Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 126 of 349
Found at i:40172570 original size:14 final size:14
Alignment explanation
Indices: 40172551--40172584 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
40172541 GTGTAAATAT
40172551 GCAAAAGTTTAGGG
1 GCAAAAGTTTAGGG
40172565 GCAAAAGTTTAGGG
1 GCAAAAGTTTAGGG
40172579 GCAAAA
1 GCAAAA
40172585 TCATAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.32, T:0.18
Consensus pattern (14 bp):
GCAAAAGTTTAGGG
Found at i:40174181 original size:198 final size:198
Alignment explanation
Indices: 40173843--40174234 Score: 703
Period size: 198 Copynumber: 2.0 Consensus size: 198
40173833 CCCCTGTTCC
*
40173843 AAATTTGGAAAATCACTAGAAATTTTAAAAAAAGAATTATAAGTCAAAGTTTATATTTATAGATT
1 AAATTTGGAAAATCACTAGAAATTGTAAAAAAAGAATTATAAGTCAAAGTTTATATTTATAGATT
* *
40173908 CCTTAGTGAGTATATTTTCATTAGAAACAAACAGAAACATTATCTGATTTTTGCATAATGAGATA
66 CCTTAGTGAGTATATTTTCATTAGAAACAAACAGAAACATTATCCGATTTCTGCATAATGAGATA
* *
40173973 ATTTATTTTTAGTGAAGAGAGGTTAGGTCTGCTGAACTGTGAAACAGAGGAATCTTTAATGAATT
131 ATTTATTTTTAGTGAAGAGAGGTTAGGTATGCTGAACTGTGAAACAGAGGAACCTTTAATGAATT
40174038 TCA
196 TCA
40174041 AAATTTGGAAAATCACTAGAAATTGTAAAAAAAGAATTATAAGTCAAAGTTTATATTTATAGATT
1 AAATTTGGAAAATCACTAGAAATTGTAAAAAAAGAATTATAAGTCAAAGTTTATATTTATAGATT
* *
40174106 CCTTAGTGAGTCTATTTTCATTAGAAATAAACAGAAACATTATCCGATTTCTGCATAATGAGATA
66 CCTTAGTGAGTATATTTTCATTAGAAACAAACAGAAACATTATCCGATTTCTGCATAATGAGATA
* *
40174171 ATTTATTTTTAGTGAAGAGAGGTTAGGTATGTTGAACTGTGAAACAGGGGAACCTTTAATGAAT
131 ATTTATTTTTAGTGAAGAGAGGTTAGGTATGCTGAACTGTGAAACAGAGGAACCTTTAATGAAT
40174235 AAACTGTACT
Statistics
Matches: 185, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
198 185 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.35
Consensus pattern (198 bp):
AAATTTGGAAAATCACTAGAAATTGTAAAAAAAGAATTATAAGTCAAAGTTTATATTTATAGATT
CCTTAGTGAGTATATTTTCATTAGAAACAAACAGAAACATTATCCGATTTCTGCATAATGAGATA
ATTTATTTTTAGTGAAGAGAGGTTAGGTATGCTGAACTGTGAAACAGAGGAACCTTTAATGAATT
TCA
Found at i:40175968 original size:11 final size:10
Alignment explanation
Indices: 40175954--40176001 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
40175944 AAACAACAAG
40175954 AAAATAGTAA
1 AAAATAGTAA
*
40175964 CAAAACAGTAA
1 -AAAATAGTAA
* *
40175975 AAAACAGCAA
1 AAAATAGTAA
40175985 TAAAATAGTAA
1 -AAAATAGTAA
40175996 AAAATA
1 AAAATA
40176002 TTTTTTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 15 0.47
11 17 0.53
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (10 bp):
AAAATAGTAA
Found at i:40179274 original size:41 final size:41
Alignment explanation
Indices: 40179217--40179295 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
40179207 TCTTACACTT
*
40179217 CATACTTATGCTAAGGTCTATCCATAGACTAATTTAGTTAC
1 CATACTAATGCTAAGGTCTATCCATAGACTAATTTAGTTAC
40179258 CATACTAATGCTAAGGTCTATCCATAGACTAATTTAGT
1 CATACTAATGCTAAGGTCTATCCATAGACTAATTTAGT
40179296 CACTTTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (41 bp):
CATACTAATGCTAAGGTCTATCCATAGACTAATTTAGTTAC
Found at i:40179282 original size:22 final size:22
Alignment explanation
Indices: 40179217--40179283 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
40179207 TCTTACACTT
*
40179217 CATACTTATGCTAAGGTCTATC
1 CATACTAATGCTAAGGTCTATC
*
40179239 CATAGACTAAT--TTA-GT-TA-C
1 CAT--ACTAATGCTAAGGTCTATC
40179258 CATACTAATGCTAAGGTCTATC
1 CATACTAATGCTAAGGTCTATC
40179280 CATA
1 CATA
40179284 GACTAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
17 6 0.17
19 6 0.17
20 4 0.11
21 4 0.11
22 10 0.29
24 5 0.14
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (22 bp):
CATACTAATGCTAAGGTCTATC
Found at i:40180757 original size:48 final size:48
Alignment explanation
Indices: 40180680--40180817 Score: 179
Period size: 48 Copynumber: 2.9 Consensus size: 48
40180670 GGGTAAAATA
* * * ***
40180680 CGATGTCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCAT-ATCAACGC
*
40180728 TGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATATCAACGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATATCAACGC
* *
40180776 CGATGCCATGTCCCAGACATTGTCTTACACTAGCACACATAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATAT
40180818 AAACCAAATG
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 2 0.03
48 77 0.97
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATATCAACGC
Found at i:40183346 original size:68 final size:67
Alignment explanation
Indices: 40183274--40183423 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
40183264 CATCATGTGT
* * * *
40183274 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
40183336 ATGTAG
62 ATGTAG
** * *
40183342 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
40183407 AG
66 AG
40183409 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
40183424 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:40183379 original size:64 final size:64
Alignment explanation
Indices: 40183298--40183481 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
40183288 AGACATTATG
* *
40183298 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
40183362 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
40183427 AA
63 AA
* * * *
40183429 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
40183482 CAACTATATG
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:40190953 original size:144 final size:145
Alignment explanation
Indices: 40190691--40190958 Score: 418
Period size: 144 Copynumber: 1.8 Consensus size: 145
40190681 AATGCCGATA
*
40190691 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATACATCGGTGCCGATGCCATATCCTAGACAT
1 CCATGTCCCAGACATGGTCTTACACCGGCTCTCATACATCGGTGCCGATGCCATATCCTAGACAT
* *
40190756 GGTCTTACACTGACACATATAACAATGCCGATGCCATGTTCCAAACATAGTCTTACACTGGCTCA
66 GGTCTTACACTGACACATAT-ACAACGCCGATGCCATGTCCCAAACATAGTCTTACACTGGCTCA
40190821 CATATTGAGGCCAATG
130 CATATTGAGGCCAATG
* *
40190837 CCATGTCCCAGACATGGTCTTACACCGGTTCTCATA-AT-GAG-GCCGATGCCATGTCCTAGACA
1 CCATGTCCCAGACATGGTCTTACACCGGCTCTCATACATCG-GTGCCGATGCCATATCCTAGACA
*
40190899 TGGTCTTACACTAGCACACATAT-CAACGCCGATGCCATGTCCCAAACATGGTCTTACACT
65 TGGTCTTACACT-G-ACACATATACAACGCCGATGCCATGTCCCAAACATAGTCTTACACT
40190959 AGAACACATA
Statistics
Matches: 113, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
144 67 0.59
145 4 0.04
146 42 0.37
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (145 bp):
CCATGTCCCAGACATGGTCTTACACCGGCTCTCATACATCGGTGCCGATGCCATATCCTAGACAT
GGTCTTACACTGACACATATACAACGCCGATGCCATGTCCCAAACATAGTCTTACACTGGCTCAC
ATATTGAGGCCAATG
Found at i:40190970 original size:48 final size:48
Alignment explanation
Indices: 40190684--40190973 Score: 269
Period size: 48 Copynumber: 6.0 Consensus size: 48
40190674 AGGGTAAAAT
* * * *
40190684 GCCGATACCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-CATC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAC
* * * * * *
40190731 GGTGCCGATGCCATATCCTAGACATGGTCTTACACTGACACATATAACAAT
1 ---GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAC
* * * * ** *
40190782 GCCGATGCCATGTTCCAAACATAGTCTTACACTGGCTCACATATTGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAC
* * ** * * *
40190830 GCCAATGCCATGTCCCAGACATGGTCTTACACCGGTTCTCATAAT-GAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACAT-ATCAAC
* *
40190878 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCACACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAC
* * *
40190926 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGAACACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAC
40190974 CAAATGTCTT
Statistics
Matches: 197, Mismatches: 40, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
47 2 0.01
48 155 0.79
49 2 0.01
50 36 0.18
51 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAC
Found at i:40193745 original size:15 final size:15
Alignment explanation
Indices: 40193704--40193746 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
40193694 CTTGTTTAAA
* *
40193704 TTTTTGTATATTTAT
1 TTTTTATATTTTTAT
40193719 TTTTTATAATTTTTAT
1 TTTTTAT-ATTTTTAT
40193735 TTTTTATATTTT
1 TTTTTATATTTT
40193747 AAATAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTTATATTTTTAT
Found at i:40193746 original size:14 final size:14
Alignment explanation
Indices: 40193703--40193747 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
40193693 ACTTGTTTAA
40193703 ATTTTTGTATA-TTT
1 ATTTTT-TATATTTT
40193717 ATTTTTTATAATTTTT
1 ATTTTTTAT-A-TTTT
40193733 ATTTTTTATATTTT
1 ATTTTTTATATTTT
40193747 A
1 A
40193748 AATAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.11
14 12 0.43
15 1 0.04
16 12 0.43
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (14 bp):
ATTTTTTATATTTT
Found at i:40195638 original size:25 final size:24
Alignment explanation
Indices: 40195568--40195638 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
40195558 TATTGCTCTT
* * *
40195568 ATGAGCTTCCCGTTATATAGCCTAG
1 ATGAGCTT-CCGTTATATGGCTTAC
* *
40195593 ATGTGCTTCCGTTACATGGCTTAC
1 ATGAGCTTCCGTTATATGGCTTAC
*
40195617 ATGAGCTTCCTATTATATGGCT
1 ATGAGCTTCC-GTTATATGGCT
40195639 CGAGAGAGGG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 21 0.57
25 16 0.43
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.37
Consensus pattern (24 bp):
ATGAGCTTCCGTTATATGGCTTAC
Found at i:40207402 original size:55 final size:53
Alignment explanation
Indices: 40207311--40207500 Score: 183
Period size: 53 Copynumber: 3.6 Consensus size: 53
40207301 ATTAGGGTTT
* * *
40207311 AAGGATACCATGTAAGACTATGTCAAGACATGGCATTGATAAGTTTCTATACGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAG-TTC-ATAAGGC
* * * *
40207366 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGC
** * * * *
40207419 AAGGATACCATGTAAGACCATATCGAGACATGGCAATGGTAAGTT-TTAA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGC
* *
40207468 AAGGATACCACGTAAGACCATGTCAAGACATGG
1 AAGGATACCATGTAAGACCATGCCAAGACATGG
40207501 AAATGGTAAG
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
49 30 0.26
52 7 0.06
53 39 0.34
54 3 0.03
55 32 0.28
56 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCATAAGGC
Found at i:40207438 original size:53 final size:53
Alignment explanation
Indices: 40207311--40207510 Score: 212
Period size: 49 Copynumber: 3.8 Consensus size: 53
40207301 ATTAGGGTTT
* * *
40207311 AAGGATACCATGTAAGACTATGTCAAGACATGGCATTGATAAGTTTCTATACGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAG-TTC-ATAAGGC
* * * *
40207366 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGC
* * * *
40207419 AAGGATACCATGTAAGACCATATCGAGACATGGCAATGGTAAGTT-TTAA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGC
* * *
40207468 AAGGATACCACGTAAGACCATGTCAAGACATGGAAATGGTAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAG
40207511 GTACCCGTGT
Statistics
Matches: 124, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
49 39 0.31
52 7 0.06
53 39 0.31
54 3 0.02
55 32 0.26
56 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:40207722 original size:16 final size:16
Alignment explanation
Indices: 40207701--40207731 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40207691 ATAAATTTGA
40207701 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
40207717 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
40207732 AGTGCAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:40207821 original size:14 final size:14
Alignment explanation
Indices: 40207802--40207829 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40207792 CCAAGTAGTA
40207802 AGATAATTCTTATG
1 AGATAATTCTTATG
40207816 AGATAATTCTTATG
1 AGATAATTCTTATG
40207830 GATGTTGTTA
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:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
AGATAATTCTTATG
Found at i:40211378 original size:27 final size:27
Alignment explanation
Indices: 40211340--40211397 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
40211330 AACACTAGTC
40211340 TAGCCTTATCAGATGATGGATTTATCT
1 TAGCCTTATCAGATGATGGATTTATCT
40211367 TAGCCTTATCAGATGATGGATTTATCT
1 TAGCCTTATCAGATGATGGATTTATCT
40211394 TAGC
1 TAGC
40211398 TGAGTTGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (27 bp):
TAGCCTTATCAGATGATGGATTTATCT
Found at i:40212645 original size:17 final size:18
Alignment explanation
Indices: 40212619--40212652 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40212609 TTTTTGTTTA
40212619 AATAAATTAATA-GCATT
1 AATAAATTAATATGCATT
*
40212636 AATAATTTAATATGCAT
1 AATAAATTAATATGCAT
40212653 ATATTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAAATTAATATGCATT
Found at i:40224590 original size:7 final size:7
Alignment explanation
Indices: 40224580--40224604 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40224570 TGATGAATGA
40224580 ATGAGGG
1 ATGAGGG
40224587 ATGAGGG
1 ATGAGGG
40224594 ATGAGGG
1 ATGAGGG
40224601 ATGA
1 ATGA
40224605 TTGAAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (7 bp):
ATGAGGG
Found at i:40227552 original size:144 final size:143
Alignment explanation
Indices: 40227288--40227586 Score: 342
Period size: 144 Copynumber: 2.1 Consensus size: 143
40227278 TTTACATGCG
*
40227288 TTATTACATATATACATATACTTTATAATAAAGTTAATTTTATTTCATGCATATTATTAATGTTA
1 TTATTATATATATACATATACTTTATAATAAAGTTAATTTTATTTCATGCATATTATTAATGTTA
* *
40227353 TATTATTTTATACATGTAATTTCCTTTAAATTTATTCTTATATTATATAACATAATCCTACATAA
66 TATTATTTTACACATATAATTTCCTTTAAATTTATTCTTATATTATATAACATAATCCTACATAA
*
40227418 TAAATCTTTTAAA
131 CAAATCTTTTAAA
* *
40227431 TTATTATATATATATATACGTACTTTATAGT-AAGATT-ATTTTA-TTCTATGCATATTATTAAT
1 TTATTATATATATACATA--TACTTTATAATAAAG-TTAATTTTATTTC-ATGCATATTATTAAT
* * * * * * *
40227493 -TCTATATTATTTTACGCATATAGTTTCTTTTAAATTTATTCTCGTCTTTTA-AT-ATATAATCT
62 GT-TATATTATTTTACACATATAATTTCCTTTAAATTTATTCT--TATATTATATAACATAATCC
* * *
40227555 TATATAACATATCTTTTAAT
124 TACATAACAAATCTTTTAAA
40227575 TTATTAT-TATAT
1 TTATTATATATAT
40227587 GTCTTTCATC
Statistics
Matches: 133, Mismatches: 16, Indels: 14
0.82 0.10 0.09
Matches are distributed among these distances:
143 25 0.19
144 89 0.67
145 14 0.11
146 5 0.04
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (143 bp):
TTATTATATATATACATATACTTTATAATAAAGTTAATTTTATTTCATGCATATTATTAATGTTA
TATTATTTTACACATATAATTTCCTTTAAATTTATTCTTATATTATATAACATAATCCTACATAA
CAAATCTTTTAAA
Found at i:40230392 original size:47 final size:47
Alignment explanation
Indices: 40230329--40230632 Score: 437
Period size: 47 Copynumber: 6.4 Consensus size: 47
40230319 CCCTTCGGGA
* * *
40230329 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
40230376 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
40230423 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
40230470 CTTATCACATATATACACTTTCACATTCATCACGTTGGTCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
40230517 CCTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
40230564 CCTATCACATATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
40230613 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
40230633 GTACATCAAT
Statistics
Matches: 238, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
47 193 0.81
49 45 0.19
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
Found at i:40241828 original size:26 final size:26
Alignment explanation
Indices: 40241798--40241879 Score: 164
Period size: 26 Copynumber: 3.2 Consensus size: 26
40241788 TGAAATTCCC
40241798 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40241824 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40241850 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
40241876 ATCA
1 ATCA
40241880 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:40243657 original size:128 final size:128
Alignment explanation
Indices: 40243424--40243657 Score: 308
Period size: 128 Copynumber: 1.8 Consensus size: 128
40243414 AGATGAGATT
* * *
40243424 TGATATTTGACAATTCGCGGAATCTTGCCCTTACATGTTGGGTTGCATTCGCGTTTGCTCAAAAT
1 TGATATTTGACAATTCGCGGAATCCTGCCCTAACATGTTGGGTTGCATTCGCGATTGCTCAAAAT
* * *
40243489 AATCAAATATCACTTCAAAATTTCACTCATGTCTTTTAAAATCCCTTGAACGAAGGTGATACG
66 AATCAAATATCACTTCAAAACTTCACTCATATCTTCTAAAATCCCTTGAACGAAGGTGATACG
* * * * * * *
40243552 TGATATTTGGCAATTTGTGGAATCCTGCCCTAACGTGTTGGGTTGCAATT-TCGATTGTTTAAAA
1 TGATATTTGACAATTCGCGGAATCCTGCCCTAACATGTTGGGTTGC-ATTCGCGATTGCTCAAAA
* * *
40243616 TAATCAAATATCCCTTCAAGACTTCATTCATATCTTCTAAAA
65 TAATCAAATATCACTTCAAAACTTCACTCATATCTTCTAAAA
40243658 ATTATTTAAA
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
128 86 0.97
129 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (128 bp):
TGATATTTGACAATTCGCGGAATCCTGCCCTAACATGTTGGGTTGCATTCGCGATTGCTCAAAAT
AATCAAATATCACTTCAAAACTTCACTCATATCTTCTAAAATCCCTTGAACGAAGGTGATACG
Found at i:40245005 original size:52 final size:52
Alignment explanation
Indices: 40244921--40245067 Score: 222
Period size: 52 Copynumber: 2.8 Consensus size: 52
40244911 TAAGATTTTT
* ** *
40244921 CACACGGCCTGGCACACGGGCGTGTGGTTTGGCTGTGTGACCCCTGTACCTA
1 CACACGGCCTAGCACACGGGCGTGTGACTTGGCCGTGTGACCCCTGTACCTA
*
40244973 CACACGGCCTAGCACATGGGCGTGTGACTTGGCCGTGTGACCCCTGTACCTA
1 CACACGGCCTAGCACACGGGCGTGTGACTTGGCCGTGTGACCCCTGTACCTA
* * *
40245025 CACACGGCCTAGCACACGAGCATGTGACTTGGCCATGTGACCC
1 CACACGGCCTAGCACACGGGCGTGTGACTTGGCCGTGTGACCC
40245068 AAGTCAGATA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 86 1.00
ACGTcount: A:0.18, C:0.33, G:0.29, T:0.20
Consensus pattern (52 bp):
CACACGGCCTAGCACACGGGCGTGTGACTTGGCCGTGTGACCCCTGTACCTA
Found at i:40246942 original size:20 final size:20
Alignment explanation
Indices: 40246905--40246942 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40246895 GCATTACTGT
*
40246905 ATAATTCATAACATTTACAG
1 ATAATTCATAACAATTACAG
*
40246925 ATAATTCATGACAATTAC
1 ATAATTCATAACAATTAC
40246943 TATTCATTTT
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:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
ATAATTCATAACAATTACAG
Found at i:40250267 original size:28 final size:28
Alignment explanation
Indices: 40250216--40250270 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
40250206 ACAGGGGTTT
*
40250216 TCACATGGCTTGACACACGCCCGTGTCTC
1 TCACATGGCATGACACAC-CCCGTGTCTC
40250245 TCACATGGCCATGACACA-CCCGTGTC
1 TCACATGG-CATGACACACCCCGTGTC
40250271 CTAGCCCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 8 0.33
30 8 0.33
ACGTcount: A:0.20, C:0.38, G:0.20, T:0.22
Consensus pattern (28 bp):
TCACATGGCATGACACACCCCGTGTCTC
Found at i:40262936 original size:34 final size:34
Alignment explanation
Indices: 40262893--40262962 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
40262883 AAACACACTT
40262893 TCGGGAATACCGATTGAGTCTTACCAATTTCCGC
1 TCGGGAATACCGATTGAGTCTTACCAATTTCCGC
40262927 TCGGGAATACCGATTGAGTCTTACCAATTTCCGC
1 TCGGGAATACCGATTGAGTCTTACCAATTTCCGC
40262961 TC
1 TC
40262963 ATACTCTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (34 bp):
TCGGGAATACCGATTGAGTCTTACCAATTTCCGC
Found at i:40274794 original size:48 final size:48
Alignment explanation
Indices: 40274723--40275025 Score: 482
Period size: 48 Copynumber: 6.3 Consensus size: 48
40274713 CAAGATAAAT
* * *
40274723 ATATATATGTGTGGTAAAGCCGAATGGCTCGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
40274771 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
40274819 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
40274867 ATTTGTATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
40274915 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
40274963 ATATGTATATTTGGTAAAG-CGAATGGCTAATGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
40275010 ATGTTGTATATTGTGG
1 AT-ATGTATA-TGTGG
40275026 CCGAATGACC
Statistics
Matches: 237, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
47 28 0.12
48 205 0.86
49 4 0.02
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:40275212 original size:36 final size:37
Alignment explanation
Indices: 40275151--40275251 Score: 179
Period size: 37 Copynumber: 2.8 Consensus size: 37
40275141 GGAAATATAT
40275151 TCCGGGTAAGACCC-ATGACTACGTGTGGAGA-TTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
40275186 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
*
40275223 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
40275252 GGACTATTCG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
35 14 0.22
36 17 0.27
37 32 0.51
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:40277094 original size:22 final size:19
Alignment explanation
Indices: 40277055--40277096 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
40277045 TAGAAAGTTG
40277055 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
40277074 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
40277096 A
1 A
40277097 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:40279184 original size:50 final size:49
Alignment explanation
Indices: 40279080--40279400 Score: 274
Period size: 50 Copynumber: 6.7 Consensus size: 49
40279070 TGACATGTGT
* *
40279080 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC-A-TTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCCTCGAGATATGAGA
*
40279126 GCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAGATATGAAA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCCTCGAGATATGAGA
* * * *
40279176 GCTAGTGTAAGACCATGTCTAGGACATGTCATCAG-CT--TGATATGTG-
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GCCTCGAGATATGAGA
* * *
40279222 TC-AGTGTAAGACCATGTCTGGGACATGGCATCGACAC-CGACAGATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCG-C-CTCGAGATATGAGA
* * * *
40279271 GCCAATGTAAGACCATGTCTGGGACATGGCATTGGCCTCGATATATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCA-TCGCCTCGAGATATGAGA
* ** * * *
40279321 G-TCAGTGTAAGACCAAGTCAAGGACAT-GCAATCGACCT--TGATGTGTGA
1 GCT-AGTGTAAGACCATGTCTGGGACATGGC-ATCG-CCTCGAGATATGAGA
*
40279369 GCTAGTGTAAGACCATGTCCGGGACATGGCAT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCAT
40279401 TGGCATCTTA
Statistics
Matches: 223, Mismatches: 34, Indels: 34
0.77 0.12 0.12
Matches are distributed among these distances:
44 1 0.00
45 28 0.13
46 13 0.06
47 21 0.09
48 44 0.20
49 12 0.05
50 102 0.46
51 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (49 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGCCTCGAGATATGAGA
Found at i:40279282 original size:145 final size:145
Alignment explanation
Indices: 40279074--40279400 Score: 416
Period size: 145 Copynumber: 2.3 Consensus size: 145
40279064 TTTGGGTGAC
* * * *
40279074 ATGTGTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGAGCTAGTGTAAG
1 ATGTGT-CTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACATGATGAGAGCCAATGTAAG
* *
40279137 ACCATGTCTGGGACATGGCATCAGCCTCGAGATATGAAAG-CTAGTGTAAGACCATGTCTAGGAC
65 ACCATGTCTGGGACATGGCATCAGCCTCGAGATATGAAAGTC-AGTGTAAGACCAAGTCAAGGAC
*
40279201 ATGTC-ATC-AGCTTGAT
129 ATG-CAATCGACCTTGAT
40279217 ATGTGTC-AGTGTAAGACCATGTCTGGGACATGGCATCGACACCGACA-GATGAGAGCCAATGTA
1 ATGTGTCTAGTGTAAGACCATGTCTGGGACATGGCATCG--ACC-ACATGATGAGAGCCAATGTA
** * *
40279280 AGACCATGTCTGGGACATGGCATTGGCCTCGATATATGAGAGTCAGTGTAAGACCAAGTCAAGGA
63 AGACCATGTCTGGGACATGGCATCAGCCTCGAGATATGAAAGTCAGTGTAAGACCAAGTCAAGGA
40279345 CATGCAATCGACCTTGAT
128 CATGCAATCGACCTTGAT
* * *
40279363 GTGTGAGCTAGTGTAAGACCATGTCCGGGACATGGCAT
1 ATGTG-TCTAGTGTAAGACCATGTCTGGGACATGGCAT
40279401 TGGCATCTTA
Statistics
Matches: 160, Mismatches: 14, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
141 9 0.06
142 15 0.09
143 12 0.08
144 1 0.01
145 79 0.49
146 15 0.09
147 1 0.01
148 28 0.17
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (145 bp):
ATGTGTCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACATGATGAGAGCCAATGTAAGA
CCATGTCTGGGACATGGCATCAGCCTCGAGATATGAAAGTCAGTGTAAGACCAAGTCAAGGACAT
GCAATCGACCTTGAT
Found at i:40284905 original size:24 final size:24
Alignment explanation
Indices: 40284845--40284909 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
40284835 CCGATATATC
*
40284845 AGCTCATAAGAGCTTACTGTTATT
1 AGCTCATTAGAGCTTACTGTTATT
40284869 AGCTCATTAGAGCTTACTGTTATT
1 AGCTCATTAGAGCTTACTGTTATT
* *
40284893 AGCTTATTGGAGCTTAC
1 AGCTCATTAGAGCTTAC
40284910 CATTTCAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (24 bp):
AGCTCATTAGAGCTTACTGTTATT
Found at i:40284952 original size:22 final size:22
Alignment explanation
Indices: 40284927--40284983 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
40284917 GCTCGTATGG
* *
40284927 GCTTATTGTTCAACTCGATAGA
1 GCTTACTGTTCAACTCAATAGA
* *
40284949 GCTTACCGTTTCAGCTCAATAGA
1 GCTTACTG-TTCAACTCAATAGA
40284972 GCTTACTGTTCA
1 GCTTACTGTTCA
40284984 TTAGCTCGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (22 bp):
GCTTACTGTTCAACTCAATAGA
Found at i:40284970 original size:23 final size:23
Alignment explanation
Indices: 40284843--40284981 Score: 95
Period size: 24 Copynumber: 6.0 Consensus size: 23
40284833 GACCGATATA
40284843 TCAGCTC-ATAAGAGCTTACTGTT
1 TCAGCTCAAT-AGAGCTTACTGTT
* *
40284866 ATTAGCTCATTAGAGCTTACTGTT
1 -TCAGCTCAATAGAGCTTACTGTT
* * * * **
40284890 ATTAGCTTATTGGAGCTTACCATT
1 -TCAGCTCAATAGAGCTTACTGTT
* * *
40284914 TCAGCTC-GTATGGGCTTATTG-T
1 TCAGCTCAATA-GAGCTTACTGTT
* * *
40284936 TCAACTCGATAGAGCTTACCGTT
1 TCAGCTCAATAGAGCTTACTGTT
40284959 TCAGCTCAATAGAGCTTACTGTT
1 TCAGCTCAATAGAGCTTACTGTT
40284982 CATTAGCTCG
Statistics
Matches: 89, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
22 15 0.17
23 34 0.38
24 39 0.44
25 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (23 bp):
TCAGCTCAATAGAGCTTACTGTT
Found at i:40285377 original size:25 final size:26
Alignment explanation
Indices: 40285349--40285399 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
40285339 CTTATTTCAT
*
40285349 TAAATAAAAAAT-TTTAAAAATATAA
1 TAAATAAAAAATATTTAAAAACATAA
* *
40285374 TAAATCAAATATATTTAAAAACATAA
1 TAAATAAAAAATATTTAAAAACATAA
40285400 AAACAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAATAAAAAATATTTAAAAACATAA
Found at i:40285391 original size:26 final size:24
Alignment explanation
Indices: 40285361--40285409 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
40285351 AATAAAAAAT
*
40285361 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
40285387 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
40285410 TAAAGCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:40287140 original size:40 final size:38
Alignment explanation
Indices: 40287091--40287190 Score: 128
Period size: 40 Copynumber: 2.6 Consensus size: 38
40287081 TACGGTATCT
*
40287091 CTTGGTGTGTAGGGTTGGATGGGTTGATTTTATCCCCATA
1 CTTGGTGTGTAGGGTTGGATGGGTTGATCTTATCCCC--A
* * *
40287131 CTTGATGTGTAGGGCTGGGTGGGTTGATCTTATCCCCA
1 CTTGGTGTGTAGGGTTGGATGGGTTGATCTTATCCCCA
* *
40287169 CATGGTGTGTTGGGTTGGATGG
1 CTTGGTGTGTAGGGTTGGATGG
40287191 AGATGGTGTG
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 18 0.35
40 33 0.65
ACGTcount: A:0.13, C:0.13, G:0.37, T:0.37
Consensus pattern (38 bp):
CTTGGTGTGTAGGGTTGGATGGGTTGATCTTATCCCCA
Found at i:40297686 original size:6 final size:6
Alignment explanation
Indices: 40297672--40297706 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
40297662 GAGACAATGG
* *
40297672 AATAAA AATAGA AATAAA GATAAA AATAAA AATAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAA
40297707 TAGTAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:40302285 original size:37 final size:37
Alignment explanation
Indices: 40302235--40302308 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
40302225 GTGTTACTAG
*
40302235 GTAAACTTCCTGGTGGTCTTTCTGAAATCATCTTAGC
1 GTAAACTTCCTGGTGGTCTTTCTAAAATCATCTTAGC
40302272 GTAAACTTCCTGGTGGTCTTTCTAAAATCATCTTAGC
1 GTAAACTTCCTGGTGGTCTTTCTAAAATCATCTTAGC
40302309 CAACTACCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (37 bp):
GTAAACTTCCTGGTGGTCTTTCTAAAATCATCTTAGC
Found at i:40304450 original size:40 final size:40
Alignment explanation
Indices: 40304273--40304450 Score: 247
Period size: 40 Copynumber: 4.5 Consensus size: 40
40304263 AAACCAAGTA
* *
40304273 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
40304312 CCTTTGGGACTTAGCCC-GATTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-TATAGTAACTCGCACAAATG
*
40304352 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40304392 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40304432 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40304451 TTATCATCCG
Statistics
Matches: 126, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
39 16 0.13
40 108 0.86
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40307181 original size:26 final size:26
Alignment explanation
Indices: 40307152--40307204 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40307142 AAAAGTAAAA
40307152 TGGCTAAAGTAATAAAAATTGAGTGT
1 TGGCTAAAGTAATAAAAATTGAGTGT
40307178 TGGCTAAAGTAATAAAAATTGAGTGT
1 TGGCTAAAGTAATAAAAATTGAGTGT
40307204 T
1 T
40307205 CCTAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.32
Consensus pattern (26 bp):
TGGCTAAAGTAATAAAAATTGAGTGT
Found at i:40309117 original size:89 final size:89
Alignment explanation
Indices: 40308994--40309172 Score: 272
Period size: 89 Copynumber: 2.0 Consensus size: 89
40308984 AACGATAATG
* * *
40308994 AATTGACGGATTACGATTATTATTCACTCGAGTATCCTTTGAATTTCAAATAGGTACAAC-GAGT
1 AATTGACGGATTACGATTATTATTCACCCCAGTATCCTTTGAATTTCAAATAGGTACAACAG-GC
40309058 ACAAATAATGTTATACAGATGAGTT
65 ACAAATAATGTTATACAGATGAGTT
* *
40309083 AATTGACGGATTACTGA-TATTATTCACCCCAGTATCCTTTGAATTTCTAATAGGTTCAACAGGC
1 AATTGACGGATTAC-GATTATTATTCACCCCAGTATCCTTTGAATTTCAAATAGGTACAACAGGC
*
40309147 ACAAATAATGTTATACGGATGAGTT
65 ACAAATAATGTTATACAGATGAGTT
40309172 A
1 A
40309173 CGGTTTATAA
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
89 79 0.96
90 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (89 bp):
AATTGACGGATTACGATTATTATTCACCCCAGTATCCTTTGAATTTCAAATAGGTACAACAGGCA
CAAATAATGTTATACAGATGAGTT
Found at i:40317433 original size:27 final size:27
Alignment explanation
Indices: 40317403--40317516 Score: 158
Period size: 27 Copynumber: 4.3 Consensus size: 27
40317393 GGGGCAAAAT
* * *
40317403 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
40317430 GGTAATTCTACCCTACAAGGGTA-TTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
40317456 CGTAACTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
40317483 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
40317510 GGTAATT
1 GGTAATT
40317517 TCACAAATCA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
26 23 0.30
27 53 0.70
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:40317585 original size:27 final size:27
Alignment explanation
Indices: 40317474--40317573 Score: 130
Period size: 27 Copynumber: 3.7 Consensus size: 27
40317464 TACCCTACAA
* **
40317474 GGGTATTTTGGTAATTCTACCCTA-CAG
1 GGGTATTTTGGTAATTTTA-CAAACCAG
* * *
40317501 GGGTATTTCGGTAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
40317528 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
40317555 GGGTATTTTGGTAATTTTA
1 GGGTATTTTGGTAATTTTA
40317574 TTGATCGAGG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.03
27 62 0.97
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:40317635 original size:54 final size:55
Alignment explanation
Indices: 40317474--40317635 Score: 150
Period size: 54 Copynumber: 3.0 Consensus size: 55
40317464 TACCCTACAA
* ** * * *
40317474 GGGTATTTTGGTAATTCTACCCTA-CAGGGGTATTTCGGTAATTTCACAAATC-AG
1 GGGTATTTTGGTAATTTTA-CAAACCAAGGGTATTTCGGTAATTTTATAAATCGAG
* * **
40317528 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATTGATCGA-
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTATAAATCGAG
* ** * * *
40317582 GGGTCTTTTGGTAATTTTGTAAACCAATGGTATTTCAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTATAAATCGA
40317636 TGGTAAAATG
Statistics
Matches: 88, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
53 2 0.02
54 85 0.97
55 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (55 bp):
GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTATAAATCGAG
Found at i:40317649 original size:27 final size:27
Alignment explanation
Indices: 40317619--40317680 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
40317609 TGGTATTTCA
* *
40317619 GTAATTTTGTAAATCGATGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
40317646 GTAATTCTGTAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40317673 ATAATTCT
1 GTAATTCT
40317681 ATCTTATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.35
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:40317715 original size:27 final size:27
Alignment explanation
Indices: 40317685--40317779 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
40317675 AATTCTATCT
*
40317685 TATTTCGGTAATTTTACAAATCGAGGA
1 TATTTCGGTAATTTTACAAATCGAGGG
* * *
40317712 TATTTGGGTAATTTTATAAATCGGGGG
1 TATTTCGGTAATTTTACAAATCGAGGG
* *
40317739 TACTTT-GGTAATTTTACAAGTTGAGGG
1 TA-TTTCGGTAATTTTACAAATCGAGGG
*
40317766 TATTTCAGTAATTT
1 TATTTCGGTAATTT
40317780 AGTAAACTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
26 3 0.05
27 51 0.89
28 3 0.05
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.42
Consensus pattern (27 bp):
TATTTCGGTAATTTTACAAATCGAGGG
Found at i:40318875 original size:26 final size:25
Alignment explanation
Indices: 40318847--40318936 Score: 89
Period size: 24 Copynumber: 3.7 Consensus size: 25
40318837 CTCACCATAG
*
40318847 CTCGTATGAGCTTACTGATATATCAG
1 CTCGTATGAGCTTACTGAT-TATCAA
* *
40318873 CTCCTAAGAGCTTACT-ATTATCAA
1 CTCGTATGAGCTTACTGATTATCAA
* *
40318897 CTCAT-TGGAGCTTACCG-TT-TCAA
1 CTCGTAT-GAGCTTACTGATTATCAA
40318920 CTCGTATGAGCTTACTG
1 CTCGTATGAGCTTACTG
40318937 TTCAGCTCAA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
23 17 0.32
24 20 0.38
25 2 0.04
26 14 0.26
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (25 bp):
CTCGTATGAGCTTACTGATTATCAA
Found at i:40318952 original size:22 final size:22
Alignment explanation
Indices: 40318927--40318985 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 22
40318917 CAACTCGTAT
*
40318927 GAGCTTACTGTTCAGCTCAATA
1 GAGCTTACTATTCAGCTCAATA
*
40318949 GAGCTTACCACTTCAGCTCAATA
1 GAGCTTACTA-TTCAGCTCAATA
40318972 GAGCTTACTATTCA
1 GAGCTTACTATTCA
40318986 TTAGCTCGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 12 0.36
23 21 0.64
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (22 bp):
GAGCTTACTATTCAGCTCAATA
Found at i:40325321 original size:25 final size:25
Alignment explanation
Indices: 40325293--40325362 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
40325283 CTCTTTTAAT
*
40325293 AACTGGGGCAAAGCTCTTTCTGATA
1 AACTGGGGCAAAGCCCTTTCTGATA
* *
40325318 AACTGGGGCAAAGCCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTCTGATA
*
40325343 AACTGGGGCAGAGCCCTTTC
1 AACTGGGGCAAAGCCCTTTC
40325363 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTCTGATA
Found at i:40326201 original size:27 final size:27
Alignment explanation
Indices: 40326171--40326235 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
40326161 GGGCATATTC
40326171 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
40326198 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
40326225 GTCTTTTTACC
1 GTCATTTTACC
40326236 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:40338244 original size:8 final size:8
Alignment explanation
Indices: 40338231--40338255 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40338221 TTATCAGCTC
40338231 TTATTATT
1 TTATTATT
40338239 TTATTATT
1 TTATTATT
40338247 TTATTATT
1 TTATTATT
40338255 T
1 T
40338256 CGACTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTATT
Found at i:40338732 original size:17 final size:17
Alignment explanation
Indices: 40338710--40338748 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
40338700 TTTATTGTTC
*
40338710 TATTTATTTATCTTAGT
1 TATTTATTTATCTTAAT
*
40338727 TATTTATTTATTTTAAT
1 TATTTATTTATCTTAAT
40338744 TATTT
1 TATTT
40338749 TATCTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TATTTATTTATCTTAAT
Found at i:40342283 original size:40 final size:40
Alignment explanation
Indices: 40342239--40342320 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
40342229 TATCTCTGTC
*
40342239 AACCTTATCATGAAA-CTTTGTAATAAATAAATTAAATCAA
1 AACCTTATCATCAAACCTTT-TAATAAATAAATTAAATCAA
* *
40342279 AACCTTATCATCAAACCTTTTAATAATTTAATTAAATCAA
1 AACCTTATCATCAAACCTTTTAATAAATAAATTAAATCAA
40342319 AA
1 AA
40342321 GTCAAATGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 34 0.89
41 4 0.11
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (40 bp):
AACCTTATCATCAAACCTTTTAATAAATAAATTAAATCAA
Found at i:40346680 original size:18 final size:18
Alignment explanation
Indices: 40346645--40346682 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
40346635 TTGCAGCTCC
*
40346645 ATATTTTCTCTTCTTTTT
1 ATATTTTCTCTTCATTTT
40346663 ATATTTTCT-TATCATTTT
1 ATATTTTCTCT-TCATTTT
40346681 AT
1 AT
40346683 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (18 bp):
ATATTTTCTCTTCATTTT
Found at i:40353100 original size:17 final size:17
Alignment explanation
Indices: 40353078--40353111 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40353068 GAATATACAT
40353078 TCAACTCACTCAGCCAC
1 TCAACTCACTCAGCCAC
40353095 TCAACTCACTCAGCCAC
1 TCAACTCACTCAGCCAC
40353112 AAACAAGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.47, G:0.06, T:0.18
Consensus pattern (17 bp):
TCAACTCACTCAGCCAC
Found at i:40356335 original size:30 final size:30
Alignment explanation
Indices: 40356301--40356361 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40356291 TCCTTAACTC
40356301 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40356331 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40356361 A
1 A
40356362 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40357204 original size:15 final size:15
Alignment explanation
Indices: 40357184--40357213 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40357174 ATAACCTTAT
40357184 CGAGGGATTCATCAC
1 CGAGGGATTCATCAC
40357199 CGAGGGATTCATCAC
1 CGAGGGATTCATCAC
40357214 ATATCTAGCT
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:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (15 bp):
CGAGGGATTCATCAC
Found at i:40357483 original size:41 final size:41
Alignment explanation
Indices: 40357373--40357493 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 41
40357363 TACCATACAA
* *
40357373 ATGCCATATCCCAAATATGGTCTTACA-TGGGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACT--AATCTCATATCG
* * *
40357415 ATGCCAATAGCCCAGCTATGGTTTTACACTAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACTAATCTCATATCG
40357457 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACAC-TAATCTCA
40357494 AATAACCCCA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
41 20 0.29
42 29 0.43
43 18 0.26
44 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.31
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACACTAATCTCATATCG
Found at i:40365062 original size:42 final size:41
Alignment explanation
Indices: 40364945--40365062 Score: 137
Period size: 43 Copynumber: 2.8 Consensus size: 41
40364935 ATACCAATGA
40364945 CATATCCCAGATATGGTCTTACATGAGATCTCATATAGATGG
1 CATATCCCAGATATGGTCTTACATGA-ATCTCATATAGATGG
* * * * *
40364987 CAATAGCCTAGCTATGGTCTTACATGAAGTCTCATATCGATGT
1 C-ATATCCCAGATATGGTCTTACATGAA-TCTCATATAGATGG
* *
40365030 CATATCCCAGATATAGTCTTACACGTAATCTCA
1 CATATCCCAGATATGGTCTTACATG-AATCTCA
40365063 AATAACCCCA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
42 26 0.41
43 37 0.59
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (41 bp):
CATATCCCAGATATGGTCTTACATGAATCTCATATAGATGG
Found at i:40366426 original size:24 final size:24
Alignment explanation
Indices: 40366399--40366454 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
40366389 TGGAGGAACG
* * *
40366399 AGATGAAGGTGAAGATAAAGATGA
1 AGATGAAGCTCAAGATAAAAATGA
* *
40366423 AGATGGAGCTCAAGGTAAAAATGA
1 AGATGAAGCTCAAGATAAAAATGA
40366447 AGATGAAG
1 AGATGAAG
40366455 AATATGAGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.04, G:0.32, T:0.16
Consensus pattern (24 bp):
AGATGAAGCTCAAGATAAAAATGA
Found at i:40371077 original size:27 final size:27
Alignment explanation
Indices: 40371039--40371108 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
40371029 TTCTCTATAG
* *
40371039 AGGCGTTCCTTTCATGTTGCGCCAAAA
1 AGGCGTTCCTTTCATATTGCACCAAAA
* *
40371066 AGGCTTTCCTTTCATATTGCACCACAA
1 AGGCGTTCCTTTCATATTGCACCAAAA
*
40371093 AGACGTTCCTTTCATA
1 AGGCGTTCCTTTCATA
40371109 ATTCATCAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (27 bp):
AGGCGTTCCTTTCATATTGCACCAAAA
Found at i:40371243 original size:27 final size:27
Alignment explanation
Indices: 40371160--40371244 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
40371150 TTGCGCCATA
* * * * *
40371160 TTCCTTTCATAATGCGCTATAAAGGCT
1 TTCCTTTCATAATTCACCACAAAGGCG
* *
40371187 TTCCTTTCAT-ATTGCACCACAAATGTG
1 TTCCTTTCATAATT-CACCACAAAGGCG
40371214 TTCCTTTCATAATTCACCACAAAGGCG
1 TTCCTTTCATAATTCACCACAAAGGCG
40371241 TTCC
1 TTCC
40371245 ATTCCTAACA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
26 2 0.04
27 42 0.89
28 3 0.06
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (27 bp):
TTCCTTTCATAATTCACCACAAAGGCG
Found at i:40375287 original size:42 final size:43
Alignment explanation
Indices: 40375179--40375340 Score: 145
Period size: 43 Copynumber: 3.8 Consensus size: 43
40375169 AGCTCATACA
* *
40375179 ATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCAAACATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACATGAAATCAAACATCG
* * * *
40375222 ATGCCACTGTCCCAGGCAGGGTCTTAAATGAAATCAAATA-CG
1 ATGCCACTGTCCCAGACATGGTCTTACATGAAATCAAACATCG
* *
40375264 ATGTCGA-TGTCCCAGACATGGTCTTACATGTAAATCATAA-GTCG
1 ATG-CCACTGTCCCAGACATGGTCTTACATG-AAATCA-AACATCG
* * *
40375308 ATGCCAAC-GTCCTAGACGTGGTCTTACACGAAA
1 ATGCC-ACTGTCCCAGACATGGTCTTACATGAAA
40375341 ACACATATCG
Statistics
Matches: 97, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
42 27 0.28
43 43 0.44
44 27 0.28
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACATGAAATCAAACATCG
Found at i:40392353 original size:40 final size:40
Alignment explanation
Indices: 40392248--40392398 Score: 189
Period size: 40 Copynumber: 3.8 Consensus size: 40
40392238 TGGATGATAA
* * * **
40392248 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
40392288 CCGGGC-AAGTCCCAAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
40392327 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
* *
40392367 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
40392399 AGCTATATCC
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
39 33 0.34
40 62 0.64
41 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:40400398 original size:40 final size:40
Alignment explanation
Indices: 40400301--40400449 Score: 185
Period size: 40 Copynumber: 3.8 Consensus size: 40
40400291 GACGATAACT
* * * * **
40400301 GGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACTAGTTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
40400341 GGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
* *
40400380 GGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAA-CC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAATCC
* *
40400420 GGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT
40400450 AGCTATATCC
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 33 0.34
40 61 0.64
41 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:40418883 original size:27 final size:27
Alignment explanation
Indices: 40418853--40418970 Score: 82
Period size: 27 Copynumber: 4.4 Consensus size: 27
40418843 ATACTATCCC
* *
40418853 TTCATGATT-CACTACAAAGGCGTTCCT
1 TTCAT-ATTGCACTACAAAAGCATTCCT
*
40418880 TTCATATTGCCCTACAAAAGCATTCCT
1 TTCATATTGCACTACAAAAGCATTCCT
* * *
40418907 TTAATAAATTGC-C-A-TAAAGACATTTCT
1 TTCAT--ATTGCACTACAAAAG-CATTCCT
* * * *
40418934 TTTATATTGCACCACAAAGGCTTTCCT
1 TTCATATTGCACTACAAAAGCATTCCT
40418961 TTCATATTGC
1 TTCATATTGC
40418971 GCCAAAAAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
25 5 0.07
26 8 0.11
27 50 0.69
28 4 0.06
29 5 0.07
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (27 bp):
TTCATATTGCACTACAAAAGCATTCCT
Found at i:40429970 original size:21 final size:21
Alignment explanation
Indices: 40429946--40429994 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
40429936 TAGGGACACG
*
40429946 CCCGTGTGACCCTAAGGCACA
1 CCCGTGCGACCCTAAGGCACA
40429967 CCCGTGCGACCCTAAGGCACA
1 CCCGTGCGACCCTAAGGCACA
40429988 CCCGTGC
1 CCCGTGC
40429995 TACAGGTCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.24, T:0.12
Consensus pattern (21 bp):
CCCGTGCGACCCTAAGGCACA
Found at i:40439781 original size:30 final size:30
Alignment explanation
Indices: 40439745--40439802 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
40439735 TTTTATTATT
40439745 AATTTTGTTATTATTTTAAAGACATTTGTA
1 AATTTTGTTATTATTTTAAAGACATTTGTA
* *
40439775 AATTTTGTTATTATTTTAGAGGCATTTG
1 AATTTTGTTATTATTTTAAAGACATTTG
40439803 CTTGTTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.53
Consensus pattern (30 bp):
AATTTTGTTATTATTTTAAAGACATTTGTA
Found at i:40439906 original size:18 final size:18
Alignment explanation
Indices: 40439885--40439924 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
40439875 AAAATATTTA
*
40439885 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
40439903 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
40439921 TTTT
1 TTTT
40439925 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:40454491 original size:24 final size:23
Alignment explanation
Indices: 40454396--40454494 Score: 82
Period size: 24 Copynumber: 4.3 Consensus size: 23
40454386 AAACTTTATT
40454396 GAGCT-AAAACGGTAAGCTCTATC
1 GAGCTGAAAACGGTAAGCTCTA-C
*
40454419 GAGCTGAATAA---TAAGCTCATAA
1 GAGCTGAA-AACGGTAAGCTC-TAC
* * *
40454441 GAG-TTAAAACGGTAAGCTCCAAT
1 GAGCTGAAAACGGTAAGCT-CTAC
40454464 GAGCTGAAAACGGTAAGCTCTTAC
1 GAGCTGAAAACGGTAAGCTC-TAC
40454488 GAGCTGA
1 GAGCTGA
40454495 TATAGGAGCT
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
20 2 0.03
21 3 0.05
22 10 0.17
23 18 0.30
24 25 0.42
25 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.21
Consensus pattern (23 bp):
GAGCTGAAAACGGTAAGCTCTAC
Found at i:40455022 original size:29 final size:27
Alignment explanation
Indices: 40454980--40455040 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
40454970 ATCTTTCATT
40454980 ATTTTACATATTTAACCACCATATTTTAC
1 ATTTTACATATTTAACC-CC-TATTTTAC
* *
40455009 ATTTTCACA-ATTTAATCCCTATTTTGC
1 ATTTT-ACATATTTAACCCCTATTTTAC
40455036 ATTTT
1 ATTTT
40455041 TGCCAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 12 0.41
28 2 0.07
29 12 0.41
30 3 0.10
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.49
Consensus pattern (27 bp):
ATTTTACATATTTAACCCCTATTTTAC
Found at i:40456927 original size:19 final size:19
Alignment explanation
Indices: 40456900--40456938 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
40456890 AAGATCTGGA
*
40456900 TCCAATTAATTGGATTGGG
1 TCCAATTAATTGGATCGGG
*
40456919 TCCAGTTAATTGGATCGGG
1 TCCAATTAATTGGATCGGG
40456938 T
1 T
40456939 TGAGGGAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (19 bp):
TCCAATTAATTGGATCGGG
Found at i:40458934 original size:48 final size:48
Alignment explanation
Indices: 40458848--40459134 Score: 243
Period size: 48 Copynumber: 6.0 Consensus size: 48
40458838 AAAAGGGTGA
* ** * * * *
40458848 AATGCCGATGCCATGTCCCGGACGTGGTCTTGCACTGGCTCACATAAC
1 AATGCCGATGCCATGTTCCAAACATGGACTTACACTGGCTCACATATC
* * * * *
40458896 AATGCTGATGGCATGTTCCAAACATGGACTTACGCTGGCTCATATATT
1 AATGCCGATGCCATGTTCCAAACATGGACTTACACTGGCTCACATATC
* * * * * * *
40458944 GAGGCCAATGCCATGTCCCAGACAT-GATCTTACACTAGCTCTCATATC
1 AATGCCGATGCCATGTTCCAAACATGGA-CTTACACTGGCTCACATATC
* * * *
40458992 AATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGATCACATATT
1 AATGCCGATGCCATGTTCCAAACATGGACTTACACTGGCTCACATATC
* * * * * * *
40459040 GAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC
1 AATGCCGATGCCATGTTCCAAACATGGACTTACACTGGCTCACATATC
* * * * *
40459088 AGTGCCGATGCCATGCTCCAAAAATGGCCTTACACTGGCTCATATAT
1 AATGCCGATGCCATGTTCCAAACATGGACTTACACTGGCTCACATAT
40459135 TGAGGTTAAT
Statistics
Matches: 182, Mismatches: 55, Indels: 4
0.76 0.23 0.02
Matches are distributed among these distances:
47 2 0.01
48 179 0.98
49 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (48 bp):
AATGCCGATGCCATGTTCCAAACATGGACTTACACTGGCTCACATATC
Found at i:40459024 original size:96 final size:95
Alignment explanation
Indices: 40458855--40459181 Score: 438
Period size: 96 Copynumber: 3.4 Consensus size: 95
40458845 TGAAATGCCG
* * * * * * *
40458855 ATGCCATGTCCCGGACGTGGTCTTGCACTGGCTCACATAACAATGCTGATGGCATGTTCCAAACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGC-GATGCCATGTTCCAAACA
*
40458920 TGGACTTACGCTGGCTCATATATTGAGGCCA
65 TGGACTTACACTGGCTCATATATTGAGGCCA
*
40458951 ATGCCATGTCCCAGACATGATCTTACACTAGCTCTCATATCAATGTCGATGCCATGTTCCAAACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATG-CGATGCCATGTTCCAAACA
* * * *
40459016 TGGTCTTACACTGGATCACATATTGAGGCCG
65 TGGACTTACACTGGCTCATATATTGAGGCCA
* * *
40459047 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAGTGCCGATGCCATGCTCCAAAAA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATG-CGATGCCATGTTCCAAACA
* **
40459112 TGGCCTTACACTGGCTCATATATTGAGGTTA
65 TGGACTTACACTGGCTCATATATTGAGGCCA
* *
40459143 ATGTCATTTCCCAGACATGGTCTTACACTAGCTCTCATA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATA
40459182 ACCCTAGTAT
Statistics
Matches: 204, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
96 203 1.00
97 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (95 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCGATGCCATGTTCCAAACAT
GGACTTACACTGGCTCATATATTGAGGCCA
Found at i:40459168 original size:48 final size:48
Alignment explanation
Indices: 40458917--40459176 Score: 215
Period size: 48 Copynumber: 5.4 Consensus size: 48
40458907 CATGTTCCAA
* * * * *
40458917 ACATGGACTTACGCTGGCTCATATATTGAGGCCAATGCCATGTCCCAG
1 ACATGGTCTTACACTAGCTCATATATTGAGGCCGATGCCATTTCCCAG
* ** * * *
40458965 ACATGATCTTACACTAGCTC-TCATATCAATGTCGATGCCATGTT-CCAA
1 ACATGGTCTTACACTAGCTCAT-ATATTGAGGCCGATGCCAT-TTCCCAG
* * * *
40459013 ACATGGTCTTACACTGGATCACATATTGAGGCCGATGCCATGTCCCAG
1 ACATGGTCTTACACTAGCTCATATATTGAGGCCGATGCCATTTCCCAG
* * *
40459061 ACATGGTCTTACACTAGCTC-TCATA-TCAGTGCCGATGCCA-TGCTCCAA
1 ACATGGTCTTACACTAGCTCAT-ATATTGAG-GCCGATGCCATTTC-CCAG
* * * *** *
40459109 AAATGGCCTTACACTGGCTCATATATTGAGGTTAATGTCATTTCCCAG
1 ACATGGTCTTACACTAGCTCATATATTGAGGCCGATGCCATTTCCCAG
40459157 ACATGGTCTTACACTAGCTC
1 ACATGGTCTTACACTAGCTC
40459177 TCATAACCCT
Statistics
Matches: 161, Mismatches: 41, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
47 6 0.04
48 148 0.92
49 7 0.04
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (48 bp):
ACATGGTCTTACACTAGCTCATATATTGAGGCCGATGCCATTTCCCAG
Found at i:40462039 original size:19 final size:19
Alignment explanation
Indices: 40462003--40462039 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40461993 TAGCCCATCG
*
40462003 GGCCCATTTAGCCTATTCT
1 GGCCCATTTAGCCAATTCT
*
40462022 GGCCCATTTGGCCAATTC
1 GGCCCATTTAGCCAATTC
40462040 GTAACCCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.32, G:0.19, T:0.32
Consensus pattern (19 bp):
GGCCCATTTAGCCAATTCT
Found at i:40462150 original size:8 final size:8
Alignment explanation
Indices: 40462137--40462185 Score: 64
Period size: 8 Copynumber: 6.1 Consensus size: 8
40462127 GTAGCCTAAC
40462137 TTTCGGCT
1 TTTCGGCT
40462145 TTTCGG-T
1 TTTCGGCT
40462152 ATTTCGGCT
1 -TTTCGGCT
40462161 TTTCGGCT
1 TTTCGGCT
*
40462169 TTTCGGCA
1 TTTCGGCT
*
40462177 TTTCAGCT
1 TTTCGGCT
40462185 T
1 T
40462186 GCCGATTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
7 1 0.03
8 34 0.94
9 1 0.03
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.49
Consensus pattern (8 bp):
TTTCGGCT
Found at i:40462167 original size:24 final size:24
Alignment explanation
Indices: 40462137--40462185 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
40462127 GTAGCCTAAC
* *
40462137 TTTCGGCTTTTCGGTATTTCGGCT
1 TTTCGGCTTTTCGGCATTTCAGCT
40462161 TTTCGGCTTTTCGGCATTTCAGCT
1 TTTCGGCTTTTCGGCATTTCAGCT
40462185 T
1 T
40462186 GCCGATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.49
Consensus pattern (24 bp):
TTTCGGCTTTTCGGCATTTCAGCT
Found at i:40465356 original size:49 final size:47
Alignment explanation
Indices: 40465293--40465597 Score: 439
Period size: 47 Copynumber: 6.4 Consensus size: 47
40465283 ATTGATGTAC
* * *
40465293 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * *
40465340 AAGTATATATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
1 AAG--TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * *
40465389 AAGTGTATATATGTGATAGGGTCGAAGTGACCAACGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAA-TGGCCAATGTGATGAATGTGA
40465437 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
40465484 AAGTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
40465531 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
40465578 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
40465598 TCCCGAAGGG
Statistics
Matches: 238, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
47 148 0.62
48 44 0.18
49 46 0.19
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:40465440 original size:24 final size:24
Alignment explanation
Indices: 40465366--40465441 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
40465356 GATAGGGCCG
*
40465366 AGTGGCCAACGTGATGAATGTGAA
1 AGTGACCAACGTGATGAATGTGAA
* * **
40465390 AGTGTA-TATATGTGAT-AGGGTCG-A
1 AGTG-ACCA-ACGTGATGAATGT-GAA
40465414 AGTGACCAACGTGATGAATGTGAA
1 AGTGACCAACGTGATGAATGTGAA
40465438 AGTG
1 AGTG
40465442 TATATATGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 12
0.64 0.16 0.21
Matches are distributed among these distances:
23 8 0.22
24 22 0.59
25 7 0.19
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.25
Consensus pattern (24 bp):
AGTGACCAACGTGATGAATGTGAA
Found at i:40465604 original size:142 final size:143
Alignment explanation
Indices: 40465293--40465604 Score: 421
Period size: 142 Copynumber: 2.2 Consensus size: 143
40465283 ATTGATGTAC
* * * * * *
40465293 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAAAGTATATATATATGTGA
1 AAGTGTATAAATGTGATAAGCCCGAATGGCCAATGTGATGAATGTGAAAG-ATATATATATGAGA
* * * * *
40465358 TAGGGCCGAGTGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAGGGTCGAAGTGACCAA
65 TAAGACCGAATGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAGTGACCAA
40465423 CGTGATGAATGTGA
130 CGTGATGAATGTGA
* * *
40465437 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG-TGTATATATGAGAT
1 AAGTGTATAAATGTGATAAGCCCGAATGGCCAATGTGATGAATGTGAAAGATATATATATGAGAT
* * * *
40465501 AAGACCTAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAA-TGGCCAAT
66 AAGACCGAATGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAGTGACCAAC
*
40465565 GTGATGGATGTGA
131 GTGATGAATGTGA
40465578 AAGTGTATAAATGTGATAAGTCCCGAA
1 AAGTGTATAAATGTGATAAG-CCCGAA
40465605 GGGCATTTGT
Statistics
Matches: 150, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
141 37 0.25
142 66 0.44
144 47 0.31
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.27
Consensus pattern (143 bp):
AAGTGTATAAATGTGATAAGCCCGAATGGCCAATGTGATGAATGTGAAAGATATATATATGAGAT
AAGACCGAATGGCCAACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAAGTGACCAAC
GTGATGAATGTGA
Found at i:40468087 original size:38 final size:38
Alignment explanation
Indices: 40468023--40468097 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
40468013 AATCCGAGTT
*
40468023 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
40468061 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCGG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCGG
40468098 ATTAAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:40468210 original size:40 final size:40
Alignment explanation
Indices: 40468151--40468418 Score: 421
Period size: 40 Copynumber: 6.7 Consensus size: 40
40468141 AGGTCTCGAC
40468151 GATG-ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
40468190 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
40468230 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* *
40468270 GATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
40468310 GATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * **
40468350 GATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * *
40468390 GTTATATCCGGGCTAGGTCCCGAAGAGCA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCA
40468419 ATCATGCTGG
Statistics
Matches: 209, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
39 4 0.02
40 205 0.98
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:40471825 original size:47 final size:47
Alignment explanation
Indices: 40471768--40472071 Score: 437
Period size: 47 Copynumber: 6.4 Consensus size: 47
40471758 ATTGATGTAC
* * *
40471768 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * *
40471815 AAGTATATATATATGTGATAGGGCCGAGTGGCCAACGTGATGAATGTGA
1 AAG--TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * * * *
40471864 AAGTGTATATATGTGATAGGGTCGAGTGACCAACGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
40471911 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
40471958 AAGTGTATATATGAGATAAGACCTAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
40472005 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
40472052 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
40472072 TCCCGAAGGG
Statistics
Matches: 238, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
47 192 0.81
49 46 0.19
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:40477692 original size:42 final size:42
Alignment explanation
Indices: 40477633--40477791 Score: 203
Period size: 42 Copynumber: 3.6 Consensus size: 42
40477623 CCAGACATAA
*
40477633 TCTTACATTGGCTCACATATTGAGGCCATGATCCAAACAAGG
1 TCTTACACTGGCTCACATATTGAGGCCATGATCCAAACAAGG
* * *
40477675 TCTTACACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATA-A
1 TCTTACACTGGCTCACATATTGAGGCC---ATGA--T-CCAAACA-AGG
40477723 TCTTACACTGGCTCACATATTGAGGCCATGATCCAAACAAGG
1 TCTTACACTGGCTCACATATTGAGGCCATGATCCAAACAAGG
*
40477765 TCTTACACTGGCTCACATATTAAGGCC
1 TCTTACACTGGCTCACATATTGAGGCC
40477792 GATGTCATGT
Statistics
Matches: 101, Mismatches: 8, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
41 1 0.01
42 58 0.57
43 1 0.01
45 6 0.06
47 1 0.01
48 33 0.33
49 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (42 bp):
TCTTACACTGGCTCACATATTGAGGCCATGATCCAAACAAGG
Found at i:40477743 original size:90 final size:90
Alignment explanation
Indices: 40477590--40477826 Score: 420
Period size: 90 Copynumber: 2.6 Consensus size: 90
40477580 GCTCTAATAC
*
40477590 CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTACATTGGCTCACATATTG
1 CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTACACTGGCTCACATATTG
40477655 AGGCCATGATCCAAACAAGGTCTTA
66 AGGCCATGATCCAAACAAGGTCTTA
*
40477680 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAATCTTACACTGGCTCACATATTG
1 CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTACACTGGCTCACATATTG
40477745 AGGCCATGATCCAAACAAGGTCTTA
66 AGGCCATGATCCAAACAAGGTCTTA
* ** *
40477770 CACTGGCTCACATATTAAGGCCGATGTCATGTCCCAGACATGGTCTTACACTAGCTC
1 CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTACACTGGCTC
40477827 TCGTAACCCT
Statistics
Matches: 140, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 140 1.00
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (90 bp):
CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTACACTGGCTCACATATTG
AGGCCATGATCCAAACAAGGTCTTA
Found at i:40477746 original size:48 final size:48
Alignment explanation
Indices: 40477590--40477826 Score: 250
Period size: 48 Copynumber: 5.2 Consensus size: 48
40477580 GCTCTAATAC
* *
40477590 CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTA
1 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAGTCTTA
* * *
40477638 CATTGGCTCACATATTGAGGCC---ATGA--T-CCAAACA-AGGTCTTA
1 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATA-GTCTTA
*
40477680 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAATCTTA
1 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAGTCTTA
* *
40477728 CACTGGCTCACATATTGAGGCC---ATGA--T-CCAAACA-AGGTCTTA
1 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATA-GTCTTA
* * *
40477770 CACTGGCTCACATATTAAGGCCGATGTCATGTCCCAGACATGGTCTTA
1 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAGTCTTA
*
40477818 CACTAGCTC
1 CACTGGCTC
40477827 TCGTAACCCT
Statistics
Matches: 155, Mismatches: 18, Indels: 32
0.76 0.09 0.16
Matches are distributed among these distances:
41 2 0.01
42 64 0.41
43 2 0.01
45 10 0.06
47 2 0.01
48 74 0.48
49 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (48 bp):
CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAGTCTTA
Found at i:40480406 original size:46 final size:46
Alignment explanation
Indices: 40480353--40480441 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
40480343 TATATATACA
* *
40480353 CATCTCATCCATATCTCACATTAGCCATTTGGCTTTACCACATGTC
1 CATCTCATACATATCTCACATTAGCCATTCGGCTTTACCACATGTC
* * * *
40480399 CATCTCATACATGTTTCGCATTAGCCGTTCGGCTTTACCACAT
1 CATCTCATACATATCTCACATTAGCCATTCGGCTTTACCACAT
40480442 ATATACACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.22, C:0.31, G:0.11, T:0.35
Consensus pattern (46 bp):
CATCTCATACATATCTCACATTAGCCATTCGGCTTTACCACATGTC
Found at i:40480490 original size:47 final size:47
Alignment explanation
Indices: 40480457--40480701 Score: 409
Period size: 47 Copynumber: 5.2 Consensus size: 47
40480447 CACTTCCATG
* *
40480457 TTCATCACATTGGCCATTCTGCCTTGTCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
40480504 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* * *
40480551 TTCATCACATTGGCTATTCGACCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
40480598 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
* * **
40480645 TTCATCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
40480692 TTCATCACAT
1 TTCATCACAT
40480702 AAAATCCTAA
Statistics
Matches: 186, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 186 1.00
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACA
Found at i:40480605 original size:25 final size:25
Alignment explanation
Indices: 40480529--40480606 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
40480519 ATTCGGCCTT
*
40480529 ATCACATATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
* *
40480554 AT--CACAT-TGGC-TATTCGACCTT-
1 ATCACACATAT-GCATGTTC-ACATTC
40480576 ATCACACATATGCATGTTCACATTC
1 ATCACACATATGCATGTTCACATTC
40480601 ATCACA
1 ATCACA
40480607 TTGGCCATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
22 7 0.17
23 10 0.24
24 11 0.27
25 13 0.32
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (25 bp):
ATCACACATATGCATGTTCACATTC
Found at i:40480628 original size:22 final size:22
Alignment explanation
Indices: 40480601--40480672 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
40480591 GTTCACATTC
40480601 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
40480623 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
40480647 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
40480670 ATC
1 ATC
40480673 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:40495730 original size:13 final size:13
Alignment explanation
Indices: 40495712--40495738 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40495702 AGATCCTCGC
40495712 TCTCTTCAACTCA
1 TCTCTTCAACTCA
40495725 TCTCTTCAACTCA
1 TCTCTTCAACTCA
40495738 T
1 T
40495739 TATTGTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (13 bp):
TCTCTTCAACTCA
Found at i:40497447 original size:22 final size:19
Alignment explanation
Indices: 40497408--40497449 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
40497398 TGCAAAGTTG
40497408 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
40497427 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
40497449 A
1 A
40497450 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:40508643 original size:39 final size:39
Alignment explanation
Indices: 40508599--40508674 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
40508589 TTCCAACGCG
*
40508599 TAGCCTACAGACCTTAAGTCCGGTTATAATTCCAGCACA
1 TAGCCTACAGACCTTAAGTCCGGGTATAATTCCAGCACA
* *
40508638 TAGCCTGCGGACCTTAAGTCCGGGTATAATTCCAGCA
1 TAGCCTACAGACCTTAAGTCCGGGTATAATTCCAGCA
40508675 TATATCCTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
TAGCCTACAGACCTTAAGTCCGGGTATAATTCCAGCACA
Found at i:40508706 original size:40 final size:39
Alignment explanation
Indices: 40508612--40508743 Score: 165
Period size: 40 Copynumber: 3.3 Consensus size: 39
40508602 CCTACAGACC
* * * * * *
40508612 TTAAGTCCGGTTATAATTCCAGCACATAGCCTGCGGACC
1 TTAAGCCCGGATATAATTCCAGCATATAGCCTGGGGTCT
* * *
40508651 TTAAGTCCGGGTATAATTCCAGCATATATCCTGTGGGTCT
1 TTAAGCCCGGATATAATTCCAGCATATAGCCTG-GGGTCT
40508691 TTAAGCCCGGATATAATTCCAGCATATAGCCTGCGGGTCT
1 TTAAGCCCGGATATAATTCCAGCATATAGCCTG-GGGTCT
40508731 TTAAGCCCGGATA
1 TTAAGCCCGGATA
40508744 CACATCAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 30 0.37
40 52 0.63
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (39 bp):
TTAAGCCCGGATATAATTCCAGCATATAGCCTGGGGTCT
Found at i:40516583 original size:35 final size:37
Alignment explanation
Indices: 40516513--40516636 Score: 117
Period size: 35 Copynumber: 3.3 Consensus size: 37
40516503 TTTCAGCGCG
40516513 TAGCCTGCGGACCTTAAGTCCGGTTATAATTCCAGCACA
1 TAGCCTGCGGACCTTAAG--CGGTTATAATTCCAGCACA
* *
40516552 TAGCCTGCGGACCTTCAG-GG-TATAATTCCAGCATA
1 TAGCCTGCGGACCTTAAGCGGTTATAATTCCAGCACA
* * * * * *
40516587 TAGCCTGTGGGTCTTTAAGCCCGGATATAATTCTAGCATA
1 TAGCCTG-CGGACCTTAAG--CGGTTATAATTCCAGCACA
40516627 TAGCCTGCGG
1 TAGCCTGCGG
40516637 GTCTTTAAGC
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
35 21 0.29
36 9 0.12
39 21 0.29
40 21 0.29
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.27
Consensus pattern (37 bp):
TAGCCTGCGGACCTTAAGCGGTTATAATTCCAGCACA
Found at i:40516627 original size:40 final size:40
Alignment explanation
Indices: 40516436--40516653 Score: 150
Period size: 39 Copynumber: 5.7 Consensus size: 40
40516426 TACCAACACA
** * *
40516436 AGCCTGCGGGAATTTAAACCC-GATATAATACCAGC-TCGA-
1 AGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCAT--AT
* * * * * ***
40516475 AGCCTGCGGGACTTT-TGCCCGGACATATTTTCAGCGCGT
1 AGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATAT
* * * * *
40516514 AGCCTGC-GGACCTTAAGTCCGGTTATAATTCCAGCACAT
1 AGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATAT
* * *
40516553 AGCCTGC-GGACCTTCAG---GG-TATAATTCCAGCATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATAT
* *
40516588 AGCCTGTGGGTCTTTAAGCCCGGATATAATTCTAGCATAT
1 AGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATAT
40516628 AGCCTGCGGGTCTTTAAGCCCGGATA
1 AGCCTGCGGGTCTTTAAGCCCGGATA
40516654 CACATCAAAT
Statistics
Matches: 144, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
35 21 0.15
36 9 0.06
38 9 0.06
39 65 0.45
40 40 0.28
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
AGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATAT
Found at i:40520609 original size:27 final size:27
Alignment explanation
Indices: 40520579--40520776 Score: 252
Period size: 27 Copynumber: 7.3 Consensus size: 27
40520569 TACTGAAATG
* *
40520579 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* *
40520606 CCCTCGATTTATAGAATTACGGTTTCA
1 CCCTCGATTTATAGAATTACCGTTTTA
* * * *
40520633 CTCTCGATTTACAAAATTACTGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
*
40520660 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
*
40520687 CCCTCGATTTATAGAATTACTGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* * *
40520714 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* * *
40520741 CCCTCAATTTACAAAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
40520768 CCCTCGATT
1 CCCTCGATT
40520777 GTGAAATTAC
Statistics
Matches: 148, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCGTTTTA
Found at i:40520694 original size:81 final size:81
Alignment explanation
Indices: 40520579--40520776 Score: 306
Period size: 81 Copynumber: 2.4 Consensus size: 81
40520569 TACTGAAATG
* *
40520579 CCCTCGATTTGTAGAATTACCATTTTACCCTCGATTTATAGAATTACGGTTTCACTCTCGATTTA
1 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACGGTTTCACCCTCGATTTA
**
40520644 CAAAATTACTGTTTTA
66 CAAAATTACCATTTTA
* *
40520660 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTCGATTTA
1 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACGGTTTCACCCTCGATTTA
40520725 CAAAATTACCATTTTA
66 CAAAATTACCATTTTA
* * * *
40520741 CCCTCAATTTACAAAATTACCGTTTTACCCTCGATT
1 CCCTCGATTTATAGAATTACCATTTTACCCTCGATT
40520777 GTGAAATTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 107 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (81 bp):
CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTACGGTTTCACCCTCGATTTA
CAAAATTACCATTTTA
Found at i:40520838 original size:27 final size:27
Alignment explanation
Indices: 40520808--40520904 Score: 124
Period size: 27 Copynumber: 3.6 Consensus size: 27
40520798 TATAGGATAG
40520808 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * *
40520835 AATTACCGAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
40520862 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
40520889 AATTACCAAAATACCC
1 AATTACCAAAATACCC
40520905 TTGATTTACA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
26 3 0.05
27 54 0.92
28 2 0.03
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:40520919 original size:27 final size:27
Alignment explanation
Indices: 40520808--40520989 Score: 84
Period size: 27 Copynumber: 6.7 Consensus size: 27
40520798 TATAGGATAG
* * **
40520808 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTAATTTACAA
* ** ***
40520835 AATTACCGAAATACCAC-TGGTTTGTGA
1 AATTACCAAAATACC-CTTAATTTACAA
* * **
40520862 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCTTAATTTACAA
* *
40520889 AATTACCAAAATACCCTTGATTTACAC
1 AATTACCAAAATACCCTTAATTTACAA
*
40520916 AATTA-TAGAAATACCCTTAACTTT-CTAAA
1 AATTACCA-AAATACCCTTAA-TTTAC--AA
* * *
40520945 AATTA-TAGAAATACCATTAGTTTACAA
1 AATTACCA-AAATACCCTTAATTTACAA
**
40520972 AATTACTGAAATACCCTT
1 AATTACCAAAATACCCTT
40520990 GGATTGTAGA
Statistics
Matches: 127, Mismatches: 20, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.02
27 97 0.76
28 8 0.06
29 20 0.16
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCTTAATTTACAA
Found at i:40520920 original size:54 final size:53
Alignment explanation
Indices: 40520808--40520988 Score: 136
Period size: 54 Copynumber: 3.3 Consensus size: 53
40520798 TATAGGATAG
* * * * **
40520808 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCGAAATACCAC-TGGTTTGTGA
1 AATTACCGAAATACCCTC-AATTTGTAAAATTACCAAAATACC-CTTGATTT-ACA
40520862 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCTTGATTTACA
1 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCTTGATTTACA
** * * * *
40520915 CAATTATAGAAATACCCTTAACTTTCTAAAAATTA-TAGAAATACCATT-AGTTTACAA
1 -AATTACCGAAATACCCTCAA-TTTGT-AAAATTACCA-AAATACCCTTGA-TTTAC-A
*
40520972 AATTACTGAAATACCCT
1 AATTACCGAAATACCCT
40520989 TGGATTGTAG
Statistics
Matches: 105, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
53 2 0.02
54 59 0.56
55 7 0.07
56 36 0.34
57 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (53 bp):
AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCTTGATTTACA
Found at i:40521765 original size:25 final size:25
Alignment explanation
Indices: 40521737--40521784 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40521727 TTATAGTATG
* * *
40521737 AAAATGACTATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
40521762 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
40521785 GTTTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:40521845 original size:20 final size:20
Alignment explanation
Indices: 40521820--40521886 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
40521810 GATATGATAT
*
40521820 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
40521840 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
40521860 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
40521880 ACATGAT
1 ACATGAT
40521887 GTATTCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:40522020 original size:52 final size:51
Alignment explanation
Indices: 40521936--40522058 Score: 196
Period size: 52 Copynumber: 2.4 Consensus size: 51
40521926 GAGGAAGTGC
* *
40521936 AAAAGGGCTTATGCCCTAGTTTATTGAGAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAGAAGGGCTT-TGCCCCAGTTTACCA
40521988 AAAAGGGCTTATGCCCCAGTTTATTGTA-AAGGGCTTTGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTATTG-AGAAGGGCTTTGCCCCAGTTTACCA
40522039 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40522059 ATTAAAAGAG
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
50 10 0.15
51 24 0.35
52 33 0.49
53 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAGAAGGGCTTTGCCCCAGTTTACCA
Found at i:40522033 original size:25 final size:26
Alignment explanation
Indices: 40521936--40522058 Score: 160
Period size: 26 Copynumber: 4.8 Consensus size: 26
40521926 GAGGAAGTGC
* **
40521936 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
40521962 AGAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
**
40521988 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* *
40522014 TAAAGGGCTT-TGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCG
40522039 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
40522059 ATTAAAAGAG
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 31 0.36
26 54 0.64
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:40522226 original size:42 final size:42
Alignment explanation
Indices: 40522167--40522258 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
40522157 TAGTCTCCCC
* ** *
40522167 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTAATATTACATATGATATTG
*
40522209 AAATGGGCTTGCATACATCCATTAATATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTAATATTACATATGATATTG
40522251 AAATGGGC
1 AAATGGGC
40522259 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTAATATTACATATGATATTG
Found at i:40522317 original size:31 final size:31
Alignment explanation
Indices: 40522282--40522360 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
40522272 CGTTTACAGT
40522282 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
*
40522313 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
*
40522344 AAAGGCTTCAGCCCAGT
1 AAAGGCTTCGGCCCAGT
40522361 AACCGTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTTATGA
Found at i:40524032 original size:45 final size:45
Alignment explanation
Indices: 40523948--40524035 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
40523938 CTATGCGATC
* * *
40523948 TGAACTCATTGAGTTGTGGTCTGATTTCATGATATATGTGACATT
1 TGAACTCATTGAGTTGTGGTCTGAGTTCATAATACATGTGACATT
* *
40523993 TGAACTTATTGAGTTGTGGTCTGAGTTCATAATGCATGTGACA
1 TGAACTCATTGAGTTGTGGTCTGAGTTCATAATACATGTGACA
40524036 CATGTTTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (45 bp):
TGAACTCATTGAGTTGTGGTCTGAGTTCATAATACATGTGACATT
Found at i:40526699 original size:48 final size:47
Alignment explanation
Indices: 40526611--40526789 Score: 162
Period size: 48 Copynumber: 3.7 Consensus size: 47
40526601 GGTCTACATA
* * ** *
40526611 CCGATGCCATATCCCAGATATGGTTTTACA-TGAAATCACATACCAAGG
1 CCGATGCCATATCCCAGACATGGTCTTACACTGGCA-CACATACC-ATG
* * *
40526659 CCGATGCCATATCCTAGATATGGTCTTACACTGGCACACATATCGATG
1 CCGATGCCATATCCCAGACATGGTCTTACACTGGCACACATA-CCATG
** * * * *
40526707 CCGATGTTATGTCCCAGACATGGTCTTATACTGGCTCTCATATCCATG
1 CCGATGCCATATCCCAGACATGGTCTTACACTGGCACACATA-CCATG
* * *
40526755 TCGATGCCATGTCTCAGACATGGTCTTACACTGGC
1 CCGATGCCATATCCCAGACATGGTCTTACACTGGC
40526790 TCTCATAAAT
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
48 105 0.96
49 4 0.04
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (47 bp):
CCGATGCCATATCCCAGACATGGTCTTACACTGGCACACATACCATG
Found at i:40526790 original size:48 final size:47
Alignment explanation
Indices: 40526658--40526796 Score: 170
Period size: 48 Copynumber: 2.9 Consensus size: 47
40526648 ACATACCAAG
* * * * *
40526658 GCCGATGCCATATCCTAGATATGGTCTTACACTGGCACACATATCGAT
1 GCCGATGCCATGTCC-AGACATGGTCTTACACTGGCTCTCATATCCAT
** *
40526706 GCCGATGTTATGTCCCAGACATGGTCTTATACTGGCTCTCATATCCAT
1 GCCGATGCCATGT-CCAGACATGGTCTTACACTGGCTCTCATATCCAT
*
40526754 GTCGATGCCATGTCTCAGACATGGTCTTACACTGGCTCTCATA
1 GCCGATGCCATGTC-CAGACATGGTCTTACACTGGCTCTCATA
40526797 AATCGTGGTG
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
47 1 0.01
48 74 0.96
49 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (47 bp):
GCCGATGCCATGTCCAGACATGGTCTTACACTGGCTCTCATATCCAT
Found at i:40531053 original size:25 final size:25
Alignment explanation
Indices: 40531025--40531073 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
40531015 TTGTTTTTGA
*
40531025 TAGTATATCTTGAAACTGCTATAGG
1 TAGTATATCTTGAAACTACTATAGG
* *
40531050 TAGTATATGTTGAGACTACTATAG
1 TAGTATATCTTGAAACTACTATAG
40531074 ATATACTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (25 bp):
TAGTATATCTTGAAACTACTATAGG
Found at i:40536939 original size:18 final size:18
Alignment explanation
Indices: 40536916--40536957 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
40536906 AAGGCCAATT
*
40536916 TGGGCAGTGTCGG-CCACA
1 TGGGCA-TGTAGGCCCACA
40536934 TGGGCATGTAGGCCCACA
1 TGGGCATGTAGGCCCACA
*
40536952 CGGGCA
1 TGGGCA
40536958 AGCAACATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.19, C:0.29, G:0.38, T:0.14
Consensus pattern (18 bp):
TGGGCATGTAGGCCCACA
Found at i:40538775 original size:21 final size:21
Alignment explanation
Indices: 40538736--40538775 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40538726 CCATATATCA
* *
40538736 AGCTAATCACTAAAGGTATTT
1 AGCTAATCACCAAAAGTATTT
*
40538757 AGCTAATGACCAAAAGTAT
1 AGCTAATCACCAAAAGTAT
40538776 ATCAAGTTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
AGCTAATCACCAAAAGTATTT
Found at i:40539694 original size:46 final size:46
Alignment explanation
Indices: 40539590--40539800 Score: 162
Period size: 46 Copynumber: 4.6 Consensus size: 46
40539580 GATCGGAGGG
* * * * *
40539590 TGCCAT-GATGTCTTTCAACCATGGTCTTTTTTATTCTCGA-C-TTT
1 TGCCATAG-TGTCTTTCAACCATGGTCTTATTCATTTTCTATCGTGT
* *
40539634 ATGCCATAGTGTCTTTCAGCCATTGTCTTATTCATTTT-TCATCGTGT
1 -TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCT-ATCGTGT
** *
40539681 TGCCATAGTGTCTTTCAATTATGGTTTTATTCATTTTCTATCGTGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCTATCGTGT
* * ** * ** * *
40539727 TGCTATAGTGTCTTTTAATTATGGTCTTATTCGTTTGAT-TCATGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCTATCGTGT
* * *
40539772 TGCCATAGCGTCTTTCAGCTATGGTCTTA
1 TGCCATAGTGTCTTTCAACCATGGTCTTA
40539801 CTCGGTAGAA
Statistics
Matches: 136, Mismatches: 25, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
45 59 0.43
46 74 0.54
47 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (46 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCTATCGTGT
Found at i:40539797 original size:45 final size:45
Alignment explanation
Indices: 40539634--40539942 Score: 187
Period size: 45 Copynumber: 6.8 Consensus size: 45
40539624 TCTCGACTTT
* *
40539634 ATGCCATAGTGTCTTTCAGCCATTGTCTTATTCATTT--TTCATCGTG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGATTCA---TG
* ** * ** *
40539680 TTGCCATAGTGTCTTTCAATTATGGTTTTATTCATTTTCTATCGTG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGAT-TCATG
* * * ** *
40539726 TTGCTATAGTGTCTTTTAATTATGGTCTTATTCGTTTGATTCATG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGATTCATG
* * ** * *
40539771 ATGCCATAGCGTCTTTCAGCTATGGTCTTACTCGGTAGAAT-AGTG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGATTCA-TG
* * * * * * * * *
40539816 CTGTCATAATGTCTTTCAGCTATGGCCTTACTCAATAGAATCGTG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGATTCATG
** * *
40539861 ATGCCATAACGTCTTTCAGCTATGGTCTTACTCATTTCTG-GT-ATG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCA-TT-TGATTCATG
* * *
40539906 GTGCCATAGTGTCTTTCATCTATGGTCTTATTTATTT
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTT
40539943 CTGGTATAGA
Statistics
Matches: 210, Mismatches: 46, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
43 1 0.00
44 3 0.01
45 133 0.63
46 69 0.33
47 1 0.00
48 1 0.00
49 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.44
Consensus pattern (45 bp):
ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGATTCATG
Found at i:40539964 original size:45 final size:45
Alignment explanation
Indices: 40539768--40539968 Score: 142
Period size: 45 Copynumber: 4.5 Consensus size: 45
40539758 CGTTTGATTC
** ** * *
40539768 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTC-GGT-AGAAT
1 ATGATGCCATAATGTCTTTCAGCTATGGTCTTACTCATTTCTG-GT
* * * * * *
40539812 AGTGCTGTCATAATGTCTTTCAGCTATGGCCTTACTCA-AT-AGAAT
1 A-TGATGCCATAATGTCTTTCAGCTATGGTCTTACTCATTTCTG-GT
* *
40539857 CGTGATGCCATAACGTCTTTCAGCTATGGTCTTACTCATTTCTGGT
1 -ATGATGCCATAATGTCTTTCAGCTATGGTCTTACTCATTTCTGGT
* * * * *
40539903 ATGGTGCCATAGTGTCTTTCATCTATGGTCTTATTTATTTCTGGT
1 ATGATGCCATAATGTCTTTCAGCTATGGTCTTACTCATTTCTGGT
*
40539948 ATAGAT-TCATAATGTCTTTCA
1 AT-GATGCCATAATGTCTTTCA
40539969 ACTAATGTCT
Statistics
Matches: 127, Mismatches: 24, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
44 1 0.01
45 121 0.95
46 4 0.03
47 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (45 bp):
ATGATGCCATAATGTCTTTCAGCTATGGTCTTACTCATTTCTGGT
Done.