Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 123 of 167
Found at i:41117374 original size:14 final size:15
Alignment explanation
Indices: 41117355--41117383 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41117345 AAATATTATA
41117355 TTTAAA-TTTTAAAT
1 TTTAAATTTTTAAAT
41117369 TTTAAATTTTTAAAT
1 TTTAAATTTTTAAAT
41117384 GAATAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAAATTTTTAAAT
Found at i:41118370 original size:29 final size:29
Alignment explanation
Indices: 41118338--41118394 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
41118328 TGAAAGTATA
41118338 AAAAAAGGTAATAAATAAATAAATAATAT
1 AAAAAAGGTAATAAATAAATAAATAATAT
*
41118367 AAAAAAGGTACTAAATAAATAAATAATA
1 AAAAAAGGTAATAAATAAATAAATAATA
41118395 ATGAAATAAT
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:0.68, C:0.02, G:0.07, T:0.23
Consensus pattern (29 bp):
AAAAAAGGTAATAAATAAATAAATAATAT
Found at i:41118534 original size:16 final size:15
Alignment explanation
Indices: 41118491--41118532 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
41118481 AAAGTAAAGG
*
41118491 AAATAATAAATAAATA
1 AAATAATATATAAA-A
41118507 AAATAATATAT-AAA
1 AAATAATATATAAAA
41118521 AAATAATATATA
1 AAATAATATATA
41118533 TATATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 12 0.50
15 2 0.08
16 10 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAATATATAAAA
Found at i:41118542 original size:18 final size:19
Alignment explanation
Indices: 41118492--41118541 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
41118482 AAGTAAAGGA
41118492 AATA-ATAAATAAATAAAAT
1 AATATATAAA-AAATAAAAT
*
41118511 AATATATAAAAAATAATAT
1 AATATATAAAAAATAAAAT
41118530 ATATATATAAAA
1 A-ATATATAAAA
41118542 TCTATACAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATATATAAAAAATAAAAT
Found at i:41120520 original size:51 final size:51
Alignment explanation
Indices: 41120453--41120698 Score: 199
Period size: 51 Copynumber: 5.0 Consensus size: 51
41120443 GGGAGATTAG
* *
41120453 ACTTATAGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTA
1 ACTTATAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTA
* * * * *
41120504 ACTTGTAGCTTTAATCTATTTCACTGCAACTTCAGAGAAATAAGATTTG--
1 ACTTATAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTA
* ** *
41120553 -----TAGCTTCAATCTACTCCACCACAA-ATCTAGGGAGATAAGATTTGTA
1 ACTTATAGCTTTAATCTACTCCACTGCAACTTC-AGGGAGATAAGATTTGTA
* * ** * * *
41120599 ACGTATAGCTTTAATTTGTTCCACTGTAACTTCAGAGAAATAAGATTTGTA
1 ACTTATAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTA
* * * *
41120650 GC-TAT--TTTTCAATTTACTCCATTGCAACTTCAGGGAGATAAGATTTGTA
1 ACTTATAGCTTT-AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTA
41120699 GCTTCAATCT
Statistics
Matches: 152, Mismatches: 33, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
43 2 0.01
44 33 0.22
48 3 0.02
49 33 0.22
50 3 0.02
51 76 0.50
52 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.35
Consensus pattern (51 bp):
ACTTATAGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTA
Found at i:41120557 original size:95 final size:95
Alignment explanation
Indices: 41120428--41120698 Score: 310
Period size: 95 Copynumber: 2.8 Consensus size: 95
41120418 TTTAATTTGC
* * * * * * *
41120428 TCCACTGCAACTTCTGGGAGATTAGACTTATAGCTTTAATCTGCTCCACTACAACTTCAGGGAGA
1 TCCACTGCAACTTCAGAGAAATAAGATTTGTAGCTTTAATCTACTCCACTACAACTTCAGGGAGA
* *
41120493 TAAGATTTGTAACTTGTAGCTTTAATCTAT
66 TAAGATTTGTAACGTATAGCTTTAATCTAT
* * * *
41120523 TTCACTGCAACTTCAGAGAAATAAGATTTGTAGCTTCAATCTACTCCACCACAA-ATCTAGGGAG
1 TCCACTGCAACTTCAGAGAAATAAGATTTGTAGCTTTAATCTACTCCACTACAACTTC-AGGGAG
* *
41120587 ATAAGATTTGTAACGTATAGCTTTAATTTGT
65 ATAAGATTTGTAACGTATAGCTTTAATCTAT
* * * *
41120618 TCCACTGTAACTTCAGAGAAATAAGATTTGTAGCTATTTTTCAATTTACTCCATTGCAACTTCAG
1 TCCACTGCAACTTCAGAGAAATAAGATTTGTAGC----TTT-AATCTACTCCACTACAACTTCAG
41120683 GGAGATAAGATTTGTA
61 GGAGATAAGATTTGTA
41120699 GCTTCAATCT
Statistics
Matches: 146, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
94 2 0.01
95 109 0.75
99 2 0.01
100 31 0.21
101 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (95 bp):
TCCACTGCAACTTCAGAGAAATAAGATTTGTAGCTTTAATCTACTCCACTACAACTTCAGGGAGA
TAAGATTTGTAACGTATAGCTTTAATCTAT
Found at i:41139541 original size:78 final size:78
Alignment explanation
Indices: 41139412--41139567 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
41139402 AACTATTTGT
41139412 CTACAATTCTATTTATCCATCAAAGGGAAAACTGAAGTCTTAAACATACGACGAGCACATTTTCT
1 CTACAATTCTATTTATCCATCAAAGGGAAAACTGAAGTCTTAAACATACGACGAGCACATTTTCT
41139477 TCCCTTAGTGAGA
66 TCCCTTAGTGAGA
*
41139490 CTACAATTCTATTTATCCATCGAAGGGAAAACTGAAGTCTTAAACATACGACGAGCACATTTTCT
1 CTACAATTCTATTTATCCATCAAAGGGAAAACTGAAGTCTTAAACATACGACGAGCACATTTTCT
41139555 TCCCTTAGTGAGA
66 TCCCTTAGTGAGA
41139568 AGGACAAATA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (78 bp):
CTACAATTCTATTTATCCATCAAAGGGAAAACTGAAGTCTTAAACATACGACGAGCACATTTTCT
TCCCTTAGTGAGA
Found at i:41140400 original size:7 final size:7
Alignment explanation
Indices: 41140388--41140441 Score: 65
Period size: 7 Copynumber: 7.4 Consensus size: 7
41140378 TAAGTTATGG
41140388 TTTTAAT
1 TTTTAAT
41140395 TTTTAAT
1 TTTTAAT
41140402 TTTTAATT
1 TTTTAA-T
41140410 TTTTATAT
1 TTTTA-AT
41140418 TTTTAAT
1 TTTTAAT
*
41140425 TTTGAGA-
1 TTTTA-AT
41140432 TTTTAAT
1 TTTTAAT
41140439 TTT
1 TTT
41140442 GACTAAATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 1 0.02
7 26 0.63
8 13 0.32
9 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (7 bp):
TTTTAAT
Found at i:41141217 original size:11 final size:10
Alignment explanation
Indices: 41141191--41141220 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41141181 TTAATCTGAT
41141191 TTAAAAATTA
1 TTAAAAATTA
*
41141201 TTAAAAATTT
1 TTAAAAATTA
41141211 TTAAAAATTA
1 TTAAAAATTA
41141221 AAAAATCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:41142918 original size:7 final size:7
Alignment explanation
Indices: 41142906--41142936 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
41142896 ATAGAGTAGT
41142906 TGGAGAA
1 TGGAGAA
41142913 TGGAGAA
1 TGGAGAA
41142920 TGGAGAA
1 TGGAGAA
41142927 TGGAGAA
1 TGGAGAA
41142934 TGG
1 TGG
41142937 GAAAGGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.45, T:0.16
Consensus pattern (7 bp):
TGGAGAA
Found at i:41145205 original size:6 final size:6
Alignment explanation
Indices: 41145194--41145220 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41145184 TTGGATATTT
41145194 CTGGTG CTGGTG CTGGTG CTGGTG CTG
1 CTGGTG CTGGTG CTGGTG CTGGTG CTG
41145221 ATGAAGATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.48, T:0.33
Consensus pattern (6 bp):
CTGGTG
Found at i:41152315 original size:6 final size:6
Alignment explanation
Indices: 41152297--41152409 Score: 63
Period size: 6 Copynumber: 18.3 Consensus size: 6
41152287 AAGAAACATT
* * *
41152297 ATCAGA A-CTAGA ATCAGA ATCAAA ATCAGA ATCAG- GTGACAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * * * *
41152346 ATCAAA ATTAGA ATCAGA ATTAGGTA A-CAGA ATCAGA ATCAGT ATTAGGTA
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCA-G-A
41152397 A-CAGA ATCAGA AT
1 ATCAGA ATCAGA AT
41152410 AGCGAAGCCA
Statistics
Matches: 82, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
5 6 0.07
6 64 0.78
7 8 0.10
8 4 0.05
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:41152385 original size:25 final size:25
Alignment explanation
Indices: 41152355--41152409 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
41152345 AATCAAAATT
41152355 AGAATCAGAATTAGGTAACAGAATC
1 AGAATCAGAATTAGGTAACAGAATC
*
41152380 AGAATCAGTATTAGGTAACAGAATC
1 AGAATCAGAATTAGGTAACAGAATC
41152405 AGAAT
1 AGAAT
41152410 AGCGAAGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (25 bp):
AGAATCAGAATTAGGTAACAGAATC
Found at i:41152393 original size:37 final size:37
Alignment explanation
Indices: 41152306--41152406 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 37
41152296 TATCAGAACT
* * *
41152306 AGAATCAGAATCAAAATCAGAATCAGGTGACAGAATC
1 AGAATCAGAATTAGAATCAGAATCAGGTAACAGAATC
* * *
41152343 AAAATCAAAATTAGAATCAGAATTAGGTAACAGAATC
1 AGAATCAGAATTAGAATCAGAATCAGGTAACAGAATC
*
41152380 AGAATCAGTATTAGGTAA-CAGAATCAG
1 AGAATCAGAATTA-G-AATCAGAATCAG
41152407 AATAGCGAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
37 41 0.79
38 9 0.17
39 2 0.04
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.20
Consensus pattern (37 bp):
AGAATCAGAATTAGAATCAGAATCAGGTAACAGAATC
Found at i:41152680 original size:27 final size:27
Alignment explanation
Indices: 41152650--41152781 Score: 147
Period size: 27 Copynumber: 4.9 Consensus size: 27
41152640 AACACCCTAG
*
41152650 GGGTAAAATGGTAATTTTATAAATCAA
1 GGGTAAAATGGTAATTTTATAAATCGA
*
41152677 GGGTAAAATGGTAATTTTGTAAATCGA
1 GGGTAAAATGGTAATTTTATAAATCGA
* ** *
41152704 TGGTAAAATAATAATTTTCTAAATCGA
1 GGGTAAAATGGTAATTTTATAAATCGA
* * * *
41152731 GGGTAAAATAGTAATTCTGTCAATCGA
1 GGGTAAAATGGTAATTTTATAAATCGA
* * *
41152758 GGGTAAAACGATAATTCTATAAAT
1 GGGTAAAATGGTAATTTTATAAAT
41152782 TAAGGGTACT
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 89 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.33
Consensus pattern (27 bp):
GGGTAAAATGGTAATTTTATAAATCGA
Found at i:41152800 original size:54 final size:54
Alignment explanation
Indices: 41152650--41152789 Score: 181
Period size: 54 Copynumber: 2.6 Consensus size: 54
41152640 AACACCCTAG
* *
41152650 GGGTAAAATGGTAATTTTATAAATCAAGGGTAAAATGGTAATTTTGTAAATCGA
1 GGGTAAAATGATAATTTTATAAATCAAGGGTAAAATGGTAATTCTGTAAATCGA
* * * * * *
41152704 TGGTAAAATAATAATTTTCTAAATCGAGGGTAAAATAGTAATTCTGTCAATCGA
1 GGGTAAAATGATAATTTTATAAATCAAGGGTAAAATGGTAATTCTGTAAATCGA
* * *
41152758 GGGTAAAACGATAATTCTATAAATTAAGGGTA
1 GGGTAAAATGATAATTTTATAAATCAAGGGTA
41152790 CTTTGGTAAT
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 71 1.00
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.32
Consensus pattern (54 bp):
GGGTAAAATGATAATTTTATAAATCAAGGGTAAAATGGTAATTCTGTAAATCGA
Found at i:41152814 original size:27 final size:26
Alignment explanation
Indices: 41152784--41152943 Score: 149
Period size: 27 Copynumber: 6.0 Consensus size: 26
41152774 CTATAAATTA
* *
41152784 AGGGTACTTTGGTAATTTTACAAGCC
1 AGGGTATTTTGGTAATTTTACAAACC
*** ** *
41152810 GAGGGTATTTCAATAATTTTACAGGTCG
1 -AGGGTATTTTGGTAATTTTACA-AACC
** * *
41152838 AGGGTATTTCAGTAATTTCACAAATC
1 AGGGTATTTTGGTAATTTTACAAACC
*
41152864 AGGGATATTTTGGTAATTTTACAAACT
1 AGGG-TATTTTGGTAATTTTACAAACC
*
41152891 AGGGGTATTTTGATAATTTTACAAACC
1 A-GGGTATTTTGGTAATTTTACAAACC
41152918 AGGGGTATTTTGGTAATTTTACAAAC
1 A-GGGTATTTTGGTAATTTTACAAAC
41152944 GTAGCCATCC
Statistics
Matches: 109, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
26 4 0.04
27 101 0.93
28 4 0.04
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAACC
Found at i:41152924 original size:81 final size:81
Alignment explanation
Indices: 41152791--41152942 Score: 182
Period size: 81 Copynumber: 1.9 Consensus size: 81
41152781 TTAAGGGTAC
* * ***
41152791 TTTGGTAATTTTACAAGCCGAGGGTATTTCAATAATTTTACAGGTCGAGGGTATTTCAGTAATTT
1 TTTGGTAATTTTACAAACAGAGGGTATTTCAATAATTTTACAAACCGAGGGTATTTCAGTAATTT
41152856 CACAAATCAGGGATAT
66 CACAAATCAGGGATAT
** **
41152872 TTTGGTAATTTTACAAACTAG-GGGTATTTTGATAATTTTACAAACC-AGGGGTATTTTGGTAAT
1 TTTGGTAATTTTACAAAC-AGAGGGTATTTCAATAATTTTACAAACCGA-GGGTATTTCAGTAAT
*
41152935 TTTACAAA
64 TTCACAAA
41152943 CGTAGCCATC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
80 1 0.02
81 57 0.97
82 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (81 bp):
TTTGGTAATTTTACAAACAGAGGGTATTTCAATAATTTTACAAACCGAGGGTATTTCAGTAATTT
CACAAATCAGGGATAT
Found at i:41155193 original size:30 final size:30
Alignment explanation
Indices: 41155159--41155227 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
41155149 ACGCAGTATG
41155159 TCATGT-ATAACTATCTAATTATTTTATTAA
1 TCATGTCA-AACTATCTAATTATTTTATTAA
** *
41155189 TCATGTCAATTTATTTAATTATTTTATTAA
1 TCATGTCAAACTATCTAATTATTTTATTAA
41155219 TCATGTCAA
1 TCATGTCAA
41155228 TTTTTACCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (30 bp):
TCATGTCAAACTATCTAATTATTTTATTAA
Found at i:41155203 original size:17 final size:17
Alignment explanation
Indices: 41155181--41155230 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
41155171 ATCTAATTAT
41155181 TTTATTAATCATGTCAA
1 TTTATTAATCATGTCAA
* *
41155198 TTTATT--TAAT-T-AT
1 TTTATTAATCATGTCAA
41155211 TTTATTAATCATGTCAA
1 TTTATTAATCATGTCAA
41155228 TTT
1 TTT
41155231 TTACCAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
13 7 0.28
14 1 0.04
15 6 0.24
16 1 0.04
17 10 0.40
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTATTAATCATGTCAA
Found at i:41155228 original size:30 final size:30
Alignment explanation
Indices: 41155174--41155230 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
41155164 TATAACTATC
41155174 TAATTATTTTATTAATCATGTCAATTTATT
1 TAATTATTTTATTAATCATGTCAATTTATT
41155204 TAATTATTTTATTAATCATGTCAATTT
1 TAATTATTTTATTAATCATGTCAATTT
41155231 TTACCAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (30 bp):
TAATTATTTTATTAATCATGTCAATTTATT
Found at i:41155792 original size:15 final size:15
Alignment explanation
Indices: 41155749--41155819 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
41155739 TATCGTTTAT
* *
41155749 TAAAAACTAAAATTT
1 TAAAAACTAAAAATA
**
41155764 TAAAATTTAAAAAATA
1 TAAAAACT-AAAAATA
*
41155780 TAAAAACTAAAAATG
1 TAAAAACTAAAAATA
**
41155795 TTCAAACT-AAAATA
1 TAAAAACTAAAAATA
*
41155809 TAAAAATTAAA
1 TAAAAACTAAA
41155820 TCCATAACTT
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
14 10 0.24
15 20 0.49
16 11 0.27
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.28
Consensus pattern (15 bp):
TAAAAACTAAAAATA
Found at i:41156263 original size:13 final size:12
Alignment explanation
Indices: 41156244--41156276 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41156234 TCATAATAGT
41156244 TTATTATTTCTA
1 TTATTATTTCTA
41156256 TATATTA-TTCTA
1 T-TATTATTTCTA
41156268 TTATTATTT
1 TTATTATTT
41156277 GTGTCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.26
12 9 0.47
13 5 0.26
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATTATTTCTA
Found at i:41158721 original size:3 final size:3
Alignment explanation
Indices: 41158713--41158743 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41158703 GAACATACTA
41158713 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
41158744 CAATAGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41160274 original size:39 final size:39
Alignment explanation
Indices: 41160174--41160323 Score: 142
Period size: 39 Copynumber: 3.8 Consensus size: 39
41160164 AGCGGCGCTT
** *
41160174 TTAGCGGCGATTGGACAACAAACGCCGCTAAAAATTAAGCA
1 TTAGCGGCGATTTTACAA-AAACGCCGCTAAATA-TAAGCA
* * * *
41160215 TTAGCGGCGATTTAAAAAAAACGCCGCTAAATATCAGTA
1 TTAGCGGCGATTTTACAAAAACGCCGCTAAATATAAGCA
* * *
41160254 TTACCGGCGCTTTTACAAAAACGCCGCT-AATAATGAGCA
1 TTAGCGGCGATTTTACAAAAACGCCGCTAAAT-ATAAGCA
* *
41160293 TTAGCGGCGTTTCTTA-AAAAGCGCCGCTAAA
1 TTAGCGGCGATT-TTACAAAAACGCCGCTAAA
41160324 AACCTAAACC
Statistics
Matches: 91, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
38 3 0.03
39 54 0.59
40 19 0.21
41 15 0.16
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (39 bp):
TTAGCGGCGATTTTACAAAAACGCCGCTAAATATAAGCA
Found at i:41160614 original size:114 final size:114
Alignment explanation
Indices: 41160293--41160619 Score: 406
Period size: 113 Copynumber: 2.9 Consensus size: 114
41160283 ATAATGAGCA
* * * *
41160293 TTAGCGGCGTTTCTTAAAAAGCGCCGCTAAAAACCTAAACCAAACGACGTCGTTTTTCTTAGTTT
1 TTAGCGGCGTTTCTTAAAAAGCGCCGCAAAAAACCTAAGCCCAACGACATCGTTTTTCTTAGTTT
* * * *
41160358 TCGAGGCTTTGGTGGCGTTTTTGGAGAAGCGCAAG-TAATTCTCAGGGCT
66 TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGC-CGCTAATGCTCAAGGCT
* * * *
41160407 TTAGCAGCGTTTCTTAAAAAGCGCCGCAAAAGACCTAAGCCCAACGTCATC-ATTTTCTTAGTTT
1 TTAGCGGCGTTTCTTAAAAAGCGCCGCAAAAAACCTAAGCCCAACGACATCGTTTTTCTTAGTTT
* * * *
41160471 TCGAGGCTTTGGTGGCGTTTTCGGGAAAGCGCCGCTAATGCTCAATGTT
66 TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAGGCT
* * * * *
41160520 TTAGCGGCATTTTTTAAAAATCGCCACAAAAAACCGAAGCCCAACGACATCGTTTTTCTTAGTTT
1 TTAGCGGCGTTTCTTAAAAAGCGCCGCAAAAAACCTAAGCCCAACGACATCGTTTTTCTTAGTTT
** * *
41160585 GGGAGGCTTTAGTGGCGTTTTTGTAAAAGCGCCGC
66 TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGCCGC
41160620 AAAAAGCCTA
Statistics
Matches: 180, Mismatches: 31, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
112 1 0.01
113 94 0.52
114 85 0.47
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (114 bp):
TTAGCGGCGTTTCTTAAAAAGCGCCGCAAAAAACCTAAGCCCAACGACATCGTTTTTCTTAGTTT
TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAGGCT
Found at i:41160638 original size:73 final size:72
Alignment explanation
Indices: 41160519--41160656 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 72
41160509 TGCTCAATGT
*
41160519 TTTAGCGGCATTTTTTAAAAATCGCCACAAAAAACCGAAGCCCAACGACATCGTTTTTCTTAGTT
1 TTTAGCGGCATTTTTTAAAAAGCGCCACAAAAAACCGAAGCCCAACGACATCG-TTTTCTTAGTT
41160584 TGGGAGGC
65 TGGGAGGC
* * * * *
41160592 TTTAGTGGCGTTTTTGT-AAAAGCGCCGCAAAAAGCCTAAGCCCAACGACATCGTTTTCTTAGTT
1 TTTAGCGGCATTTTT-TAAAAAGCGCCACAAAAAACCGAAGCCCAACGACATCGTTTTCTTAGTT
41160656 T
65 T
41160657 TCGAGTCTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
72 12 0.21
73 45 0.78
74 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (72 bp):
TTTAGCGGCATTTTTTAAAAAGCGCCACAAAAAACCGAAGCCCAACGACATCGTTTTCTTAGTTT
GGGAGGC
Found at i:41160680 original size:73 final size:73
Alignment explanation
Indices: 41160519--41160680 Score: 184
Period size: 73 Copynumber: 2.2 Consensus size: 73
41160509 TGCTCAATGT
* * *
41160519 TTTAGCGGC-ATTTTTTAAAAATCGCCACAAAAAACCGAAGCCCAACGACATCGTTTTTCTTAGT
1 TTTAGTGGCGATTTTGT-AAAAGCGCCACAAAAAACCGAAGCCCAACGACATCGTTTTTCTTAGT
*
41160583 TTGGGAGGC
65 TTGCGAGGC
* * * *
41160592 TTTAGTGGCGTTTTTGTAAAAGCGCCGCAAAAAGCCTAAGCCCAACGACATCG-TTTTCTTAGTT
1 TTTAGTGGCGATTTTGTAAAAGCGCCACAAAAAACCGAAGCCCAACGACATCGTTTTTCTTAGTT
* *
41160656 TTCGAGTC
66 TGCGAGGC
* *
41160664 TTTGGTTGGGGATTTTG
1 TTTAG-TGGCGATTTTG
41160681 CGGCGTTTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
72 20 0.27
73 49 0.66
74 5 0.07
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (73 bp):
TTTAGTGGCGATTTTGTAAAAGCGCCACAAAAAACCGAAGCCCAACGACATCGTTTTTCTTAGTT
TGCGAGGC
Found at i:41161121 original size:7 final size:7
Alignment explanation
Indices: 41161088--41161261 Score: 51
Period size: 7 Copynumber: 25.1 Consensus size: 7
41161078 TGCAAATTAT
41161088 GGGTTTA
1 GGGTTTA
* *
41161095 GTGATTA
1 GGGTTTA
*
41161102 TGGTTTA
1 GGGTTTA
**
41161109 CAGTTTA
1 GGGTTTA
41161116 GGGTTTA
1 GGGTTTA
* *
41161123 CGAG-TTG
1 -GGGTTTA
41161130 GGGTTTA
1 GGGTTTA
*
41161137 AGGTTTA
1 GGGTTTA
41161144 CGGG-TT-
1 -GGGTTTA
* *
41161150 GGGGTTG
1 GGGTTTA
41161157 GGGTTTA
1 GGGTTTA
*
41161164 AGGTTTA
1 GGGTTTA
*
41161171 CGGG-TTG
1 -GGGTTTA
*
41161178 GGGTTCA
1 GGGTTTA
*
41161185 GGGTCTA
1 GGGTTTA
*
41161192 -GG-CTA
1 GGGTTTA
41161197 -GGTTTA
1 GGGTTTA
*
41161203 GGGATTA
1 GGGTTTA
* *
41161210 TGATTT-
1 GGGTTTA
41161216 GGGTTTA
1 GGGTTTA
41161223 GGGTTTAA
1 GGGTTT-A
41161231 GGGATTTAA
1 GGG-TTT-A
41161240 GGG-TTA
1 GGGTTTA
*
41161246 TGTGTTTA
1 -GGGTTTA
41161254 GGGTTTA
1 GGGTTTA
41161261 G
1 G
41161262 ATTGATTAGT
Statistics
Matches: 120, Mismatches: 33, Indels: 28
0.66 0.18 0.15
Matches are distributed among these distances:
5 8 0.07
6 16 0.13
7 75 0.62
8 13 0.11
9 8 0.07
ACGTcount: A:0.17, C:0.04, G:0.39, T:0.40
Consensus pattern (7 bp):
GGGTTTA
Found at i:41161135 original size:21 final size:21
Alignment explanation
Indices: 41161111--41161163 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
41161101 ATGGTTTACA
41161111 GTTTAGGGTTTACGAGTTGGG
1 GTTTAGGGTTTACGAGTTGGG
* *
41161132 GTTTAAGGTTTACGGGTTGGG
1 GTTTAGGGTTTACGAGTTGGG
*
41161153 G-TTGGGGTTTA
1 GTTTAGGGTTTA
41161164 AGGTTTACGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.13, C:0.04, G:0.43, T:0.40
Consensus pattern (21 bp):
GTTTAGGGTTTACGAGTTGGG
Found at i:41161163 original size:27 final size:27
Alignment explanation
Indices: 41161126--41161182 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
41161116 GGGTTTACGA
41161126 GTTGGGGTTTAAGGTTTACGGGTTGGG
1 GTTGGGGTTTAAGGTTTACGGGTTGGG
41161153 GTTGGGGTTTAAGGTTTACGGGTTGGG
1 GTTGGGGTTTAAGGTTTACGGGTTGGG
41161180 GTT
1 GTT
41161183 CAGGGTCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.11, C:0.04, G:0.47, T:0.39
Consensus pattern (27 bp):
GTTGGGGTTTAAGGTTTACGGGTTGGG
Found at i:41161832 original size:75 final size:74
Alignment explanation
Indices: 41161709--41161854 Score: 177
Period size: 75 Copynumber: 1.9 Consensus size: 74
41161699 ATTTAAAGGA
* * *
41161709 ATTTTGTTTCAATAAAAACGGCAGTGTTCTATAGGATATATTAGTGGCGTTTTGGGTAAAACACC
1 ATTTTGTTTCAATAAAAACGGCA-CGTTCTATAAGATATATTACTGGCGTTTTGGGTAAAACACC
41161774 GCAAAATGTG
65 GCAAAATGTG
* * * * *
41161784 ATTTTGTTTCAATAAAAACGTTGC-CGTTCTGTAAGATTTCTTACTGGCGTTTTTGGTAAAACGC
1 ATTTTGTTTCAATAAAAACG--GCACGTTCTATAAGATATATTACTGGCGTTTTGGGTAAAACAC
*
41161848 CGGAAAA
64 CGCAAAA
41161855 GATCAAAAGT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
75 58 0.97
77 2 0.03
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (74 bp):
ATTTTGTTTCAATAAAAACGGCACGTTCTATAAGATATATTACTGGCGTTTTGGGTAAAACACCG
CAAAATGTG
Found at i:41163927 original size:55 final size:55
Alignment explanation
Indices: 41163843--41163959 Score: 234
Period size: 55 Copynumber: 2.1 Consensus size: 55
41163833 TTACGTACTA
41163843 AAAAATTTCATAACGTAGGATCGTGAACAAGTTGGAATAAGCAGCAGGCAGAAAC
1 AAAAATTTCATAACGTAGGATCGTGAACAAGTTGGAATAAGCAGCAGGCAGAAAC
41163898 AAAAATTTCATAACGTAGGATCGTGAACAAGTTGGAATAAGCAGCAGGCAGAAAC
1 AAAAATTTCATAACGTAGGATCGTGAACAAGTTGGAATAAGCAGCAGGCAGAAAC
41163953 AAAAATT
1 AAAAATT
41163960 CACCCACACA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (55 bp):
AAAAATTTCATAACGTAGGATCGTGAACAAGTTGGAATAAGCAGCAGGCAGAAAC
Found at i:41164670 original size:21 final size:21
Alignment explanation
Indices: 41164644--41164714 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
41164634 CTACAACTTA
* *
41164644 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
41164665 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
41164686 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
41164707 AAGCAGAG
1 AAGCAGAG
41164715 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:41164957 original size:14 final size:14
Alignment explanation
Indices: 41164938--41164971 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
41164928 ATTGCTATTG
41164938 GTTGCTTTTGAAAT
1 GTTGCTTTTGAAAT
41164952 GTTGCTTTTGAAAT
1 GTTGCTTTTGAAAT
*
41164966 TTTGCT
1 GTTGCT
41164972 ACAGGAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.21, T:0.53
Consensus pattern (14 bp):
GTTGCTTTTGAAAT
Found at i:41165088 original size:40 final size:41
Alignment explanation
Indices: 41165038--41165411 Score: 192
Period size: 42 Copynumber: 8.9 Consensus size: 41
41165028 GTTTTTGTAT
* * *
41165038 AAAAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTG-T
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAA
* *
41165078 AAAAATGCCACTAAAGAACATGTTCTTTAGCGGCGATTAGAAAA
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG-TTTG--AA
* * ***
41165122 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCC
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG-TTTGAA
** * * ***
41165164 TTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG-TTTGAA
** * * * * * ***
41165206 CTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGC-GTTTGAA
* * ***
41165248 ACAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG-TTTGAA
** * * * * * ***
41165290 CTAAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGC-GTTTGAA
* * ***
41165332 ACAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG-TTTGAA
** * * *
41165374 CTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTT
41165412 TTTTCTAAGC
Statistics
Matches: 280, Mismatches: 46, Indels: 15
0.82 0.13 0.04
Matches are distributed among these distances:
40 32 0.11
41 6 0.02
42 208 0.74
44 34 0.12
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTTGAA
Found at i:41165141 original size:44 final size:40
Alignment explanation
Indices: 41165038--41165200 Score: 146
Period size: 40 Copynumber: 3.9 Consensus size: 40
41165028 GTTTTTGTAT
* * * *
41165038 AAAAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTGT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTAGA
*
41165078 AAAAATGCCACTAAAGAACATGTTCTTTAGCGGCGATTAGAAAA
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG-TTAG---A
* * ***
41165122 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCC
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCG--TTAGA
** * *
41165164 TTAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTT
1 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTT
41165201 TTTTTCTAAG
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
40 34 0.33
41 3 0.03
42 31 0.30
44 32 0.31
45 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (40 bp):
AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGTTAGA
Found at i:41165191 original size:42 final size:42
Alignment explanation
Indices: 41165127--41165455 Score: 484
Period size: 42 Copynumber: 7.8 Consensus size: 42
41165117 GAAAAAAAAA
* **
41165127 CGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTCCCTTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTC-TAAG
*
41165169 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* * *
41165211 CGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC-AAA
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT-CTAAG
*
41165253 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* * *
41165295 CGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTAC-AAA
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT-CTAAG
*
41165337 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
41165379 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
41165421 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
41165456 GTTTGTAAAC
Statistics
Matches: 260, Mismatches: 22, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
41 2 0.01
42 251 0.97
43 7 0.03
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:41165215 original size:84 final size:83
Alignment explanation
Indices: 41165040--41165455 Score: 503
Period size: 84 Copynumber: 5.0 Consensus size: 83
41165030 TTTTGTATAA
* * * * * * * *
41165040 AAGCGCCACTAAAGAACATGTTCTTTTGCGGC-GTTTGTAAAAATGCCACTAAAGAACATGTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTAAAACGCCGCTAAAGAACATGTTCT
*******
41165104 TTAGCGGCGATTAGAAAAAA
66 TTAGCGGCG-TT-TTTTTCT
* * * *
41165124 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCTT-AAGCGCCGCTAAAGAACATGTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTT--TTTAAAACGCCGCTAAAGAACATGTT
41165188 CTTTAGCGGCGTTTTTTTCT
64 CTTTAGCGGCGTTTTTTTCT
* *
41165208 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTACAAACGCCGCTAAAGAACATGTTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTA-AAACGCCGCTAAAGAACATGTTC
41165273 TTTAGCGGCGTTTTTTTCT
65 TTTAGCGGCGTTTTTTTCT
* *
41165292 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTACAAACGCCGCTAAAGAACATGTTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTA-AAACGCCGCTAAAGAACATGTTC
41165357 TTTAGCGGCGTTTTTTTCT
65 TTTAGCGGCGTTTTTTTCT
* * * *
41165376 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTT-AAAACGCCGCTAAAGAACATGTTC
*
41165441 TTTAACGGCGTTTTT
65 TTTAGCGGCGTTTTT
41165456 GTTTGTAAAC
Statistics
Matches: 296, Mismatches: 30, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
82 2 0.01
84 258 0.87
85 5 0.02
86 30 0.10
87 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (83 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTAAAACGCCGCTAAAGAACATGTTCT
TTAGCGGCGTTTTTTTCT
Found at i:41165254 original size:126 final size:126
Alignment explanation
Indices: 41165040--41165455 Score: 509
Period size: 126 Copynumber: 3.3 Consensus size: 126
41165030 TTTTGTATAA
* * * * * * * *
41165040 AAGCGCCACTAAAGAACATGTTCTTTTGCGGCG--TTTGTAAAAATGCCACTAAAGAACATGTTC
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTACAAACGCCGCTAAAGAACATGGTC
******* **
41165103 TTTAGCGGCGATTAGAAAAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTCCCTT
66 TTTAGCGGC-ATT-TTTTTCTAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC-T
* *
41165166 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTT-CTAAGCGCCGCTAAAGAACATGGT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTAC-AAACGCCGCTAAAGAACATGGT
* *
41165230 CTTTAGTGGCATTTTTTTAC-AAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCT
65 CTTTAGCGGCATTTTTTT-CTAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
* * *
41165292 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTTTTACAAACGCCGCTAAAGAACATGTTC
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTACAAACGCCGCTAAAGAACATGGTC
* *
41165357 TTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
66 TTTAGCGGCATTTTTTTCTAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
*
41165418 AAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
41165456 GTTTGTAAAC
Statistics
Matches: 253, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
125 1 0.00
126 212 0.84
127 9 0.04
128 31 0.12
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (126 bp):
AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTACAAACGCCGCTAAAGAACATGGTC
TTTAGCGGCATTTTTTTCTAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
Found at i:41170462 original size:728 final size:728
Alignment explanation
Indices: 41169066--41170516 Score: 2884
Period size: 728 Copynumber: 2.0 Consensus size: 728
41169056 GTAATAATTT
41169066 AAGTCTTACAACTTATCATATAGCAATTTCATACTCCCACACAAATCTGAATTACTCTCCACTAA
1 AAGTCTTACAACTTATCATATAGCAATTTCATACTCCCACACAAATCTGAATTACTCTCCACTAA
41169131 GACTTTTCTTCTGAAAGCTTAGTTGTAAAACCAAGTGTCTCACTTGAGTTTTACTTAAAAATTGC
66 GACTTTTCTTCTGAAAGCTTAGTTGTAAAACCAAGTGTCTCACTTGAGTTTTACTTAAAAATTGC
41169196 ACTCTAAATAGGTTTCTTACTAAACAAATGATAAGTGTTAACTCTTGTACAAACTACCAAATGCA
131 ACTCTAAATAGGTTTCTTACTAAACAAATGATAAGTGTTAACTCTTGTACAAACTACCAAATGCA
41169261 AGCCTACCATATATAAGAGTTTTAAGCTTTCTAAGATTTCAATCGATTACCATCAAAGTTCCTTA
196 AGCCTACCATATATAAGAGTTTTAAGCTTTCTAAGATTTCAATCGATTACCATCAAAGTTCCTTA
41169326 CAAATAGCCTTACAAAAAGGACTACATTTATCTGAATAAATACTGAGATTTAATTCTTCTGTGAT
261 CAAATAGCCTTACAAAAAGGACTACATTTATCTGAATAAATACTGAGATTTAATTCTTCTGTGAT
41169391 TTGATTATGCACAAGTGATTTTTATAGATGGGCCAAAGTTACTCAACAAAATAAACAAATACATA
326 TTGATTATGCACAAGTGATTTTTATAGATGGGCCAAAGTTACTCAACAAAATAAACAAATACATA
41169456 GCATAATAGATTTTGTTTCAAAAGACTGCCAACTTAAAATAAGACGAGTTACGATCCAATTCAAC
391 GCATAATAGATTTTGTTTCAAAAGACTGCCAACTTAAAATAAGACGAGTTACGATCCAATTCAAC
41169521 TATACCTCAAGTTGCAATTGCTGTTTTAGCGGGAACCATAATTGCTCCAACAATCTAACCTTTTG
456 TATACCTCAAGTTGCAATTGCTGTTTTAGCGGGAACCATAATTGCTCCAACAATCTAACCTTTTG
41169586 AAAATTTTTGAACAAAATCATAGTCATCATAAACAAAAGGATCTATATAAATAGATTTTCCTTTT
521 AAAATTTTTGAACAAAATCATAGTCATCATAAACAAAAGGATCTATATAAATAGATTTTCCTTTT
41169651 TAATCAATAAGAAGCTTCTGTTAATCCGAAACCTTAACTATAAATATAACCAAATATTGTAATCA
586 TAATCAATAAGAAGCTTCTGTTAATCCGAAACCTTAACTATAAATATAACCAAATATTGTAATCA
*
41169716 TTGATGCTTAAGAATTAGATGCATCAGTAATCAAAGTAACCATGATTAATATTATAGAGAATCAA
651 TTGATGCTTAAGAATTAGATGCATCAGTAATCAAAGTAACCATGATTAATATCATAGAGAATCAA
41169781 AGGGAAAGCGCTC
716 AGGGAAAGCGCTC
41169794 AAGTCTTACAACTTATCATATAGCAATTTCATACTCCCACACAAATCTGAATTACTCTCCACTAA
1 AAGTCTTACAACTTATCATATAGCAATTTCATACTCCCACACAAATCTGAATTACTCTCCACTAA
41169859 GACTTTTCTTCTGAAAGCTTAGTTGTAAAACCAAGTGTCTCACTTGAGTTTTACTTAAAAATTGC
66 GACTTTTCTTCTGAAAGCTTAGTTGTAAAACCAAGTGTCTCACTTGAGTTTTACTTAAAAATTGC
41169924 ACTCTAAATAGGTTTCTTACTAAACAAATGATAAGTGTTAACTCTTGTACAAACTACCAAATGCA
131 ACTCTAAATAGGTTTCTTACTAAACAAATGATAAGTGTTAACTCTTGTACAAACTACCAAATGCA
41169989 AGCCTACCATATATAAGAGTTTTAAGCTTTCTAAGATTTCAATCGATTACCATCAAAGTTCCTTA
196 AGCCTACCATATATAAGAGTTTTAAGCTTTCTAAGATTTCAATCGATTACCATCAAAGTTCCTTA
41170054 CAAATAGCCTTACAAAAAGGACTACATTTATCTGAATAAATACTGAGATTTAATTCTTCTGTGAT
261 CAAATAGCCTTACAAAAAGGACTACATTTATCTGAATAAATACTGAGATTTAATTCTTCTGTGAT
41170119 TTGATTATGCACAAGTGATTTTTATAGATGGGCCAAAGTTACTCAACAAAATAAACAAATACATA
326 TTGATTATGCACAAGTGATTTTTATAGATGGGCCAAAGTTACTCAACAAAATAAACAAATACATA
41170184 GCATAATAGATTTTGTTTCAAAAGACTGCCAACTTAAAATAAGACGAGTTACGATCCAATTCAAC
391 GCATAATAGATTTTGTTTCAAAAGACTGCCAACTTAAAATAAGACGAGTTACGATCCAATTCAAC
41170249 TATACCTCAAGTTGCAATTGCTGTTTTAGCGGGAACCATAATTGCTCCAACAATCTAACCTTTTG
456 TATACCTCAAGTTGCAATTGCTGTTTTAGCGGGAACCATAATTGCTCCAACAATCTAACCTTTTG
41170314 AAAATTTTTGAACAAAATCATAGTCATCATAAACAAAAGGATCTATATAAATAGATTTTCCTTTT
521 AAAATTTTTGAACAAAATCATAGTCATCATAAACAAAAGGATCTATATAAATAGATTTTCCTTTT
41170379 TAATCAATAAGAAGCTTCTGTTAATCCGAAACCTTAACTATAAATATAACCAAATATTGTAATCA
586 TAATCAATAAGAAGCTTCTGTTAATCCGAAACCTTAACTATAAATATAACCAAATATTGTAATCA
41170444 TTGATGCTTAAGAATTAGATGCATCAGTAATCAAAGTAACCATGATTAATATCATAGAGAATCAA
651 TTGATGCTTAAGAATTAGATGCATCAGTAATCAAAGTAACCATGATTAATATCATAGAGAATCAA
*
41170509 AGGTAAAG
716 AGGGAAAG
41170517 AGTTCAAAGT
Statistics
Matches: 721, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
728 721 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (728 bp):
AAGTCTTACAACTTATCATATAGCAATTTCATACTCCCACACAAATCTGAATTACTCTCCACTAA
GACTTTTCTTCTGAAAGCTTAGTTGTAAAACCAAGTGTCTCACTTGAGTTTTACTTAAAAATTGC
ACTCTAAATAGGTTTCTTACTAAACAAATGATAAGTGTTAACTCTTGTACAAACTACCAAATGCA
AGCCTACCATATATAAGAGTTTTAAGCTTTCTAAGATTTCAATCGATTACCATCAAAGTTCCTTA
CAAATAGCCTTACAAAAAGGACTACATTTATCTGAATAAATACTGAGATTTAATTCTTCTGTGAT
TTGATTATGCACAAGTGATTTTTATAGATGGGCCAAAGTTACTCAACAAAATAAACAAATACATA
GCATAATAGATTTTGTTTCAAAAGACTGCCAACTTAAAATAAGACGAGTTACGATCCAATTCAAC
TATACCTCAAGTTGCAATTGCTGTTTTAGCGGGAACCATAATTGCTCCAACAATCTAACCTTTTG
AAAATTTTTGAACAAAATCATAGTCATCATAAACAAAAGGATCTATATAAATAGATTTTCCTTTT
TAATCAATAAGAAGCTTCTGTTAATCCGAAACCTTAACTATAAATATAACCAAATATTGTAATCA
TTGATGCTTAAGAATTAGATGCATCAGTAATCAAAGTAACCATGATTAATATCATAGAGAATCAA
AGGGAAAGCGCTC
Found at i:41177622 original size:34 final size:34
Alignment explanation
Indices: 41177583--41177658 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
41177573 TTAGCACCTT
* * *
41177583 TTTCAGTAACAGTATCAATCTGGGCCTGGGCCCA
1 TTTCAGTAACAGGAGCAATCTGGGCCTGAGCCCA
* * *
41177617 TTTCAGTAACAGGGGCAGTCTGGGCCTTAGCCCA
1 TTTCAGTAACAGGAGCAATCTGGGCCTGAGCCCA
41177651 TTTCAGTA
1 TTTCAGTA
41177659 CTGTATTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (34 bp):
TTTCAGTAACAGGAGCAATCTGGGCCTGAGCCCA
Found at i:41181597 original size:25 final size:25
Alignment explanation
Indices: 41181542--41181598 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
41181532 TTTACCAAGG
** * *
41181542 GTAAAATCGTCAAAATTTTATTGGG
1 GTAAAATAATCAAAACTTTATTGGA
*
41181567 GAAAAATAATCAAAACTTTATTGGA
1 GTAAAATAATCAAAACTTTATTGGA
41181592 GTAAAAT
1 GTAAAAT
41181599 TGAGATAAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.32
Consensus pattern (25 bp):
GTAAAATAATCAAAACTTTATTGGA
Found at i:41195801 original size:26 final size:26
Alignment explanation
Indices: 41195771--41195838 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
41195761 TGTTATATGA
* *
41195771 CTCTTTGTGAGCTTCCCGTTTAAAGG
1 CTCTTTGTGAGCTTCCCGATTAAAAG
*
41195797 CTCTTTGTGAGCTTCCCGATTAAAAT
1 CTCTTTGTGAGCTTCCCGATTAAAAG
* *
41195823 TTCTTTGTGAACTTCC
1 CTCTTTGTGAGCTTCC
41195839 TATTTATGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (26 bp):
CTCTTTGTGAGCTTCCCGATTAAAAG
Found at i:41197410 original size:47 final size:47
Alignment explanation
Indices: 41197356--41197480 Score: 133
Period size: 47 Copynumber: 2.7 Consensus size: 47
41197346 AATAATACCG
* * * *
41197356 TGATTTGGTTATGGGCCATGGTATAGGTATTCAGAGAGGAGTTAACT
1 TGATTTGGCTATGGGCCATGGTATAGGTACTCAGAAAGAAGTTAACT
* * * ** * *
41197403 TGATTTGGCTACGGGCCATGATATTGGTACTCCTAAATAAGTTACCT
1 TGATTTGGCTATGGGCCATGGTATAGGTACTCAGAAAGAAGTTAACT
* *
41197450 TGACTTGACTATGGGCCATGGTATAGGTACT
1 TGATTTGGCTATGGGCCATGGTATAGGTACT
41197481 TATCGATTGA
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
47 62 1.00
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (47 bp):
TGATTTGGCTATGGGCCATGGTATAGGTACTCAGAAAGAAGTTAACT
Found at i:41200987 original size:28 final size:28
Alignment explanation
Indices: 41200947--41201003 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
41200937 CAATACAAAA
*
41200947 TCTTGGTAATTAATTAGGCGTTCAACTT
1 TCTTGGTAATTAATTAAGCGTTCAACTT
*
41200975 TCTTGGTAATTAATTAAGCGTTCAGCTT
1 TCTTGGTAATTAATTAAGCGTTCAACTT
41201003 T
1 T
41201004 TTCATCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.44
Consensus pattern (28 bp):
TCTTGGTAATTAATTAAGCGTTCAACTT
Found at i:41205867 original size:19 final size:19
Alignment explanation
Indices: 41205845--41205882 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41205835 TGAGTTGGCA
* *
41205845 AATTTTATTTTATTATTTT
1 AATTTGATTTTAATATTTT
41205864 AATTTGATTTTAATATTTT
1 AATTTGATTTTAATATTTT
41205883 CTTGAATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
AATTTGATTTTAATATTTT
Found at i:41206195 original size:17 final size:18
Alignment explanation
Indices: 41206163--41206196 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41206153 GATTTTTCTT
*
41206163 AAAAAAATTTATAATTTC
1 AAAAAAATATATAATTTC
41206181 AAAAAAATATA-AATTT
1 AAAAAAATATATAATTT
41206197 TGAAAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAAAATATATAATTTC
Found at i:41207599 original size:12 final size:12
Alignment explanation
Indices: 41207582--41207611 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41207572 TGGGTTAAGT
41207582 CACACGGCCAGC
1 CACACGGCCAGC
*
41207594 CACACGGCCAGT
1 CACACGGCCAGC
41207606 CACACG
1 CACACG
41207612 CCCGTGTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.47, G:0.23, T:0.03
Consensus pattern (12 bp):
CACACGGCCAGC
Found at i:41215872 original size:12 final size:12
Alignment explanation
Indices: 41215850--41215895 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
41215840 TGACTAATTC
41215850 ATTTAATTAAAAA
1 ATTT-ATTAAAAA
41215863 ATTTATTAAAAA
1 ATTTATTAAAAA
41215875 ATTTA--AAAAA
1 ATTTATTAAAAA
*
41215885 A-CTATTAAAAA
1 ATTTATTAAAAA
41215896 TTATAAACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
9 2 0.07
10 6 0.20
11 5 0.17
12 13 0.43
13 4 0.13
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (12 bp):
ATTTATTAAAAA
Found at i:41215902 original size:21 final size:21
Alignment explanation
Indices: 41215856--41215895 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41215846 ATTCATTTAA
**
41215856 TTAAAAAATTTATTAAAAAAT
1 TTAAAAAAACTATTAAAAAAT
41215877 TTAAAAAAACTATTAAAAA
1 TTAAAAAAACTATTAAAAA
41215896 TTATAAACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAAAAAACTATTAAAAAAT
Found at i:41216643 original size:20 final size:20
Alignment explanation
Indices: 41216618--41216655 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41216608 TAATATTGTA
* *
41216618 AATTATACAAATAATTATCT
1 AATTATAAAAAAAATTATCT
41216638 AATTATAAAAAAAATTAT
1 AATTATAAAAAAAATTAT
41216656 TTTAGATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTATAAAAAAAATTATCT
Found at i:41228583 original size:19 final size:20
Alignment explanation
Indices: 41228541--41228583 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
41228531 AAAATTACTA
**
41228541 AATATTAAATAAAATAGCAT
1 AATATTAAATAAAATAAAAT
41228561 -ATATTAAA-AAAATAAAAT
1 AATATTAAATAAAATAAAAT
41228579 AATAT
1 AATAT
41228584 AGGTGAGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AATATTAAATAAAATAAAAT
Found at i:41231440 original size:19 final size:20
Alignment explanation
Indices: 41231418--41231455 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
41231408 AATATTTTTT
*
41231418 AATATTATTAAAAT-TTTAA
1 AATATTAATAAAATGTTTAA
41231437 AATATTAATAAAATGTTTA
1 AATATTAATAAAATGTTTA
41231456 TATCTCCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AATATTAATAAAATGTTTAA
Found at i:41235796 original size:22 final size:22
Alignment explanation
Indices: 41235778--41235819 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41235768 GTCATATTAC
41235778 TAAAATTCAATTTAAATATAAA
1 TAAAATTCAATTTAAATATAAA
* *
41235800 TATAATTTAATTTAAA-ATAA
1 TAAAATTCAATTTAAATATAA
41235820 TTTATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAATTCAATTTAAATATAAA
Found at i:41235806 original size:17 final size:16
Alignment explanation
Indices: 41235786--41235823 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
41235776 ACTAAAATTC
41235786 AATTTAAATATAAATAT
1 AATTTAAATATAAA-AT
*
41235803 AATTT-AATTTAAAAT
1 AATTTAAATATAAAAT
41235818 AATTTA
1 AATTTA
41235824 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 7 0.37
16 7 0.37
17 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAAATATAAAAT
Found at i:41236893 original size:18 final size:17
Alignment explanation
Indices: 41236870--41236929 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
41236860 GTTCAAGTGG
41236870 TAAGGTGTTAGTTTGCCC
1 TAAGGT-TTAGTTTGCCC
41236888 TAAGGTTTCAGTTTGCCC
1 TAAGGTTT-AGTTTGCCC
* *
41236906 TAAGGTCTCAGTTTGCCT
1 TAAGGT-TTAGTTTGCCC
41236924 TAAGGT
1 TAAGGT
41236930 CTCCTGTTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.05
18 35 0.92
19 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (17 bp):
TAAGGTTTAGTTTGCCC
Found at i:41236930 original size:18 final size:18
Alignment explanation
Indices: 41236879--41236932 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
41236869 GTAAGGTGTT
*
41236879 AGTTTGCCCTAAGGTTTC
1 AGTTTGCCCTAAGGTCTC
41236897 AGTTTGCCCTAAGGTCTC
1 AGTTTGCCCTAAGGTCTC
*
41236915 AGTTTGCCTTAAGGTCTC
1 AGTTTGCCCTAAGGTCTC
41236933 CTGTTCGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (18 bp):
AGTTTGCCCTAAGGTCTC
Found at i:41239014 original size:34 final size:34
Alignment explanation
Indices: 41238971--41239039 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
41238961 AGGTATAGGG
*
41238971 TGTTACATATTTCCTCTTTCTTATGTTTCAGTCT
1 TGTTACATATTTCCTCTTTCTTATATTTCAGTCT
41239005 TGTTACATATTTCCTCTTTCTTATATTTCAGTCT
1 TGTTACATATTTCCTCTTTCTTATATTTCAGTCT
41239039 T
1 T
41239040 CTTTTAAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.57
Consensus pattern (34 bp):
TGTTACATATTTCCTCTTTCTTATATTTCAGTCT
Found at i:41239032 original size:16 final size:16
Alignment explanation
Indices: 41238977--41239033 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
41238967 AGGGTGTTAC
41238977 ATATTTCCTCTTTCTT
1 ATATTTCCTCTTTCTT
* * *
41238993 ATGTTTCAGTCTTGT-TAC
1 ATATTTC-CTCTT-TCT-T
41239011 ATATTTCCTCTTTCTT
1 ATATTTCCTCTTTCTT
41239027 ATATTTC
1 ATATTTC
41239034 AGTCTTCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
16 14 0.45
17 10 0.32
18 7 0.23
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (16 bp):
ATATTTCCTCTTTCTT
Found at i:41239039 original size:17 final size:17
Alignment explanation
Indices: 41238985--41239039 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
41238975 ACATATTTCC
*
41238985 TCTTTCTTATGTTTCAG
1 TCTTTCTTATATTTCAG
* *
41239002 TCTTGT-TACATATTTC-C
1 TCTT-TCT-TATATTTCAG
41239019 TCTTTCTTATATTTCAG
1 TCTTTCTTATATTTCAG
41239036 TCTT
1 TCTT
41239040 CTTTTAAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
16 8 0.28
17 14 0.48
18 7 0.24
ACGTcount: A:0.15, C:0.20, G:0.07, T:0.58
Consensus pattern (17 bp):
TCTTTCTTATATTTCAG
Found at i:41239071 original size:20 final size:20
Alignment explanation
Indices: 41239046--41239086 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
41239036 TCTTCTTTTA
*
41239046 AAGTTTTTCCAAAATGGAGG
1 AAGTTTGTCCAAAATGGAGG
* *
41239066 AAGTTTGTCTATAATGGAGG
1 AAGTTTGTCCAAAATGGAGG
41239086 A
1 A
41239087 TACAAAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (20 bp):
AAGTTTGTCCAAAATGGAGG
Found at i:41240308 original size:20 final size:21
Alignment explanation
Indices: 41240270--41240310 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41240260 TGCCGAAATT
41240270 CTTTTCTTTTCTTTCTTTTTC
1 CTTTTCTTTTCTTTCTTTTTC
* *
41240291 CTTTT-TTTTTTTTGTTTTTC
1 CTTTTCTTTTCTTTCTTTTTC
41240311 TTCTATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (21 bp):
CTTTTCTTTTCTTTCTTTTTC
Found at i:41241398 original size:40 final size:40
Alignment explanation
Indices: 41241336--41241412 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
41241326 ACGGTACCTT
* *
41241336 TTGGTGTGTAGGGTTGGATGGGTTGATTATATCCCCATAC
1 TTGGCGTGTAGGGTTGGATGGGTCGATTATATCCCCATAC
*
41241376 TTGGCGTGTAGGGTTAGG-TGGGTCGATTCTATCCCCA
1 TTGGCGTGTAGGGTT-GGATGGGTCGATTATATCCCCA
41241413 CATGGTGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.35
Consensus pattern (40 bp):
TTGGCGTGTAGGGTTGGATGGGTCGATTATATCCCCATAC
Found at i:41249437 original size:25 final size:24
Alignment explanation
Indices: 41249398--41249444 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
41249388 TGAAATGAAT
41249398 ATGAAATGGATAATACAATTGTGTA
1 ATGAAATGGATAATA-AATTGTGTA
41249423 ATGAAATGTGA-AATAAATTGTG
1 ATGAAATG-GATAATAAATTGTG
41249445 AAAAGCTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.33
25 12 0.57
26 2 0.10
ACGTcount: A:0.45, C:0.02, G:0.21, T:0.32
Consensus pattern (24 bp):
ATGAAATGGATAATAAATTGTGTA
Found at i:41251691 original size:42 final size:43
Alignment explanation
Indices: 41251579--41251703 Score: 105
Period size: 44 Copynumber: 2.9 Consensus size: 43
41251569 TGTTTTACGT
* * * * *
41251579 GTAAGACCACGTCTGTGACGTTGGCATCGACT-TCTG-TTTTGTG
1 GTAAGACCATGTCTGGGACATGGGCATCGA-TATTTGATTTTG-G
*
41251622 TGTAAGATCATGTCTGGGACATGGGCATCG-TATTTGATTTTGG
1 -GTAAGACCATGTCTGGGACATGGGCATCGATATTTGATTTTGG
* * *
41251665 GTAAGACCCTGTCTGGGATA-GTGGCATCGATGTTTGATT
1 GTAAGACCATGTCTGGGACATG-GGCATCGATATTTGATT
41251704 ACCTATAAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
41 1 0.01
42 25 0.37
43 12 0.18
44 29 0.43
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (43 bp):
GTAAGACCATGTCTGGGACATGGGCATCGATATTTGATTTTGG
Found at i:41263180 original size:20 final size:20
Alignment explanation
Indices: 41263155--41263193 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41263145 ACCATCGTGT
*
41263155 CGTCGCTCCTCCGGCCACTC
1 CGTCGCTCATCCGGCCACTC
41263175 CGTCGCTCATCCGGCCACT
1 CGTCGCTCATCCGGCCACT
41263194 GGTCCTCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.51, G:0.21, T:0.21
Consensus pattern (20 bp):
CGTCGCTCATCCGGCCACTC
Found at i:41263522 original size:29 final size:30
Alignment explanation
Indices: 41263466--41263522 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
41263456 GTTAGATTGC
* *
41263466 TTTTGGTTGAGTCTTGTTAGTGTCATTAGT
1 TTTTGGTTGAATCTTGTTAGTGTAATTAGT
*
41263496 TTTTGGTTGAAT-TTGTTAGTTTAATTA
1 TTTTGGTTGAATCTTGTTAGTGTAATTA
41263523 TATTCATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.18, C:0.04, G:0.23, T:0.56
Consensus pattern (30 bp):
TTTTGGTTGAATCTTGTTAGTGTAATTAGT
Found at i:41276206 original size:43 final size:43
Alignment explanation
Indices: 41276159--41276263 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 43
41276149 GACGCCACTG
* * *
41276159 TCCCAGACAGGGTCTTACACGAAATC-GATTAGCAATGCCAATA
1 TCCCAGACATGGTCTTACACGAAATCTCAATA-CAATGCCAATA
* * *
41276202 TCCCAAACATGGTCTTACACGTAATCTCAATACAATGCCAATG
1 TCCCAGACATGGTCTTACACGAAATCTCAATACAATGCCAATA
41276245 TCCCAGACATGGTCTTACA
1 TCCCAGACATGGTCTTACA
41276264 TGTTATCACA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 51 0.94
44 3 0.06
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGAAATCTCAATACAATGCCAATA
Found at i:41283026 original size:12 final size:13
Alignment explanation
Indices: 41283007--41283032 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41282997 TATTACCAAG
41283007 GTTTTTTTAATTT
1 GTTTTTTTAATTT
41283020 GTTTTTTTAATTT
1 GTTTTTTTAATTT
41283033 AATGTAACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTTTTTTAATTT
Found at i:41283698 original size:20 final size:20
Alignment explanation
Indices: 41283663--41283716 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
41283653 TTCAATAGCA
41283663 ATTAATCAATCAGTAATATTC
1 ATTAA-CAATCAGTAATATTC
*
41283684 ATTAACAACCAGTAATATTC
1 ATTAACAATCAGTAATATTC
41283704 ATTAACAATCAGT
1 ATTAACAATCAGT
41283717 CAATCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 26 0.84
21 5 0.16
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (20 bp):
ATTAACAATCAGTAATATTC
Found at i:41283756 original size:18 final size:18
Alignment explanation
Indices: 41283733--41283883 Score: 97
Period size: 18 Copynumber: 7.9 Consensus size: 18
41283723 AAATAATTAT
* *
41283733 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAATCAA
*
41283751 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAA
* * *
41283769 TTTTTCAATAATAATCAA
1 TTATTCAGTAACAATCAA
*
41283787 TTATTCAGTATCAATCAA
1 TTATTCAGTAACAATCAA
*
41283805 TTGATCGGTTATCCAGTAACAGTCAA
1 TT-A-----T-T-CAGTAACAATCAA
* *
41283831 TTCTTCAGTAAAAATCAGA
1 TTATTCAGTAACAATCA-A
* *
41283850 -TATACAGTAACAATTAAA
1 TTATTCAGTAACAA-TCAA
41283868 TTATTCAGTAACAATC
1 TTATTCAGTAACAATC
41283884 GATCTTTCCA
Statistics
Matches: 100, Mismatches: 22, Indels: 22
0.69 0.15 0.15
Matches are distributed among these distances:
18 67 0.67
19 17 0.17
20 1 0.01
24 1 0.01
25 1 0.01
26 13 0.13
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:41284063 original size:53 final size:53
Alignment explanation
Indices: 41284001--41284119 Score: 168
Period size: 53 Copynumber: 2.2 Consensus size: 53
41283991 CAGGAACAGT
* * * *
41284001 AACAGTAACAGTAGCAGTACGGTACACAGAGTACCTCATCAGAACAAA-TCTGA
1 AACAGTAACAATAACAGTACAGTACACAAAGTACCTCATCAGAACAAATTC-GA
* *
41284054 AACGGTAACAATAACAGTACAGTACACAAAGTACCTCATCGGAACAAATTCGA
1 AACAGTAACAATAACAGTACAGTACACAAAGTACCTCATCAGAACAAATTCGA
41284107 AACAGTAACAATA
1 AACAGTAACAATA
41284120 TTCGACAAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 56 0.97
54 2 0.03
ACGTcount: A:0.45, C:0.22, G:0.16, T:0.17
Consensus pattern (53 bp):
AACAGTAACAATAACAGTACAGTACACAAAGTACCTCATCAGAACAAATTCGA
Found at i:41286653 original size:40 final size:40
Alignment explanation
Indices: 41286376--41286639 Score: 349
Period size: 40 Copynumber: 6.6 Consensus size: 40
41286366 CGAATGATGT
* * * *
41286376 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
41286416 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
41286456 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
41286494 TCCGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
41286535 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
41286575 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
41286615 CCGGGCTATGTCCCAAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
41286640 AACGAGTAGC
Statistics
Matches: 201, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
39 33 0.16
40 158 0.79
41 10 0.05
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:41286670 original size:159 final size:159
Alignment explanation
Indices: 41286376--41286672 Score: 379
Period size: 159 Copynumber: 1.9 Consensus size: 159
41286366 CGAATGATGT
*
41286376 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTG
* * ** *
41286441 TGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCCGAGTTAAGT
66 TGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAATCCGAGTTAAAT
41286506 CCCGAAGGCATTTGTGCGAGTTACTATAA
131 CCCGAAGGCATTTGTGCGAGTTACTATAA
* * * *
41286535 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCATT
* * * *
41286598 TGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAGGCATTTGAACGAG-TAGCTATATCCG-GT
64 TGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-CTAAATCCGAGT
*
41286660 TAAATTCCGAAGG
126 TAAATCCCGAAGG
41286673 TACGTGATTT
Statistics
Matches: 118, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
158 3 0.03
159 84 0.71
160 31 0.26
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (159 bp):
CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTTG
TGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAAATCCGAGTTAAAT
CCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:41288524 original size:16 final size:16
Alignment explanation
Indices: 41288475--41288530 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
41288465 TACTATATGG
*
41288475 TTTTTTTTAAATG-TG
1 TTTTTTTTAAATGATA
* * *
41288490 TTTTTTTTAATTTAAA
1 TTTTTTTTAAATGATA
41288506 TTTTTTTTAAATGATA
1 TTTTTTTTAAATGATA
41288522 TTTTATTTT
1 TTTT-TTTT
41288531 GGGTGGCTCC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
15 11 0.34
16 17 0.53
17 4 0.12
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTTTTTTAAATGATA
Found at i:41295440 original size:13 final size:14
Alignment explanation
Indices: 41295406--41295433 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41295396 TAATCTGTTT
41295406 CCGCAAGAGGGATC
1 CCGCAAGAGGGATC
41295420 CCGCAAGAGGGATC
1 CCGCAAGAGGGATC
41295434 TGCAAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.36, T:0.07
Consensus pattern (14 bp):
CCGCAAGAGGGATC
Found at i:41298947 original size:39 final size:40
Alignment explanation
Indices: 41298902--41299086 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
41298892 GCTCCTCGTT
* * *
41298902 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
41298942 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
41298981 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
41299021 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
41299062 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
41299087 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:41299002 original size:40 final size:39
Alignment explanation
Indices: 41298869--41299086 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
41298859 AAATCACGTA
* * **
41298869 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
41298908 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
41298947 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
41298987 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
41299027 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
41299067 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
41299087 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:41305574 original size:40 final size:39
Alignment explanation
Indices: 41305476--41305738 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
41305466 TCCTCGTTCA
* * * *
41305476 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
41305515 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
41305554 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
41305594 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
41305634 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
41305674 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
41305715 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41305739 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:41305698 original size:120 final size:119
Alignment explanation
Indices: 41305476--41305738 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
41305466 TCCTCGTTCA
* * *
41305476 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
41305541 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
41305594 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
41305659 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
41305715 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41305739 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:41305747 original size:41 final size:41
Alignment explanation
Indices: 41305670--41305747 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41305660 TTTGTATCTC
* * *
41305670 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41305711 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41305748 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41307371 original size:22 final size:22
Alignment explanation
Indices: 41307346--41307390 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
41307336 TTTGTATCGA
41307346 GGTAAGTACATGTGTAAATAAT
1 GGTAAGTACATGTGTAAATAAT
41307368 GGTAAGTACATGTGTAAATAAT
1 GGTAAGTACATGTGTAAATAAT
41307390 G
1 G
41307391 CGACAATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.31
Consensus pattern (22 bp):
GGTAAGTACATGTGTAAATAAT
Found at i:41308335 original size:30 final size:32
Alignment explanation
Indices: 41308301--41308368 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 32
41308291 GCACAAGAGA
* * *
41308301 AAATATTCAAAATTTTAGAGG-TTAA-AGTGT
1 AAATATTCAAAAATTTAAAGGACTAATAGTGT
*
41308331 AAATA-TGAAAAATTTAAAGGACTAATAGTGT
1 AAATATTCAAAAATTTAAAGGACTAATAGTGT
41308362 AAATATT
1 AAATATT
41308369 TTAAGGGTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 12 0.39
30 8 0.26
31 10 0.32
32 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.34
Consensus pattern (32 bp):
AAATATTCAAAAATTTAAAGGACTAATAGTGT
Found at i:41308615 original size:24 final size:25
Alignment explanation
Indices: 41308586--41308649 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 25
41308576 ATATTTTATA
41308586 ATTATTTAATTAGATAAATATTATTTT
1 ATTATTTAATTAGAT-AATA-TATTTT
*
41308613 ATTA-ATATATTA-ATAATATATTTT
1 ATTATTTA-ATTAGATAATATATTTT
*
41308637 ATTATTTTATTAG
1 ATTATTTAATTAG
41308650 TATATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
24 14 0.45
25 5 0.16
26 4 0.13
27 8 0.26
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
ATTATTTAATTAGATAATATATTTT
Found at i:41310578 original size:46 final size:46
Alignment explanation
Indices: 41310533--41310886 Score: 471
Period size: 46 Copynumber: 7.7 Consensus size: 46
41310523 ATAAAATGTG
* * * **
41310533 TAAGACCATAGTTGAAAGATACCATGGCAATATGATATGAAATGTG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
*
41310579 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
* * **
41310625 TAAGACCATGGTTAAAAGATACCATGTCAACATGACGGGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
* *
41310671 TAAGACCATGGTTGAAAGATACCATGACAACGTGACATGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
* *
41310717 TAAGA-C-TGGTTGAAAAATACCATGGCAACATGACAGGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
* ** *
41310761 TAAGACCATGGTTGAAAGATATCATGGCAATGTGATATGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
*
41310807 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAA
* * * *
41310853 TAAGACCATAGTTGAAAGACACTATGGCATCATG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATG
41310887 TCGAAGATAA
Statistics
Matches: 270, Mismatches: 35, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
44 39 0.14
45 3 0.01
46 228 0.84
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAA
Found at i:41310777 original size:21 final size:21
Alignment explanation
Indices: 41310753--41310823 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
41310743 AACATGACAG
41310753 GAAATGAATAAGACCATGGTT
1 GAAATGAATAAGACCATGGTT
* * *
41310774 GAAA-GATATCATGGCAATGTGATAT
1 GAAATGA-AT-AAGACCATG-G-T-T
41310799 GAAATGAATAAGACCATGGTT
1 GAAATGAATAAGACCATGGTT
41310820 GAAA
1 GAAA
41310824 GATACCATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
20 2 0.05
21 11 0.29
22 7 0.18
23 2 0.05
24 7 0.18
25 7 0.18
26 2 0.05
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (21 bp):
GAAATGAATAAGACCATGGTT
Found at i:41310859 original size:182 final size:182
Alignment explanation
Indices: 41310543--41310871 Score: 523
Period size: 182 Copynumber: 1.8 Consensus size: 182
41310533 TAAGACCATA
* * * * **
41310543 GTTGAAAGATACCATGGCAATATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
1 GTTGAAAAATACCATGGCAACATGACAGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCA
* * *
41310608 ACGTGACATGAAATGAATAAGACCATGGTTAAAAGATACCATGTCAACATGACGGGAAATGAATA
66 ACGTGACATGAAATGAATAAGACCATGGTTAAAAGATACCATGGCAACATGACAGAAAATGAATA
*
41310673 AGACCATGGTTGAAAGATACCATGACAACGTGACATGAAATGAATAAGACTG
131 AGACCATAGTTGAAAGATACCATGACAACGTGACATGAAATGAATAAGACTG
*
41310725 GTTGAAAAATACCATGGCAACATGACAGGAAATGAATAAGACCATGGTTGAAAGATATCATGGCA
1 GTTGAAAAATACCATGGCAACATGACAGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCA
* * * *
41310790 ATGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTA
66 ACGTGACATGAAATGAATAAGACCATGGTTAAAAGATACCATGGCAACATGACAGAAAATGAATA
41310855 AGACCATAGTTGAAAGA
131 AGACCATAGTTGAAAGA
41310872 CACTATGGCA
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
182 132 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (182 bp):
GTTGAAAAATACCATGGCAACATGACAGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCA
ACGTGACATGAAATGAATAAGACCATGGTTAAAAGATACCATGGCAACATGACAGAAAATGAATA
AGACCATAGTTGAAAGATACCATGACAACGTGACATGAAATGAATAAGACTG
Found at i:41324983 original size:16 final size:16
Alignment explanation
Indices: 41324964--41324998 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41324954 CATATAATAA
*
41324964 ATTATATTAATAATTT
1 ATTATATTAATAAATT
*
41324980 ATTATTTTAATAAATT
1 ATTATATTAATAAATT
41324996 ATT
1 ATT
41324999 TAATGTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATATTAATAAATT
Found at i:41325059 original size:16 final size:15
Alignment explanation
Indices: 41325014--41325059 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 15
41325004 TTTTAATTTT
*
41325014 ATTTTAATAATAA--
1 ATTTTAAAAATAATC
41325027 ATTTTAAAAATAATC
1 ATTTTAAAAATAATC
*
41325042 ATTTTAAATAATATTC
1 ATTTTAAA-AATAATC
41325058 AT
1 AT
41325060 CACATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 12 0.43
15 8 0.29
16 8 0.29
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTTTAAAAATAATC
Found at i:41325105 original size:15 final size:15
Alignment explanation
Indices: 41325087--41325144 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
41325077 TTTCAATACT
41325087 AATATTTTAATAATA
1 AATATTTTAATAATA
*
41325102 AATATTCGTTAAAATTATA
1 AATATT--TT--AATAATA
*
41325121 AATATATTAATAATA
1 AATATTTTAATAATA
*
41325136 AATGTTTTA
1 AATATTTTA
41325145 TAGTATAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 19 0.56
17 4 0.12
19 11 0.32
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:41334108 original size:25 final size:23
Alignment explanation
Indices: 41334078--41334142 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
41334068 AAATAAAAAT
*
41334078 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
41334103 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
*
41334124 -TTAAAACA-AGAAACAAATA
1 TTTAAAACATAAAAACAAATA
41334143 AAAAAATAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 5 0.14
24 3 0.08
25 11 0.30
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.25
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:41334139 original size:19 final size:20
Alignment explanation
Indices: 41334104--41334142 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
41334094 TCAAATACAT
41334104 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
*
41334124 TTAAAACA-AGAAACAAATA
1 TTAAAACATAAAAACAAATA
41334143 AAAAAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.69, C:0.10, G:0.03, T:0.18
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:41334148 original size:19 final size:19
Alignment explanation
Indices: 41334115--41334153 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41334105 TAAAACATAA
**
41334115 AAACAAATATTAAAACAAG
1 AAACAAATAAAAAAACAAG
*
41334134 AAACAAATAAAAAAATAAG
1 AAACAAATAAAAAAACAAG
41334153 A
1 A
41334154 CTAAAATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (19 bp):
AAACAAATAAAAAAACAAG
Found at i:41334757 original size:11 final size:11
Alignment explanation
Indices: 41334741--41334772 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
41334731 AATAACAATG
41334741 AATTTTTTTAA
1 AATTTTTTTAA
41334752 AATTTTTTTAA
1 AATTTTTTTAA
*
41334763 AATCTTTTTA
1 AATTTTTTTA
41334773 GTGATATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
AATTTTTTTAA
Found at i:41342158 original size:19 final size:19
Alignment explanation
Indices: 41342134--41342170 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41342124 ATAATTTGAT
41342134 AAGTTAAAATTTTGAACTA
1 AAGTTAAAATTTTGAACTA
*
41342153 AAGTTAAAATTTTTAACT
1 AAGTTAAAATTTTGAACT
41342171 TTTCTCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
AAGTTAAAATTTTGAACTA
Found at i:41343218 original size:10 final size:10
Alignment explanation
Indices: 41343203--41343230 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41343193 TCAATCTCGA
41343203 TTTCTTTTTT
1 TTTCTTTTTT
41343213 TTTCTTTTTT
1 TTTCTTTTTT
41343223 TTTCTTTT
1 TTTCTTTT
41343231 CATATTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:41348121 original size:22 final size:22
Alignment explanation
Indices: 41348087--41348137 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
41348077 TTTTAATAAA
41348087 AAAACTATCTACAAAATATTCCT
1 AAAA-TATCTACAAAATATTCCT
* *
41348110 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
41348132 ACAAAT
1 A-AAAT
41348138 TGTGTTCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:41356784 original size:20 final size:21
Alignment explanation
Indices: 41356759--41356798 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41356749 ATGTTTATAT
*
41356759 TTTTTTTA-TTAATTTAACCC
1 TTTTTTTACTAAATTTAACCC
41356779 TTTTTTTACTAAATTTAACC
1 TTTTTTTACTAAATTTAACC
41356799 TGCAACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTTTACTAAATTTAACCC
Found at i:41358388 original size:29 final size:29
Alignment explanation
Indices: 41358346--41358411 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
41358336 AAAAAATCAC
41358346 TTGAGCCACTACACTAAATCTGCACCCAA
1 TTGAGCCACTACACTAAATCTGCACCCAA
* *
41358375 TTGAGCTC-CTACACTAAATTTGCACCTAA
1 TTGAGC-CACTACACTAAATCTGCACCCAA
41358404 TTGAGCCA
1 TTGAGCCA
41358412 TTATCATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 1 0.03
29 31 0.94
30 1 0.03
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.26
Consensus pattern (29 bp):
TTGAGCCACTACACTAAATCTGCACCCAA
Found at i:41358645 original size:50 final size:48
Alignment explanation
Indices: 41358564--41358712 Score: 122
Period size: 50 Copynumber: 3.0 Consensus size: 48
41358554 TAAAAAATAC
* * *
41358564 AAAAATAT-AATAATAATAATAACATTA-AAAATTTTAAAAATTTAAAAT
1 AAAAATATAAAT-ATTATAAAAAC-TTATAAAATTCTAAAAATTTAAAAT
* * ** * *
41358612 AAAAATATTAAAATTTTATATAAACTTATAAAATAGTAAAAATTCATAAT
1 AAAAATA-T-AAATATTATAAAAACTTATAAAATTCTAAAAATTTAAAAT
*
41358662 AAAATTATAAATATTATAAAAACTTATATAATATTCTAATAAATTATAAAA
1 AAAAATATAAATATTATAAAAACTTATA-AA-ATTCTAA-AAATT-TAAAA
41358713 ATATTTAAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 12
0.74 0.14 0.11
Matches are distributed among these distances:
48 25 0.32
49 7 0.09
50 35 0.45
51 8 0.10
52 3 0.04
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (48 bp):
AAAAATATAAATATTATAAAAACTTATAAAATTCTAAAAATTTAAAAT
Found at i:41358651 original size:28 final size:29
Alignment explanation
Indices: 41358606--41358672 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
41358596 TTTAAAAATT
* * *
41358606 TAAAA-TA-AAAATATTAAAATTTTAT-A
1 TAAAATTATAAAATAGTAAAAATTCATAA
*
41358632 TAAACTTATAAAATAGTAAAAATTCATAA
1 TAAAATTATAAAATAGTAAAAATTCATAA
41358661 TAAAATTATAAA
1 TAAAATTATAAA
41358673 TATTATAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.12
27 2 0.06
28 15 0.45
29 12 0.36
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (29 bp):
TAAAATTATAAAATAGTAAAAATTCATAA
Found at i:41358653 original size:29 final size:28
Alignment explanation
Indices: 41358606--41358683 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 28
41358596 TTTAAAAATT
* *
41358606 TAAAA-TA-AAAATATTAAAATT-TTATA
1 TAAAATTATAAAATATAAAAATTCATA-A
*
41358632 TAAACTTATAAAATAGTAAAAATTCATAA
1 TAAAATTATAAAATA-TAAAAATTCATAA
41358661 TAAAATTATAAATATTATAAAAA
1 TAAAATTATAAA-A-TATAAAAA
41358684 CTTATATAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 4 0.10
27 2 0.05
28 6 0.14
29 19 0.45
30 9 0.21
31 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (28 bp):
TAAAATTATAAAATATAAAAATTCATAA
Found at i:41358672 original size:21 final size:21
Alignment explanation
Indices: 41358639--41358714 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 21
41358629 ATATAAACTT
41358639 ATAAAA-TAGTAAAAATTCATA
1 ATAAAATTA-TAAAAATTCATA
*
41358660 ATAAAATTATAAATATT-ATA
1 ATAAAATTATAAAAATTCATA
* *
41358680 A-AAACTTATATAATATTC-TA
1 ATAAAATTATA-AAAATTCATA
41358700 AT-AAATTATAAAAAT
1 ATAAAATTATAAAAAT
41358715 ATTTAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
19 12 0.26
20 20 0.43
21 13 0.28
22 2 0.04
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (21 bp):
ATAAAATTATAAAAATTCATA
Found at i:41358692 original size:29 final size:27
Alignment explanation
Indices: 41358627--41358730 Score: 79
Period size: 29 Copynumber: 3.7 Consensus size: 27
41358617 TATTAAAATT
*
41358627 TTATATAAACTTATAAAA-TAGTAAAAA
1 TTATATAAAATTATAAAATTA-TAAAAA
41358654 TTCATAATAAAATTATAAATATTATAAAAA
1 TT-AT-ATAAAATTATAAA-ATTATAAAAA
* *
41358684 CTTATATAATATTCTAATAAATTATAAAAA
1 -TTATATAAAATTAT-A-AAATTATAAAAA
* *
41358714 -TATTTAAAA-AATAAAAT
1 TTATATAAAATTATAAAAT
41358731 CTTTCAAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
25 4 0.06
26 1 0.02
27 3 0.05
28 9 0.14
29 20 0.32
30 20 0.32
31 6 0.10
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.37
Consensus pattern (27 bp):
TTATATAAAATTATAAAATTATAAAAA
Found at i:41358694 original size:20 final size:17
Alignment explanation
Indices: 41358662--41358741 Score: 63
Period size: 20 Copynumber: 4.3 Consensus size: 17
41358652 AATTCATAAT
41358662 AAAATTATAAATATTATA
1 AAAATTATAAATATT-TA
41358680 AAAACTTATATAATATTCTA
1 AAAA-TTATA-AATATT-TA
41358700 ATAAATTATAAAAATATTTA
1 A-AAATTAT--AAATATTTA
* *
41358720 AAAAATA-AAATCTTTCA
1 AAAATTATAAATATTT-A
41358737 AAAAT
1 AAAAT
41358742 ATTTTAAACT
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
16 7 0.13
17 5 0.10
18 4 0.08
19 10 0.19
20 16 0.31
21 9 0.17
22 1 0.02
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATTATAAATATTTA
Found at i:41358808 original size:29 final size:28
Alignment explanation
Indices: 41358775--41358839 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
41358765 AAAAATTATT
*
41358775 AAAAATTATA-AATAATTATAAAACTTCCA
1 AAAAATTATAGAA-AATTATAAAA-ATCCA
* *
41358804 AAAAATCATAGAAACTTATAAAAATCCA
1 AAAAATTATAGAAAATTATAAAAATCCA
41358832 AAACAATT
1 AAA-AATT
41358840 TGTAATAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 7 0.23
29 21 0.70
30 2 0.07
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (28 bp):
AAAAATTATAGAAAATTATAAAAATCCA
Found at i:41358826 original size:20 final size:19
Alignment explanation
Indices: 41358763--41358827 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
41358753 GCTATGAACT
* *
41358763 TAAAAAATTATTAAAAATTA
1 TAAAAAATCA-TAAAACTTA
* * *
41358783 TAAATAATTATAAAACTTC
1 TAAAAAATCATAAAACTTA
*
41358802 CAAAAAATCATAGAAACTTA
1 TAAAAAATCATA-AAACTTA
41358822 TAAAAA
1 TAAAAA
41358828 TCCAAAACAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
19 16 0.44
20 20 0.56
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.29
Consensus pattern (19 bp):
TAAAAAATCATAAAACTTA
Found at i:41362204 original size:19 final size:19
Alignment explanation
Indices: 41362182--41362231 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
41362172 TTTAAACTTT
*
41362182 TTTTTTTATAATTTCTAAC
1 TTTTTTTATAATTTATAAC
* * *
41362201 TTTTTATATTATTTATAAG
1 TTTTTTTATAATTTATAAC
41362220 TTTTATTTATAA
1 TTTT-TTTATAA
41362232 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTTTATAATTTATAAC
Found at i:41362910 original size:15 final size:15
Alignment explanation
Indices: 41362890--41362919 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41362880 TTTTACCGAC
41362890 GAAGAAGAGGAGGAA
1 GAAGAAGAGGAGGAA
41362905 GAAGAAGAGGAGGAA
1 GAAGAAGAGGAGGAA
41362920 TGATGGCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (15 bp):
GAAGAAGAGGAGGAA
Found at i:41365871 original size:23 final size:23
Alignment explanation
Indices: 41365834--41365879 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
41365824 ATGGTCAAGG
* *
41365834 TGTTCATTGCTCATGTGGTTTGA
1 TGTTCACTGCCCATGTGGTTTGA
41365857 TGTTCACTGCCCATGTGGTTTGA
1 TGTTCACTGCCCATGTGGTTTGA
41365880 ATTCGAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.17, G:0.26, T:0.43
Consensus pattern (23 bp):
TGTTCACTGCCCATGTGGTTTGA
Found at i:41365959 original size:18 final size:18
Alignment explanation
Indices: 41365936--41365970 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41365926 TTGTAATTCA
41365936 TAAAAAAAAATTATAAAT
1 TAAAAAAAAATTATAAAT
**
41365954 TAAAAAATGATTATAAA
1 TAAAAAAAAATTATAAA
41365971 AGGAAGATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAAAAAAATTATAAAT
Found at i:41366041 original size:19 final size:18
Alignment explanation
Indices: 41366014--41366061 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
41366004 ATATTACTAG
*
41366014 ATTTGTAAAAGTTATAAAT
1 ATTTTTAAAAGTTA-AAAT
41366033 ATTTTTAAAAAAGTTAAAAT
1 ATTTTT--AAAAGTTAAAAT
41366053 ATTTTTAAA
1 ATTTTTAAA
41366062 TTGATAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.12
19 5 0.19
20 10 0.38
21 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTTTAAAAGTTAAAAT
Found at i:41366052 original size:20 final size:21
Alignment explanation
Indices: 41366020--41366061 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
41366010 CTAGATTTGT
41366020 AAAAGTTATAAATATTTTTAA
1 AAAAGTTATAAATATTTTTAA
41366041 AAAAGTTA-AAATATTTTTAA
1 AAAAGTTATAAATATTTTTAA
41366061 A
1 A
41366062 TTGATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAAGTTATAAATATTTTTAA
Found at i:41379287 original size:15 final size:15
Alignment explanation
Indices: 41379237--41379288 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
41379227 CTTAAAAAAC
*
41379237 ATTTATATTTTTTTA
1 ATTTATATATTTTTA
*
41379252 ATTTA-ATATTTAATA
1 ATTTATATATTT-TTA
*
41379267 ATTTTATATATTTTTC
1 A-TTTATATATTTTTA
41379283 ATTTAT
1 ATTTAT
41379289 TAAAACTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.17
15 13 0.43
16 6 0.20
17 6 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTATATATTTTTA
Found at i:41399654 original size:47 final size:47
Alignment explanation
Indices: 41399594--41399684 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
41399584 TCTAGCTCAG
* *
41399594 GTATTGAAGAGAGATAACAGGTCAAGGCCGTGACATTTGATATTGAA
1 GTATTGAAAAGAGATAACAGGTCAAGGCCATGACATTTGATATTGAA
41399641 GTATTGAAAAGAGATAACAGGTCAAGGCCATGACATTTGATATT
1 GTATTGAAAAGAGATAACAGGTCAAGGCCATGACATTTGATATT
41399685 TTCAACTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.26
Consensus pattern (47 bp):
GTATTGAAAAGAGATAACAGGTCAAGGCCATGACATTTGATATTGAA
Found at i:41400249 original size:27 final size:28
Alignment explanation
Indices: 41400212--41400264 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
41400202 AAATTAAAAT
*
41400212 ATTTTTGAAAGGTTGATGGTTAAATTCA
1 ATTTTTGAAAGGTTGATGGTCAAATTCA
41400240 ATTTTT-AAAGGTTGATGGTCAAATT
1 ATTTTTGAAAGGTTGATGGTCAAATT
41400265 TAACTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (28 bp):
ATTTTTGAAAGGTTGATGGTCAAATTCA
Found at i:41403295 original size:79 final size:81
Alignment explanation
Indices: 41403186--41403368 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
41403176 TACTCGTTCA
* *
41403186 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
41403249 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
41403266 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
41403329 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
41403345 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41403369 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:41403368 original size:40 final size:40
Alignment explanation
Indices: 41403165--41403368 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
41403155 CGGAATTTAA
** *
41403165 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41403205 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41403245 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
41403284 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
41403324 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
41403364 CCGGA
1 CCGGA
41403369 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:41404565 original size:56 final size:56
Alignment explanation
Indices: 41404498--41404617 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
41404488 TATTAGTTTA
41404498 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
41404554 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
41404610 TTGCCCAT
1 TTGCCCAT
41404618 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Done.