Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 7 of 125
Found at i:945461 original size:31 final size:31
Alignment explanation
Indices: 945317--945466 Score: 117
Period size: 31 Copynumber: 4.7 Consensus size: 31
945307 TCTTATATAG
* *
945317 GTACCAACTAAACTGAACTTAAATCTTATC-
1 GTACCAGCTAAACTGGACTTAAATCTTATCA
* *
945347 GATGCTAGCTAAACT-GAGCTTAAATCTTATCA
1 G-TACCAGCTAAACTGGA-CTTAAATCTTATCA
* * * *
945379 GTACTAGTTAAATTAGG-CTTATAATCTTATTTA
1 GTACCAGCTAAACT-GGACTTA-AATCTTA-TCA
** * *
945412 GGTGTCAACTAAATTGGACTTAAATCTTATCA
1 -GTACCAGCTAAACTGGACTTAAATCTTATCA
945444 GTACCAGCTAAACTGGACTTAAA
1 GTACCAGCTAAACTGGACTTAAA
945467 ATCTCATTTG
Statistics
Matches: 93, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
30 2 0.02
31 56 0.60
32 10 0.11
33 12 0.13
34 13 0.14
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (31 bp):
GTACCAGCTAAACTGGACTTAAATCTTATCA
Found at i:946924 original size:14 final size:16
Alignment explanation
Indices: 946891--946928 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
946881 TTAAGCCCTA
946891 AATTTTATTTATATTTT
1 AATTTT-TTTATATTTT
946908 AATTTTTTTA-A-TTT
1 AATTTTTTTATATTTT
946922 AATTTTT
1 AATTTTT
946929 GGTTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.48
15 1 0.05
16 4 0.19
17 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
AATTTTTTTATATTTT
Found at i:946926 original size:26 final size:26
Alignment explanation
Indices: 946891--946940 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
946881 TTAAGCCCTA
* *
946891 AATTTTATTTATATTTTAATTTTTTT
1 AATTTAATTTATAGTTTAATTTTTTT
* *
946917 AATTTAATTTTTGGTTTAATTTTT
1 AATTTAATTTATAGTTTAATTTTT
946941 ATTTTTTTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (26 bp):
AATTTAATTTATAGTTTAATTTTTTT
Found at i:947013 original size:22 final size:21
Alignment explanation
Indices: 946972--947011 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
946962 AAAATCAATT
946972 GGTAAAAAAAAATAAAAAAGG
1 GGTAAAAAAAAATAAAAAAGG
*
946993 GGTAAAAATAAATAAAAAA
1 GGTAAAAAAAAATAAAAAA
947012 AGAAGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12
Consensus pattern (21 bp):
GGTAAAAAAAAATAAAAAAGG
Found at i:947654 original size:21 final size:20
Alignment explanation
Indices: 947630--947683 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
947620 TATTTACATG
* *
947630 ATTAATATATTTGTGTGATTT
1 ATTAATATATTTGTATGA-CT
* *
947651 ATTAAAAAATTTGTATGACT
1 ATTAATATATTTGTATGACT
*
947671 ATTAATATGTTTG
1 ATTAATATATTTG
947684 CTTGATTAGT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (20 bp):
ATTAATATATTTGTATGACT
Found at i:947728 original size:20 final size:20
Alignment explanation
Indices: 947659--947742 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 20
947649 TTATTAAAAA
* * *
947659 ATTTGTATGACTATTAATAT
1 ATTTGCATGATTATTAATTT
* * *
947679 GTTTGCTTGATTAGTAATTT
1 ATTTGCATGATTATTAATTT
* * *
947699 CTCTGGATGATTATTAATTT
1 ATTTGCATGATTATTAATTT
* *
947719 ATTTGCATGATTATCAACTT
1 ATTTGCATGATTATTAATTT
947739 ATTT
1 ATTT
947743 ATTTGTGTGC
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.51
Consensus pattern (20 bp):
ATTTGCATGATTATTAATTT
Found at i:947812 original size:21 final size:20
Alignment explanation
Indices: 947787--947825 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
947777 AATTGCATGT
947787 TTATTTGCATGATTTATATTA
1 TTATTTGCATGA-TTATATTA
947808 TTATTTGCATGATTATAT
1 TTATTTGCATGATTATAT
947826 GTGTGATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.56
Consensus pattern (20 bp):
TTATTTGCATGATTATATTA
Found at i:947943 original size:19 final size:19
Alignment explanation
Indices: 947921--947980 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
947911 TTTTTTGTTA
947921 TTATTGCATGATTTTATAT
1 TTATTGCATGATTTTATAT
*
947940 TTATCGCATGA---TATAT
1 TTATTGCATGATTTTATAT
947956 GTTATTGCATG-TTTTATAT
1 -TTATTGCATGATTTTATAT
947975 TTATTG
1 TTATTG
947981 TGTTCATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 5 0.14
17 9 0.26
18 6 0.17
19 15 0.43
ACGTcount: A:0.25, C:0.07, G:0.13, T:0.55
Consensus pattern (19 bp):
TTATTGCATGATTTTATAT
Found at i:947954 original size:64 final size:64
Alignment explanation
Indices: 947886--948006 Score: 153
Period size: 64 Copynumber: 1.9 Consensus size: 64
947876 ATGATTATTA
*
947886 ATATAT-TTATTTGCATGGTTATT-TATTT-TT-TGTT-ATTATTGCATGATTTTATATTTATCG
1 ATATATGTTA-TTGCAT-GTT-TTATATTTATTGTGTTCATAATTGCATGA--TTATATTTATCG
947946 CATG
61 CATG
947950 ATATATGTTATTGCATGTTTTATATTTATTGTGTTCATAATTGCATGATTATATTTA
1 ATATATGTTATTGCATGTTTTATATTTATTGTGTTCATAATTGCATGATTATATTTA
948007 ATTTCATAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
62 2 0.04
63 8 0.16
64 23 0.45
65 7 0.14
66 11 0.22
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (64 bp):
ATATATGTTATTGCATGTTTTATATTTATTGTGTTCATAATTGCATGATTATATTTATCGCATG
Found at i:947965 original size:17 final size:17
Alignment explanation
Indices: 947921--948006 Score: 60
Period size: 19 Copynumber: 5.2 Consensus size: 17
947911 TTTTTTGTTA
947921 TTATTGCATGATTTTATAT
1 TTATTGCATGA--TTATAT
*
947940 TTATCGCATGA-TATAT
1 TTATTGCATGATTATAT
*
947956 GTTATTGCATGTTTTATAT
1 -TTATTGCATG-ATTATAT
947975 TTATTG--TG-TTCATA-
1 TTATTGCATGATT-ATAT
947989 --ATTGCATGATTATAT
1 TTATTGCATGATTATAT
948004 TTA
1 TTA
948007 ATTTCATAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 22
0.68 0.04 0.28
Matches are distributed among these distances:
12 4 0.07
14 7 0.13
15 5 0.09
16 7 0.13
17 10 0.19
18 6 0.11
19 15 0.28
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (17 bp):
TTATTGCATGATTATAT
Found at i:948045 original size:18 final size:19
Alignment explanation
Indices: 948017--948090 Score: 91
Period size: 18 Copynumber: 4.0 Consensus size: 19
948007 ATTTCATAAT
948017 TATTAATATATTTGCATGA
1 TATTAATATATTTGCATGA
*
948036 TATT-ATATATTTACATGA
1 TATTAATATATTTGCATGA
* *
948054 TTTTCAT-TA-TTGCATGA
1 TATTAATATATTTGCATGA
948071 TAATTAATATATTTGCATGA
1 T-ATTAATATATTTGCATGA
948091 CATTCTTGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.17
18 22 0.48
19 8 0.17
20 8 0.17
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (19 bp):
TATTAATATATTTGCATGA
Found at i:949680 original size:63 final size:63
Alignment explanation
Indices: 949552--949682 Score: 140
Period size: 63 Copynumber: 2.1 Consensus size: 63
949542 ATGAATGGGG
* * * *
949552 TTATTTAAGGCGTTTTATAACAAAAAATACCTTGAATAATCTCCAAAAATTTTTATGAAGGGA
1 TTATTGAAGGCGTTTTATAACAAAAAACACCTTGAATAACCTCCAAAAATTTTTATGAAAGGA
* * * * * *
949615 TTATTGAAGGCGTTTTTTGAC-AGAAACACCTTGAATAACCTCTATTAAATTTTT-TGTAAATGA
1 TTATTGAAGGCGTTTTATAACAAAAAACACCTTGAATAACCTCCA-AAAATTTTTATG-AAAGGA
949678 TTATT
1 TTATT
949683 CAATGTATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
62 21 0.38
63 35 0.62
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (63 bp):
TTATTGAAGGCGTTTTATAACAAAAAACACCTTGAATAACCTCCAAAAATTTTTATGAAAGGA
Found at i:949754 original size:61 final size:60
Alignment explanation
Indices: 949676--950052 Score: 262
Period size: 61 Copynumber: 6.1 Consensus size: 60
949666 TTTTGTAAAT
* * *
949676 GATTATTCAATGTATTTTTAGCCAAAAATGCCTTCAATAATCTCTTATAAATTTGTT-TTAG
1 GATTATTCAAGGTATTTTTGGCCAAAAATGCCTTCAATAATCCCTT-TAAATTT-TTATTAG
* * *
949737 GATTATTCAAGGTATTTTTGGCTAAAAATGCCTTCAATAATCCAC-TTCAATTTTTATGAAG
1 GATTATTCAAGGTATTTTTGGCCAAAAATGCCTTCAATAATCC-CTTTAAATTTTTAT-TAG
* * * *
949798 TGATTATTCAAGGTGTTTTT-GCCAAAAATGTCTTGAATAATCCCTTCAAATTTTTTATTAGG
1 -GATTATTCAAGGTATTTTTGGCCAAAAATGCCTTCAATAATCCCTTTAAA-TTTTTATTA-G
* * * ** *
949860 GATTATTCAAGGTGTTTTTGGCCAGAAAACGCCTTGAATAATCCCTTATGAAAAATTTAATAG
1 GATTATTCAAGGTATTTTTGGCCA-AAAATGCCTTCAATAATCCCTT-T-AAATTTTTATTAG
* * * * ** * * * ** *
949923 GGTTATTGAAGGTATTTCTGGCTAAAAACACCTTGAATAATCACCTCATAAAAATTGAAGT-G
1 GATTATTCAAGGTATTTTTGGCCAAAAATGCCTTCAATAATC-CCT--TTAAATTTTTATTAG
* * * * * *
949985 GATTATTAAAGGTATTTTTTGCTAGAAACG-CTTCGAATAA-CCCTATTAAATTTTTTATAAG
1 GATTATTCAAGGTATTTTTGGCCAAAAATGCCTTC-AATAATCCCT-TTAAA-TTTTTATTAG
950046 GATTATT
1 GATTATT
950053 AAAAATGTTT
Statistics
Matches: 256, Mismatches: 43, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
59 7 0.03
60 14 0.05
61 97 0.38
62 78 0.30
63 50 0.20
64 6 0.02
65 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (60 bp):
GATTATTCAAGGTATTTTTGGCCAAAAATGCCTTCAATAATCCCTTTAAATTTTTATTAG
Found at i:949802 original size:123 final size:124
Alignment explanation
Indices: 949662--949903 Score: 321
Period size: 123 Copynumber: 2.0 Consensus size: 124
949652 ACCTCTATTA
* * *
949662 AATTTTTTGTAAATGATTATTCAATGTATTTTTAGCCAAAAATGCCTTCAATAATCTCTTATAAA
1 AATTTTTTGTAAATGATTATTCAAGGTATTTTT-GCCAAAAATGCCTTCAATAATCCCTT-CAAA
* *
949727 TTTGTT-TTA-GGATTATTCAAGGTATTTTTGGCTA-AAAATGCCTTCAATAATCCACTTC
64 TTTGTTATTAGGGATTATTCAAGGTATTTTTGGCCAGAAAACGCCTTCAATAATCCACTTC
* * * *
949785 AATTTTTATG-AAGTGATTATTCAAGGTGTTTTTGCCAAAAATGTCTTGAATAATCCCTTCAAAT
1 AATTTTT-TGTAAATGATTATTCAAGGTATTTTTGCCAAAAATGCCTTCAATAATCCCTTCAAAT
* * *
949849 TTTTTATTAGGGATTATTCAAGGTGTTTTTGGCCAGAAAACGCCTTGAATAATCC
65 TTGTTATTAGGGATTATTCAAGGTATTTTTGGCCAGAAAACGCCTTCAATAATCC
949904 CTTATGAAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
121 8 0.08
122 26 0.25
123 50 0.49
124 19 0.18
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (124 bp):
AATTTTTTGTAAATGATTATTCAAGGTATTTTTGCCAAAAATGCCTTCAATAATCCCTTCAAATT
TGTTATTAGGGATTATTCAAGGTATTTTTGGCCAGAAAACGCCTTCAATAATCCACTTC
Found at i:949937 original size:186 final size:186
Alignment explanation
Indices: 949599--949964 Score: 416
Period size: 186 Copynumber: 2.0 Consensus size: 186
949589 AATCTCCAAA
* * *
949599 AATTTTTATGAAGGGATTATTGAAGGCGTTTTTTGACAGAAACACCTTGAATAACCTCTATTAAA
1 AATTTTTATGAAGGGATTATTCAAGGCGTTTTTTGACAAAAACACCTTGAATAACCTCTATCAAA
* * * * * *
949664 TTTTTTGTAAATGATTATTCAATGTATTTTTAGCCAAAAATGCCTTCAATAATCTCTTATAAATT
66 TTTTTTATAAAGGATTATTCAAGGTATTTTTAGCCAAAAACGCCTTCAATAATCCCTTATAAAAT
** * **
949729 TGTTTTAGGATTATTCAAGGTATTTTTGGCTAAAAATGCCTTCAATAATCCACTTC
131 TGTAATAGGATTATTCAAGGTATTTCTGGCTAAAAACACCTTCAATAATCCACTTC
* * * ***
949785 AATTTTTATGAAGTGATTATTCAAGGTG-TTTTTGCCAAAAATGTCTTGAATAATCC-CT-TCAA
1 AATTTTTATGAAGGGATTATTCAAGGCGTTTTTTGACAAAAACACCTTGAATAA-CCTCTATCAA
* * * * *
949847 ATTTTTTATTAGGGATTATTCAAGGTGTTTTTGGCCAGAAAACGCCTTGAATAATCCCTTATGAA
65 ATTTTTTATAAAGGATTATTCAAGGTATTTTTAGCCA-AAAACGCCTTCAATAATCCCTTAT--A
* * *
949912 AAATT-TAATAGGGTTATTGAAGGTATTTCTGGCTAAAAACACCTTGAATAATC
127 AAATTGTAATAGGATTATTCAAGGTATTTCTGGCTAAAAACACCTTCAATAATC
949965 ACCTCATAAA
Statistics
Matches: 148, Mismatches: 28, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
184 33 0.22
185 43 0.29
186 67 0.45
187 5 0.03
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (186 bp):
AATTTTTATGAAGGGATTATTCAAGGCGTTTTTTGACAAAAACACCTTGAATAACCTCTATCAAA
TTTTTTATAAAGGATTATTCAAGGTATTTTTAGCCAAAAACGCCTTCAATAATCCCTTATAAAAT
TGTAATAGGATTATTCAAGGTATTTCTGGCTAAAAACACCTTCAATAATCCACTTC
Found at i:950023 original size:62 final size:61
Alignment explanation
Indices: 949859--950028 Score: 166
Period size: 62 Copynumber: 2.7 Consensus size: 61
949849 TTTTTATTAG
* * * * *
949859 GGATTATTCAAGGTGTTTTTGGCCAGAAAACGCCTTGAATAATCCCTTATGAAAAATTTAATA
1 GGATTATTAAAGGTATTTTTGGCTAG-AAACG-CTTGAATAATCCCTCATGAAAAATTGAATA
* * * * *
949922 GGGTTATTGAAGGTATTTCTGGCTAAAAACACCTTGAATAATCACCTCAT-AAAAATTGAAGT-
1 GGATTATTAAAGGTATTTTTGGCTAGAAAC-GCTTGAATAATC-CCTCATGAAAAATTGAA-TA
*
949984 GGATTATTAAAGGTATTTTTTGCTAGAAACGCTTCGAATAA-CCCT
1 GGATTATTAAAGGTATTTTTGGCTAGAAACGCTT-GAATAATCCCT
950029 ATTAAATTTT
Statistics
Matches: 88, Mismatches: 15, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
60 3 0.03
61 4 0.05
62 55 0.62
63 26 0.30
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (61 bp):
GGATTATTAAAGGTATTTTTGGCTAGAAACGCTTGAATAATCCCTCATGAAAAATTGAATA
Found at i:950200 original size:62 final size:62
Alignment explanation
Indices: 950115--950254 Score: 149
Period size: 62 Copynumber: 2.3 Consensus size: 62
950105 GGATTATTCA
* * * **
950115 ACCTTGAATAATTCCTTACAAAAATTTAATCGAGATTATTCAAGGCATTTTT-GCTAAAAACT
1 ACCTTGAATAATCCCTAACAAAAAATTAAAAGAGATTATTCAAGGCATTTTTGGCTAAAAA-T
* * * ** *
950177 ACCTTGAATAATCCCTAATAAAAAATTAAAAGGGATTATTTAAGGTGTTTTTGGCTAGAAAT
1 ACCTTGAATAATCCCTAACAAAAAATTAAAAGAGATTATTCAAGGCATTTTTGGCTAAAAAT
*
950239 GCCTTGAATAA-CCCTA
1 ACCTTGAATAATCCCTA
950255 TTCAATTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
61 5 0.08
62 53 0.82
63 7 0.11
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (62 bp):
ACCTTGAATAATCCCTAACAAAAAATTAAAAGAGATTATTCAAGGCATTTTTGGCTAAAAAT
Found at i:957521 original size:42 final size:42
Alignment explanation
Indices: 957452--957602 Score: 191
Period size: 42 Copynumber: 3.6 Consensus size: 42
957442 AAATGATTTC
957452 ATTTTATTTTTCAAAAGTTTCAAAGCCTTAATTATGGGAGAGA
1 ATTTTATTTTTCAAAAGTTTCAAAGCCTTAATTATGGG-GAGA
*
957495 ATTTTATTTTTC-AAAGTTTCAAAGCCTCT-ACTATGGGGA-A
1 ATTTTATTTTTCAAAAGTTTCAAAGCCT-TAATTATGGGGAGA
* * * *
957535 CATTTTATTTTTCAAAAGTTTCAAAGCCTCAGTTGTGGGGAGC
1 -ATTTTATTTTTCAAAAGTTTCAAAGCCTTAATTATGGGGAGA
*
957578 ATTTTATTTTTTAGAAAGTTTCAAA
1 ATTTTATTTTTCA-AAAGTTTCAAA
957603 TCTTTGTTAG
Statistics
Matches: 95, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
40 1 0.01
41 14 0.15
42 56 0.59
43 24 0.25
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (42 bp):
ATTTTATTTTTCAAAAGTTTCAAAGCCTTAATTATGGGGAGA
Found at i:958614 original size:20 final size:20
Alignment explanation
Indices: 958488--958681 Score: 122
Period size: 20 Copynumber: 10.2 Consensus size: 20
958478 TTTTGCATGA
* * *
958488 ATTTGCATGACTAATATTAT
1 ATTTGCATGATTATTAATAT
* * *
958508 ATTTGCGTGATTAATATTAT
1 ATTTGCATGATTATTAATAT
*
958528 ATTTGCATG---A-TAATTT
1 ATTTGCATGATTATTAATAT
*
958544 ATTTGCCT-ATTATT--T-T
1 ATTTGCATGATTATTAATAT
*
958560 ATTTACATG---ATTAATAT
1 ATTTGCATGATTATTAATAT
**
958577 ATTTGTGTGATTTATTAATAT
1 ATTTGCATGA-TTATTAATAT
* *
958598 ATTTGCATAACTATTAATAT
1 ATTTGCATGATTATTAATAT
* *
958618 TTTTGCATGATTATTAATTT
1 ATTTGCATGATTATTAATAT
* * *
958638 ATCTGGATGATTATTAATTT
1 ATTTGCATGATTATTAATAT
* *
958658 ATTTGCATGATTATCAATTT
1 ATTTGCATGATTATTAATAT
958678 ATTT
1 ATTT
958682 ATTTGTGTGA
Statistics
Matches: 137, Mismatches: 25, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
14 3 0.02
16 19 0.14
17 9 0.07
18 1 0.01
19 1 0.01
20 89 0.65
21 15 0.11
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (20 bp):
ATTTGCATGATTATTAATAT
Found at i:958752 original size:21 final size:22
Alignment explanation
Indices: 958726--958767 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
958716 AATTGCATGT
958726 TTATTTGCATGATT-TATATTA
1 TTATTTGCATGATTATATATTA
*
958747 TTATTTTCATGATTATATATT
1 TTATTTGCATGATTATATATT
958768 TAATTGCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.60
Consensus pattern (22 bp):
TTATTTGCATGATTATATATTA
Found at i:958777 original size:20 final size:20
Alignment explanation
Indices: 958725--958777 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
958715 TAATTGCATG
958725 TTTATTTGCATGATTTATAT
1 TTTATTTGCATGATTTATAT
*
958745 TATTATTTTCATGA-TTATAT
1 T-TTATTTGCATGATTTATAT
*
958765 ATTTAATTGCATG
1 -TTTATTTGCATG
958778 TCTATTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTATTTGCATGATTTATAT
Found at i:958970 original size:38 final size:36
Alignment explanation
Indices: 958928--959003 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
958918 TTATATTTAA
958928 TTACATAATTATTAATATATTTGCATAAT-ATTATATAT
1 TTACATAATTATT-AT-TA-TTGCATAATAATTATATAT
* * *
958966 TTACATCATTGTTATTATTGCATGATAATTATATAT
1 TTACATAATTATTATTATTGCATAATAATTATATAT
959002 TT
1 TT
959004 GCATGACATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 8 0.24
36 13 0.38
37 2 0.06
38 11 0.32
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (36 bp):
TTACATAATTATTATTATTGCATAATAATTATATAT
Found at i:960639 original size:17 final size:17
Alignment explanation
Indices: 960619--960676 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
960609 TATCATTTTC
960619 TCATTTTCATTTTTCTT
1 TCATTTTCATTTTTCTT
960636 TCATTTTC-TTTATT-TT
1 TCATTTTCATTT-TTCTT
*
960652 TCCACTTT-ATTTTTCTT
1 T-CATTTTCATTTTTCTT
960669 TCACTTTT
1 TCA-TTTT
960677 TTTTTCCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 10 0.29
17 24 0.71
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (17 bp):
TCATTTTCATTTTTCTT
Found at i:960675 original size:16 final size:16
Alignment explanation
Indices: 960627--960682 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
960617 TCTCATTTTC
*
960627 ATTTTTCTTTCATTTT
1 ATTTTTCTTTCACTTT
*
960643 CTTTATT-TTTCCACTTT
1 ATTT-TTCTTT-CACTTT
960660 ATTTTTCTTTCACTTT
1 ATTTTTCTTTCACTTT
*
960676 TTTTTTC
1 ATTTTTC
960683 CTTTTCTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 20 0.61
17 13 0.39
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTCTTTCACTTT
Found at i:967412 original size:18 final size:18
Alignment explanation
Indices: 967389--967423 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
967379 AGCCAACTAG
967389 CCTCCAAGCTTCCACCCT
1 CCTCCAAGCTTCCACCCT
**
967407 CCTCCAATTTTCCACCC
1 CCTCCAAGCTTCCACCC
967424 AATCAATGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.54, G:0.03, T:0.26
Consensus pattern (18 bp):
CCTCCAAGCTTCCACCCT
Found at i:969464 original size:8 final size:8
Alignment explanation
Indices: 969451--969508 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
969441 AAATTATGAA
969451 AAACCCTT
1 AAACCCTT
*
969459 AAACCCTA
1 AAACCCTT
* *
969467 AAACTCTA
1 AAACCCTT
*
969475 AAACCTTT
1 AAACCCTT
*
969483 AAACCCTG
1 AAACCCTT
*
969491 AAACCTTT
1 AAACCCTT
969499 AAA-CCTT
1 AAACCCTT
969506 AAA
1 AAA
969509 ACCTCAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
7 6 0.15
8 34 0.85
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (8 bp):
AAACCCTT
Found at i:969502 original size:24 final size:24
Alignment explanation
Indices: 969450--969511 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
969440 AAAATTATGA
*
969450 AAAACCCTTAAACCCTAAAACTCT
1 AAAACCTTTAAACCCTAAAACTCT
*
969474 AAAACCTTTAAACCCTGAAAC-CTT
1 AAAACCTTTAAACCCTAAAACTC-T
* *
969498 TAAACCTTAAAACC
1 AAAACCTTTAAACC
969512 TCAAAATCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAACCTTTAAACCCTAAAACTCT
Found at i:969510 original size:8 final size:8
Alignment explanation
Indices: 969450--969517 Score: 50
Period size: 8 Copynumber: 8.5 Consensus size: 8
969440 AAAATTATGA
969450 AAAACCCTT
1 AAAA-CCTT
*
969459 -AAACCCT
1 AAAACCTT
969466 AAAA-CTCT
1 AAAACCT-T
969474 AAAACCTT
1 AAAACCTT
* *
969482 TAAACCCT
1 AAAACCTT
*
969490 GAAACCTT
1 AAAACCTT
*
969498 TAAACCTT
1 AAAACCTT
*
969506 AAAACCTC
1 AAAACCTT
969514 AAAA
1 AAAA
969518 TCCTGAAACA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
7 4 0.09
8 41 0.87
9 2 0.04
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.22
Consensus pattern (8 bp):
AAAACCTT
Found at i:981132 original size:12 final size:12
Alignment explanation
Indices: 981105--981161 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
981095 NNNNNNAGGT
*
981105 TTTTTTTTTTGAA
1 TTTTTTTTTT-CA
981118 TTTTTTTTTTCA
1 TTTTTTTTTTCA
981130 TTTATTTTTTT-A
1 TTT-TTTTTTTCA
*
981142 -TTTGTTTTTCTA
1 TTTTTTTTTTC-A
981154 TTTTTTTT
1 TTTTTTTT
981162 ATTTATTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 6 0.16
11 2 0.05
12 6 0.16
13 23 0.62
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:981168 original size:13 final size:12
Alignment explanation
Indices: 981104--981168 Score: 67
Period size: 12 Copynumber: 5.2 Consensus size: 12
981094 NNNNNNNAGG
981104 TTTTTTTTTTTGAA
1 TTTTTTTTTTT--A
*
981118 TTTTTTTTTTCA
1 TTTTTTTTTTTA
*
981130 TTTATTTTTTTA
1 TTTTTTTTTTTA
* *
981142 TTTGTTTTTCTA
1 TTTTTTTTTTTA
981154 TTTTTTTTATTTA
1 TTTTTTTT-TTTA
981167 TT
1 TT
981169 AGATTAGATT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
12 28 0.65
13 5 0.12
14 10 0.23
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:981227 original size:16 final size:16
Alignment explanation
Indices: 981208--981269 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
981198 TTATCTTATT
981208 TTTATTTTTGTTTTAC
1 TTTATTTTTGTTTTAC
*
981224 TTTATTTTT-TTTCTTC
1 TTTATTTTTGTTT-TAC
**
981240 TTTA-TTTACTTTTAC
1 TTTATTTTTGTTTTAC
981255 TTT-TATTTTGTTTTA
1 TTTAT-TTTTGTTTTA
981270 TATTCTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
15 11 0.30
16 26 0.70
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTATTTTTGTTTTAC
Found at i:981351 original size:57 final size:58
Alignment explanation
Indices: 981287--981621 Score: 500
Period size: 57 Copynumber: 5.8 Consensus size: 58
981277 TAAATAAAAA
981287 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
1 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
* ** *
981345 TCAAAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGGAAATCAAAGTT
1 TC--AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTT
*
981406 TCAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TT
1 TC-AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
*
981464 TCCAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TT
1 TCAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
* *
981521 TCAAAAAAATATTTTT-ATGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAATTT
1 TCAAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
*
981579 TC-AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
981622 CTACACAAGA
Statistics
Matches: 256, Mismatches: 15, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
56 1 0.00
57 139 0.54
58 10 0.04
59 3 0.01
60 96 0.38
61 7 0.03
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (58 bp):
TCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTT
Found at i:991813 original size:46 final size:46
Alignment explanation
Indices: 991761--991907 Score: 143
Period size: 46 Copynumber: 3.2 Consensus size: 46
991751 TCAGTTTTAG
*
991761 ATTTTTAAAATTGTCGA-CTCATTGCACCAAAACTTTTACTAATTAA
1 ATTTTTAAAATTGTCGAGC-CATTGCACCAAAACTTTTACAAATTAA
* * * * * * *
991807 ATTTTTAAAGTTGTTGAGCCTTTGCATCGAAACTTTTTCAAATTAG
1 ATTTTTAAAATTGTCGAGCCATTGCACCAAAACTTTTACAAATTAA
* * * * * * *
991853 ATTTTTAAAATTGTCAAGCCTTTACACCAAAGCTTTTCCATATTAG
1 ATTTTTAAAATTGTCGAGCCATTGCACCAAAACTTTTACAAATTAA
991899 ATTTTTAAA
1 ATTTTTAAA
991908 GTTATTGGAC
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
46 82 0.99
47 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (46 bp):
ATTTTTAAAATTGTCGAGCCATTGCACCAAAACTTTTACAAATTAA
Found at i:992079 original size:47 final size:47
Alignment explanation
Indices: 991901--992126 Score: 240
Period size: 47 Copynumber: 4.8 Consensus size: 47
991891 CATATTAGAT
* * *
991901 TTTTAAAGTTATTGGA-CCTTTGCTTAAAGGAG-TTTTTAGGATGAGC
1 TTTTAAAGTTA-TGAAGCCTTTGCTTAAAGGAGTTTTTTAAGATGAGA
* * * *
991947 TTTTAAAGTTATTAAGCCTTTGCTTAAATGAGTTTTTCAAAATGAGA
1 TTTTAAAGTTATGAAGCCTTTGCTTAAAGGAGTTTTTTAAGATGAGA
* * * * * * *
991994 TTTTTAAAAGTTTTTAAGCCTTTACTTATAGTAGTTTTTTAGGGTGAGA
1 -TTTT-AAAGTTATGAAGCCTTTGCTTAAAGGAGTTTTTTAAGATGAGA
* *
992043 TTTTAAAGTTATGAAGCATTTGTTTAAAGGAGTTTTTTAAGATGAGA
1 TTTTAAAGTTATGAAGCCTTTGCTTAAAGGAGTTTTTTAAGATGAGA
* * *
992090 TTTTAAAATTATGGAGTCTTTGCTTAAAGGAGTTTTT
1 TTTTAAAGTTATGAAGCCTTTGCTTAAAGGAGTTTTT
992127 AAATTTATTT
Statistics
Matches: 146, Mismatches: 30, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
45 2 0.01
46 26 0.18
47 76 0.52
48 8 0.05
49 34 0.23
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (47 bp):
TTTTAAAGTTATGAAGCCTTTGCTTAAAGGAGTTTTTTAAGATGAGA
Found at i:992308 original size:10 final size:10
Alignment explanation
Indices: 992293--992332 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
992283 AAAGAGACAC
992293 ACAAAAAAAA
1 ACAAAAAAAA
*
992303 ACAAAAAAGA
1 ACAAAAAAAA
992313 ACAAAAACAAA
1 ACAAAAA-AAA
992324 A-AAAAAAAA
1 ACAAAAAAAA
992333 GAATCAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.88, C:0.10, G:0.03, T:0.00
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:992308 original size:23 final size:23
Alignment explanation
Indices: 992263--992340 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 23
992253 TTTTATTCAA
992263 AACAAAAACAAAATAAATAAAAAGAG
1 AACAAAAACAAAA-AAA-AAAAA-AG
* *
992289 ACACACAAA-AAAAAACAAAAAAG
1 A-ACAAAAACAAAAAAAAAAAAAG
992312 AACAAAAAC-AAAAAAAAAAAAG
1 AACAAAAACAAAAAAAAAAAAAG
992334 AATCAAA
1 AA-CAAA
992341 CGAAGTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
22 20 0.44
23 7 0.16
24 5 0.11
25 2 0.04
26 5 0.11
27 6 0.13
ACGTcount: A:0.79, C:0.12, G:0.05, T:0.04
Consensus pattern (23 bp):
AACAAAAACAAAAAAAAAAAAAG
Found at i:992386 original size:18 final size:18
Alignment explanation
Indices: 992365--992404 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
992355 AAATTTTCCC
992365 AAAAAAA-CTAAAAAAGAA
1 AAAAAAATCTAAAAAA-AA
992383 AAAAAAATCTAAAAAAAA
1 AAAAAAATCTAAAAAAAA
992401 AAAA
1 AAAA
992405 CTCTTCCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.85, C:0.05, G:0.03, T:0.07
Consensus pattern (18 bp):
AAAAAAATCTAAAAAAAA
Found at i:992387 original size:19 final size:18
Alignment explanation
Indices: 992365--992404 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
992355 AAATTTTCCC
992365 AAAAAAACTAAAAAAGAAA
1 AAAAAAACTAAAAAA-AAA
*
992384 AAAAAATCTAAAAAAAAA
1 AAAAAAACTAAAAAAAAA
992402 AAA
1 AAA
992405 CTCTTCCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.85, C:0.05, G:0.03, T:0.07
Consensus pattern (18 bp):
AAAAAAACTAAAAAAAAA
Found at i:993779 original size:14 final size:14
Alignment explanation
Indices: 993741--993788 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
993731 TCTGCGAACC
993741 AAAAAAA-AAA-A-
1 AAAAAAAGAAAGAG
993752 AAAAAAA-AAA-AG
1 AAAAAAAGAAAGAG
*
993764 AAAGAAAGAAAGAG
1 AAAAAAAGAAAGAG
993778 AAAAAAAGAAA
1 AAAAAAAGAAA
993789 CAACAGGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
11 11 0.34
12 6 0.19
13 3 0.09
14 12 0.38
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAGAG
Found at i:993787 original size:18 final size:18
Alignment explanation
Indices: 993759--993801 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
993749 AAAAAAAAAA
*
993759 AAAAGAAAGAAAGAA-AGAG
1 AAAA-AAAGAAACAACAG-G
993778 AAAAAAAGAAACAACAGG
1 AAAAAAAGAAACAACAGG
993796 AAAAAA
1 AAAAAA
993802 CCAGTCTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.77, C:0.05, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAACAACAGG
Found at i:1008855 original size:61 final size:62
Alignment explanation
Indices: 1008710--1008935 Score: 240
Period size: 61 Copynumber: 3.8 Consensus size: 62
1008700 GCTCTTGTAC
* * * *
1008710 AAGAAAAATTGATACTTTTAAC-TTTTTCT--TAAA-ATA-TTTTTTT-ACAATTTTTATATTT
1 AAGAAAAATTGATACTTTCAACTTTTTTCTCAAAAATATATTTTTTTTGA-AAATTTAAT-TTT
* * * *
1008768 AAGGAAAATTGGTACTTCCAACTTTTTTC-CAAAAATAT-TTTTTATCTTGAAATTTTAATTTT
1 AAGAAAAATTGATACTTTCAACTTTTTTCTCAAAAATATATTTTT-T-TTGAAAATTTAATTTT
*
1008830 GAGAAAAATTGAT-CTTTCAAC-TTTTTCTCAAAAATATATTTTTTTTGAAAATTTAATTTT
1 AAGAAAAATTGATACTTTCAACTTTTTTCTCAAAAATATATTTTTTTTGAAAATTTAATTTT
* *
1008890 AAGAAAAATTGATACTTTCAAC-TTTTCCTTAAAAATATATTTTTTT
1 AAGAAAAATTGATACTTTCAACTTTTTTCTCAAAAATATATTTTTTT
1008936 GGAATTTTTA
Statistics
Matches: 143, Mismatches: 14, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
58 18 0.13
59 6 0.04
60 36 0.25
61 53 0.37
62 19 0.13
63 10 0.07
64 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (62 bp):
AAGAAAAATTGATACTTTCAACTTTTTTCTCAAAAATATATTTTTTTTGAAAATTTAATTTT
Found at i:1008887 original size:60 final size:61
Alignment explanation
Indices: 1008710--1008956 Score: 269
Period size: 60 Copynumber: 4.1 Consensus size: 61
1008700 GCTCTTGTAC
* * *
1008710 AAGAAAAATTGATACTTTTAACTTTTTCT--TAAA-ATA-TTTTTTT-ACAATTTTTATATTT
1 AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTTTGA-AATTTTAAT-TTT
* * *
1008768 AAGGAAAATTGGTACTTCCAACTTTTT-TCCAAAAATAT-TTTTTATCTTGAAATTTTAATTTT
1 AAGAAAAATTGATACTTTCAACTTTTTCT-CAAAAATATATTTTT-T-TTGAAATTTTAATTTT
* *
1008830 GAGAAAAATTGAT-CTTTCAACTTTTTCTCAAAAATATATTTTTTTTGAAAATTTAATTTT
1 AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTTTGAAATTTTAATTTT
* * * *
1008890 AAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATA-TTTTTTTGGAATTTTTATTTT
1 AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTTTGAAATTTTAATTTT
*
1008950 AGGAAAA
1 AAGAAAA
1008957 TCATTAAAGT
Statistics
Matches: 160, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
57 1 0.01
58 23 0.14
60 54 0.34
61 51 0.32
62 20 0.12
63 10 0.06
64 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (61 bp):
AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTTTGAAATTTTAATTTT
Found at i:1008974 original size:3 final size:3
Alignment explanation
Indices: 1008966--1009086 Score: 144
Period size: 3 Copynumber: 41.0 Consensus size: 3
1008956 ATCATTAAAG
* *
1008966 TAA TAA TAA TAA -AA TAA TAA -AA TAA -AA -AA TAA AAA TTAA GGAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA -TAA
* *
1009009 TAA TGA TAA -ATA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1009054 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1009087 ATCAAAGAAA
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
2 9 0.09
3 90 0.87
4 4 0.04
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1009550 original size:11 final size:11
Alignment explanation
Indices: 1009534--1009558 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1009524 TGGATTTTGG
1009534 AAATTTTCCAA
1 AAATTTTCCAA
1009545 AAATTTTCCAA
1 AAATTTTCCAA
1009556 AAA
1 AAA
1009559 AAAACTCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTTTCCAA
Found at i:1009876 original size:4 final size:4
Alignment explanation
Indices: 1009844--1009964 Score: 64
Period size: 4 Copynumber: 32.2 Consensus size: 4
1009834 CAAGAAAAAG
*
1009844 ATAA AGTAA A-AA AT-A AT-A AT-A AT-A ATAA AT-A A-AA ATAT ATAA
1 ATAA A-TAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * * * *
1009886 ATTA ATAT AT-A GTAA ATAA ATAA ATAT ATTA ATAG ATAA AT-A ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * *
1009932 A-AA ATAT ATTA ATAA ATAA ATAA TAAAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA -ATAA ATAA A
1009965 AATAAAAATA
Statistics
Matches: 88, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
3 26 0.30
4 55 0.62
5 7 0.08
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (4 bp):
ATAA
Found at i:1009885 original size:23 final size:22
Alignment explanation
Indices: 1009852--1009974 Score: 76
Period size: 22 Copynumber: 5.3 Consensus size: 22
1009842 AGATAAAGTA
1009852 AAAAATAATAATAATAATAAAT
1 AAAAATAATAATAATAATAAAT
1009874 AAAAATATATAAATTAATATATAGTAAAT
1 AAAAATA-AT-AA-T-A-ATA-A-TAAAT
*
1009903 AAATAA-ATATATTAATAGATAAAT
1 AAA-AATA-ATAATAATA-ATAAAT
* *
1009927 AATAAAAAAT-ATATTAATAAAT
1 AA-AAATAATAATAATAATAAAT
*
1009949 --AAATAATAAAAATAA-AAAT
1 AAAAATAATAATAATAATAAAT
1009968 AAAAATA
1 AAAAATA
1009975 CAAATGAGCT
Statistics
Matches: 81, Mismatches: 7, Indels: 27
0.70 0.06 0.23
Matches are distributed among these distances:
19 10 0.12
20 5 0.06
21 5 0.06
22 13 0.16
23 6 0.07
24 13 0.16
25 7 0.09
26 2 0.02
27 4 0.05
28 2 0.02
29 12 0.15
30 2 0.02
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATAATAATAATAATAAAT
Found at i:1009916 original size:27 final size:27
Alignment explanation
Indices: 1009842--1009958 Score: 113
Period size: 26 Copynumber: 4.5 Consensus size: 27
1009832 ATCAAGAAAA
*
1009842 AGATAAAGTAAAAAAT-AATA-A-TAAT
1 AGATAAA-TAATAAATAAATATATTAAT
* *
1009867 A-ATAAATAA-AAATATATAAATTAAT
1 AGATAAATAATAAATAAATATATTAAT
* *
1009892 ATAT-AGTAAATAAATAAATATATTAAT
1 AGATAAAT-AATAAATAAATATATTAAT
1009919 AGATAAATAATAAA-AAATATATTAAT
1 AGATAAATAATAAATAAATATATTAAT
*
1009945 AAATAAATAATAAA
1 AGATAAATAATAAA
1009959 AATAAAAATA
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
22 4 0.05
23 6 0.08
24 6 0.08
25 8 0.10
26 29 0.37
27 23 0.29
28 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (27 bp):
AGATAAATAATAAATAAATATATTAAT
Found at i:1009943 original size:53 final size:53
Alignment explanation
Indices: 1009845--1009945 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
1009835 AAGAAAAAGA
*
1009845 TAAAGTAAAAAATAATAATAATAATAAATAAAAATATATAAATTAATATATAG
1 TAAAGTAAAAAATAATAATAATAATAAATAAAAATAAATAAATTAATATATAG
* *
1009898 TAAA-TAAATAAAT-ATATTAATAGATAAATAATAAA-AAATATATTAATA
1 TAAAGTAAA-AAATAATAATAATA-ATAAATAA-AAATAAATAAATTAATA
1009946 AATAAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
52 12 0.29
53 27 0.64
54 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (53 bp):
TAAAGTAAAAAATAATAATAATAATAAATAAAAATAAATAAATTAATATATAG
Found at i:1009979 original size:6 final size:6
Alignment explanation
Indices: 1009945--1009979 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
1009935 ATATATTAAT
*
1009945 AAATAA ATAATAA AAATAA AAATAA AAATAC AAAT
1 AAATAA A-AATAA AAATAA AAATAA AAATAA AAAT
1009980 GAGCTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:1010046 original size:3 final size:3
Alignment explanation
Indices: 1010038--1010102 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
1010028 TTGGATGTCT
* *
1010038 ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA TATA A-A ATG ATT ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA -ATA ATA ATA ATA ATA
*
1010084 AAA ATA AT- ATAA ATA ATA A
1 ATA ATA ATA AT-A ATA ATA A
1010103 AAAAAATTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.08
3 40 0.77
4 8 0.15
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1010440 original size:21 final size:21
Alignment explanation
Indices: 1010416--1010539 Score: 61
Period size: 22 Copynumber: 6.2 Consensus size: 21
1010406 TCAAAATCCC
1010416 AAACCTCAAACCCTAAAATCG
1 AAACCTCAAACCCTAAAATCG
* * * *
1010437 AAACCCTAAAACCTTAAACTTG
1 AAA-CCTCAAACCCTAAAATCG
1010459 AAA-CT-AAACCCTAAAA-C-
1 AAACCTCAAACCCTAAAATCG
* * *
1010476 ---CTTTAAACCCTAAAATTG
1 AAACCTCAAACCCTAAAATCG
**
1010494 AAACC-CTAAACCCTAAAACTAA
1 AAACCTC-AAACCCTAAAA-TCG
*
1010516 AAACCTCAAA-CCT-CAATCG
1 AAACCTCAAACCCTAAAATCG
1010535 AAACC
1 AAACC
1010540 CTAAAATCTA
Statistics
Matches: 76, Mismatches: 16, Indels: 24
0.66 0.14 0.21
Matches are distributed among these distances:
15 1 0.01
16 11 0.14
19 15 0.20
20 4 0.05
21 18 0.24
22 26 0.34
23 1 0.01
ACGTcount: A:0.48, C:0.31, G:0.03, T:0.18
Consensus pattern (21 bp):
AAACCTCAAACCCTAAAATCG
Found at i:1010442 original size:14 final size:14
Alignment explanation
Indices: 1010363--1010447 Score: 68
Period size: 14 Copynumber: 6.0 Consensus size: 14
1010353 CCCTAAACCC
* *
1010363 TCGAAATCCTAATA
1 TCGAAACCCTAAAA
1010377 TCGAAACCCTAAAA
1 TCGAAACCCTAAAA
*
1010391 CTTC-AAACCCCAAAA
1 --TCGAAACCCTAAAA
* *
1010406 TCAAAATCCC-AAACC
1 TCGAAA-CCCTAAA-A
1010421 TC-AAACCCTAAAA
1 TCGAAACCCTAAAA
1010434 TCGAAACCCTAAAA
1 TCGAAACCCTAAAA
1010448 CCTTAAACTT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
13 7 0.12
14 35 0.59
15 15 0.25
16 2 0.03
ACGTcount: A:0.48, C:0.32, G:0.04, T:0.16
Consensus pattern (14 bp):
TCGAAACCCTAAAA
Found at i:1010476 original size:35 final size:34
Alignment explanation
Indices: 1010441--1010559 Score: 105
Period size: 34 Copynumber: 3.4 Consensus size: 34
1010431 AAATCGAAAC
1010441 CCTAAAACCTTAAACTTGAAACTAAACCCTAAAA
1 CCTAAAACCTTAAACTTGAAACTAAACCCTAAAA
* * *
1010475 CCTTTAAACCCTAAAATTGAAACCCTAAACCCTAAAA
1 CC-TAAAACCTTAAACTTGAAA--CTAAACCCTAAAA
* * * * *
1010512 -CTAAAAACCTCAAACCTCAATCGAAACCCTAAAA
1 CCT-AAAACCTTAAACTTGAAACTAAACCCTAAAA
* *
1010546 TCTAAAACTTTAAA
1 CCTAAAACCTTAAA
1010560 ATCCAAAATT
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
34 23 0.34
35 19 0.28
36 12 0.18
37 13 0.19
ACGTcount: A:0.49, C:0.28, G:0.03, T:0.21
Consensus pattern (34 bp):
CCTAAAACCTTAAACTTGAAACTAAACCCTAAAA
Found at i:1010499 original size:14 final size:14
Alignment explanation
Indices: 1010365--1010503 Score: 61
Period size: 14 Copynumber: 9.8 Consensus size: 14
1010355 CTAAACCCTC
* * *
1010365 GAAATCCTAATATC
1 GAAACCCTAAAATT
1010379 GAAACCCTAAAACTT
1 GAAACCCTAAAA-TT
* * *
1010394 CAAACCCCAAAATC
1 GAAACCCTAAAATT
* **
1010408 AAAATCCC-AAACCT
1 GAAA-CCCTAAAATT
* *
1010422 CAAACCCTAAAATC
1 GAAACCCTAAAATT
1010436 GAAACCCTAAAACCTT
1 GAAACCCTAAAA--TT
* * *
1010452 -AAA-CTTGAAACT
1 GAAACCCTAAAATT
1010464 -AAACCCTAAAACCTT
1 GAAACCCTAAAA--TT
*
1010479 TAAACCCTAAAATT
1 GAAACCCTAAAATT
1010493 GAAACCCTAAA
1 GAAACCCTAAA
1010504 CCCTAAAACT
Statistics
Matches: 93, Mismatches: 23, Indels: 18
0.69 0.17 0.13
Matches are distributed among these distances:
12 4 0.04
13 8 0.09
14 51 0.55
15 18 0.19
16 12 0.13
ACGTcount: A:0.48, C:0.29, G:0.04, T:0.19
Consensus pattern (14 bp):
GAAACCCTAAAATT
Found at i:1012454 original size:2 final size:2
Alignment explanation
Indices: 1012447--1012496 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1012437 AATATTACAT
1012447 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1012489 TA TA TA TA
1 TA TA TA TA
1012497 CACACATAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1014339 original size:145 final size:145
Alignment explanation
Indices: 1014088--1014454 Score: 344
Period size: 145 Copynumber: 2.5 Consensus size: 145
1014078 AAAATTTTTG
* * * * *
1014088 TGAAATTTCGAGCTCGGAAAGGCTAAATTACGAAAATACCCCTATGAGAGTATTTTGGTAATTTC
1 TGAAATTTAGAGCTCGAAAAGGCCAAATTACGAAAATACCCCTATAAGAGTATTTTAGTAATTTC
* ** * * ** * * *
1014153 ACACTTCTCGGGGTACTGTTATAATTTCAAATGTATTAAAAATTATGAAATATTATAAAACTAGG
66 ACACTTCTCGGGATACTACTATAATTCCAAATGCACCAAAAATCATGAAATATTACAAAACTAAG
*
1014218 ATATGAAAAGTTTCA
131 ATATAAAAAGTTTCA
* * *
1014233 TGAAATTTAGAGCTCGAAAAGGCCAAATTACGAAAATACTCCTCA-AAGGGTATTTTAGTCATTT
1 TGAAATTTAGAGCTCGAAAAGGCCAAATTACGAAAATACCCCT-ATAAGAGTATTTTAGTAATTT
* * * * * *
1014297 CATACTTCTTGGGATACTACTATGATTCCGAACT-CACCAAAAATCATGAAATGTTACAAAAGTA
65 CACACTTCTCGGGATACTACTATAATTCC-AAATGCACCAAAAATCATGAAATATTACAAAACTA
*
1014361 AGATCTAAAAAGTTTCA
129 AGATATAAAAAGTTTCA
** * ** * * * ** *
1014378 CAAAATTTTGAGCTCGAAAAGGTGAAATTAC-AAAGAAACTCCTATAAGGGTGGTTTGGTAATTT
1 TGAAATTTAGAGCTCGAAAAGGCCAAATTACGAAA-ATACCCCTATAAGAGTATTTTAGTAATTT
*
1014442 CACACTTATCGGG
65 CACACTTCTCGGG
1014455 GGTACCACTG
Statistics
Matches: 179, Mismatches: 39, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
144 4 0.02
145 171 0.96
146 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (145 bp):
TGAAATTTAGAGCTCGAAAAGGCCAAATTACGAAAATACCCCTATAAGAGTATTTTAGTAATTTC
ACACTTCTCGGGATACTACTATAATTCCAAATGCACCAAAAATCATGAAATATTACAAAACTAAG
ATATAAAAAGTTTCA
Found at i:1015377 original size:18 final size:18
Alignment explanation
Indices: 1015356--1015396 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1015346 ATATTATATT
1015356 TTTTAGGTCTATATTTTA
1 TTTTAGGTCTATATTTTA
* * *
1015374 TTTTAGTTCTGTTTTTTA
1 TTTTAGGTCTATATTTTA
1015392 TTTTA
1 TTTTA
1015397 TTTATTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (18 bp):
TTTTAGGTCTATATTTTA
Found at i:1016092 original size:19 final size:18
Alignment explanation
Indices: 1016038--1016091 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 18
1016028 CCCAGATTAA
*
1016038 GAAAATTTTTTGTTTATG
1 GAAAATTTTTTGTTTTTG
*
1016056 GAATAATTTTTTGCTTTTG
1 GAA-AATTTTTTGTTTTTG
*
1016075 GAAAATTTTTTATTTTT
1 GAAAATTTTTTGTTTTT
1016092 TTCACTGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.59
Consensus pattern (18 bp):
GAAAATTTTTTGTTTTTG
Found at i:1027895 original size:21 final size:20
Alignment explanation
Indices: 1027842--1027882 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1027832 CTTAACGATC
1027842 CCTAATTGATCTCTAATGAT
1 CCTAATTGATCTCTAATGAT
* *
1027862 CCTAAGCTAATCTCTAATGAT
1 CCTAA-TTGATCTCTAATGAT
1027883 TTTAATATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (20 bp):
CCTAATTGATCTCTAATGAT
Found at i:1027981 original size:98 final size:98
Alignment explanation
Indices: 1027812--1028001 Score: 344
Period size: 98 Copynumber: 1.9 Consensus size: 98
1027802 ATAAAAAATT
* * *
1027812 ATAAACATACAATCTTAATTCTTAACGATCCCTAATTGATCTCTAATGATCCTAAGCTAATCTCT
1 ATAAACATACAATCTTAATTATTAACGATCCCTAATTGAACTCTAATGATCCTAAACTAATCTCT
1027877 AATGATTTTAATATGATCTTTATCCCATTTATC
66 AATGATTTTAATATGATCTTTATCCCATTTATC
*
1027910 ATAAACATACAATCTTAATTATTAACGATCCCTAATTGAACTCTAATGGTCCTAAACTAATCTCT
1 ATAAACATACAATCTTAATTATTAACGATCCCTAATTGAACTCTAATGATCCTAAACTAATCTCT
1027975 AATGATTTTAATATGATCTTTATCCCA
66 AATGATTTTAATATGATCTTTATCCCA
1028002 AATTGATTTC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.38
Consensus pattern (98 bp):
ATAAACATACAATCTTAATTATTAACGATCCCTAATTGAACTCTAATGATCCTAAACTAATCTCT
AATGATTTTAATATGATCTTTATCCCATTTATC
Found at i:1028831 original size:18 final size:18
Alignment explanation
Indices: 1028804--1028846 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1028794 ATTATTGGTT
1028804 AAAAATTA-TTAAATTCA
1 AAAAATTATTTAAATTCA
*
1028821 AAAATATTATTTTAATTCA
1 AAAA-ATTATTTAAATTCA
1028840 AATAAAT
1 AA-AAAT
1028847 CATAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 4 0.18
19 12 0.55
20 2 0.09
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAATTATTTAAATTCA
Found at i:1028924 original size:2 final size:2
Alignment explanation
Indices: 1028917--1028948 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1028907 ATCTTTTCTC
*
1028917 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1028949 GCCCATCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1033731 original size:16 final size:16
Alignment explanation
Indices: 1033710--1033740 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1033700 TTATGCATAT
1033710 TAAATTTGAATGATAA
1 TAAATTTGAATGATAA
1033726 TAAATTTGAATGATA
1 TAAATTTGAATGATA
1033741 TTGAATCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (16 bp):
TAAATTTGAATGATAA
Found at i:1036315 original size:244 final size:246
Alignment explanation
Indices: 1035865--1036329 Score: 729
Period size: 244 Copynumber: 1.9 Consensus size: 246
1035855 CTCAAAAAAT
*
1035865 GCTTGAATATTTATTTATTTATTGTATAGAAGTCTAATAATATAAAAAAAGAGTTTAAATTACAA
1 GCTTGAATATTTATTTATTTATTGTATAAAAGTCTAATAATATAAAAAAAGAGTTTAAATTACAA
* *
1035930 TTTTTAAGAAGTCTAATAATAAAAGAGTTCAAATTATAATTTATCTCAATAAAAATTTAATAATA
66 TTTTTAAAAAATCTAATAATAAAAGAGTTCAAATTATAATTTATCTCAATAAAAATTTAATAATA
* ** **
1035995 AAAAATCATTTTAATTAAAATTTATTAAAAATTTTACTAAGAGTATTTTGGTTGTTCATTATTAT
131 AAAAATCATTTTAATTAAAATTTATTAAAAATTTTACTAAGAGTATATTAATCATTCATTATTAT
*
1036060 CACCTTTGATTTACTAAGGGTATTTTGGTTGTAATTGATTTCTCTAAAGGA
196 CACCTTTGATTTACTAAGAGTATTTTGGTTGTAATTGATTTCTCTAAAGGA
* * *
1036111 GCTTGAA-ATTT-TTTTTTTTTTGTATAAAAGTCTAATAATATAAAGAAAGAGTTTAAATTACAA
1 GCTTGAATATTTATTTATTTATTGTATAAAAGTCTAATAATATAAAAAAAGAGTTTAAATTACAA
* * *
1036174 TTTTTAAAAAATTTGATAATAAAAGAGTTCAAATTATAATTTATTTCAATAAAAATTTAATAATA
66 TTTTTAAAAAATCTAATAATAAAAGAGTTCAAATTATAATTTATCTCAATAAAAATTTAATAATA
* *
1036239 AAAAGTCATTTTAATTAAAATTTATTAAAAATTTTACTGAG-GATATATTAATCATTCATTATTA
131 AAAAATCATTTTAATTAAAATTTATTAAAAATTTTACTAAGAG-TATATTAATCATTCATTATTA
* *
1036303 TCACTTTTGATTTATTAAGAGTATTTT
195 TCACCTTTGATTTACTAAGAGTATTTT
1036330 AGTCATTCAC
Statistics
Matches: 199, Mismatches: 19, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
243 1 0.01
244 187 0.94
245 4 0.02
246 7 0.04
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (246 bp):
GCTTGAATATTTATTTATTTATTGTATAAAAGTCTAATAATATAAAAAAAGAGTTTAAATTACAA
TTTTTAAAAAATCTAATAATAAAAGAGTTCAAATTATAATTTATCTCAATAAAAATTTAATAATA
AAAAATCATTTTAATTAAAATTTATTAAAAATTTTACTAAGAGTATATTAATCATTCATTATTAT
CACCTTTGATTTACTAAGAGTATTTTGGTTGTAATTGATTTCTCTAAAGGA
Found at i:1036373 original size:2 final size:2
Alignment explanation
Indices: 1036366--1036407 Score: 50
Period size: 2 Copynumber: 20.5 Consensus size: 2
1036356 TTCACACTTT
*
1036366 TA TA TA TA GA TGA TA TA TA TA TA TA TA TA TA T- TA TA TCA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
1036408 TTAACGTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 1 0.03
2 30 0.86
3 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1036401 original size:19 final size:20
Alignment explanation
Indices: 1036366--1036407 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
1036356 TTCACACTTT
1036366 TATATATAGATGATATAT-A
1 TATATATAGATGATATATCA
*
1036385 TATATATATAT-ATTATATCA
1 TATATATAGATGA-TATATCA
1036405 TAT
1 TAT
1036408 TTAACGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.75
20 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (20 bp):
TATATATAGATGATATATCA
Found at i:1041024 original size:143 final size:142
Alignment explanation
Indices: 1040830--1041115 Score: 563
Period size: 142 Copynumber: 2.0 Consensus size: 142
1040820 GTATTATATC
1040830 TTACTTTTCTTTGATACGTAAATTCTTAAATTGACTTTATTTTTATTATTTATTTCTTAGCATAT
1 TTACTTTTCTTTGATACGTAAATTCTTAAATTGACTTTATTTTTATTATTTATTTCTTAGCATAT
1040895 TGTTTTTTCAATAAATAAAAATTGTATATATTTTAAATTTTTAATTATACTAAATAAAAAAAAAC
66 TG-TTTTTCAATAAATAAAAATTGTATATATTTTAAATTTTTAATTATACTAAATAAAAAAAAAC
1040960 CCATAGTGAAGCA
130 CCATAGTGAAGCA
1040973 TTACTTTTCTTTGATACGTAAATTCTTAAATTGACTTTATTTTTATTATTTATTTCTTAGCATAT
1 TTACTTTTCTTTGATACGTAAATTCTTAAATTGACTTTATTTTTATTATTTATTTCTTAGCATAT
1041038 TGTTTTTCAATAAATAAAAATTGTATATATTTTAAATTTTTAATTATACTAAATAAAAAAAAACC
66 TGTTTTTCAATAAATAAAAATTGTATATATTTTAAATTTTTAATTATACTAAATAAAAAAAAACC
1041103 CATAGTGAAGCA
131 CATAGTGAAGCA
1041115 T
1 T
1041116 GGGCATCACA
Statistics
Matches: 143, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
142 76 0.53
143 67 0.47
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (142 bp):
TTACTTTTCTTTGATACGTAAATTCTTAAATTGACTTTATTTTTATTATTTATTTCTTAGCATAT
TGTTTTTCAATAAATAAAAATTGTATATATTTTAAATTTTTAATTATACTAAATAAAAAAAAACC
CATAGTGAAGCA
Found at i:1046237 original size:63 final size:61
Alignment explanation
Indices: 1046171--1046589 Score: 473
Period size: 61 Copynumber: 6.9 Consensus size: 61
1046161 ATTTTTTGCA
*
1046171 AAAAATAAAAATTTTCAAAAAGAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAAT-AAAATTTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* * *
1046233 AAAAAT-AAATTTTCAAAAAAAAAAAACTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAATAAAATTTTC-AAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* ** * *
1046294 GAAAATAAGCTTTCCAAAAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAATAAAATTTTC-AAAAAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* *
1046357 AAAAAT-AAATTTTCAAAAAAAAAAAGATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAATAAAATTTTCAAAAAAAAATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
** * * * *
1046418 AAAAATAAGCTTTCCACAAAAAAAATATTTTGGGGAGAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAATAAAATTTTCA-AAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTT
** * *
1046481 AAAAAT-AAATTTTC---AAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTC
1 AAAAATAAAATTTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* * * *
1046538 AAAATTAAAA-TTTC---AAAAGATA-TTTTGGGGAAAAGTCGAAAGTATCAATTTT
1 AAAAATAAAATTTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTT
1046590 TCCTACACAA
Statistics
Matches: 308, Mismatches: 42, Indels: 20
0.83 0.11 0.05
Matches are distributed among these distances:
56 28 0.09
57 40 0.13
58 15 0.05
60 8 0.03
61 96 0.31
62 43 0.14
63 78 0.25
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (61 bp):
AAAAATAAAATTTTCAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
Found at i:1046338 original size:124 final size:122
Alignment explanation
Indices: 1046187--1046589 Score: 563
Period size: 124 Copynumber: 3.3 Consensus size: 122
1046177 AAAAATTTTC
* *
1046187 AAAAAGAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAA
1 AAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAA
*
1046252 AAAAAAACTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTCCA
66 AAAAAAA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGCTTTCCA
1046310 AAAAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAA
1 AAAAAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAA
*
1046375 AAAAAAAGATTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCCA
65 AAAAAAA-ATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGCTTTCCA
* * *
1046434 CAAAAAAAATATTTTGGGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC---A
1 AAAAAAAAATATTTTTGGG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAA
*** * * **
1046496 AAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAATTAAAATTT-C-
65 AAAAAAAATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGCTTTCCA
* *
1046552 ---AAAAGATA-TTTTGGGGAAAAGTCGAAAGTATCAATTTT
1 AAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1046590 TCCTACACAA
Statistics
Matches: 259, Mismatches: 18, Indels: 16
0.88 0.06 0.05
Matches are distributed among these distances:
113 22 0.08
114 6 0.02
115 7 0.03
119 1 0.00
120 42 0.16
121 6 0.02
123 17 0.07
124 157 0.61
125 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (122 bp):
AAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAA
AAAAAAATTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAGCTTTCCA
Found at i:1051056 original size:13 final size:12
Alignment explanation
Indices: 1051032--1051092 Score: 76
Period size: 12 Copynumber: 5.3 Consensus size: 12
1051022 ACAATGGATG
1051032 AAAAATGAGAAA
1 AAAAATGAGAAA
1051044 AAAAATGATGAAA
1 AAAAATGA-GAAA
1051057 AAAAAT-AGAAA
1 AAAAATGAGAAA
*
1051068 AAAAA--A-AGA
1 AAAAATGAGAAA
1051077 AAAAATGAGAAA
1 AAAAATGAGAAA
1051089 AAAA
1 AAAA
1051093 GAAGAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 7 0.16
10 1 0.02
11 10 0.23
12 15 0.35
13 10 0.23
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (12 bp):
AAAAATGAGAAA
Found at i:1051068 original size:10 final size:11
Alignment explanation
Indices: 1051032--1051102 Score: 67
Period size: 11 Copynumber: 6.4 Consensus size: 11
1051022 ACAATGGATG
1051032 AAAAATGAGAAA
1 AAAAATGAG-AA
1051044 AAAAATGATGAAA
1 AAAAATGA-G-AA
1051057 AAAAAT-AGAA
1 AAAAATGAGAA
**
1051067 AAAAAAAAG-A
1 AAAAATGAGAA
1051077 AAAAATGAGAA
1 AAAAATGAGAA
1051088 AAAAA-GAAGAA
1 AAAAATG-AGAA
1051099 AAAA
1 AAAA
1051103 TAAGAAAATG
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
10 16 0.31
11 17 0.33
12 9 0.17
13 10 0.19
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (11 bp):
AAAAATGAGAA
Found at i:1051079 original size:21 final size:21
Alignment explanation
Indices: 1051032--1051110 Score: 88
Period size: 21 Copynumber: 3.6 Consensus size: 21
1051022 ACAATGGATG
*
1051032 AAAAATGAGAAAAAAAATGATGAAA
1 AAAAATGAGAAAAAAAA--A--AGA
1051057 AAAAAT-AGAAAAAAAAAAGA
1 AAAAATGAGAAAAAAAAAAGA
*
1051077 AAAAATGAGAAAAAAAGAAGA
1 AAAAATGAGAAAAAAAAAAGA
*
1051098 AAAAATAAGAAAA
1 AAAAATGAGAAAA
1051111 TGAAAAAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.16
21 25 0.50
22 1 0.02
24 10 0.20
25 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (21 bp):
AAAAATGAGAAAAAAAAAAGA
Found at i:1051107 original size:10 final size:10
Alignment explanation
Indices: 1051056--1051110 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
1051046 AAATGATGAA
1051056 AAAAAAT-AG
1 AAAAAATAAG
*
1051065 AAAAAAAAAAG
1 -AAAAAATAAG
*
1051076 AAAAAATGAG
1 AAAAAATAAG
*
1051086 AAAAAAAGAAG
1 -AAAAAATAAG
1051097 AAAAAATAAG
1 AAAAAATAAG
1051107 AAAA
1 AAAA
1051111 TGAAAAAAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
10 27 0.73
11 10 0.27
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (10 bp):
AAAAAATAAG
Found at i:1051117 original size:45 final size:45
Alignment explanation
Indices: 1051032--1051121 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
1051022 ACAATGGATG
* *
1051032 AAAAATGAGAAAAAAAATGATGAAAAAAAATAGAAAAAAAAAAGA
1 AAAAATGAGAAAAAAAATGAAGAAAAAAAAGAGAAAAAAAAAAGA
1051077 AAAAATGAG-AAAAAAA-GAAGAAAAAATAAGA-AAATGAAAAAAAGA
1 AAAAATGAGAAAAAAAATGAAGAAAAAA-AAGAGAAA--AAAAAAAGA
1051122 TATTCAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
43 12 0.30
44 10 0.25
45 18 0.45
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (45 bp):
AAAAATGAGAAAAAAAATGAAGAAAAAAAAGAGAAAAAAAAAAGA
Found at i:1052874 original size:41 final size:40
Alignment explanation
Indices: 1052812--1053311 Score: 504
Period size: 41 Copynumber: 12.2 Consensus size: 40
1052802 ATGATTGTCA
* *
1052812 AGGAGCAATTTACTTTCCAAAGTTTCGTTGCCTCTATTTAG
1 AGGAGCAATTTACTTTTCAAAG-TTCGTTGCCTCTGTTTAG
1052853 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
*
1052894 AGGAGCAATTTA-TTTTCCAAAG-TCATGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTTC--GTTGCCTCTGTTTAG
*
1052935 AGGAGCAATTTACTTTTCAAAGATGT-GGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAG-T-TCGTTGCCTCTGTTTAG
* *
1052976 AGGAGCAATTTACTTTTTCAAAG-TCATGGTGCCTCTATTTAG
1 AGGAGCAATTTAC-TTTTCAAAGTTC--GTTGCCTCTGTTTAG
* *
1053018 AGGAGCAATATA-TTTTCCAAAG-TCATGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTT-CAAAGTTC--GTTGCCTCTGTTTAG
* *
1053059 AGGAGTAATTTATTTTTCAAAG-TCGTGATGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
*
1053100 AGGAGCAATTTATTTTTCAAAGTT-GTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
* *
1053141 AGGAGCAATTTACTTTTCAAAG-TCGTGGTGCCTCTATTTAA
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
*
1053182 AGTAGCAATTTACTTTTCAAAAG-TCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTC-AAAGTTCGT--TGCCTCTGTTTAG
* *
1053224 AGGAGCAATTTAATTTTCAAAG-TCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAG
*
1053265 AGGAGCAATTTACTTTCCAAAGTT-GTTGAGCCTCTGTTTAG
1 AGGAGCAATTTACTTTTCAAAGTTCGTT--GCCTCTGTTTAG
*
1053306 AAGAGC
1 AGGAGC
1053312 TTTGAAAAAA
Statistics
Matches: 412, Mismatches: 24, Indels: 46
0.85 0.05 0.10
Matches are distributed among these distances:
39 7 0.02
40 9 0.02
41 313 0.76
42 81 0.20
43 1 0.00
44 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (40 bp):
AGGAGCAATTTACTTTTCAAAGTTCGTTGCCTCTGTTTAG
Found at i:1053093 original size:165 final size:165
Alignment explanation
Indices: 1052812--1053311 Score: 772
Period size: 165 Copynumber: 3.0 Consensus size: 165
1052802 ATGATTGTCA
* * *
1052812 AGGAGCAATTTACTTTCCAAAGT-TTCGTTGCCTCTATTTAGAGGAGCAATTTACTTTT-CAAAG
1 AGGAGCAATTTACTTTTCAAAGTCAT-GGTGCCTCTATTTAGAGGAGCAATTTACTTTTCCAAAG
* *
1052875 TCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAG
65 TCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
*
1052940 CAATTTACTTTTCAAAGATGTGGTGCCTCTGTTTAG
130 CAATTTACTTTTCAAAGTTGTGGTGCCTCTGTTTAG
*
1052976 AGGAGCAATTTACTTTTTCAAAGTCATGGTGCCTCTATTTAGAGGAGCAATATA-TTTTCCAAAG
1 AGGAGCAATTTAC-TTTTCAAAGTCATGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCCAAAG
* * *
1053040 TCATGGTGCCTCTGTTTAGAGGAGTAATTTATTTTTCAAAGTCGTGATGCCTCTGTTTAGAGGAG
65 TCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAG
*
1053105 CAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAG
130 CAATTTACTTTTCAAAGTTGTGGTGCCTCTGTTTAG
* * * *
1053141 AGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTATTTAAAGTAGCAATTTACTTTTCAAAAGT
1 AGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCCAAAGT
* *
1053206 CGTGGTGCCTCTGTTTAGAGGAGCAATTTAATTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGC
66 CGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
* * *
1053271 AATTTACTTTCCAAAGTTGTTGAGCCTCTGTTTAG
131 AATTTACTTTTCAAAGTTGTGGTGCCTCTGTTTAG
*
1053306 AAGAGC
1 AGGAGC
1053312 TTTGAAAAAA
Statistics
Matches: 306, Mismatches: 26, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
164 53 0.17
165 252 0.82
166 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (165 bp):
AGGAGCAATTTACTTTTCAAAGTCATGGTGCCTCTATTTAGAGGAGCAATTTACTTTTCCAAAGT
CGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
AATTTACTTTTCAAAGTTGTGGTGCCTCTGTTTAG
Found at i:1053171 original size:206 final size:206
Alignment explanation
Indices: 1052812--1053311 Score: 731
Period size: 206 Copynumber: 2.4 Consensus size: 206
1052802 ATGATTGTCA
* * * *
1052812 AGGAGCAATTTACTTTCCAAAGT-TTCGTTGCCTCTATTTAGAGGAGCAATTTACTTTTCAAAGT
1 AGGAGCAATTTATTTTCCAAAGTCAT-GGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
*
1052876 CGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGC
65 CGTGATGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGC
* *
1052941 AATTTACTTTTCAAAGATGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTC-AAAGTCATGG
130 AATTTACTTTTCAAAGATGTGGTGCCTCTATTTAAAGGAGCAATTTAC-TTTTCAAAAGTCATGG
1053005 TGCCTCTATTTAG
194 TGCCTCTATTTAG
* * *
1053018 AGGAGCAATATATTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGTAATTTATTTTTCAAAGTC
1 AGGAGCAATTTATTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
* **
1053083 GTGATGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCA
66 GTGATGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCA
* *
1053148 ATTTACTTTTCAAAG-TCGTGGTGCCTCTATTTAAAGTAGCAATTTACTTTTCAAAAGTCGTGGT
131 ATTTACTTTTCAAAGAT-GTGGTGCCTCTATTTAAAGGAGCAATTTACTTTTCAAAAGTCATGGT
*
1053212 GCCTCTGTTTAG
195 GCCTCTATTTAG
* * *
1053224 AGGAGCAATTTAATTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
1 AGGAGCAATTT-ATTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGT
* *
1053288 TGTTGA-GCCTCTGTTTAGAAGAGC
65 CG-TGATGCCTCTGTTTAGAGGAGC
1053312 TTTGAAAAAA
Statistics
Matches: 265, Mismatches: 24, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
205 6 0.02
206 250 0.94
207 9 0.03
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (206 bp):
AGGAGCAATTTATTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTC
GTGATGCCTCTGTTTAGAGGAGCAATTTATTTTCCAAAGTCATGGTGCCTCTGTTTAGAGGAGCA
ATTTACTTTTCAAAGATGTGGTGCCTCTATTTAAAGGAGCAATTTACTTTTCAAAAGTCATGGTG
CCTCTATTTAG
Found at i:1053322 original size:1 final size:1
Alignment explanation
Indices: 1053316--1053384 Score: 57
Period size: 1 Copynumber: 69.0 Consensus size: 1
1053306 AAGAGCTTTG
* * * * * * * * *
1053316 AAAAAAAAATAAAAACAAAACAAAAAACAAAAAAAATAAGAAACAAAAAAACAAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1053381 AAAA
1 AAAA
1053385 TTGCCTCTGT
Statistics
Matches: 50, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.87, C:0.07, G:0.01, T:0.04
Consensus pattern (1 bp):
A
Found at i:1053375 original size:23 final size:23
Alignment explanation
Indices: 1053317--1053384 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 23
1053307 AGAGCTTTGA
1053317 AAAAAAAATAAAAACAAAACAAAAAAC
1 AAAAAAAATAAAAAC---A-AAAAAAC
1053344 AAAAAAAATAAGAAACAAAAAAAC
1 AAAAAAAATAA-AAACAAAAAAAC
1053368 -AAAAAAATAAAAA-AAAA
1 AAAAAAAATAAAAACAAAA
1053385 TTGCCTCTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.10
22 3 0.08
23 10 0.25
24 7 0.17
25 1 0.03
27 11 0.28
28 4 0.10
ACGTcount: A:0.87, C:0.07, G:0.01, T:0.04
Consensus pattern (23 bp):
AAAAAAAATAAAAACAAAAAAAC
Found at i:1053514 original size:110 final size:105
Alignment explanation
Indices: 1053360--1053565 Score: 324
Period size: 110 Copynumber: 1.9 Consensus size: 105
1053350 AATAAGAAAC
*
1053360 AAAAAAACAAAAAAATAAAAAAAAATTGCCTCTGTTTAAGGGAGCTTTGTTTATGTTTCTCAAAG
1 AAAAAAACAAAAAAAAAAAAAAAAATTGCCTCTGTTTAAGGGAGCTTTGTTTATGTTTCTCAAAG
*
1053425 TCGTTGAGCCTCTATTTAGAGGAGCTTTGATCAATTTAAA
66 TCGTTGAGCCTCTACTTAGAGGAGCTTTGATCAATTTAAA
*
1053465 AAAAAAAGAAAGAAAACAAAAAAAAAAGTTGAGCCTCTGTTT-AGAGGAGCTTTGTTTATGTTTC
1 AAAAAAACAAA-AAAA-AAAAAAAAAA-TT--GCCTCTGTTTAAG-GGAGCTTTGTTTATGTTTC
1053529 TCAAAGTCGTTGAGCCTCTACTTAGAGGAGCTTTGAT
60 TCAAAGTCGTTGAGCCTCTACTTAGAGGAGCTTTGAT
1053566 TAAAATTTTT
Statistics
Matches: 92, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
105 10 0.11
106 4 0.04
107 9 0.10
108 2 0.02
109 2 0.02
110 65 0.71
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (105 bp):
AAAAAAACAAAAAAAAAAAAAAAAATTGCCTCTGTTTAAGGGAGCTTTGTTTATGTTTCTCAAAG
TCGTTGAGCCTCTACTTAGAGGAGCTTTGATCAATTTAAA
Found at i:1053787 original size:13 final size:13
Alignment explanation
Indices: 1053771--1053800 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1053761 TTATTTTTTT
1053771 ATTTTTATTTCAG
1 ATTTTTATTTCAG
*
1053784 ATTTTTATTTTAG
1 ATTTTTATTTCAG
1053797 ATTT
1 ATTT
1053801 ATCATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (13 bp):
ATTTTTATTTCAG
Found at i:1055708 original size:6 final size:6
Alignment explanation
Indices: 1055697--1055737 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
1055687 TTCAGGAGTA
*
1055697 TTATTT TTATTT TTA-TT TTA-TT TTA-TC TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TT
1055738 TGCAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 14 0.44
6 18 0.56
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:1055912 original size:60 final size:61
Alignment explanation
Indices: 1055757--1056088 Score: 412
Period size: 59 Copynumber: 5.5 Consensus size: 61
1055747 TAAAAATTTT
* * * *
1055757 CAAAAAGAAATATTTTTGAGGAAAAGTTGAAATTATCAATTTTTCTTGAAATTAAAG-TTTT
1 CAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAGCTTTC
*
1055818 C--AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
1 CAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
* * * *
1055877 CAAAAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAA-ATTTT
1 CAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
* *
1055936 CAAAAAAAAAGA-TTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTC
1 CAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
* * * * * *
1055996 CACAAAAAAAAAATTTTGGGGGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGTTTC
1 CA-AAAAAAAATATTTT-TGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
*
1056059 C---AAAAAATATTTTTGGGGAAAAGTTGAAAG
1 CAAAAAAAAATATTTTTGAGGAAAAGTTGAAAG
1056089 GAAAAGTTGA
Statistics
Matches: 240, Mismatches: 23, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
58 24 0.10
59 110 0.46
60 38 0.16
61 25 0.10
62 3 0.01
63 40 0.17
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (61 bp):
CAAAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
Found at i:1056093 original size:13 final size:13
Alignment explanation
Indices: 1056075--1056101 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1056065 ATATTTTTGG
1056075 GGAAAAGTTGAAA
1 GGAAAAGTTGAAA
1056088 GGAAAAGTTGAAA
1 GGAAAAGTTGAAA
1056101 G
1 G
1056102 TATCAATTTT
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:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (13 bp):
GGAAAAGTTGAAA
Found at i:1056135 original size:71 final size:71
Alignment explanation
Indices: 1056017--1056159 Score: 187
Period size: 71 Copynumber: 2.0 Consensus size: 71
1056007 AATTTTGGGG
* * * * * * * *
1056017 GGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGTTTCCAAAAAATATTTTTGGGGAAAAG
1 GGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAAAAAGATTTTTGAGAAAAAG
1056082 TTGAAA
66 TTGAAA
* * *
1056088 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTTTTTGAGAAAAAG
1 GGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAAAAAGATTTTTGAGAAAAAG
1056153 TTGAAA
66 TTGAAA
1056159 G
1 G
1056160 TATCAATTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.31
Consensus pattern (71 bp):
GGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAAAAAGATTTTTGAGAAAAAG
TTGAAA
Found at i:1056157 original size:58 final size:57
Alignment explanation
Indices: 1056089--1056226 Score: 172
Period size: 58 Copynumber: 2.4 Consensus size: 57
1056079 AAGTTGAAAG
* *
1056089 GAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTCAAAAAA-AGGTTTTTGA
1 GAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAATTTTCAAAAAATA--TTTTGGA
* * * *
1056146 GAAAAAGTTGAAAGTATCAATTTTCCTCGAGATTAAAATTTTTAAAAAATATTTTGGA
1 G-AAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAATTTTCAAAAAATATTTTGGA
*
1056204 GAAAAGTCGAAAGTATCAATTTT
1 GAAAAGTTGAAAGTATCAATTTT
1056227 TCCTGTACAA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
57 22 0.31
58 35 0.49
59 13 0.18
60 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (57 bp):
GAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAATTTTCAAAAAATATTTTGGA
Found at i:1059879 original size:27 final size:27
Alignment explanation
Indices: 1059841--1059893 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1059831 TTAACATATA
1059841 TATAGATGTATAACTGACATTTGAGCC
1 TATAGATGTATAACTGACATTTGAGCC
*
1059868 TATAGATGTATAATTGACATTTGAGC
1 TATAGATGTATAACTGACATTTGAGC
1059894 TAACAAGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (27 bp):
TATAGATGTATAACTGACATTTGAGCC
Found at i:1060369 original size:13 final size:13
Alignment explanation
Indices: 1060343--1060408 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
1060333 ATAAAAAACG
1060343 AAAAGCAAATAGAA
1 AAAAGCAAA-AGAA
*
1060357 AAAAGTAAAAGAA
1 AAAAGCAAAAGAA
*
1060370 AAAAGGAAAA-AA
1 AAAAGCAAAAGAA
*
1060382 AATAAGCATAAATTAA
1 AA-AAGCA-AAA-GAA
*
1060398 AAAAGGAAAAG
1 AAAAGCAAAAG
1060409 TAAATAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 4 0.09
13 17 0.40
14 14 0.33
15 4 0.09
16 4 0.09
ACGTcount: A:0.73, C:0.03, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAAGCAAAAGAA
Found at i:1061415 original size:10 final size:10
Alignment explanation
Indices: 1061400--1061424 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1061390 GCTAAAATCC
1061400 ACTTTTATTG
1 ACTTTTATTG
1061410 ACTTTTATTG
1 ACTTTTATTG
1061420 ACTTT
1 ACTTT
1061425 GTTTGCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (10 bp):
ACTTTTATTG
Found at i:1062502 original size:91 final size:92
Alignment explanation
Indices: 1062407--1062582 Score: 246
Period size: 91 Copynumber: 1.9 Consensus size: 92
1062397 GTGGTCACCG
* * * * *
1062407 GTAAGATTCGAACAAAGATGTGCACTATCTGACAATATAAGACAGGTGACTGCAAGTTGTATATT
1 GTAAGACTCAAACAAAGATGTGCACTACCTGACAACATAAGACAGGTGACTGCAAGTTATATATT
1062472 CGAGACGATCC-AATAAGTGGCCACTA
66 CGAGACGATCCTAATAAGTGGCCACTA
* * * * *
1062498 GTAAGACTCAAACAAATATGTGCACTACCTGACAACCTAAGATAGGTGGCTGCAAGTTATGTATT
1 GTAAGACTCAAACAAAGATGTGCACTACCTGACAACATAAGACAGGTGACTGCAAGTTATATATT
*
1062563 CGAGATGATCCTAATAAGTG
66 CGAGACGATCCTAATAAGTG
1062583 ATCAACAATA
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
91 65 0.89
92 8 0.11
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (92 bp):
GTAAGACTCAAACAAAGATGTGCACTACCTGACAACATAAGACAGGTGACTGCAAGTTATATATT
CGAGACGATCCTAATAAGTGGCCACTA
Found at i:1062980 original size:16 final size:17
Alignment explanation
Indices: 1062942--1062981 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
1062932 AACAAAGCCA
1062942 ATTTCCTTTATTTTGTCG
1 ATTT-CTTTATTTTGTCG
1062960 A-TTCTTTATTTTGTC-
1 ATTTCTTTATTTTGTCG
1062975 ATTTCTT
1 ATTTCTT
1062982 GATATGCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 17 0.81
17 2 0.10
18 1 0.05
ACGTcount: A:0.12, C:0.15, G:0.07, T:0.65
Consensus pattern (17 bp):
ATTTCTTTATTTTGTCG
Found at i:1064734 original size:11 final size:11
Alignment explanation
Indices: 1064716--1064755 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
1064706 AATCTCATAA
1064716 GAGATTTGTTT
1 GAGATTTGTTT
* *
1064727 GGGATTTGTTA
1 GAGATTTGTTT
1064738 GAGATTTGTTT
1 GAGATTTGTTT
1064749 GAGATTT
1 GAGATTT
1064756 ATTAGATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:1064743 original size:22 final size:22
Alignment explanation
Indices: 1064715--1064761 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1064705 AAATCTCATA
* *
1064715 AGAGATTTGTTTGGGATTTGTT
1 AGAGATTTGTTTGAGATTTATT
1064737 AGAGATTTGTTTGAGATTTATT
1 AGAGATTTGTTTGAGATTTATT
1064759 AGA
1 AGA
1064762 TATTGCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTATT
Found at i:1064870 original size:52 final size:52
Alignment explanation
Indices: 1064782--1064937 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
1064772 TGGACAAGAA
* *
1064782 GACTTGCAAAAAAAGAATTCTAAGA-GAAAGATGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAAAAGAATTCTAAGAGGAAAG-GGATTCTTAATAGGTAAGTTT
* * *
1064834 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAAAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
* * * *
1064886 GACTTACAGGAAAAGAATTCTAAGAGGAGAGGGA-TCTTAATGGGTAAGTTT
1 GACTTGCAAGAAAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
1064937 G
1 G
1064938 TATGGTTATA
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
51 16 0.18
52 70 0.77
53 5 0.05
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.26
Consensus pattern (52 bp):
GACTTGCAAGAAAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGTAAGTTT
Found at i:1065410 original size:25 final size:24
Alignment explanation
Indices: 1065382--1065437 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1065372 TGAAGATTCA
*
1065382 AGATGTGAAAAGAGCCGAATGTTCG
1 AGATGTGAAAA-AGCCGAAAGTTCG
* *
1065407 AGATGTGAAAAAGCTGAAAGTTTG
1 AGATGTGAAAAAGCCGAAAGTTCG
1065431 AGATGTG
1 AGATGTG
1065438 GGAAGAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.38, C:0.07, G:0.32, T:0.23
Consensus pattern (24 bp):
AGATGTGAAAAAGCCGAAAGTTCG
Found at i:1065720 original size:11 final size:11
Alignment explanation
Indices: 1065702--1065763 Score: 88
Period size: 11 Copynumber: 5.6 Consensus size: 11
1065692 AATCCCATAA
1065702 GAGATTTGTTT
1 GAGATTTGTTT
* *
1065713 GGGATTTGTTA
1 GAGATTTGTTT
1065724 GAGATTTGTTT
1 GAGATTTGTTT
* *
1065735 GGGATTTGTTA
1 GAGATTTGTTT
1065746 GAGATTTGTTT
1 GAGATTTGTTT
1065757 GAGATTT
1 GAGATTT
1065764 ATCAGATATT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:1065726 original size:22 final size:22
Alignment explanation
Indices: 1065701--1065763 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
1065691 AAATCCCATA
1065701 AGAGATTTGTTTGGGATTTGTT
1 AGAGATTTGTTTGGGATTTGTT
1065723 AGAGATTTGTTTGGGATTTGTT
1 AGAGATTTGTTTGGGATTTGTT
*
1065745 AGAGATTTGTTTGAGATTT
1 AGAGATTTGTTTGGGATTT
1065764 ATCAGATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGGGATTTGTT
Found at i:1065878 original size:52 final size:52
Alignment explanation
Indices: 1065791--1065945 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
1065781 GAACAAGAAA
*
1065791 ACTTGCAAAAGAAGAATTCTAAGA-GAAAGATGATTCTTAATAGGTAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGGAAAGA-GATTCTTAATAGGTAAGTTTG
* *
1065843 ACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGTAAGTTTG
* * * *
1065895 ACTTACAGGAGAAGAATTCTAAGAGGAGAGGGA-TCTTAAT-GGATAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGG-TAAGTTTG
1065946 TATGGTTATA
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
50 2 0.02
51 14 0.15
52 70 0.76
53 6 0.07
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.26
Consensus pattern (52 bp):
ACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGTAAGTTTG
Found at i:1066428 original size:24 final size:25
Alignment explanation
Indices: 1066367--1066431 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
1066357 GAGAAAAATT
*
1066367 AAAGATTCAAGATGTGAAAAGAGCCG
1 AAAG-TTCGAGATGTGAAAAGAGCCG
* *
1066393 AATGTTCGAGATGTGAAAA-AGCTG
1 AAAGTTCGAGATGTGAAAAGAGCCG
1066417 AAAGTTCGAGATGTG
1 AAAGTTCGAGATGTG
1066432 GGAAGAGCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 18 0.51
25 14 0.40
26 3 0.09
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (25 bp):
AAAGTTCGAGATGTGAAAAGAGCCG
Found at i:1066715 original size:11 final size:12
Alignment explanation
Indices: 1066696--1066737 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
1066686 AATCCCATAA
1066696 GAGATTTGTTTG
1 GAGATTTGTTTG
*
1066708 GA-ATTTG-TTA
1 GAGATTTGTTTG
1066718 GAGATTTGTTT-
1 GAGATTTGTTTG
1066729 GAGATTTGT
1 GAGATTTGT
1066738 CAGATATTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 19 0.70
12 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (12 bp):
GAGATTTGTTTG
Found at i:1066723 original size:22 final size:22
Alignment explanation
Indices: 1066695--1066737 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1066685 AAATCCCATA
1066695 AGAGATTTGTTTG-GAATTTGTT
1 AGAGATTTGTTTGAG-ATTTGTT
1066717 AGAGATTTGTTTGAGATTTGT
1 AGAGATTTGTTTGAGATTTGT
1066738 CAGATATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTT
Found at i:1066850 original size:52 final size:52
Alignment explanation
Indices: 1066762--1066917 Score: 199
Period size: 52 Copynumber: 3.0 Consensus size: 52
1066752 TGGACAAGAA
* *
1066762 GACTTGCAAAAGAAGAATTCTAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGA-GATTCTTAATAGGCAAGTTT
* *
1066814 GACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGCTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
* * * * * *
1066866 GACTTACAGGAGAAAAATTCTAAGAGGAGAGGGA-TCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
1066917 G
1 G
1066918 TATGGTTATA
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
51 16 0.18
52 69 0.76
53 6 0.07
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:1067408 original size:24 final size:25
Alignment explanation
Indices: 1067361--1067416 Score: 96
Period size: 24 Copynumber: 2.3 Consensus size: 25
1067351 TGAAGATTCA
*
1067361 AGATGTGAAAAGAGCCGAATGTTCG
1 AGATGTGAAAAGAGCCGAAAGTTCG
1067386 AGATGTGAAAA-AGCCGAAAGTTCG
1 AGATGTGAAAAGAGCCGAAAGTTCG
1067410 AGATGTG
1 AGATGTG
1067417 GGAAGAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.38, C:0.11, G:0.32, T:0.20
Consensus pattern (25 bp):
AGATGTGAAAAGAGCCGAAAGTTCG
Found at i:1067566 original size:985 final size:986
Alignment explanation
Indices: 1064689--1068296 Score: 6210
Period size: 985 Copynumber: 3.7 Consensus size: 986
1064679 GTGTACACTT
* *
1064689 TTGGAAATATTGACTCAAATCTCATAAGAGATTTGTTTGGGATTTGTTAGAGATTTGTTTGAGAT
1 TTGGAAATATTGACTCAAATCCCATAAGAGATTTGTTTGGAATTTGTTAGAGATTTGTTTGAGAT
* * *
1064754 TTATTAGATATTGCTTGATGGACAAGAAGACTTGCAAAAAAAGAATTCTAAGAGAAAGATGATTC
66 TTATCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAGAAGAATTCTAAGAGAAAGAGGATTC
*
1064819 TTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGCAAGT
131 TTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGT
*
1064884 TTGACTTACAGGA-AAAGAATTCTAAGAGGAGAGGGATCTTAATGGGTAAGTTTGTATGGTTATA
196 TTGACTTACAGGAGAAA-AATTCTAAGAGGAGAGGGATCTTAATGGGCAAGTTTGTATGGTTATA
*
1064948 AATAGGTGAAGTCTCTACAGGATTAGGTATGAGAAAAAGATGTAAGAGAGTTGCAGGGTTTTGTG
260 AATAGGTGAAGTCTCTACAGGATTAGGTATGAGAAAAAGATGTAAGAGAGTTGTAGGGTTTTGTG
1065013 GGATAAACACCCCATAGGAGTATTGGGGCTCTACGTCTTATGGGTGTGTATGTTTGTTTGTGAGT
325 GGATAAACACCCCATAGGAGTATTGGGGCTCTACGTCTTATGGGTGTGTATGTTTGTTTGTGAGT
1065078 GGACTAGAAGAAGATTGAGAGTATCTTATGAGTATTGATTGTTGAGTGAGGTTGATGATTTGATG
390 GGACTAGAAGAAGATTGAGAGTATCTTATGAGTATTGATTGTTGAGTGAGGTTGATGATTTGATG
1065143 TAAGCTTATAATTCTCTACAACTAGTGGATCTTGTTTCTCATCCGTGGATGTAGGTCAGTTGGAC
455 TAAGCTTATAATTCTCTACAACTAGTGGATCTTGTTTCTCATCCGTGGATGTAGGTCAGTTGGAC
*
1065208 CGAACCACGTTAAATTGCTGTCTCTTGTGTGTTTGATTTATTGTTTGATTTCACTTCCGTTGGTG
520 CGAACCACGTTAAATTGCTGTCTCTTGTGTGTTTGATTTATTGTTTGATTTCGCTTCCGTTGGTG
1065273 TGATTGGATTGGAGGCTTTTAGCCCAACAAATGGTATTAGAGCTGTGGTGTTCCCCAACAAGTGG
585 TGATTGGATTGGAGGCTTTTAGCCCAACAAATGGTATTAGAGCTGTGGTGTTCCCCAACAAGTGG
* *
1065338 TATCAGAGCTGAAGGTTCGAAATGTGAGAAAAGTTGAAGATTCAAGATGTGAAAAGAGCCGAATG
650 TATCAGAGCTGAAGGTTCAAAATGTGAGAAAAATTGAAGATTCAAGATGTGAAAAGAGCCGAATG
* *
1065403 TTCGAGATGTGAAAAAGCTGAAAGTTTGAGATGTGGGAAGAGCTAAAGGTTTGGAAAGTGCATGG
715 TTCGAGATGTGAAAAAGCTGAAAGTTCGAGATGTGGGAAGAGCTAAAGGTTTGGGAAGTGCATGG
*
1065468 TTTGAGACATGGGAAGAAGCAAGTCCAGAAGAGCTTGATTCGAAAGAAGAGTTCGAGTTTAAGTT
780 TTTGAGACATGGGAAGAAGCAAGTCCAGAAGAGCTCGATTCGAAAGAAGAGTTCGAGTTTAAGTT
*
1065533 TTGAAGATTGATGATTGATTTGTATGAAGCGTGAAGACACAAGAGAAGAGAACATGATTGTGAGA
845 TTGAAGATTGATGATTGATTTGTATGAAGCGTGAAGACACAAGAGAAGAGAAGATGATTGTGAGA
* * *
1065598 CTTTTATTGTAGGTGGAGCCAAGCATGTCTAGCATGAAGACAGATAATTGATGAAATTTGAGTCA
910 CTTTCATTGTAGGTGGAGCCAAGCATGTCTAGCATGAAGACAGATGATTGATGGAATTTGAGTCA
1065663 AGGTGGAGATTG
975 AGGTGGAGATTG
1065675 TT-GAGAATATTGACTCAAATCCCATAAGAGATTTGTTTGGGATTTGTTAGAGATTTGTTTGGGA
1 TTGGA-AATATTGACTCAAATCCCATAAGAGA----TTT--G---T-TT-G-GA----------A
* *
1065739 TTTGTTAGAGATTTGTTTGAGATTTATCAGATATTGCTTGATGAACAAGAAAACTTGCAAAAGAA
43 TTTGTTAGAGATTTGTTTGAGATTTATCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAGAA
*
1065804 GAATTCTAAGAGAAAGATGATTCTTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAAGG
108 GAATTCTAAGAGAAAGAGGATTCTTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAAGG
*
1065869 AAAGAGATTCTTAATAGGCAAGTTTGACTTACAGGAGAAGAATTCTAAGAGGAGAGGGATCTTAA
173 AAAGAGATTCTTAATAGGCAAGTTTGACTTACAGGAGAAAAATTCTAAGAGGAGAGGGATCTTAA
**
1065934 TGGATAAGTTTGTATGGTTATAAATAGGTGAAGTCTCTACAGGATTAGGTATGAGAAAAAGATGT
238 TGGGCAAGTTTGTATGGTTATAAATAGGTGAAGTCTCTACAGGATTAGGTATGAGAAAAAGATGT
1065999 AAGAGAGTTGTAGGGTTTTGTGGGATAAACACCCCATAGGAGTATTGGGGCTCTACGTCTTATGG
303 AAGAGAGTTGTAGGGTTTTGTGGGATAAACACCCCATAGGAGTATTGGGGCTCTACGTCTTATGG
1066064 G-GTGTATG-TTGTTTGTGAGTGGACTAGAAGAAGA-TGAGAGTTATCTTATGAGTATTGATTGT
368 GTGTGTATGTTTGTTTGTGAGTGGACTAGAAGAAGATTGAGAG-TATCTTATGAGTATTGATTGT
1066126 TGAGTGAGGTTGATGATTTGATGTAAGCTTATAATTCTCTACAACTAGTGGATCTTGTTTCTCAT
432 TGAGTGAGGTTGATGATTTGATGTAAGCTTATAATTCTCTACAACTAGTGGATCTTGTTTCTCAT
1066191 CCGTGGATGTAGGTCAGTTGGACCGAACCACGTTAAATTGCTGTCTC---T-TG--TG------T
497 CCGTGGATGTAGGTCAGTTGGACCGAACCACGTTAAATTGCTGTCTCTTGTGTGTTTGATTTATT
* *
1066244 GTTTGATTTCACTTTCGTTGGTGTGATTGGATTGGAGGCTTTTAGCCCAACAAATGGTATTAGAG
562 GTTTGATTTCGCTTCCGTTGGTGTGATTGGATTGGAGGCTTTTAGCCCAACAAATGGTATTAGAG
*
1066309 CTGTGGTGTTCCCCAACAAGTGGTATCAGAGCTGAAGGTTCAAAATGTGAGAAAAATTAAAGATT
627 CTGTGGTGTTCCCCAACAAGTGGTATCAGAGCTGAAGGTTCAAAATGTGAGAAAAATTGAAGATT
1066374 CAAGATGTGAAAAGAGCCGAATGTTCGAGATGTGAAAAAGCTGAAAGTTCGAGATGTGGGAAGAG
692 CAAGATGTGAAAAGAGCCGAATGTTCGAGATGTGAAAAAGCTGAAAGTTCGAGATGTGGGAAGAG
*
1066439 CTAAAGGTTTGGGAAGTGCATGGTTTGAGACATGAGAAGAAGCAAGTCCAGAAGAGCTCGATTCG
757 CTAAAGGTTTGGGAAGTGCATGGTTTGAGACATGGGAAGAAGCAAGTCCAGAAGAGCTCGATTCG
1066504 AAAGAAGAGTTCGAGTTTAAGTTTTGAAGATTGATGATTGATTTGTATGAAGCGTGAAGACACAA
822 AAAGAAGAGTTCGAGTTTAAGTTTTGAAGATTGATGATTGATTTGTATGAAGCGTGAAGACACAA
*
1066569 GAGAAGAGAAGATGATTGTGAGACTTTCATTGCAGGTGGAGCCAAGCATGTCTAGCATGAAGACA
887 GAGAAGAGAAGATGATTGTGAGACTTTCATTGTAGGTGGAGCCAAGCATGTCTAGCATGAAGACA
1066634 GATGATTGATGGAATTTGAGTCAAGGTGGAGATTG
952 GATGATTGATGGAATTTGAGTCAAGGTGGAGATTG
1066669 TTGGAAATATTGACTCAAATCCCATAAGAGATTTGTTTGGAATTTGTTAGAGATTTGTTTGAGAT
1 TTGGAAATATTGACTCAAATCCCATAAGAGATTTGTTTGGAATTTGTTAGAGATTTGTTTGAGAT
*
1066734 TTGTCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAGAAGAATTCTAAGAGAAAGAGGATTC
66 TTATCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAGAAGAATTCTAAGAGAAAGAGGATTC
*
1066799 TTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGC
131 TTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGT
1066864 TTGACTTACAGGAGAAAAATTCTAAGAGGAGAGGGATCTTAATGGGCAAGTTTGTATGGTTATAA
196 TTGACTTACAGGAGAAAAATTCTAAGAGGAGAGGGATCTTAATGGGCAAGTTTGTATGGTTATAA
* * *
1066929 ATAGGTGAAGTCTTTATAGGGTTAGGTATGAGAAAAAGATGTAAGAGAGTTGTAGGGTTTTGTGG
261 ATAGGTGAAGTCTCTACAGGATTAGGTATGAGAAAAAGATGTAAGAGAGTTGTAGGGTTTTGTGG
* *
1066994 GATAGACACCCCATAGGAGTATTGGGGCTCTACGTCTTATGGGTATGTATGTTTGTTTGTGAGTG
326 GATAAACACCCCATAGGAGTATTGGGGCTCTACGTCTTATGGGTGTGTATGTTTGTTTGTGAGTG
*
1067059 GACTAGAAG-AGATTGAGAGTGTCTTATGAGTATTGATTGTTGAGTGAGGTTGATGATTTGATGT
391 GACTAGAAGAAGATTGAGAGTATCTTATGAGTATTGATTGTTGAGTGAGGTTGATGATTTGATGT
* * *
1067123 AAGTTTATAATTCTCTACAACTAGTGGATCTTGTTTCTCATCCATGGATGTAGGTCAGTTGGATC
456 AAGCTTATAATTCTCTACAACTAGTGGATCTTGTTTCTCATCCGTGGATGTAGGTCAGTTGGACC
* * *
1067188 GAATCACGTTAAATTGTTGTCTCTTGTGTGTTTGATTTATTGTTTGATTTCGCTTCTGTTGGTGT
521 GAACCACGTTAAATTGCTGTCTCTTGTGTGTTTGATTTATTGTTTGATTTCGCTTCCGTTGGTGT
*
1067253 GATTGGATTGGAGGCTTTTAGCCCAACAAATGGTATTAGAGCTGTGGTGTTCCCTAACAAGTGGT
586 GATTGGATTGGAGGCTTTTAGCCCAACAAATGGTATTAGAGCTGTGGTGTTCCCCAACAAGTGGT
1067318 ATCAGAGCTGAAGGTTCAAAATGTGAGAAAAATTGAAGATTCAAGATGTGAAAAGAGCCGAATGT
651 ATCAGAGCTGAAGGTTCAAAATGTGAGAAAAATTGAAGATTCAAGATGTGAAAAGAGCCGAATGT
*
1067383 TCGAGATGTGAAAAAGCCGAAAGTTCGAGATGTGGGAAGAGCTAAAGGTTTGGGAAGTGCATGGT
716 TCGAGATGTGAAAAAGCTGAAAGTTCGAGATGTGGGAAGAGCTAAAGGTTTGGGAAGTGCATGGT
* *
1067448 TTGAGACGTGGGAAGAAGCAAGTCCAGAAGAGCTCGATTCGAAAGAAGAGTTCGAGTTTAAATTT
781 TTGAGACATGGGAAGAAGCAAGTCCAGAAGAGCTCGATTCGAAAGAAGAGTTCGAGTTTAAGTTT
*
1067513 TGAAGATTGATGATTGATTTTTATGAAGCGTGAAGACACAAGAGAAGAGAAGATGATTGTGAGAC
846 TGAAGATTGATGATTGATTTGTATGAAGCGTGAAGACACAAGAGAAGAGAAGATGATTGTGAGAC
*
1067578 TTTCATTGTAGGTGGAGCCACGCATGTCTAGCATGAAGACAGATGATTGATGGAATTTGAGTCAA
911 TTTCATTGTAGGTGGAGCCAAGCATGTCTAGCATGAAGACAGATGATTGATGGAATTTGAGTCAA
1067643 GGTGGAGATTG
976 GGTGGAGATTG
* * *
1067654 TTGGGAATATTGACTCAAATCCCATAAGAGATTTGTTTGGGATTTGTTTGAGATTTGTTTGAGAT
1 TTGGAAATATTGACTCAAATCCCATAAGAGATTTGTTTGGAATTTGTTAGAGATTTGTTTGAGAT
*
1067719 TTGTCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAGAAGAATTCTAAGAGAAAGAGGATTC
66 TTATCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAGAAGAATTCTAAGAGAAAGAGGATTC
* * * *
1067784 TTAATAGGAAAGTTTGACTTGGAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGTAAGT
131 TTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGT
* * *
1067849 TTGACTTACAAGAGAAGAATTCTAAGAGGAGAAGGATCTTAATGGGCAAGTTTGTATGGTTATAA
196 TTGACTTACAGGAGAAAAATTCTAAGAGGAGAGGGATCTTAATGGGCAAGTTTGTATGGTTATAA
* *
1067914 ATAGGTGAAGTCTCTACAGGGTTAGGTATGAGAAAAAGATGTAAGAGAGTTGTAGGGTTTTGTAG
261 ATAGGTGAAGTCTCTACAGGATTAGGTATGAGAAAAAGATGTAAGAGAGTTGTAGGGTTTTGTGG
*
1067979 GATAAACACCCCATAGGAGTATTGGGGCTCTACGTCTTATGGGTGTGTATGTTTGTGTGTGAGTG
326 GATAAACACCCCATAGGAGTATTGGGGCTCTACGTCTTATGGGTGTGTATGTTTGTTTGTGAGTG
* *
1068044 GACTAG-AGGAGATTGAGAGTGTCTTATGAGTATTGATTGTTGAGTGAGGTTGATGATTTGATGT
391 GACTAGAAGAAGATTGAGAGTATCTTATGAGTATTGATTGTTGAGTGAGGTTGATGATTTGATGT
*
1068108 AAGTTTATAATTCTCTACAACTAGTGGATCTTGTTTCTCATCCGTGGATGTAGGTCAGTTGGACC
456 AAGCTTATAATTCTCTACAACTAGTGGATCTTGTTTCTCATCCGTGGATGTAGGTCAGTTGGACC
* * * *
1068173 GAATCACGTTAAATTGTTGTCTCTTGTGTGTTTGATTTATTATTTGATTTCGCTTCCGTTGATGT
521 GAACCACGTTAAATTGCTGTCTCTTGTGTGTTTGATTTATTGTTTGATTTCGCTTCCGTTGGTGT
* *
1068238 GATTGAATTGGAGGCTTTTAGCCCATCAAATGGTATTAGAGCTGTGGTGTTCCCCAACA
586 GATTGGATTGGAGGCTTTTAGCCCAACAAATGGTATTAGAGCTGTGGTGTTCCCCAACA
1068297 TACACTTCAT
Statistics
Matches: 2501, Mismatches: 79, Indels: 85
0.94 0.03 0.03
Matches are distributed among these distances:
972 315 0.13
973 136 0.05
974 28 0.01
976 1 0.00
977 2 0.00
979 2 0.00
982 2 0.00
983 1 0.00
984 4 0.00
985 1032 0.41
986 27 0.01
988 1 0.00
990 6 0.00
992 1 0.00
994 441 0.18
995 3 0.00
996 2 0.00
997 1 0.00
998 1 0.00
1000 2 0.00
1002 2 0.00
1003 1 0.00
1005 6 0.00
1006 159 0.06
1007 7 0.00
1008 316 0.13
1009 2 0.00
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (986 bp):
TTGGAAATATTGACTCAAATCCCATAAGAGATTTGTTTGGAATTTGTTAGAGATTTGTTTGAGAT
TTATCAGATATTGCTTGATGGACAAGAAGACTTGCAAAAGAAGAATTCTAAGAGAAAGAGGATTC
TTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAAGGAAAGAGATTCTTAATAGGCAAGT
TTGACTTACAGGAGAAAAATTCTAAGAGGAGAGGGATCTTAATGGGCAAGTTTGTATGGTTATAA
ATAGGTGAAGTCTCTACAGGATTAGGTATGAGAAAAAGATGTAAGAGAGTTGTAGGGTTTTGTGG
GATAAACACCCCATAGGAGTATTGGGGCTCTACGTCTTATGGGTGTGTATGTTTGTTTGTGAGTG
GACTAGAAGAAGATTGAGAGTATCTTATGAGTATTGATTGTTGAGTGAGGTTGATGATTTGATGT
AAGCTTATAATTCTCTACAACTAGTGGATCTTGTTTCTCATCCGTGGATGTAGGTCAGTTGGACC
GAACCACGTTAAATTGCTGTCTCTTGTGTGTTTGATTTATTGTTTGATTTCGCTTCCGTTGGTGT
GATTGGATTGGAGGCTTTTAGCCCAACAAATGGTATTAGAGCTGTGGTGTTCCCCAACAAGTGGT
ATCAGAGCTGAAGGTTCAAAATGTGAGAAAAATTGAAGATTCAAGATGTGAAAAGAGCCGAATGT
TCGAGATGTGAAAAAGCTGAAAGTTCGAGATGTGGGAAGAGCTAAAGGTTTGGGAAGTGCATGGT
TTGAGACATGGGAAGAAGCAAGTCCAGAAGAGCTCGATTCGAAAGAAGAGTTCGAGTTTAAGTTT
TGAAGATTGATGATTGATTTGTATGAAGCGTGAAGACACAAGAGAAGAGAAGATGATTGTGAGAC
TTTCATTGTAGGTGGAGCCAAGCATGTCTAGCATGAAGACAGATGATTGATGGAATTTGAGTCAA
GGTGGAGATTG
Found at i:1067699 original size:11 final size:11
Alignment explanation
Indices: 1067681--1067722 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
1067671 AATCCCATAA
1067681 GAGATTTGTTT
1 GAGATTTGTTT
*
1067692 GGGATTTGTTT
1 GAGATTTGTTT
1067703 GAGATTTGTTT
1 GAGATTTGTTT
1067714 GAGATTTGT
1 GAGATTTGT
1067723 CAGATATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:1067834 original size:52 final size:52
Alignment explanation
Indices: 1067747--1067902 Score: 210
Period size: 52 Copynumber: 3.0 Consensus size: 52
1067737 TGGACAAGAA
*
1067747 GACTTGCAAAAGAAGAATTCTAAGA-GAAAGAGGATTCTTAATAGGAAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAG-GGATTCTTAATAGGAAAGTTT
* * *
1067799 GACTTGGAAGAGAAGAATTCTAAAAGGAAAGGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGAAAGTTT
* * *
1067851 GACTTACAAGAGAAGAATTCTAAGAGGAGAA-GGA-TCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGA-AAGGGATTCTTAATAGGAAAGTTT
1067902 G
1 G
1067903 TATGGTTATA
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
51 16 0.17
52 70 0.75
53 7 0.08
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.25
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGAAAGTTT
Found at i:1073022 original size:25 final size:25
Alignment explanation
Indices: 1072994--1073044 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1072984 TCTGGGAAGG
1072994 TTTGCCATTCGCATAAGTCTCTATA
1 TTTGCCATTCGCATAAGTCTCTATA
*
1073019 TTTGCCATTCGCATAGGTCTCTATA
1 TTTGCCATTCGCATAAGTCTCTATA
1073044 T
1 T
1073045 GGTCCTAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (25 bp):
TTTGCCATTCGCATAAGTCTCTATA
Found at i:1074343 original size:12 final size:12
Alignment explanation
Indices: 1074326--1074379 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
1074316 TTGTAATTTG
1074326 ATTTTGATTTTA
1 ATTTTGATTTTA
*
1074338 ATTTTGGTTTTA
1 ATTTTGATTTTA
**
1074350 ATTTTTTTATTTA
1 ATTTTGAT-TTTA
*
1074363 GTTTTGATTTTA
1 ATTTTGATTTTA
1074375 ATTTT
1 ATTTT
1074380 ATGATTTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 25 0.74
13 9 0.26
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70
Consensus pattern (12 bp):
ATTTTGATTTTA
Found at i:1074362 original size:25 final size:25
Alignment explanation
Indices: 1074334--1074395 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
1074324 TGATTTTGAT
* *
1074334 TTTAATTTTGGTTTTAATTTTTTTA
1 TTTAATTTTGGTTTTAATTTTATGA
* *
1074359 TTTAGTTTTGATTTTAATTTTATGA
1 TTTAATTTTGGTTTTAATTTTATGA
1074384 TTT-ATTTTGGTT
1 TTTAATTTTGGTT
1074396 AAATAAAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.19, C:0.00, G:0.11, T:0.69
Consensus pattern (25 bp):
TTTAATTTTGGTTTTAATTTTATGA
Found at i:1076986 original size:20 final size:19
Alignment explanation
Indices: 1076941--1077005 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 19
1076931 AAGGGGAAAG
1076941 GAAATAAAAAGAA-AAAAAAA
1 GAAA-AAAAA-AAGAAAAAAA
**
1076961 GTAAAAGTAAAAGCAAAAAAA
1 G-AAAAAAAAAAG-AAAAAAA
1076982 GAAAAAAAAAAGAGAAAAAA
1 GAAAAAAAAAAGA-AAAAAA
1077002 GAAA
1 GAAA
1077006 GACTTAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.08
20 23 0.62
21 11 0.30
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (19 bp):
GAAAAAAAAAAGAAAAAAA
Found at i:1077006 original size:13 final size:13
Alignment explanation
Indices: 1076975--1077007 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1076965 AAGTAAAAGC
1076975 AAAAAA-AGAAAA
1 AAAAAAGAGAAAA
1076987 AAAAAAGAGAAAA
1 AAAAAAGAGAAAA
*
1077000 AAGAAAGA
1 AAAAAAGA
1077008 CTTAAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:1078076 original size:25 final size:25
Alignment explanation
Indices: 1078035--1078091 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
1078025 TCTTGATAAT
*
1078035 TGCATTT-GCATCATGTTCAAGGCA
1 TGCATTTGGAATCATGTTCAAGGCA
1078059 TGCATTTGGAATCATGTTCAAGGCA
1 TGCATTTGGAATCATGTTCAAGGCA
1078084 TGCATTTG
1 TGCATTTG
1078092 CATTATGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 7 0.23
25 24 0.77
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (25 bp):
TGCATTTGGAATCATGTTCAAGGCA
Found at i:1078154 original size:13 final size:13
Alignment explanation
Indices: 1078136--1078161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1078126 TTGTTTACAG
1078136 CATGTATTTGTAT
1 CATGTATTTGTAT
1078149 CATGTATTTGTAT
1 CATGTATTTGTAT
1078162 TTAGTGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
CATGTATTTGTAT
Found at i:1078575 original size:24 final size:24
Alignment explanation
Indices: 1078450--1078575 Score: 71
Period size: 24 Copynumber: 5.4 Consensus size: 24
1078440 ATATATGACA
*
1078450 TTTTGATTGTGAATCTCTAAAATT
1 TTTTGAATGTGAATCTCTAAAATT
* * * *
1078474 TTTTTAATGTGAATCTTTGATATT
1 TTTTGAATGTGAATCTCTAAAATT
* ** * *
1078498 TTAT--ATGCAAAACCCTAAAATT
1 TTTTGAATGTGAATCTCTAAAATT
** ** * *
1078520 TTTCAAATAAGAATCTTTCAAA-T
1 TTTTGAATGTGAATCTCTAAAATT
*
1078543 TTTAG-ATGTGAATCTCTAAAATT
1 TTTTGAATGTGAATCTCTAAAATT
1078566 TTTTGAATGT
1 TTTTGAATGT
1078576 AAATATTTGA
Statistics
Matches: 69, Mismatches: 29, Indels: 8
0.65 0.27 0.08
Matches are distributed among these distances:
22 25 0.36
23 9 0.13
24 35 0.51
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (24 bp):
TTTTGAATGTGAATCTCTAAAATT
Found at i:1078585 original size:92 final size:91
Alignment explanation
Indices: 1078420--1078665 Score: 243
Period size: 92 Copynumber: 2.7 Consensus size: 91
1078410 GGCCTAATTA
* * * * * *
1078420 CTAAAATATTTCAAATGAGAATATATGACATTTT-GATTGTGAATCTCTAAAATTTTTTTAATGT
1 CTAAAATTTTTCAAATAAGAATCT-TTAAATTTTAGATTGTGAATCTCTAAAATTTTTTGAATGT
* *
1078484 GAATCTTTGATA-TTTT-ATATGCAAAACC
65 AAATATTTGA-AGTTTTGATATG--AAACC
1078512 CTAAAATTTTTCAAATAAGAATCTTTCAAATTTTAGA-TGTGAATCTCTAAAATTTTTTGAATGT
1 CTAAAATTTTTCAAATAAGAATCTTT-AAATTTTAGATTGTGAATCTCTAAAATTTTTTGAATGT
* *
1078576 AAATATTTGAAGTTTTGGATTTGAATCC
65 AAATATTTGAAGTTTT-GATATGAAACC
* * * * *
1078604 CTAAATTTTTTTCTAATGAA-AATCTTTAACTTTTA-ATTGTGAATTTCTAAAATTTTTCGAAT
1 CTAAA-ATTTTTCAAAT-AAGAATCTTTAAATTTTAGATTGTGAATCTCTAAAATTTTTTGAAT
1078666 AAAATCCTTG
Statistics
Matches: 131, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
91 3 0.02
92 104 0.79
93 18 0.14
94 6 0.05
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (91 bp):
CTAAAATTTTTCAAATAAGAATCTTTAAATTTTAGATTGTGAATCTCTAAAATTTTTTGAATGTA
AATATTTGAAGTTTTGATATGAAACC
Found at i:1078601 original size:46 final size:44
Alignment explanation
Indices: 1078450--1078670 Score: 117
Period size: 46 Copynumber: 4.8 Consensus size: 44
1078440 ATATATGACA
* ** *
1078450 TTTTGATTGTGAATCTCTAAAATTTTTTTAATGTGAATCTTTGATA-
1 TTTTGATT-TGAATCTCTAAAATTTTTTGAATGAAAATATTT-A-AC
* * * ** * *
1078496 TTTT-ATATGCAAAACCCTAAAATTTTTCAAAT-AAGAATCTTTCAAA
1 TTTTGATTTG--AATCTCTAAAATTTTTTGAATGAA-AATATTT-AAC
* * *
1078542 TTTTAGATGTGAATCTCTAAAATTTTTTGAATGTAAATATTTGAAG
1 TTTT-GATTTGAATCTCTAAAATTTTTTGAATGAAAATATTT-AAC
* * * *
1078588 TTTTGGATTTGAATCCCTAAATTTTTTTCTAATGAAAATCTTTAAC
1 TTTT-GATTTGAATCTCTAAAATTTTTT-GAATGAAAATATTTAAC
* * *
1078634 TTTTAATTGTGAATTTCTAAAATTTTTCGAAT-AAAAT
1 TTTTGATT-TGAATCTCTAAAATTTTTTGAATGAAAAT
1078671 CCTTGAATTC
Statistics
Matches: 135, Mismatches: 31, Indels: 20
0.73 0.17 0.11
Matches are distributed among these distances:
44 7 0.05
45 9 0.07
46 103 0.76
47 12 0.09
48 4 0.03
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (44 bp):
TTTTGATTTGAATCTCTAAAATTTTTTGAATGAAAATATTTAAC
Found at i:1078920 original size:18 final size:18
Alignment explanation
Indices: 1078897--1078962 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
1078887 ATGAAACTAG
1078897 AATTCTTGCAAATCTTTA
1 AATTCTTGCAAATCTTTA
* * *
1078915 AATTCTTACGAATC-TGA
1 AATTCTTGCAAATCTTTA
* * * *
1078932 AAGTCTTGCTACTCTTTG
1 AATTCTTGCAAATCTTTA
1078950 AATTCTTGCAAAT
1 AATTCTTGCAAAT
1078963 TTGAAATATT
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
17 12 0.34
18 23 0.66
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (18 bp):
AATTCTTGCAAATCTTTA
Found at i:1078968 original size:35 final size:35
Alignment explanation
Indices: 1078900--1078968 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
1078890 AAACTAGAAT
*
1078900 TCTTGCAAATCTTTAAATTCTTACGAATCTGAAAG
1 TCTTGCAAATCTTTAAATTCTTACAAATCTGAAAG
* * * * *
1078935 TCTTGCTACTCTTTGAATTCTTGCAAATTTGAAA
1 TCTTGCAAATCTTTAAATTCTTACAAATCTGAAA
1078969 TATTTATGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (35 bp):
TCTTGCAAATCTTTAAATTCTTACAAATCTGAAAG
Found at i:1079400 original size:43 final size:43
Alignment explanation
Indices: 1079353--1079450 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
1079343 ATTTGAAGTT
* * **
1079353 TTTAAAGTTGTTTAGCCTCTGTCTAGAAGAACTTATTTCTTAA
1 TTTAAAGTTGTTTAGCCTCTGTATAAAAGAACACATTTCTTAA
* *
1079396 TTTAAAGTTGTTTAGCCTTTGTATAAAAGAGCACATTTCTTAA
1 TTTAAAGTTGTTTAGCCTCTGTATAAAAGAACACATTTCTTAA
*
1079439 TTTAAAATTGTT
1 TTTAAAGTTGTT
1079451 GAACTCCTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (43 bp):
TTTAAAGTTGTTTAGCCTCTGTATAAAAGAACACATTTCTTAA
Found at i:1079762 original size:24 final size:23
Alignment explanation
Indices: 1079723--1079798 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
1079713 TTAATTATAA
*
1079723 TTTT-ATTT-TGATTTTAATTTTAG
1 TTTTAATTTGTGA-TTT-ATTTTGG
* * *
1079746 TTTTAATTTTTTATTTAGTTTGG
1 TTTTAATTTGTGATTTATTTTGG
1079769 ATTTTAATTTGTGATTTATTTTGG
1 -TTTTAATTTGTGATTTATTTTGG
1079793 TTTTAA
1 TTTTAA
1079799 AAAAAAAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
23 15 0.34
24 27 0.61
25 2 0.05
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (23 bp):
TTTTAATTTGTGATTTATTTTGG
Done.