics
Matches: 192, Mismatches: 26, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
223 2 0.01
224 165 0.86
225 25 0.13
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (225 bp):
TTAATCTCAATTGTTGTTATTTTCTAACTCGTGATTTAATCCCGGTTAATCTCGATTATTGTTAT
TTTTTGACTAGTGGTTTAATCCCGATCTCTTTATTTTCTAACTTGTGATTCAATCCAAGTTGACG
TTATTCTGACTCGCGGTTCAATCCCGATTCCTCTAATCTAAAATCACAGTTTAATCTCAATTGTT
ATTATTTTCTGACTCATGGTTTAATTTCGA
Found at i:12775208 original size:17 final size:18
Alignment explanation
Indices: 12775188--12775222 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12775178 TAATATTGGT
12775188 TTAATTAA-AATTAAAAA
1 TTAATTAATAATTAAAAA
*
12775205 TTAATTAATTATTAAAAA
1 TTAATTAATAATTAAAAA
12775223 AAAAGAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAATTAATAATTAAAAA
Found at i:12776245 original size:19 final size:18
Alignment explanation
Indices: 12776199--12776246 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
12776189 AATTTTCTAA
* *
12776199 TTTTTTATATATTATTAT
1 TTTTTTATATTTTAGTAT
*
12776217 TTTTGTTAT-TTTAAGTAT
1 TTTT-TTATATTTTAGTAT
12776235 TTTTTTATATTT
1 TTTTTTATATTT
12776247 ATGCATGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTTTTATATTTTAGTAT
Found at i:12776364 original size:3 final size:3
Alignment explanation
Indices: 12776356--12776410 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
12776346 AAATGCTTAA
12776356 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12776404 AAT AAT A
1 AAT AAT A
12776411 GAATAATTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12776701 original size:22 final size:23
Alignment explanation
Indices: 12776659--12776711 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
12776649 GAAAACCCTC
12776659 TAAAATCTGAAATCCCAAACCTT
1 TAAAATCTGAAATCCCAAACCTT
* * **
12776682 TAAACTCTTAAAT-CCAAACCCC
1 TAAAATCTGAAATCCCAAACCTT
12776704 TAAAATCT
1 TAAAATCT
12776712 AAACCCTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.26
Consensus pattern (23 bp):
TAAAATCTGAAATCCCAAACCTT
Found at i:12776730 original size:20 final size:20
Alignment explanation
Indices: 12776705--12776743 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12776695 CCAAACCCCT
12776705 AAAATC-TAAACCCTTAAATC
1 AAAATCTTAAA-CCTTAAATC
12776725 AAAATCTTAAACCTTAAAT
1 AAAATCTTAAACCTTAAAT
12776744 TTTAAAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATCTTAAACCTTAAATC
Found at i:12776774 original size:30 final size:30
Alignment explanation
Indices: 12776733--12776825 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
12776723 TCAAAATCTT
12776733 AAACCTT--AAATTTTAAAACCGAAACCCTA
1 AAACCTTCCAAATTTTAAAACC-AAACCCTA
* * *
12776762 AAATCTT-CAAATTCTAAAATCAAAACCCT-
1 AAACCTTCCAAATTTTAAAA-CCAAACCCTA
* **
12776791 AAACCTTCCATACCTTAAAACCAAACCCTA
1 AAACCTTCCAAATTTTAAAACCAAACCCTA
12776821 AAACC
1 AAACC
12776826 CTCAAAACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
29 20 0.39
30 30 0.59
31 1 0.02
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (30 bp):
AAACCTTCCAAATTTTAAAACCAAACCCTA
Found at i:12776836 original size:29 final size:29
Alignment explanation
Indices: 12776745--12776853 Score: 87
Period size: 29 Copynumber: 3.7 Consensus size: 29
12776735 ACCTTAAATT
* *
12776745 TTAAAACCGAAACCCTAAAATCTTC-AAAT
1 TTAAAACC-AAACCCTAAAACCTTCAAAAC
* * *
12776774 TCTAAAATCAAAACCCT-AAACCTTCCATACC
1 T-TAAAA-CCAAACCCTAAAACCTT-CAAAAC
*
12776805 TTAAAACCAAACCCTAAAACCCTCAAAAC
1 TTAAAACCAAACCCTAAAACCTTCAAAAC
* *
12776834 TTAAATCTAAACCCTTAAAA
1 TTAAAACCAAACCC-TAAAA
12776854 TCCGAATCTT
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
29 31 0.49
30 29 0.46
31 3 0.05
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (29 bp):
TTAAAACCAAACCCTAAAACCTTCAAAAC
Found at i:12777995 original size:26 final size:27
Alignment explanation
Indices: 12777935--12777997 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
12777925 ACGTTTTATT
*
12777935 TATTTTCTTATTTTGTATTTATAGAAAA
1 TATTTT-TTATTTTGCATTTATAGAAAA
* *
12777963 TAATTTTTATTTT-CATTTATCA-AATA
1 TATTTTTTATTTTGCATTTAT-AGAAAA
12777989 TATTTTTTA
1 TATTTTTTA
12777998 AAAAACAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 17 0.57
27 8 0.27
28 5 0.17
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (27 bp):
TATTTTTTATTTTGCATTTATAGAAAA
Found at i:12778018 original size:30 final size:31
Alignment explanation
Indices: 12777984--12778055 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
12777974 TTCATTTATC
12777984 AAATATATTTT-TTAAA-AAACAAAAAAATAA
1 AAATATATTTTATTAAATAAA-AAAAAAATAA
* *
12778014 AAATAATGTTTTATTAAATAAAAATAAAATAA
1 AAAT-ATATTTTATTAAATAAAAAAAAAATAA
12778046 AAA-ATATTTT
1 AAATATATTTT
12778056 CTCAAACCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
30 10 0.28
31 6 0.17
32 17 0.47
33 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (31 bp):
AAATATATTTTATTAAATAAAAAAAAAATAA
Found at i:12781053 original size:46 final size:46
Alignment explanation
Indices: 12780976--12781070 Score: 120
Period size: 46 Copynumber: 2.1 Consensus size: 46
12780966 TACAATACAA
** * *
12780976 AAAAAAAAGAATAAAGAAATTTTTTTATTAGAAACAAAGAGTCTTG
1 AAAAAAAAGAATAAAGAAAGGTTTTTATTAGAAAAAAAAAGTCTTG
* *
12781022 AAAACAAAGAATAAAGAAAAGGTTTTT-TTAGAAAAAAAAAGTTTTG
1 AAAAAAAAGAATAAAG-AAAGGTTTTTATTAGAAAAAAAAAGTCTTG
12781068 AAA
1 AAA
12781071 GAATTGGTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 34 0.81
47 8 0.19
ACGTcount: A:0.57, C:0.03, G:0.14, T:0.26
Consensus pattern (46 bp):
AAAAAAAAGAATAAAGAAAGGTTTTTATTAGAAAAAAAAAGTCTTG
Found at i:12781742 original size:25 final size:24
Alignment explanation
Indices: 12781714--12781761 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
12781704 AGAAAACCTA
12781714 AAAAAAGTCTAAAAATAAAAAAGAC
1 AAAAAAGTCTAAAAA-AAAAAAGAC
*
12781739 AAAAAATTCTAAAAAAAAAAAGA
1 AAAAAAGTCTAAAAAAAAAAAGA
12781762 TTCAAGCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (24 bp):
AAAAAAGTCTAAAAAAAAAAAGAC
Found at i:12782310 original size:29 final size:28
Alignment explanation
Indices: 12782259--12782314 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
12782249 AAAAAATTAA
*
12782259 ATTTATTTATAGTTTATTATATAATAAT
1 ATTTATTTATAATTTATTATATAATAAT
*
12782287 ATTTATTTACTAATTTATTGTATAATAA
1 ATTTATTTA-TAATTTATTATATAATAA
12782315 CAAAATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (28 bp):
ATTTATTTATAATTTATTATATAATAAT
Found at i:12782653 original size:2 final size:2
Alignment explanation
Indices: 12782646--12782677 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12782636 ACGAGGAAGG
12782646 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
12782678 GATAAGGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12783754 original size:29 final size:31
Alignment explanation
Indices: 12783691--12783762 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
12783681 TATTTATTAA
12783691 TAAATTATTATT-T-GATATAAAATAATTTT
1 TAAATTATTATTATAGATATAAAATAATTTT
* *
12783720 TTAATTATT-TTATAGATATTAAATAA-TTT
1 TAAATTATTATTATAGATATAAAATAATTTT
12783749 TAAATT-TTATTATA
1 TAAATTATTATTATA
12783763 TATAATTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.11
29 22 0.59
30 11 0.30
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (31 bp):
TAAATTATTATTATAGATATAAAATAATTTT
Found at i:12789114 original size:2 final size:2
Alignment explanation
Indices: 12789107--12789131 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12789097 CCATACTTAC
12789107 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
12789132 ACACCGACGA
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:12790863 original size:23 final size:23
Alignment explanation
Indices: 12790819--12790864 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12790809 AGGTATATTT
* *
12790819 TATTAATATATTATTTACATAAA
1 TATTAATATATTAATAACATAAA
* *
12790842 TATTTATATATTAATAATATAAA
1 TATTAATATATTAATAACATAAA
12790865 AAAATATTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATATATTAATAACATAAA
Found at i:12793588 original size:31 final size:32
Alignment explanation
Indices: 12793516--12793590 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
12793506 TTATTTTTTT
* *
12793516 AAAATAAAAAATAAAAATATGTTTGATAATTA
1 AAAATAAAAAATAAAAATAAGATTGATAATTA
*
12793548 AAAAT-AAAAATAAAAA-AAGATTGA-AATATG
1 AAAATAAAAAATAAAAATAAGATTGATAAT-TA
12793578 AAAATAAAAAATA
1 AAAATAAAAAATA
12793591 TATTTTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 3 0.08
30 12 0.32
31 18 0.47
32 5 0.13
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (32 bp):
AAAATAAAAAATAAAAATAAGATTGATAATTA
Found at i:12797194 original size:22 final size:24
Alignment explanation
Indices: 12797138--12797194 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
12797128 TTAAATGGAC
* *
12797138 TTAAATATAAAAACAAAAAATATT
1 TTAATTATAAAAACAAAAAATAGT
*
12797162 TTCAATTATAAAAACAAGAAAT-GT
1 TT-AATTATAAAAACAAAAAATAGT
12797186 TT-ATTATAA
1 TTAATTATAA
12797195 TTTTTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.24
24 5 0.17
25 17 0.59
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (24 bp):
TTAATTATAAAAACAAAAAATAGT
Found at i:12797553 original size:20 final size:21
Alignment explanation
Indices: 12797516--12797554 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12797506 TGTGGGCAGA
12797516 AAAAATGTTTTAAGAAAAAGT
1 AAAAATGTTTTAAGAAAAAGT
12797537 AAAAATGTTTTAA-AAAAA
1 AAAAATGTTTTAAGAAAAA
12797555 TTAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (21 bp):
AAAAATGTTTTAAGAAAAAGT
Found at i:12798549 original size:73 final size:73
Alignment explanation
Indices: 12798427--12798564 Score: 204
Period size: 73 Copynumber: 1.9 Consensus size: 73
12798417 AACAAAGGCC
* * *
12798427 ATGTTTTTTTTATAAGAAGTGTAGTATTCAAATGCCATGCTACAATAGAAATGTAGGAGAGACAA
1 ATGTTTCTTTCATAAGAAATGTAGTATTCAAATGCCATGCTACAATAGAAATGTAGGAGAGACAA
12798492 CTATGACT
66 CTATGACT
* * * * *
12798500 ATGTTTCTTTCATAAGAAATGTAGTCTTTAAATGCCATGTTGCACTAGAAATGTAGGAGAGACAA
1 ATGTTTCTTTCATAAGAAATGTAGTATTCAAATGCCATGCTACAATAGAAATGTAGGAGAGACAA
12798565 ACTTACTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
73 57 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (73 bp):
ATGTTTCTTTCATAAGAAATGTAGTATTCAAATGCCATGCTACAATAGAAATGTAGGAGAGACAA
CTATGACT
Found at i:12798723 original size:54 final size:54
Alignment explanation
Indices: 12798644--12798766 Score: 162
Period size: 54 Copynumber: 2.3 Consensus size: 54
12798634 TTTTTTTTAA
* *
12798644 TTTTTTTCAATCAAATATTACGTTTC-TACTTTAGA-AAACGTAGTCTTTGT-AATT
1 TTTTTTTCAATCAAACATTACGTTTCAT-CTTTA-ATAAACATAGTCTTTGTGAA-T
*
12798698 TTTTTTTCAATCAAACATTATGTTTCATCTTTAATAAACATAGTCTTTGTGAAT
1 TTTTTTTCAATCAAACATTACGTTTCATCTTTAATAAACATAGTCTTTGTGAAT
*
12798752 TTTTTTTGAATCAAA
1 TTTTTTTCAATCAAA
12798767 GACTACATCT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
53 1 0.02
54 58 0.94
55 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (54 bp):
TTTTTTTCAATCAAACATTACGTTTCATCTTTAATAAACATAGTCTTTGTGAAT
Found at i:12798791 original size:54 final size:52
Alignment explanation
Indices: 12798641--12798882 Score: 150
Period size: 54 Copynumber: 4.5 Consensus size: 52
12798631 GAATTTTTTT
* * * * * * *
12798641 TAATTTTTTTCAATCAAATATTACGTTTCTA-CTTTAGAAAACGTAGTCTTTG
1 TAATTTTTTTTAATAAAAGACTACATTTCTACCTTCA-AAAACATAGTCTTTG
* * * ** * *
12798693 TAATTTTTTTTTCAATCAAACATTATGTTTC-ATCTTTAATAAACATAGTCTTTG
1 TAA-TTTTTTTT-AATAAAAGACTACATTTCTACCTTCAA-AAACATAGTCTTTG
* *
12798747 TGAATTTTTTTTGAATCAAAGACTACATCTT-TACCTTGAAAAACATAGTCTTT-
1 T-AATTTTTTTT-AATAAAAGACTACAT-TTCTACCTTCAAAAACATAGTCTTTG
* * * * * * * *
12798800 TAATGTTTTTTTAATTAAAGGCTACGTTTCTACTTTCATAAGCGTAGCCTTTG
1 TAAT-TTTTTTTAATAAAAGACTACATTTCTACCTTCAAAAACATAGTCTTTG
12798853 TAAATTTTTTTTTAATAAAAGACTACATTT
1 T-AA-TTTTTTTTAATAAAAGACTACATTT
12798883 TTTTATTTTA
Statistics
Matches: 155, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
51 2 0.01
52 34 0.22
53 18 0.12
54 90 0.58
55 11 0.07
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.46
Consensus pattern (52 bp):
TAATTTTTTTTAATAAAAGACTACATTTCTACCTTCAAAAACATAGTCTTTG
Found at i:12799496 original size:12 final size:12
Alignment explanation
Indices: 12799479--12799504 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12799469 AAGGCTCAGT
12799479 AGTTACAATACA
1 AGTTACAATACA
12799491 AGTTACAATACA
1 AGTTACAATACA
12799503 AG
1 AG
12799505 GACTAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.23
Consensus pattern (12 bp):
AGTTACAATACA
Found at i:12800755 original size:128 final size:127
Alignment explanation
Indices: 12800572--12801025 Score: 397
Period size: 128 Copynumber: 3.6 Consensus size: 127
12800562 CTTTTGTATT
* * * * * *
12800572 AAAATTACTATAATACCTTATCAAATTACGTATTAAATTTCAACATAATACAAAATTAACCATAT
1 AAAATTACTATAATACCCTATTAAATTACATATTAAATTTTAACATAATATAAAATTAACCACAT
* ** * * *
12800637 ACTAAATTATTAAAACAACCTTGCCATTACTTTTTAGAAATTTGGCATTTGGCATTTTATTTG
66 ACTAAATTACTAAAA-AACCTTGCCATTACTTCATAGAAATTTGACATGTGACATTTTATTTG
* * * * *
12800700 AAAATTACTGTAATACCCTATTAAATCATATATGAAATTTTAACATAATATAAAATTAACTACAT
1 AAAATTACTATAATACCCTATTAAATTACATATTAAATTTTAACATAATATAAAATTAACCACAT
* * *
12800765 ATTAAATTACTAAAATACCTTGCCATTACTTCATAGAAATTTTACATGTGACATTTTATTTG
66 ACTAAATTACTAAAAAACCTTGCCATTACTTCATAGAAATTTGACATGTGACATTTTATTTG
* * * * * * * * **
12800827 AAATTTATTACAATACCCTTATTACATTACAAATTAAATTTTAACATAAAATAAAATTATCTATT
1 AAAATTACTATAATACCC-TATTAAATTACATATTAAATTTTAACATAATATAAAATTAACCACA
* * *** **
12800892 TATTAAATTACTAAAATAACTTTATAATCGCTTCAT-GAAAATTTGACATGTG--ATTTT-TTAT
65 TACTAAATTACTAAAA-AACCTTGCCATTACTTCATAG-AAATTTGACATGTGACATTTTATT-T
12800953 G
127 G
* * * * *
12800954 AAAATTACTATAGTACCCCT-TTGAA-TACATATTAAA--TTAA-TTACATA-AAACTTAACTAC
1 AAAATTACTATAATA-CCCTATTAAATTACATATTAAATTTTAACATA-ATATAAAATTAACCAC
12801013 ATACTAAATTACT
64 ATACTAAATTACT
12801026 TAACAAAATA
Statistics
Matches: 265, Mismatches: 55, Indels: 18
0.78 0.16 0.05
Matches are distributed among these distances:
122 22 0.08
123 6 0.02
125 10 0.04
126 5 0.02
127 73 0.28
128 124 0.47
129 25 0.09
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.39
Consensus pattern (127 bp):
AAAATTACTATAATACCCTATTAAATTACATATTAAATTTTAACATAATATAAAATTAACCACAT
ACTAAATTACTAAAAAACCTTGCCATTACTTCATAGAAATTTGACATGTGACATTTTATTTG
Found at i:12804934 original size:21 final size:21
Alignment explanation
Indices: 12804908--12804948 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12804898 AAACAAGTAG
12804908 ATAAATA-AAAAATAATAAATA
1 ATAAATACAAAAATAA-AAATA
*
12804929 ATAAATACAAATATAAAAAT
1 ATAAATACAAAAATAAAAAT
12804949 TGGCTAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
ATAAATACAAAAATAAAAATA
Found at i:12807291 original size:43 final size:42
Alignment explanation
Indices: 12807229--12807408 Score: 209
Period size: 43 Copynumber: 4.2 Consensus size: 42
12807219 ATTTAAAGAC
* *
12807229 ATTTGCATTCACTCAATGGTGATATCTGAATA-CCTATATCTAA
1 ATTTGCATTCACTCGATGGTGATAT-TGAGTATCC-ATATCTAA
* *
12807272 ATTTGCATTCACTCGATGGTGATATTCGAGTATCCATATATGA
1 ATTTGCATTCACTCGATGGTGATATT-GAGTATCCATATCTAA
* * * *
12807315 ATTTGTATTTACTCGATAGCGATATTTGAGTATCCATATCTAA
1 ATTTGCATTCACTCGATGGTGATA-TTGAGTATCCATATCTAA
* * *
12807358 ATTTGCATTCACTCGGTGGTGATATATGAGTATCCATGTCTGA
1 ATTTGCATTCACTCGATGGTGATAT-TGAGTATCCATATCTAA
12807401 ATTTGCAT
1 ATTTGCAT
12807409 CATTCCTTGG
Statistics
Matches: 116, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
42 2 0.02
43 110 0.95
44 4 0.03
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (42 bp):
ATTTGCATTCACTCGATGGTGATATTGAGTATCCATATCTAA
Found at i:12807990 original size:46 final size:46
Alignment explanation
Indices: 12807930--12808034 Score: 149
Period size: 46 Copynumber: 2.3 Consensus size: 46
12807920 GCTTTTCAGG
* * * *
12807930 ATTTATTTTT-AAAGTTGTTAATCCTTTTCTTAAATGAGTTTTTAA
1 ATTTATTTTTAAAAGTTGTTAACCCTTTACTTAAAAGAGCTTTTAA
* *
12807975 ATTTGTTTTTAAAAGTTGTTGACCCTTTACTTAAAAGAGCTTTTAA
1 ATTTATTTTTAAAAGTTGTTAACCCTTTACTTAAAAGAGCTTTTAA
12808021 ATTTATTTTTAAAA
1 ATTTATTTTTAAAA
12808035 ATTTTTTAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
45 9 0.17
46 43 0.83
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (46 bp):
ATTTATTTTTAAAAGTTGTTAACCCTTTACTTAAAAGAGCTTTTAA
Found at i:12808086 original size:11 final size:11
Alignment explanation
Indices: 12808064--12808104 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
12808054 TTGCAAAGTC
*
12808064 AAAAAAAGAAAA
1 AAAAAAA-AAAG
12808076 AAAATAAAAAAG
1 AAAA-AAAAAAG
12808088 AAAAAAAAAAG
1 AAAAAAAAAAG
12808099 AAAAAA
1 AAAAAA
12808105 GGGGAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 13 0.48
12 11 0.41
13 3 0.11
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:12808102 original size:16 final size:16
Alignment explanation
Indices: 12808065--12808095 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12808055 TGCAAAGTCA
12808065 AAAAAAGAAAAAAAAT
1 AAAAAAGAAAAAAAAT
12808081 AAAAAAGAAAAAAAA
1 AAAAAAGAAAAAAAA
12808096 AAGAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.06, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAT
Found at i:12810013 original size:21 final size:20
Alignment explanation
Indices: 12809966--12810015 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
12809956 TTCTCATTCA
12809966 AAAATTTTATTAATTATTTT
1 AAAATTTTATTAATTATTTT
*
12809986 ATTAATTTTATTAATT-TTAATT
1 A-AAATTTTATTAATTATT--TT
12810008 AAAATTTT
1 AAAATTTT
12810016 GAAGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AAAATTTTATTAATTATTTT
Found at i:12810381 original size:203 final size:208
Alignment explanation
Indices: 12810039--12810585 Score: 797
Period size: 213 Copynumber: 2.6 Consensus size: 208
12810029 AATTTAATCA
* * * *
12810039 TATTGAAGATTTTCTATAAATATTCCAATACGCTGGTAATATTTTACAAAAAATCTTCTCACCTA
1 TATTGAAAATTTTTTATAAATACTCCAATACGCTGGTAGTATTTTA-AAAAAATCTTCTCACCTA
* * * * * *
12810104 GAGATTTCTTAAAGCATCTCTACTCGGAATACTTTTAGAATCTCATCATTGGAT-TAAATTT-CT
65 GAGATTTCGT-AGGCATCACTACTCGGAATACCTTT-GAATCTCATCATCGGATAAAAATTTCCT
*
12810167 TTGCTTCTTA-TTTTTATCACTTATATTTTTTATTTATTAATCAATTTTTATTTATTA-TTT-AA
128 TTGCTTCTTATTTTTTATCACTTATA-TTTTAATTTATTAATCAATTTTTATTTATTATTTTAAA
12810229 AAA-AAAATCTTTACTG
192 AAAGAAAATCTTTACTG
*
12810245 TATTGAAAATTTTTTATAAATACTCCAATACGCTGGTAGTA-CTTAAAAAAATCTTCTCACCTAG
1 TATTGAAAATTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAATCTTCTCACCTAG
12810309 AGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCTCTT
66 AGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCT-TT
* *
12810374 -C-TCTTATTTTTTATTAGTTATATTTTAATTTATTAATCAATTTTTATTTATTATTTTTTTAAA
130 GCTTCTTATTTTTTATCACTTATATTTTAATTTATTAATCAATTTTTATTTATTA---TTTT-AA
12810437 AAAAGAAAATCTTTACTG
191 AAAAGAAAATCTTTACTG
12810455 TATTGAAAATTTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAAATCTTCTCACCT
1 TATTGAAAA-TTTTTTATAAATACTCCAATACGCTGGTAGTATTTT-AAAAAAATCTTCTCACCT
*
12810520 AGAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCGTCGGATAAAAATTTCCTT
64 AGAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCTT
12810585 T
129 T
12810586 TTCTTTCATT
Statistics
Matches: 311, Mismatches: 16, Indels: 22
0.89 0.05 0.06
Matches are distributed among these distances:
202 16 0.05
203 63 0.20
204 43 0.14
205 5 0.02
206 37 0.12
207 3 0.01
209 5 0.02
210 22 0.07
211 32 0.10
212 4 0.01
213 81 0.26
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (208 bp):
TATTGAAAATTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAATCTTCTCACCTAG
AGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCTTTG
CTTCTTATTTTTTATCACTTATATTTTAATTTATTAATCAATTTTTATTTATTATTTTAAAAAAG
AAAATCTTTACTG
Found at i:12810635 original size:213 final size:206
Alignment explanation
Indices: 12810039--12810646 Score: 732
Period size: 213 Copynumber: 2.9 Consensus size: 206
12810029 AATTTAATCA
* * * * *
12810039 TATTGAAGATTTTCTATAAATATTCCAATACGCTGGTAATATTTTACAAAAAATCTTCTCACCTA
1 TATTGAAAATTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAAATCTTCTCACCTA
* * * * * *
12810104 GAGATTTCTTAAAGCATCTCTACTCGGAATACTTTTAGAATCTCATCATTGGAT-TAAATTT-CT
66 GAGATTTCGT-AGGCATCACTACTCGGAATACCTTT-GAATCTCATCATCGGATAAAAATTTCCT
* * ** *
12810167 TTGCTTC-TTATTTTTATCACTTATATTT-TTTATTTATT-AATCAATTTTTATTTATTATTTAA
129 TT--TTCTTTATTTTTTTTACTTATATTTATTTA-TTATTAAATTTATTTTTATTTATTATTAAA
12810229 AAAAAAATCTTTACTG
191 AAAAAAATCTTTACTG
*
12810245 TATTGAAAATTTTTTATAAATACTCCAATACGCTGGTAGTA-CTT-AAAAAAATCTTCTCACCTA
1 TATTGAAAATTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAAATCTTCTCACCTA
*
12810308 GAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCC-TC
66 GAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCTTT
* * *
12810372 TTCTCTTATTTTTTATTAGTTATATTTTAATTTATTAATCAATTTTTATTTATTATTT-TT-TTA
131 TTCT-TTATTTTTT-TTACTTATA-TTT-ATTTATT-ATTAA-ATTTATTT-TTATTTATTATT-
12810435 AAAAAAGAAAATCTTTACTG
188 AAAAAA-AAAATCTTTACTG
12810455 TATTGAAAATTTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAAATCTTCTCACCT
1 TATTGAAAA-TTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAAATCTTCTCACCT
*
12810520 AGAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCGTCGGATAAAAATTTCCTT
65 AGAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCTT
**
12810585 TTTCTTTCATTTTTTTTTTTTACTACTTTAGTATTATTATTAAATTTATTTTTTATGTTATT
130 TTTCTTT-ATTTTTTTTACTTA-TA-TTTA-T-TTATTATTAAATTTA-TTTTTAT-TTATT
12810647 GTTTTTAAAG
Statistics
Matches: 348, Mismatches: 29, Indels: 41
0.83 0.07 0.10
Matches are distributed among these distances:
201 3 0.01
202 16 0.05
203 37 0.11
204 35 0.10
205 5 0.01
206 39 0.11
207 6 0.02
208 3 0.01
209 12 0.03
210 28 0.08
211 32 0.09
212 2 0.01
213 96 0.28
214 27 0.08
215 7 0.02
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.45
Consensus pattern (206 bp):
TATTGAAAATTTTTTATAAATACTCCAATACGCTGGTAGTATTTTAAAAAAAATCTTCTCACCTA
GAGATTTCGTAGGCATCACTACTCGGAATACCTTTGAATCTCATCATCGGATAAAAATTTCCTTT
TTCTTTATTTTTTTTACTTATATTTATTTATTATTAAATTTATTTTTATTTATTATTAAAAAAAA
AATCTTTACTG
Found at i:12811733 original size:16 final size:16
Alignment explanation
Indices: 12811712--12811750 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
12811702 TTTCTGTTTC
12811712 TTTTGTTTGTTTATTT-
1 TTTTGTTT-TTTATTTG
*
12811728 TTTTGTTTTTTGTTTG
1 TTTTGTTTTTTATTTG
12811744 TTTTGTT
1 TTTTGTT
12811751 AAATATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (16 bp):
TTTTGTTTTTTATTTG
Found at i:12811994 original size:47 final size:47
Alignment explanation
Indices: 12811922--12812860 Score: 1493
Period size: 47 Copynumber: 19.9 Consensus size: 47
12811912 TTTTGAAAGG
*
12811922 GCTCCTCTCAGCAGAGGTTCAACAACTTTAAAATTCATCTTGGAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
* *
12811969 GCTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTTCATC-TGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TTCATCTTGGAAAA
*
12812016 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATC-TGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TCATCTTGGAAAA
12812063 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
* *
12812110 GCTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTTCATC-TGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TTCATCTTGGAAAA
*
12812157 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATC-TGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TCATCTTGGAAAA
*
12812204 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATC-TGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TCATCTTGGAAAA
*
12812251 GCTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
*
12812298 GCTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCATCTTGGAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
*
12812345 GCTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTTCATC-T-GAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TTCATCTTGGAAAA
12812391 GCTCCTCTCAGCAGAGGCTTC-ACAACTTTAAAATTCTCATCTTGGAAAA
1 GCTCCTCTCAGCAGAGGC-TCAACAACTTTAAAA-T-TCATCTTGGAAAA
*
12812440 GCTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTCATCTTGGAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
*
12812487 GCTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTTCATCTTGGAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TTCATCTTGGAAAA
12812535 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
12812582 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
*
12812629 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCTTCTTGGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TCATCTTGG-AAAA
* *
12812678 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTATC-TGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
* *
12812724 GCTCCTCTCACCAGAGGCTCAACAACTTTAAAATCTCATC-TGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TCATCTTGGAAAA
*
12812771 GCTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAAA
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGG-AAAA
*
12812819 GCTCCTCTCAGCAGAGGCTCCACAACTTTAAAATTTCATCTT
1 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TTCATCTT
12812861 CTGTTTTCAA
Statistics
Matches: 849, Mismatches: 24, Indels: 36
0.93 0.03 0.04
Matches are distributed among these distances:
46 91 0.11
47 563 0.66
48 114 0.13
49 81 0.10
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.26
Consensus pattern (47 bp):
GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCATCTTGGAAAA
Found at i:12813646 original size:12 final size:12
Alignment explanation
Indices: 12813629--12813656 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
12813619 TAAGTCATCA
12813629 TTTTTTTTCTTT
1 TTTTTTTTCTTT
12813641 TTTTTTTTCTTT
1 TTTTTTTTCTTT
12813653 TTTT
1 TTTT
12813657 AAGCAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:12821035 original size:21 final size:19
Alignment explanation
Indices: 12821011--12821052 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
12821001 GCCATGTGTC
12821011 AAAATTTTTATTTTTGAAAAA
1 AAAATTTTT-TTTTT-AAAAA
12821032 AAAATTTTTTTTTTAAAAA
1 AAAATTTTTTTTTTAAAAA
12821051 AA
1 AA
12821053 TGATGCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
AAAATTTTTTTTTTAAAAA
Found at i:12822657 original size:22 final size:23
Alignment explanation
Indices: 12822630--12822682 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
12822620 ATCAATTTTT
*
12822630 ATTTATTATTAA-AAAAATGAAA
1 ATTTATTATGAAGAAAAATGAAA
12822652 ATTTATT-TGAAGAAAAATGAAA
1 ATTTATTATGAAGAAAAATGAAA
*
12822674 TTTTATTAT
1 ATTTATTAT
12822683 ATTGAAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 23 0.85
23 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (23 bp):
ATTTATTATGAAGAAAAATGAAA
Found at i:12822856 original size:226 final size:225
Alignment explanation
Indices: 12822432--12822863 Score: 545
Period size: 226 Copynumber: 1.9 Consensus size: 225
12822422 AAATTAAAAT
* *
12822432 TTTGAAGAAAAAGGAATTTAATTATATTGAAAATTTTCTATAAATATTCCAATACGCTGGTAATA
1 TTTGAAGAAAAAGAAATTTAATTATATTGAAAATTTTCTATAAATATTCCAATACACTGGTAATA
* * * *
12822497 TTTTACAGAAAATCTTCTCACCTAGAGTTTCTTAAAGCATCTCTACTCGGAATACTTTTAGAATC
66 TTTTACAAAAAATCTTCTCACCTAGAGTTTCATAAAGCATCACTACTCGGAATACCTTTAGAATC
* * * * *
12822562 CCATCATTGGATTAAATTTCTTTCCTTCTTATTTTTATTACTTATTTTTAATATATTAATCAATT
131 CCATCATCGGATAAAATTTCTTTCCTAC-TATTTTTATTACTTATTATTAATATATAAATCAATT
12822627 TTTAT-TTATTATTAAAAAAATGAAAATTTA
195 TTTATATTATTATTAAAAAAATGAAAATTTA
* *
12822657 TTTGAAGAAAAATGAAATTTTATTATATTGAAGATTTTCTATAAATATTCCAATACACTGGTAAA
1 TTTGAAGAAAAA-GAAATTTAATTATATTGAAAATTTTCTATAAATATTCCAATACACTGGT-AA
* *
12822722 TATTTTATAAAAAATCTTCTCACCTAGAGATTTCAT-AGGCATCACTACTCGGAATACCTTT-GA
64 TATTTTACAAAAAATCTTCTCACCTAGAG-TTTCATAAAGCATCACTACTCGGAATACCTTTAGA
* * * *
12822785 ATCTCATCGTCGGATAAAAATTTCATTTTCCTAC-A-TTTTGTTAGTTTATTATT-AT-TATCAA
128 ATCCCATCATCGGAT-AAAATTTC--TTTCCTACTATTTTTATTA-CTTATTATTAATATAT-AA
**
12822846 ATTTATTTTTATATTATT
188 ATCAATTTTTATATTATT
12822864 GTTTTTAAAG
Statistics
Matches: 177, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
225 15 0.08
226 79 0.45
227 71 0.40
228 5 0.03
229 7 0.04
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (225 bp):
TTTGAAGAAAAAGAAATTTAATTATATTGAAAATTTTCTATAAATATTCCAATACACTGGTAATA
TTTTACAAAAAATCTTCTCACCTAGAGTTTCATAAAGCATCACTACTCGGAATACCTTTAGAATC
CCATCATCGGATAAAATTTCTTTCCTACTATTTTTATTACTTATTATTAATATATAAATCAATTT
TTATATTATTATTAAAAAAATGAAAATTTA
Found at i:12822861 original size:26 final size:27
Alignment explanation
Indices: 12822831--12822881 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
12822821 TTTGTTAGTT
12822831 TATTATTATTATCAAA-TTTATTTTTA
1 TATTATTATTATCAAAGTTTATTTTTA
* * *
12822857 TATTATTGTTTTTAAAGTTTATTTT
1 TATTATTATTATCAAAGTTTATTTT
12822882 AAAAATTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
TATTATTATTATCAAAGTTTATTTTTA
Found at i:12823071 original size:13 final size:13
Alignment explanation
Indices: 12823053--12823091 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
12823043 GGTCAACGTA
12823053 CGGTTCGGTTCGG
1 CGGTTCGGTTCGG
12823066 CGGTTCGG-TCTGG
1 CGGTTCGGTTC-GG
*
12823079 CGGTTTGGTTCGG
1 CGGTTCGGTTCGG
12823092 TCTGGCAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 2 0.09
13 19 0.83
14 2 0.09
ACGTcount: A:0.00, C:0.21, G:0.46, T:0.33
Consensus pattern (13 bp):
CGGTTCGGTTCGG
Found at i:12824056 original size:20 final size:20
Alignment explanation
Indices: 12824031--12824080 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
12824021 TTTTTTTCGA
12824031 TGTATTTTTTCATATTTT-TT
1 TGTATTTTTTCAT-TTTTATT
*
12824051 TGTATTATTTCATTTTTATT
1 TGTATTTTTTCATTTTTATT
12824071 T-TCATTTTTT
1 TGT-ATTTTTT
12824081 TTGTATTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (20 bp):
TGTATTTTTTCATTTTTATT
Found at i:12824309 original size:26 final size:27
Alignment explanation
Indices: 12824269--12824320 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
12824259 TCTAGTTTTG
*
12824269 TTTATTATTTCTTTTATCTAATTAATA
1 TTTATTATATCTTTTATCTAATTAATA
* *
12824296 TTTATTATAT-TTTTATTTTATTAAT
1 TTTATTATATCTTTTATCTAATTAAT
12824321 TAATAACTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTATTATATCTTTTATCTAATTAATA
Found at i:12825595 original size:2 final size:2
Alignment explanation
Indices: 12825588--12825617 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12825578 GTTTTAATCA
12825588 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
12825618 GCATAAACCG
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:12826012 original size:49 final size:49
Alignment explanation
Indices: 12825959--12826052 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
12825949 CCTTATCTCA
*
12825959 TTTTTAAATTTAAAAAATGTCATTATCAATATATAAAATTATAGCATCG
1 TTTTTAAATTTAAAAAATGTCATTAGCAATATATAAAATTATAGCATCG
* * * *
12826008 TTTTTAAATTTCAAAATTTTTATTAGCAATATATAAAATTATAGC
1 TTTTTAAATTTAAAAAATGTCATTAGCAATATATAAAATTATAGC
12826053 TGATGCATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (49 bp):
TTTTTAAATTTAAAAAATGTCATTAGCAATATATAAAATTATAGCATCG
Found at i:12826201 original size:14 final size:14
Alignment explanation
Indices: 12826182--12826213 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12826172 GGTAACATAT
*
12826182 AAATAAAGTTTTTA
1 AAATAAAGTTTGTA
12826196 AAATAAAGTTTGTA
1 AAATAAAGTTTGTA
12826210 AAAT
1 AAAT
12826214 TTTTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (14 bp):
AAATAAAGTTTGTA
Found at i:12829770 original size:19 final size:18
Alignment explanation
Indices: 12829748--12829805 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
12829738 AATTGTAATC
12829748 TTTTTAATATTAAACTATA
1 TTTTTAATA-TAAACTATA
**
12829767 TTTTTCGTACTAAAC--TA
1 TTTTTAATA-TAAACTATA
12829784 -TTTT-ATATAAACTATA
1 TTTTTAATATAAACTATA
12829800 TTTTTA
1 TTTTTA
12829806 TCTATCTGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 6 0.19
17 6 0.19
19 12 0.39
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTTTAATATAAACTATA
Found at i:12829900 original size:43 final size:43
Alignment explanation
Indices: 12829865--12829953 Score: 116
Period size: 42 Copynumber: 2.1 Consensus size: 43
12829855 TAAATTTATC
12829865 AAATT-ATT-TTTTAAAAATAAGAATAA-AATTAATTAAATAATA
1 AAATTAATTATTTT-AAAATAA-AATAATAATTAATTAAATAATA
12829907 AAATTAATTATTTTAAAATAAAATAATAATT--TTAAATAATTA
1 AAATTAATTATTTTAAAATAAAATAATAATTAATTAAATAA-TA
12829949 AAATT
1 AAATT
12829954 TGTTTAACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
41 8 0.19
42 17 0.40
43 14 0.33
44 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (43 bp):
AAATTAATTATTTTAAAATAAAATAATAATTAATTAAATAATA
Found at i:12829922 original size:22 final size:21
Alignment explanation
Indices: 12829865--12829953 Score: 71
Period size: 22 Copynumber: 4.2 Consensus size: 21
12829855 TAAATTTATC
12829865 AAATT-ATT-TTTTAAAAATA
1 AAATTAATTATTTTAAAAATA
* *
12829884 AGAATAAAATTA-ATTAAATAATA
1 A-AAT-TAATTATTTTAAA-AATA
12829907 AAATTAATTATTTT-AAAATA
1 AAATTAATTATTTTAAAAATA
*
12829927 AAA-TAATAATTTTAAATAATTA
1 AAATTAATTATTTTAAA-AA-TA
12829949 AAATT
1 AAATT
12829954 TGTTTAACAT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
19 10 0.18
20 12 0.22
21 9 0.16
22 18 0.33
23 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (21 bp):
AAATTAATTATTTTAAAAATA
Found at i:12829938 original size:19 final size:20
Alignment explanation
Indices: 12829903--12829942 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
12829893 TTAATTAAAT
*
12829903 AATAAAATTAATTATTTTAA
1 AATAAAATTAATAATTTTAA
12829923 AATAAAA-TAATAATTTTAA
1 AATAAAATTAATAATTTTAA
12829942 A
1 A
12829943 TAATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAAAATTAATAATTTTAA
Found at i:12831521 original size:52 final size:52
Alignment explanation
Indices: 12831430--12831529 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
12831420 GGCAAGAAGA
* * * *
12831430 CTTGCAAAAGAAGAATTATGAGAGAAAGGGGATTTTTAATAGGTAAGTTTAT
1 CTTGCAAAAGAAGAATTATGAGAGAAAGAGAATTCTTAATAGGCAAGTTTAT
*
12831482 CTTGCAAAAGAAGAATTTTGAGAGGAAA-AGAATTCTTAATAGGCAAGT
1 CTTGCAAAAGAAGAATTATGAGA-GAAAGAGAATTCTTAATAGGCAAGT
12831530 ATGTATGCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 38 0.90
53 4 0.10
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.28
Consensus pattern (52 bp):
CTTGCAAAAGAAGAATTATGAGAGAAAGAGAATTCTTAATAGGCAAGTTTAT
Found at i:12832097 original size:25 final size:25
Alignment explanation
Indices: 12832063--12832114 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
12832053 GTGGTATCAG
*
12832063 AGCTGAAAGTTTGAAACATGGGAAA
1 AGCTAAAAGTTTGAAACATGGGAAA
**
12832088 AGCTAAAAGTTTGAGCCATGGGAAA
1 AGCTAAAAGTTTGAAACATGGGAAA
12832113 AG
1 AG
12832115 GTAAGTCCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.29, T:0.19
Consensus pattern (25 bp):
AGCTAAAAGTTTGAAACATGGGAAA
Found at i:12835353 original size:144 final size:144
Alignment explanation
Indices: 12835146--12835970 Score: 1383
Period size: 144 Copynumber: 5.8 Consensus size: 144
12835136 ACTATCTATG
* *
12835146 TGGTTCTATCCCTGCTTCCATAGGAAACTTGACCAGTCTATCCACTCTCTACCTTCATCGAAATA
1 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTCATCGAAATA
12835211 TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGT
66 TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGT
12835276 CATAATAATTTCTC
131 CATAATAATTTCTC
* *
12835290 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTTATGGAAATA
1 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTCATCGAAATA
*
12835355 TGTTTTCTGGGTCCATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGT
66 TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGT
12835420 CATAATAATTTCTC
131 CATAATAATTTCTC
*
12835434 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACTAGCCTATCCACTCTCTACCTTCAAT-GAAAT
1 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTC-ATCGAAAT
12835498 ATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAG
65 ATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAG
* *
12835563 TGAAAATAATTTCTC
130 TCATAATAATTTCTC
* * *
12835578 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGGCTATCCACTCTCTACCTTTATGGAAATA
1 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTCATCGAAATA
12835643 TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGT
66 TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGT
* *
12835708 GAAAATAATTTCTC
131 CATAATAATTTCTC
* *
12835722 TGG-TCAAATCCCTGCTTCCATAGGAAACTTGACCAGTCTATCCACTCTCTACCTTCACCG----
1 TGGTTC-AATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTCATCGAAAT
12835782 A--------GGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAG
65 ATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAG
12835839 TCATAATAATTTCTC
130 TCATAATAATTTCTC
*
12835854 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACGAGCCTATCCACTCTCTACCTTCATCGAAATA
1 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTCATCGAAATA
12835919 TGTTTTCTGGGTCGATACCTC-AGAGATAGGGATGCTTAAATCTCTCACTGAC
66 TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGAC
12835971 NNNNNNNNNN
Statistics
Matches: 643, Mismatches: 22, Indels: 33
0.92 0.03 0.05
Matches are distributed among these distances:
132 123 0.19
133 2 0.00
136 1 0.00
140 1 0.00
143 35 0.05
144 479 0.74
145 2 0.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (144 bp):
TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTCATCGAAATA
TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGT
CATAATAATTTCTC
Found at i:12835570 original size:72 final size:72
Alignment explanation
Indices: 12835206--12835714 Score: 178
Period size: 72 Copynumber: 7.1 Consensus size: 72
12835196 ACCTTCATCG
*
12835206 AAATATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGT
1 AAATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGT
*
12835271 TGAGTCA
66 TGAGTGA
* * * * **** ** ** *
12835278 TAATAAT-TTCTCTGGTTCAATCCCTGC-TTCCATA-GGAAACTTGACCAGCCTATCCACT--CT
1 AAAT-ATGTTTTCTGGGTCAATACCT-CAAGAGATAGGGATGCTT-A--AATCTCT-CACTGACT
* * * *
12835338 CT-ACCTTTA-TGG
60 TTGA-GTTGAGTGA
*
12835350 AAATATGTTTTCTGGGTCCATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGT
1 AAATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGT
*
12835415 TGAGTCA
66 TGAGTGA
* * * * **** ** ** *
12835422 TAATAAT-TTCTCTGGTTCAATCCCTGC-TTCCATA-GGAAACTTGACTAGCCTATCCACT--CT
1 AAAT-ATGTTTTCTGGGTCAATACCT-CAAGAGATAGGGATGCTT-A--AATCTCT-CACTGACT
* * * *
12835482 CT-ACCTTCAATG-
60 TTGA-GTTGAGTGA
*
12835494 AAATATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGT
1 AAATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGT
12835559 TGAGTGA
66 TGAGTGA
* * * **** ** ** *
12835566 AAATAAT-TTCTCTGGTTCAATCCCTGC-TTCCATA-GGAAACTTGACCAGGCTATCCACT--CT
1 AAAT-ATGTTTTCTGGGTCAATACCT-CAAGAGATAGGGATGCTT-A--AATCTCT-CACTGACT
* * * *
12835626 CT-ACCTTTA-TGG
60 TTGA-GTTGAGTGA
*
12835638 AAATATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGT
1 AAATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGT
12835703 TGAGTGA
66 TGAGTGA
12835710 AAATA
1 AAATA
12835715 ATTTCTCTGG
Statistics
Matches: 286, Mismatches: 109, Indels: 84
0.60 0.23 0.18
Matches are distributed among these distances:
69 12 0.04
70 12 0.04
71 47 0.16
72 145 0.51
73 46 0.16
74 12 0.04
75 12 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (72 bp):
AAATATGTTTTCTGGGTCAATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGT
TGAGTGA
Found at i:12835895 original size:132 final size:132
Alignment explanation
Indices: 12835651--12835910 Score: 468
Period size: 132 Copynumber: 2.0 Consensus size: 132
12835641 TATGTTTTCT
*
12835651 GGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGTGAAAATAA
1 GGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGTCAAAATAA
*
12835716 TTTCTCTGGTCAAATCCCTGCTTCCATAGGAAACTTGACCAGTCTATCCACTCTCTACCTTCACC
66 TTTCTCTGGTCAAATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTCACC
12835781 GA
131 GA
*
12835783 GGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGTCATAATAA
1 GGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGTCAAAATAA
*
12835848 TTTCTCTGGTTC-AATCCCTGCTTCCATAGGAAACTTGACGAGCCTATCCACTCTCTACCTTCA
66 TTTCTCTGG-TCAAATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTCA
12835911 TCGAAATATG
Statistics
Matches: 123, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
132 121 0.98
133 2 0.02
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (132 bp):
GGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGTCAAAATAA
TTTCTCTGGTCAAATCCCTGCTTCCATAGGAAACTTGACCAGCCTATCCACTCTCTACCTTCACC
GA
Found at i:12841700 original size:29 final size:29
Alignment explanation
Indices: 12841667--12841723 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
12841657 TTAGGGGTAT
*
12841667 TTTAAAGCATTTGAATTCAGTCATTTTAA
1 TTTAAAGCACTTGAATTCAGTCATTTTAA
12841696 TTTAAAGCACTTGAATTCAGTCATTTTA
1 TTTAAAGCACTTGAATTCAGTCATTTTA
12841724 GTTTGAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (29 bp):
TTTAAAGCACTTGAATTCAGTCATTTTAA
Done.