Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000521.1 Hibiscus syriacus cultivar Beakdansim tig00000999_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1347562
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1127980 original size:16 final size:16
Alignment explanation
Indices: 1127961--1127992 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1127951 TTTTTTCCCA
1127961 CAAATATGCAAATTTT
1 CAAATATGCAAATTTT
1127977 CAAATATGCAAATTTT
1 CAAATATGCAAATTTT
1127993 TAGTGGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
CAAATATGCAAATTTT
Found at i:1128700 original size:168 final size:169
Alignment explanation
Indices: 1128422--1128760 Score: 599
Period size: 168 Copynumber: 2.0 Consensus size: 169
1128412 AGTGGGCAGA
* *
1128422 AGAGGTTCTCCATGGAGCTGGTACAGATATCAAGTACCAGAAAAGGAAAACTCAATACAGTAGGA
1 AGAGGTTCTCCATGGAGCTGGTACAAATATCAAGTACCAAAAAAGGAAAACTCAATACAGTAGGA
* *
1128487 ACTTGAAGCGTTAAAAAAGCATAAACAGACGAGTACAAATTTATACAGATTTTTCCCTCCTTTTT
66 ACTTGAAGCGTTAAAAAAGCATAAACAGACAAGTACAAATTTATACAGATTTTTCCCTCCTTTTC
1128552 AGA-GGGGGCTAGGGGATGTTGAGAAAACATGAGAATGG
131 AGAGGGGGGCTAGGGGATGTTGAGAAAACATGAGAATGG
1128590 AGAGGTTCTCCATGGAGCTGGTACAAATATCAAGTACCAAAAAAGGAAAACTCAATACAGTAGGA
1 AGAGGTTCTCCATGGAGCTGGTACAAATATCAAGTACCAAAAAAGGAAAACTCAATACAGTAGGA
* * *
1128655 ACTTGAAGCGTTAGAAAAGCATAAACAGACAAGTATACATTTATACAGATTTTTCCCTCCTTTTC
66 ACTTGAAGCGTTAAAAAAGCATAAACAGACAAGTACAAATTTATACAGATTTTTCCCTCCTTTTC
*
1128720 AGAGGGGGGGTAGGGGATGTTGAGAAAACATGAGAATGG
131 AGAGGGGGGCTAGGGGATGTTGAGAAAACATGAGAATGG
1128759 AG
1 AG
1128761 CAGTAAACTG
Statistics
Matches: 162, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
168 126 0.78
169 36 0.22
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (169 bp):
AGAGGTTCTCCATGGAGCTGGTACAAATATCAAGTACCAAAAAAGGAAAACTCAATACAGTAGGA
ACTTGAAGCGTTAAAAAAGCATAAACAGACAAGTACAAATTTATACAGATTTTTCCCTCCTTTTC
AGAGGGGGGCTAGGGGATGTTGAGAAAACATGAGAATGG
Found at i:1129931 original size:20 final size:20
Alignment explanation
Indices: 1129906--1129997 Score: 83
Period size: 20 Copynumber: 5.0 Consensus size: 20
1129896 TCTGTTAGTT
1129906 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
1129926 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
1129946 ATT--CT-G--TTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
1129958 ATTAAATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
1129978 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
1129998 TTCTATTGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
12 3 0.05
13 2 0.04
14 1 0.02
15 4 0.07
17 4 0.07
18 1 0.02
19 2 0.04
20 40 0.70
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.43
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1129952 original size:52 final size:51
Alignment explanation
Indices: 1129890--1130001 Score: 197
Period size: 52 Copynumber: 2.2 Consensus size: 51
1129880 TAACTATATA
*
1129890 TTTTATTCTGTTAGTTATTAGATAGAATCAGTTTTAATTAGATAGAATCAG
1 TTTTATTCTGTTAGTTATTAAATAGAATCAGTTTTAATTAGATAGAATCAG
*
1129941 TTTTTATTCTGTTAGTTATTAAATAGGATCAGTTTTAATTAGATAGAATCAG
1 -TTTTATTCTGTTAGTTATTAAATAGAATCAGTTTTAATTAGATAGAATCAG
1129993 TTTTATTCT
1 TTTTATTCT
1130002 ATTGCTAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 9 0.16
52 49 0.84
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.48
Consensus pattern (51 bp):
TTTTATTCTGTTAGTTATTAAATAGAATCAGTTTTAATTAGATAGAATCAG
Found at i:1130488 original size:34 final size:30
Alignment explanation
Indices: 1130450--1130518 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
1130440 TTGATATAAC
1130450 AATTTAAGTCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
1130484 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
1130513 AATTTA
1 AATTTA
1130519 TTCAAAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:1130525 original size:31 final size:31
Alignment explanation
Indices: 1130458--1130530 Score: 107
Period size: 30 Copynumber: 2.4 Consensus size: 31
1130448 ACAATTTAAG
1130458 TCAAAATGGTTTTTGGACTTGAATTGAATTTA
1 TCAAAAT-GTTTTTGGACTTGAATTGAATTTA
1130490 -CAAAATGTTTTTGGACTT-AATTGAATTTA
1 TCAAAATGTTTTTGGACTTGAATTGAATTTA
1130519 TTCAAAA-GTTTT
1 -TCAAAATGTTTT
1130531 AAAAGGTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
29 11 0.28
30 17 0.44
31 11 0.28
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (31 bp):
TCAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1130625 original size:21 final size:21
Alignment explanation
Indices: 1130599--1130656 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
1130589 AGGGTGTCAA
1130599 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
1130620 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCCCTGC
1130641 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
1130657 TGCACTAGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1130730 original size:20 final size:19
Alignment explanation
Indices: 1130705--1130776 Score: 117
Period size: 20 Copynumber: 3.7 Consensus size: 19
1130695 AATGCAATTA
1130705 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTT-T
1130725 GTGCATCGATGCATCCTTT
1 GTGCATCGATGCATCCTTT
1130744 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCT-TT
*
1130764 GTGCATCCATGCA
1 GTGCATCGATGCA
1130777 CGAAGGCTGC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 18 0.36
20 32 0.64
ACGTcount: A:0.17, C:0.28, G:0.22, T:0.33
Consensus pattern (19 bp):
GTGCATCGATGCATCCTTT
Found at i:1130897 original size:21 final size:21
Alignment explanation
Indices: 1130868--1130907 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1130858 TTTGAGTAGA
1130868 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCC-AACGGCTCC
*
1130890 AAAA-CATCCTCAACGGCT
1 AAAATCATCCCCAACGGCT
1130908 ATATACGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1142421 original size:2 final size:2
Alignment explanation
Indices: 1142414--1142442 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1142404 CAAGGAACAG
1142414 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1142443 GAGAGCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1143106 original size:34 final size:34
Alignment explanation
Indices: 1143014--1143118 Score: 147
Period size: 34 Copynumber: 3.1 Consensus size: 34
1143004 TATTAATTAA
* * * *
1143014 CCTGAATTACATAAGATACAAAATGCACTCAAAC
1 CCTGAATTACATAAGATACACATTACACTCTAAC
1143048 CCTGAATTACATAAGATACACATTACACTCTAAC
1 CCTGAATTACATAAGATACACATTACACTCTAAC
* * *
1143082 CCTGAAATACATAAGATACGCATTACACTATAAC
1 CCTGAATTACATAAGATACACATTACACTCTAAC
1143116 CCT
1 CCT
1143119 CCTTGATTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.43, C:0.26, G:0.08, T:0.24
Consensus pattern (34 bp):
CCTGAATTACATAAGATACACATTACACTCTAAC
Found at i:1153976 original size:23 final size:23
Alignment explanation
Indices: 1153947--1154001 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
1153937 AGAATTATAC
1153947 AGAAGAAAGATCTTATGCAGAGA
1 AGAAGAAAGATCTTATGCAGAGA
*
1153970 AGAAGAAAGATCTTATGCAGTGA
1 AGAAGAAAGATCTTATGCAGAGA
*
1153993 AGAAAAAAG
1 AGAAGAAAG
1154002 CATAATATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.51, C:0.07, G:0.25, T:0.16
Consensus pattern (23 bp):
AGAAGAAAGATCTTATGCAGAGA
Found at i:1162599 original size:22 final size:22
Alignment explanation
Indices: 1162571--1162615 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1162561 TTAATTTCAT
1162571 TTGATGTCCTCAAACAATGATC
1 TTGATGTCCTCAAACAATGATC
1162593 TTGATGTCCTCAAACAATGATC
1 TTGATGTCCTCAAACAATGATC
1162615 T
1 T
1162616 AGATTTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (22 bp):
TTGATGTCCTCAAACAATGATC
Found at i:1164930 original size:21 final size:21
Alignment explanation
Indices: 1164906--1164949 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1164896 AAATATGTAG
*
1164906 TAAAAGAATTTGTTATAAATT
1 TAAAAGAACTTGTTATAAATT
** *
1164927 TAAATTAACTTGTTATAGATT
1 TAAAAGAACTTGTTATAAATT
1164948 TA
1 TA
1164950 GGGAAATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (21 bp):
TAAAAGAACTTGTTATAAATT
Found at i:1164966 original size:47 final size:48
Alignment explanation
Indices: 1164915--1165025 Score: 138
Period size: 47 Copynumber: 2.4 Consensus size: 48
1164905 GTAAAAGAAT
* * * *
1164915 TTGTTATAAATTTAAATTA-ACTTGTTATAGATTT-AGGGAAATTAAAA
1 TTGTTATAAACTTAAATTAGACTTATTATAAATTTGA-GAAAATTAAAA
* *
1164962 TTGTTATAAACTTAGA-TAGACTTATTATAAATTTGAGAAAATTTAAA
1 TTGTTATAAACTTAAATTAGACTTATTATAAATTTGAGAAAATTAAAA
1165009 TTGTTATAAACTTAAAT
1 TTGTTATAAACTTAAAT
1165026 GTACTTGGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
46 2 0.04
47 51 0.94
48 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (48 bp):
TTGTTATAAACTTAAATTAGACTTATTATAAATTTGAGAAAATTAAAA
Found at i:1164976 original size:26 final size:25
Alignment explanation
Indices: 1164928--1164976 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1164918 TTATAAATTT
* * *
1164928 AAATTAACTTGTTATAGATTTAGGG
1 AAATTAAATTGTTATAAACTTAGGG
1164953 AAATTAAAATTGTTATAAACTTAG
1 AAATT-AAATTGTTATAAACTTAG
1164977 ATAGACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (25 bp):
AAATTAAATTGTTATAAACTTAGGG
Found at i:1169831 original size:44 final size:43
Alignment explanation
Indices: 1169727--1169834 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 43
1169717 TTACATGAAC
* * *
1169727 ACATGAGAAATAATATAAGTTATATGATATGATTTATATGATT
1 ACATGAGAAATAATATATGTTATATGATATGATCTATATGACT
* ** * *
1169770 ACATGCACATGTTATATATGTTATATGATATGGATCTATGTGACT
1 ACATG-AGAAATAATATATGTTATATGATAT-GATCTATATGACT
*
1169815 ACGTGAGAAATAATATATGT
1 ACATGAGAAATAATATATGT
1169835 CTATGAGAAG
Statistics
Matches: 50, Mismatches: 13, Indels: 3
0.76 0.20 0.05
Matches are distributed among these distances:
43 5 0.10
44 31 0.62
45 14 0.28
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (43 bp):
ACATGAGAAATAATATATGTTATATGATATGATCTATATGACT
Found at i:1170938 original size:23 final size:23
Alignment explanation
Indices: 1170912--1170972 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1170902 CTCGTATAAA
1170912 TGCATCGAAGTGCCACGTAGAAT
1 TGCATCGAAGTGCCACGTAGAAT
*
1170935 TGCATCGAAGTGCCGCGTAGAAT
1 TGCATCGAAGTGCCACGTAGAAT
* * *
1170958 TACACCGTAGTGCCA
1 TGCATCGAAGTGCCA
1170973 TATAAGATTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCATCGAAGTGCCACGTAGAAT
Found at i:1171267 original size:25 final size:25
Alignment explanation
Indices: 1171238--1171286 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1171228 TATAACTTCG
1171238 CATACATATTCATTTAAAACATGTA
1 CATACATATTCATTTAAAACATGTA
1171263 CATACATATTCATTTAAAACATGT
1 CATACATATTCATTTAAAACATGT
1171287 TACACCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (25 bp):
CATACATATTCATTTAAAACATGTA
Found at i:1171614 original size:20 final size:20
Alignment explanation
Indices: 1171589--1171637 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1171579 GAAGGTATGC
1171589 ATCGATGCACTACACCATGT
1 ATCGATGCACTACACCATGT
1171609 ATCGATGCACTACACCATGT
1 ATCGATGCACTACACCATGT
1171629 ATCGATGCA
1 ATCGATGCA
1171638 TCCCTTGACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGATGCACTACACCATGT
Found at i:1178973 original size:21 final size:21
Alignment explanation
Indices: 1178914--1178966 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 21
1178904 GTAACATGAT
1178914 ACTATTC--ACGGTATTGTTC
1 ACTATTCATACGGTATTGTTC
1178933 ACTACTGTTCATACGGTATTGTTC
1 ACTA---TTCATACGGTATTGTTC
1178957 ACTATTCATA
1 ACTATTCATA
1178967 TTGTATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.14
21 6 0.21
22 3 0.10
24 16 0.55
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.42
Consensus pattern (21 bp):
ACTATTCATACGGTATTGTTC
Found at i:1178985 original size:19 final size:20
Alignment explanation
Indices: 1178935--1178985 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1178925 TATTGTTCAC
1178935 TACTGTTCATACGGTATTGT
1 TACTGTTCATACGGTATTGT
* **
1178955 TCACTATTCATATTGTATT-T
1 T-ACTGTTCATACGGTATTGT
1178975 TACTGTTCATA
1 TACTGTTCATA
1178986 AAACGTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 9 0.35
20 3 0.12
21 14 0.54
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.49
Consensus pattern (20 bp):
TACTGTTCATACGGTATTGT
Found at i:1182758 original size:2 final size:2
Alignment explanation
Indices: 1182753--1182777 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1182743 TTGAATAAAT
1182753 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1182778 TATTGTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1183024 original size:31 final size:32
Alignment explanation
Indices: 1182959--1183027 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
1182949 TTGTGATTAC
* *
1182959 ATATTAATTAAATAAAAAACGAATTTGACCAA
1 ATATTAATTAAATAAAAAACGAATGTAACCAA
*
1182991 ATATTAATTAAAT-AACAACGGAA-GTAACCAA
1 ATATTAATTAAATAAAAAAC-GAATGTAACCAA
1183022 ATATTA
1 ATATTA
1183028 TGTTTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 17 0.52
32 16 0.48
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (32 bp):
ATATTAATTAAATAAAAAACGAATGTAACCAA
Found at i:1183516 original size:21 final size:20
Alignment explanation
Indices: 1183478--1183516 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1183468 ATATATCTTG
* *
1183478 AATTAATCTTATATTATTTT
1 AATTAATATTATAATATTTT
1183498 AATTAAATATTATAATATT
1 AATT-AATATTATAATATT
1183517 AAATTCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTAATATTATAATATTTT
Found at i:1184158 original size:2 final size:2
Alignment explanation
Indices: 1184151--1184183 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1184141 TCAATTAATC
1184151 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1184184 TGCCATCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1190045 original size:8 final size:8
Alignment explanation
Indices: 1190032--1190062 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
1190022 AAATTTATTA
1190032 TAATTTAT
1 TAATTTAT
1190040 TAATTTAT
1 TAATTTAT
1190048 TAATTTAT
1 TAATTTAT
1190056 TAATTTA
1 TAATTTA
1190063 ATTATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TAATTTAT
Found at i:1191144 original size:26 final size:25
Alignment explanation
Indices: 1191094--1191153 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
1191084 CAAGTGAAAT
* *
1191094 AAATAAGATAAGATAGAGAAAATAA
1 AAATAAAATAAGATAGAAAAAATAA
*
1191119 AAATAAAATAAAGAT--AAAAAATAT
1 AAATAAAAT-AAGATAGAAAAAATAA
*
1191143 AAAGAAAATAA
1 AAATAAAATAA
1191154 AAACAAATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 15 0.50
25 8 0.27
26 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (25 bp):
AAATAAAATAAGATAGAAAAAATAA
Found at i:1191150 original size:24 final size:26
Alignment explanation
Indices: 1191103--1191154 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
1191093 TAAATAAGAT
*
1191103 AAGATAGAGAAAATAAAAATAAAATA
1 AAGATAGAGAAAATAAAAAGAAAATA
*
1191129 AAGATA-A-AAAATATAAAGAAAATA
1 AAGATAGAGAAAATAAAAAGAAAATA
1191153 AA
1 AA
1191155 AACAAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 17 0.71
25 1 0.04
26 6 0.25
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (26 bp):
AAGATAGAGAAAATAAAAAGAAAATA
Found at i:1191195 original size:39 final size:39
Alignment explanation
Indices: 1191119--1191204 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 39
1191109 GAGAAAATAA
* * *
1191119 AAATAAAATAAAGATAAAAAATATAAAGAAAATAAAAAC
1 AAATAAAATAAAGATAAAAAAAAGAAAGAAAACAAAAAC
* * *
1191158 AAATGAAATAAAGATAAAGAAAAAGCAA-AAAACAAAAAT
1 AAATAAAATAAAGATAAA-AAAAAGAAAGAAAACAAAAAC
1191197 AAGATAAA
1 AA-ATAAA
1191205 GGAAATAGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
39 28 0.74
40 10 0.26
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (39 bp):
AAATAAAATAAAGATAAAAAAAAGAAAGAAAACAAAAAC
Found at i:1191221 original size:24 final size:23
Alignment explanation
Indices: 1191208--1191258 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
1191198 AGATAAAGGA
1191208 AATAGAAAATAATAAAATAAAAAT
1 AATA-AAAATAATAAAATAAAAAT
*
1191232 AATAAAAATAATATATATACAAAAT
1 AATAAAAATAATA-AAATA-AAAAT
1191257 AA
1 AA
1191259 AGATGAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 8 0.33
25 7 0.29
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (23 bp):
AATAAAAATAATAAAATAAAAAT
Found at i:1191224 original size:29 final size:28
Alignment explanation
Indices: 1191132--1191227 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 28
1191122 TAAAATAAAG
* * *
1191132 ATAAAA-AATATAAAGAAAATAAAAACAA
1 ATAAAATAAGATAAAGGAAATAGAAA-AA
* *
1191160 ATGAAATAAAGATAAA-GAAAAAGCAAAAA
1 ATAAAAT-AAGATAAAGGAAATAG-AAAAA
*
1191189 ACAAAAATAAGATAAAGGAAATAGAAAATA
1 A-TAAAATAAGATAAAGGAAATAGAAAA-A
1191219 ATAAAATAA
1 ATAAAATAA
1191228 AAATAATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
28 5 0.09
29 26 0.49
30 22 0.42
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (28 bp):
ATAAAATAAGATAAAGGAAATAGAAAAA
Found at i:1191239 original size:15 final size:14
Alignment explanation
Indices: 1191207--1191322 Score: 65
Period size: 15 Copynumber: 7.9 Consensus size: 14
1191197 AAGATAAAGG
1191207 AAATAGAAAATAATA
1 AAATA-AAAATAATA
1191222 AAATAAAAATAATAA
1 AAATAAAAATAAT-A
* *
1191237 AAATAATATATATACA
1 AAATAA-AAATA-ATA
* *
1191253 AAATAAAGATGAACA
1 AAATAAAAAT-AATA
* ** *
1191268 AGATAAGTACAATA
1 AAATAAAAATAATA
1191282 AAGATAAATAA-AATA
1 AA-ATAAA-AATAATA
1191297 AAAT-AAAATAAGTA
1 AAATAAAAATAA-TA
*
1191311 AAATAAATATAA
1 AAATAAAAATAA
1191323 AATATATATA
Statistics
Matches: 80, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
12 2 0.03
13 4 0.05
14 20 0.25
15 40 0.50
16 13 0.16
17 1 0.01
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.22
Consensus pattern (14 bp):
AAATAAAAATAATA
Found at i:1191297 original size:9 final size:9
Alignment explanation
Indices: 1191278--1191319 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
1191268 AGATAAGTAC
1191278 AATAAAGATA
1 AATAAA-ATA
1191288 AATAAAATAA
1 AATAAAAT-A
1191298 AATAAAATA
1 AATAAAATA
*
1191307 AGTAAAATA
1 AATAAAATA
1191316 AATA
1 AATA
1191320 TAAAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (9 bp):
AATAAAATA
Found at i:1191324 original size:20 final size:19
Alignment explanation
Indices: 1191090--1191326 Score: 73
Period size: 20 Copynumber: 12.3 Consensus size: 19
1191080 AAAGCAAGTG
* *
1191090 AAATAAATAAGATAAGATA
1 AAATAAATAAAATAAAATA
*
1191109 GAGA-AAATAAAAATAAAATA
1 -AAATAAAT-AAAATAAAATA
*
1191129 AAGAT-AA-AAAATATAAAGA
1 AA-ATAAATAAAATA-AAATA
* *
1191148 AAATAAAAACAAATGAAATA
1 AAATAAATA-AAATAAAATA
* **
1191168 AAGATAAAGAAAA-AGCA-A
1 AA-ATAAATAAAATAAAATA
* *
1191186 AAA-ACA-AAAATAAGATA
1 AAATAAATAAAATAAAATA
** *
1191203 AAGGAAATAGAAA-ATAATA
1 AAATAAATA-AAATAAAATA
1191222 AAATAAA-AATAATAAAAATA
1 AAATAAATAA-AAT-AAAATA
* *
1191242 ATATATATACAAAATAAAGATGA
1 A-A-ATAAATAAAATAAA-AT-A
* * * *
1191265 ACA-AGAT-AAGTACAATA
1 AAATAAATAAAATAAAATA
1191282 AAGATAAATAAAATAAAATA
1 AA-ATAAATAAAATAAAATA
*
1191302 AAATAAGTAAAATAAATATA
1 AAATAAATAAAATAAA-ATA
1191322 AAATA
1 AAATA
1191327 TATATATATA
Statistics
Matches: 160, Mismatches: 32, Indels: 50
0.66 0.13 0.21
Matches are distributed among these distances:
15 4 0.03
16 4 0.03
17 7 0.04
18 19 0.12
19 45 0.28
20 53 0.33
21 15 0.09
22 9 0.06
23 4 0.03
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (19 bp):
AAATAAATAAAATAAAATA
Found at i:1191334 original size:13 final size:11
Alignment explanation
Indices: 1191278--1191332 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
1191268 AGATAAGTAC
*
1191278 AATAAAGAT-A
1 AATAAATATAA
1191288 AATAAA-ATAA
1 AATAAATATAA
1191298 AATAAAATAAGTAA
1 AAT-AAAT-A-TAA
1191312 AATAAATATAA
1 AATAAATATAA
*
1191323 AATATATATA
1 AATAAATATA
1191333 TATATAATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 2 0.05
10 10 0.26
11 15 0.38
12 1 0.03
13 5 0.13
14 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (11 bp):
AATAAATATAA
Found at i:1191443 original size:17 final size:15
Alignment explanation
Indices: 1191423--1191456 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
1191413 TAAAAATGCA
1191423 ATAATAATAATATATAT
1 ATAATAA-AATATA-AT
1191440 ATAATAAAATATAAT
1 ATAATAAAATATAAT
1191455 AT
1 AT
1191457 TTAAATAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATAAAATATAAT
Found at i:1191454 original size:21 final size:21
Alignment explanation
Indices: 1191428--1191474 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1191418 ATGCAATAAT
*
1191428 AATAATATATATATAA-TAAA
1 AATAATATATAAATAAGTAAA
*
1191448 ATATAATATTTAAATAAGTAAA
1 A-ATAATATATAAATAAGTAAA
1191470 AATAA
1 AATAA
1191475 GAAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAATATATAAATAAGTAAA
Found at i:1192641 original size:20 final size:20
Alignment explanation
Indices: 1192593--1192641 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 20
1192583 GCTATTAAAG
*
1192593 TATATA-AC-ATAGTACATA
1 TATATATACTATAATACATA
*
1192611 TATAT-T-GTATAATACATA
1 TATATATACTATAATACATA
1192629 TATATATACTATA
1 TATATATACTATA
1192642 TGCTATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
18 19 0.79
19 1 0.04
20 4 0.17
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (20 bp):
TATATATACTATAATACATA
Found at i:1197083 original size:52 final size:51
Alignment explanation
Indices: 1196959--1197134 Score: 262
Period size: 51 Copynumber: 3.4 Consensus size: 51
1196949 ATAAGTCTTT
* * *
1196959 TCCCTATTTCTTCAGAGAGTATAAGACTTGATCTTCAACAAACGTGTCCGC
1 TCCCTATTACTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCCGC
* ** *
1197010 TCCCTATTACTTCAGAGAGTATAGGACTCGATCTTCAATAAAATATGTCTGC
1 TCCCTATTACTTCAGAGAGTATAAGACTCGATCTTCAAT-AAACGTGTCCGC
*
1197062 TCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCCGC
1 TCCCTATTACTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCCGC
*
1197113 TCCCTATTGCTTCAGAGAGTAT
1 TCCCTATTACTTCAGAGAGTAT
1197135 GGATCCCGAG
Statistics
Matches: 111, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
51 65 0.59
52 46 0.41
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (51 bp):
TCCCTATTACTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCCGC
Found at i:1197171 original size:54 final size:54
Alignment explanation
Indices: 1197146--1197532 Score: 643
Period size: 54 Copynumber: 7.2 Consensus size: 54
1197136 GATCCCGAGC
* * *
1197146 ATCTTCTTCTTACGGTTTCGCTCCCTCTTTCTCTA-GGAGTATGGAACTCAAAC
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
* * * *
1197199 ATATTATTCTTACAGGTTCGCTTCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
* *
1197253 ATCTTCTTCTTACGGGTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTCAAAT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
*
1197307 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTAT-GAACTCGAAT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
*
1197360 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCGAAT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
*
1197414 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAAT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
*
1197468 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCGAAT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
1197522 ATCTTCTTCTT
1 ATCTTCTTCTT
1197533 CTTTACTACT
Statistics
Matches: 312, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
53 82 0.26
54 230 0.74
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (54 bp):
ATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
Found at i:1197260 original size:107 final size:108
Alignment explanation
Indices: 1197146--1197532 Score: 643
Period size: 107 Copynumber: 3.6 Consensus size: 108
1197136 GATCCCGAGC
* * * * *
1197146 ATCTTCTTCTTACGGTTTCGCTCCCTCTTTCTCTA-GGAGTATGGAACTCAAACATATTATTCTT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCAAATATCTTCTTCTT
* *
1197210 ACAGGTTCGCTTCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
66 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
* *
1197253 ATCTTCTTCTTACGGGTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTCAAATATCTTCTTCTT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCAAATATCTTCTTCTT
*
1197318 ACGGGTTCGCTCCCTCTTTATCTAGGGAGTAT-GAACTCGAAT
66 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
*
1197360 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCGAATATCTTCTTCTT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCAAATATCTTCTTCTT
*
1197425 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTTGAAT
66 ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
*
1197468 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCGAATATCTTCTTCTT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCAAATATCTTCTTCTT
1197533 CTTTACTACT
Statistics
Matches: 265, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
107 136 0.51
108 129 0.49
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (108 bp):
ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCAAATATCTTCTTCTT
ACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAAT
Found at i:1197316 original size:161 final size:162
Alignment explanation
Indices: 1197146--1197517 Score: 622
Period size: 161 Copynumber: 2.3 Consensus size: 162
1197136 GATCCCGAGC
* *
1197146 ATCTTCTTCTTACGGTTTCGCTCCCTCTTTCTCTA-GGAGTATGGAACTCAAACATATTATTCTT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCAAACATATTATTCTT
* *
1197210 ACAGGTTCGCTTCCTCTTTCTCTAGGGAGTATGGAACTCGAATATCTTCTTCTTACGGGTTCACT
66 ACAGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCGAATATCTTCTTCTTACGGGTTCACT
1197275 CCCTCTTTCTCTAGGGAGTATGGAACTCAAAT
131 CCCTCTTTCTCTAGGGAGTATGGAACTCAAAT
* * * *
1197307 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTAT-GAACTCGAATATCTTCTTCTT
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCAAACATATTATTCTT
* *
1197371 ACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCGAATATCTTCTTCTTACGGGTTCGCT
66 ACAGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCGAATATCTTCTTCTTACGGGTTCACT
**
1197436 CCCTCTTTCTCTAGGGAGTATGGAACTTGAAT
131 CCCTCTTTCTCTAGGGAGTATGGAACTCAAAT
1197468 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTC
1 ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTC
1197518 GAATATCTTC
Statistics
Matches: 197, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
161 184 0.93
162 13 0.07
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (162 bp):
ATCTTCTTCTTACGGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCAAACATATTATTCTT
ACAGGTTCGCTCCCTCTTTATCTAGGGAGTATGGAACTCGAATATCTTCTTCTTACGGGTTCACT
CCCTCTTTCTCTAGGGAGTATGGAACTCAAAT
Found at i:1197604 original size:37 final size:37
Alignment explanation
Indices: 1197537--1197610 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
1197527 CTTCTTCTTT
* * *
1197537 ACTACTTTCTTGTGAAGACTTTTAGATGATTTGCTTC
1 ACTACTCTCTCGTGAAGACTTTAAGATGATTTGCTTC
*
1197574 ACTACTCTCTCGTGAAGAC-TTAAGTTTGATTTGCTTC
1 ACTACTCTCTCGTGAAGACTTTAAG-ATGATTTGCTTC
1197611 GAAAGTCGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (37 bp):
ACTACTCTCTCGTGAAGACTTTAAGATGATTTGCTTC
Found at i:1202788 original size:72 final size:72
Alignment explanation
Indices: 1202669--1202819 Score: 257
Period size: 72 Copynumber: 2.1 Consensus size: 72
1202659 CCCATAACAG
*
1202669 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAATATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
*
1202734 TTCATCT
66 TTCATAT
* *
1202741 GTTCTTGATCATTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1 GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
1202806 TTCATAT
66 TTCATAT
*
1202813 TTTCTTG
1 GTTCTTG
1202820 TGTAATAGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.37
Consensus pattern (72 bp):
GTTCTTGATCAGTTGCTATCATCACATTGGCTGCACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:1203540 original size:55 final size:56
Alignment explanation
Indices: 1203480--1203611 Score: 198
Period size: 55 Copynumber: 2.4 Consensus size: 56
1203470 AACATCTTCA
* ** *
1203480 GGATGTCTTTCTTTGTTG-ATCAGTCTTCAATCAGTTTCAAATTTCTTCATTCATC
1 GGATGTCCTTCTTTCATGAATCAGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
*
1203535 GGATGTCCTTC-TTCATGAATCATTCTTCAATCAGGTTCAAATTTCTTCATTCATC
1 GGATGTCCTTCTTTCATGAATCAGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
1203590 GGATGTCCTTC-TTCATGAATCA
1 GGATGTCCTTCTTTCATGAATCA
1203612 TCTGAACGCC
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
54 4 0.06
55 67 0.94
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (56 bp):
GGATGTCCTTCTTTCATGAATCAGTCTTCAATCAGGTTCAAATTTCTTCATTCATC
Found at i:1203612 original size:55 final size:55
Alignment explanation
Indices: 1203498--1203612 Score: 212
Period size: 55 Copynumber: 2.1 Consensus size: 55
1203488 TTCTTTGTTG
* *
1203498 ATCAGTCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGA
1 ATCATTCTTCAATCAGGTTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGA
1203553 ATCATTCTTCAATCAGGTTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGA
1 ATCATTCTTCAATCAGGTTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGA
1203608 ATCAT
1 ATCAT
1203613 CTGAACGCCT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (55 bp):
ATCATTCTTCAATCAGGTTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGA
Found at i:1205669 original size:18 final size:19
Alignment explanation
Indices: 1205625--1205670 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1205615 ATAGGTTTGC
1205625 ATTATTAAAAAAAATTAAAA
1 ATTA-TAAAAAAAATTAAAA
* *
1205645 ATT-TAAAAAAAA-TATAT
1 ATTATAAAAAAAATTAAAA
1205662 ATTATAAAA
1 ATTATAAAA
1205671 CATAAATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 6 0.26
18 14 0.61
20 3 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTATAAAAAAAATTAAAA
Found at i:1209256 original size:14 final size:13
Alignment explanation
Indices: 1209223--1209256 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1209213 ATTATTTGTT
*
1209223 TTTAAAAGATAAA
1 TTTAAAAAATAAA
1209236 TTTAAAAAATAAA
1 TTTAAAAAATAAA
1209249 TTTAAAAA
1 TTTAAAAA
1209257 TTATTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (13 bp):
TTTAAAAAATAAA
Found at i:1209831 original size:27 final size:27
Alignment explanation
Indices: 1209769--1209837 Score: 113
Period size: 26 Copynumber: 2.6 Consensus size: 27
1209759 ATATATTATT
* *
1209769 AATGAATGAAAAAGTTTTATGCAGAAA
1 AATGAATGAAAAGGTTTTATACAGAAA
1209796 AAT-AATGAAAAGGTTTTATACAGAAA
1 AATGAATGAAAAGGTTTTATACAGAAA
1209822 AATGAATGAAAAGGTT
1 AATGAATGAAAAGGTT
1209838 AATTTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 24 0.62
27 15 0.38
ACGTcount: A:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (27 bp):
AATGAATGAAAAGGTTTTATACAGAAA
Found at i:1213463 original size:12 final size:12
Alignment explanation
Indices: 1213438--1213476 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1213428 TTTGTCCGGT
1213438 TTATTA-TTATTA
1 TTATTATTTA-TA
1213450 TTATTATTTATA
1 TTATTATTTATA
*
1213462 TTTTTATTTATA
1 TTATTATTTATA
1213474 TTA
1 TTA
1213477 ATTTTACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 21 0.88
13 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTATTTATA
Found at i:1213863 original size:21 final size:21
Alignment explanation
Indices: 1213837--1213889 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1213827 GTTTCCAGAT
1213837 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
1213858 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
1213879 TCGCAATGCGA
1 TCGCAACGCGA
1213890 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:1213958 original size:44 final size:41
Alignment explanation
Indices: 1213879--1213972 Score: 122
Period size: 44 Copynumber: 2.3 Consensus size: 41
1213869 ACTTCGACTA
*
1213879 TCGCAATGCGA-TTTTCCAAATTCGTTGCAATAGTCCAAGT
1 TCGCATTGCGATTTTTCCAAATTCGTTGCAATAGTCCAAGT
*
1213919 TCGCATTGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATTT-TTCCAAATT--CGTTGCAATAGTCCAAGT
1213963 TCG--TTGCGAT
1 TCGCATTGCGAT
1213973 AGTCGAAGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
40 10 0.21
41 2 0.04
42 16 0.33
44 20 0.42
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (41 bp):
TCGCATTGCGATTTTTCCAAATTCGTTGCAATAGTCCAAGT
Found at i:1213970 original size:42 final size:41
Alignment explanation
Indices: 1213901--1214126 Score: 210
Period size: 42 Copynumber: 5.4 Consensus size: 41
1213891 TTTCCAAATT
* * * *
1213901 CGTTGC-AATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCG
1 CGTTGCGATTAGTCCAAGTTCG--TTGCGA--TAGTCCAAGTTCA
* *
1213945 CGTTGCGA-TAGTCCAAGTTCGTTGCGATAGTCGAAGTACA
1 CGTTGCGATTAGTCCAAGTTCGTTGCGATAGTCCAAGTTCA
* *
1213985 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCA
1 CGTTGCGA-TTAGTCCAAGTTCGTTGCGATAGTCCAAGTTCA
* * *
1214027 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTACA
1 CGTTGCGA-TTAGTCCAAGTTCGTTGCGATAGTCCAAGTTCA
* * *
1214069 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA-TTAGTCCAAGTTCGTTGCGA--TAGTCCAAGTTCA
1214111 CGTTGCGA-TAGTCCAA
1 CGTTGCGATTAGTCCAA
1214127 AATCGCAACG
Statistics
Matches: 164, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
40 23 0.14
42 113 0.69
44 27 0.16
45 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (41 bp):
CGTTGCGATTAGTCCAAGTTCGTTGCGATAGTCCAAGTTCA
Found at i:1214017 original size:105 final size:103
Alignment explanation
Indices: 1213885--1214126 Score: 294
Period size: 105 Copynumber: 2.3 Consensus size: 103
1213875 ACTATCGCAA
* * *
1213885 TGCGA-TT-TTCCAAATTCGTTGCAATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCACATTGCGATTTATTCCAAATT--CGT
* *
1213948 TGCGATAGTCCAAGT-TCGTTGCGA-TAGTCGAAGTACACGT
64 TGCGATAGTCCAAGTAACGTTGCGATTAGTCCAA--ACACGT
* * *
1213988 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAGTTCGTTG
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCACATTGCGATTTATTCCAAATTCGTTG
* * **
1214053 CGATAGTCGAAGTACACGTTGCGATTTATTCCAAATTCGT
66 CGATAGTCCAAGTA-ACGTTGCGA-TTAGTCCAAACACGT
1214093 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
1214127 AATCGCAACG
Statistics
Matches: 120, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
103 22 0.18
104 2 0.02
105 90 0.75
107 6 0.05
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (103 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCACATTGCGATTTATTCCAAATTCGTTG
CGATAGTCCAAGTAACGTTGCGATTAGTCCAAACACGT
Found at i:1214031 original size:63 final size:62
Alignment explanation
Indices: 1213893--1214035 Score: 180
Period size: 63 Copynumber: 2.3 Consensus size: 62
1213883 AATGCGATTT
* * * *
1213893 TCCAAATTCGTTGCAATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCGCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTACACATTGCGATTTATTCCAAATTC-CGTTGCGATAG
* * *
1213956 TCCAAGTTCGTTGCGATAGTCGAAGTACACGTTGCGATTTATTCCAAGTT-CGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTACACATTGCGATTTATTCCAAATTCCGTTGCGATAG
*
1214017 TCGAAGTTCACGTTGCGAT
1 TCCAAGTT--CGTTGCGAT
1214036 TTATTCCAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
61 18 0.26
63 52 0.74
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (62 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTACACATTGCGATTTATTCCAAATTCCGTTGCGATAG
Found at i:1214052 original size:63 final size:61
Alignment explanation
Indices: 1213912--1214119 Score: 190
Period size: 63 Copynumber: 3.3 Consensus size: 61
1213902 GTTGCAATAG
* *
1213912 TCCAAGTTCGCATTGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGTTGCGA--TAG
1 TCCAAGTTCG--TTGCGATTTATTCCAAGTT--CGTTGCGATAGTCCAAGTTCGTTGCGATTTAT
* * *
1213975 TCGAAGTACACGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCACGTTGCGATTTAT
1 TCCAAGT--TCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTT--CGTTGCGATTTAT
* * * * *
1214040 TCCAAGTTCGTTGCGA--TAGTCGAAGTACACGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATTTATTCCAAGT--TCGTTGCGA--TAGTCCAAGTTCGTTGCGATTTAT
1214103 TCCAAGTTCGTTGCGAT
1 TCCAAGTTCGTTGCGAT
1214120 AGTCCAAAAT
Statistics
Matches: 121, Mismatches: 13, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
61 26 0.21
63 77 0.64
65 18 0.15
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (61 bp):
TCCAAGTTCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGTTGCGATTTAT
Found at i:1214115 original size:84 final size:84
Alignment explanation
Indices: 1213924--1214126 Score: 299
Period size: 84 Copynumber: 2.4 Consensus size: 84
1213914 CAAGTTCGCA
*
1213924 TTGCGATTTATTCCAAATTCGCGTTGCGA-TAGTCCAAGTTCGTTGCGATAGTCGAAGTACACGT
1 TTGCGATTTATTCCAAGTTC-CGTTGCGATTAGTCCAAGTTCGTTGCGATAGTCGAAGTACACGT
*
1213988 TGCGATTTATTCCAAGTTCG
65 TGCGATTTATTCCAAATTCG
* * *
1214008 TTGCGA--TAGTCGAAGTTCACGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTACACG
1 TTGCGATTTATTCCAAGTTC-CGTTGCGA-TTAGTCCAAGTTCGTTGCGATAGTCGAAGTACACG
1214071 TTGCGATTTATTCCAAATTCG
64 TTGCGATTTATTCCAAATTCG
1214092 TTGCGATTTATTCCAAGTT-CGTTGCGA-TAGTCCAA
1 TTGCGATTTATTCCAAGTTCCGTTGCGATTAGTCCAA
1214127 AATCGCAACG
Statistics
Matches: 106, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
82 24 0.23
84 73 0.69
86 9 0.08
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (84 bp):
TTGCGATTTATTCCAAGTTCCGTTGCGATTAGTCCAAGTTCGTTGCGATAGTCGAAGTACACGTT
GCGATTTATTCCAAATTCG
Found at i:1215002 original size:42 final size:43
Alignment explanation
Indices: 1214950--1215169 Score: 276
Period size: 42 Copynumber: 5.2 Consensus size: 43
1214940 GCGATTTTGG
* * *
1214950 ACTATAGCAACAAACTTGGAATAAATCGTAACGCGAACTT-GA
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
*
1214992 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG-
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
* *
1215034 ACTATCGCAACGAACTTTGAATAAATCGCAA--CGAACTTGGA
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
* *
1215075 A-TAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTAG-
1 ACT--ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
*
1215118 ACTATCGCAACGAA-TGTGTAATAAATCGCAACGCGAACTTCG-
1 ACTATCGCAACGAACT-TGGAATAAATCGCAACGCGAACTTCGA
1215160 ACTATCGCAA
1 ACTATCGCAA
1215170 ATCAGTTTCC
Statistics
Matches: 158, Mismatches: 12, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
40 9 0.06
41 2 0.01
42 136 0.86
43 2 0.01
44 9 0.06
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (43 bp):
ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGA
Found at i:1215003 original size:21 final size:22
Alignment explanation
Indices: 1214974--1215237 Score: 76
Period size: 21 Copynumber: 12.6 Consensus size: 22
1214964 CTTGGAATAA
*
1214974 ATCGTAACGCGAACTT-GAACT
1 ATCGCAACGCGAACTTCGAACT
* *
1214995 ATCGCAA--CGAATTTGGAA-T
1 ATCGCAACGCGAACTTCGAACT
1215014 AAATCGCAACGCGAACTTCG-ACT
1 --ATCGCAACGCGAACTTCGAACT
*
1215037 ATCGCAA--CGAACTTTGAA-T
1 ATCGCAACGCGAACTTCGAACT
*
1215056 AAATCGCAA--CGAACTTGGAA-T
1 --ATCGCAACGCGAACTTCGAACT
* *
1215077 AAATCGCAA--CGAATTTGGAA-T
1 --ATCGCAACGCGAACTTCGAACT
*
1215098 AAATCGCAACGCGAACTTAG-ACT
1 --ATCGCAACGCGAACTTCGAACT
1215121 ATCGCAA--CGAA-TGT-GTAA-T
1 ATCGCAACGCGAACT-TCG-AACT
1215140 AAATCGCAACGCGAACTTCG-ACT
1 --ATCGCAACGCGAACTTCGAACT
** ** *
1215163 ATCGCAAATC-AGTTTCCAGA-T
1 ATCGCAACGCGAACTTCGA-ACT
1215184 -TCGCAACGCGAACTTCG-ACT
1 ATCGCAACGCGAACTTCGAACT
* **
1215204 ATCGCAACACGAACTT-GGTCT
1 ATCGCAACGCGAACTTCGAACT
*
1215225 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1215238 TATGTAAATC
Statistics
Matches: 192, Mismatches: 23, Indels: 56
0.71 0.08 0.21
Matches are distributed among these distances:
18 2 0.01
19 23 0.12
20 18 0.09
21 121 0.63
22 4 0.02
23 22 0.11
24 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (22 bp):
ATCGCAACGCGAACTTCGAACT
Found at i:1221483 original size:12 final size:12
Alignment explanation
Indices: 1221452--1221487 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1221442 GTTTTGAAGT
* *
1221452 TCTTAAAATTAA
1 TCTTAAATTTTA
1221464 TCTTAAATTTTA
1 TCTTAAATTTTA
1221476 TCTTAAATTTTA
1 TCTTAAATTTTA
1221488 ATTAGACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (12 bp):
TCTTAAATTTTA
Found at i:1226283 original size:21 final size:21
Alignment explanation
Indices: 1226257--1226310 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1226247 GTTTCCAGAT
* * *
1226257 TCGCAACGTGAACTTGGACTA
1 TCGCAACGCGAACTTAGAATA
*
1226278 TCGCAATGCGAACTTAGAATA
1 TCGCAACGCGAACTTAGAATA
*
1226299 TCGCAATGCGAA
1 TCGCAACGCGAA
1226311 TATGTAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAACGCGAACTTAGAATA
Found at i:1226363 original size:41 final size:41
Alignment explanation
Indices: 1226318--1226411 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
1226308 GAATATGTAA
1226318 ATCGCAATGCGAATATGTAAATCACAATGCGATAGTCG-GCT
1 ATCGCAATGCGAATATGTAAATCACAATGCGATAGTCGAG-T
* *
1226359 ATCGCAATGCGAATATGTAAATCGCATTGCGATAGTCGAGT
1 ATCGCAATGCGAATATGTAAATCACAATGCGATAGTCGAGT
*
1226400 ATCGCATTGCGA
1 ATCGCAATGCGA
1226412 TAGTCGGCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
41 48 0.98
42 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (41 bp):
ATCGCAATGCGAATATGTAAATCACAATGCGATAGTCGAGT
Found at i:1226368 original size:21 final size:21
Alignment explanation
Indices: 1226342--1226489 Score: 94
Period size: 21 Copynumber: 7.1 Consensus size: 21
1226332 ATGTAAATCA
1226342 CAATGCGATAGTCGGCTATCG
1 CAATGCGATAGTCGGCTATCG
***
1226363 CAATGCGAATA-T-GTAAATCG
1 CAATGCG-ATAGTCGGCTATCG
*
1226383 CATTGCGATAGTCGAG-TATCG
1 CAATGCGATAGTCG-GCTATCG
* *
1226404 CATTGCGATAGTCGGCTATCA
1 CAATGCGATAGTCGGCTATCG
***
1226425 CAATGCGAATA-T-GTAAATCG
1 CAATGCG-ATAGTCGGCTATCG
*
1226445 CAATGCGATAGTC--CAAGTTCG
1 CAATGCGATAGTCGGCTA--TCG
* *
1226466 CATTGCGATAGTCGACTATCG
1 CAATGCGATAGTCGGCTATCG
1226487 CAA
1 CAA
1226490 CGACTGGTGG
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
19 8 0.08
20 25 0.25
21 58 0.59
22 6 0.06
23 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (21 bp):
CAATGCGATAGTCGGCTATCG
Found at i:1226439 original size:62 final size:62
Alignment explanation
Indices: 1226297--1226489 Score: 268
Period size: 62 Copynumber: 3.1 Consensus size: 62
1226287 GAACTTAGAA
* * *
1226297 TATCGCAATGCGAATATGTAAATCGCAATGCGAATA-T-GTA-AATCACAATGCGATAGTCGGC
1 TATCGCAATGCGAATATGTAAATCGCAATGCG-ATAGTCG-AGTATCGCATTGCGATAGTCGGC
*
1226358 TATCGCAATGCGAATATGTAAATCGCATTGCGATAGTCGAGTATCGCATTGCGATAGTCGGC
1 TATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAGTATCGCATTGCGATAGTCGGC
* * *
1226420 TATCACAATGCGAATATGTAAATCGCAATGCGATAGTCCAAGT-TCGCATTGCGATAGTCGAC
1 TATCGCAATGCGAATATGTAAATCGCAATGCGATAGT-CGAGTATCGCATTGCGATAGTCGGC
1226482 TATCGCAA
1 TATCGCAA
1226490 CGACTGGTGG
Statistics
Matches: 119, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
60 3 0.03
61 33 0.28
62 79 0.66
63 4 0.03
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (62 bp):
TATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAGTATCGCATTGCGATAGTCGGC
Found at i:1227230 original size:42 final size:42
Alignment explanation
Indices: 1227183--1227265 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
1227173 TGCGATTTTG
1227183 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1227225 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTT
1227266 GGAATAAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1227289 original size:65 final size:64
Alignment explanation
Indices: 1227187--1227348 Score: 258
Period size: 65 Copynumber: 2.5 Consensus size: 64
1227177 ATTTTGGACT
*
1227187 ATCGCAA-CGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAAGCGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1227250 ATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAA-GCGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
* *
1227315 ATCGCAATGCGAACTTCGACT--ATCGCAACGCGAA
1 ATCGCAA-GCGAACTTGGAATAAATCGCAACGCGAA
1227349 TATGTAAATC
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
63 20 0.22
65 73 0.78
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (64 bp):
ATCGCAAGCGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:1227305 original size:42 final size:42
Alignment explanation
Indices: 1227250--1227344 Score: 163
Period size: 42 Copynumber: 2.2 Consensus size: 42
1227240 TTTGGAATAA
1227250 ATCGCAACGCGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTCGACT
*
1227294 ATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTCGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1227336 ATCGCAACG
1 ATCGCAACG
1227345 CGAATATGTA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 43 0.86
44 7 0.14
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (42 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:1234155 original size:13 final size:13
Alignment explanation
Indices: 1234137--1234168 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1234127 CTCCACCAAT
1234137 GAAACTTCATCTC
1 GAAACTTCATCTC
1234150 GAAACTTCATCTC
1 GAAACTTCATCTC
*
1234163 TAAACT
1 GAAACT
1234169 CACCCTCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.31
Consensus pattern (13 bp):
GAAACTTCATCTC
Found at i:1243793 original size:14 final size:14
Alignment explanation
Indices: 1243774--1243807 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1243764 TATTTTGAGA
*
1243774 CCGCCCGCATCCGC
1 CCGCCCCCATCCGC
1243788 CCGCCCCCATCCGC
1 CCGCCCCCATCCGC
1243802 CCGCCC
1 CCGCCC
1243808 AGCTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.71, G:0.18, T:0.06
Consensus pattern (14 bp):
CCGCCCCCATCCGC
Found at i:1252576 original size:138 final size:138
Alignment explanation
Indices: 1252323--1252598 Score: 498
Period size: 138 Copynumber: 2.0 Consensus size: 138
1252313 TGTTTATCTA
* * * *
1252323 GTAGTATGTATGATATAATTTATACAAACACAGAAAAGAAATTTTGGATGCCAATGTTAACCAAA
1 GTAGCATGTAAGATATAATTCACACAAACACAGAAAAGAAATTTTGGATGCCAATGTTAACCAAA
*
1252388 AGCCTCAAACTAATCAGAGATAATGATTGTTTGCGAAAACGTATAAGAGTTCCAAATGGAGAGCT
66 AGCCTCAAACTAATCAGAGAGAATGATTGTTTGCGAAAACGTATAAGAGTTCCAAATGGAGAGCT
1252453 AAACCATT
131 AAACCATT
*
1252461 GTAGCATGTAAGATATAATTCACACAAACATAGAAAAGAAATTTTGGATGCCAATGTTAACCAAA
1 GTAGCATGTAAGATATAATTCACACAAACACAGAAAAGAAATTTTGGATGCCAATGTTAACCAAA
1252526 AGCCTCAAACTAATCAGAGAGAATGATTGTTTGCGAAAACGTATAAGAGTTCCAAATGGAGAGCT
66 AGCCTCAAACTAATCAGAGAGAATGATTGTTTGCGAAAACGTATAAGAGTTCCAAATGGAGAGCT
1252591 AAACCATT
131 AAACCATT
1252599 CCATAGACAT
Statistics
Matches: 132, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 132 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.25
Consensus pattern (138 bp):
GTAGCATGTAAGATATAATTCACACAAACACAGAAAAGAAATTTTGGATGCCAATGTTAACCAAA
AGCCTCAAACTAATCAGAGAGAATGATTGTTTGCGAAAACGTATAAGAGTTCCAAATGGAGAGCT
AAACCATT
Found at i:1255091 original size:69 final size:69
Alignment explanation
Indices: 1255013--1255151 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
1255003 GGGGAAGTTA
*
1255013 ATAGTTGCAGTGGTAAGGGGTCGGATTTTGTTTCAGATAAGAATGAACAGGGGAGGACAGAAGCT
1 ATAGTTGCAGTGGCAAGGGGTCGGATTTTGTTTCAGATAAGAATGAACAGGGGAGGACAGAAGCT
1255078 TTGG
66 TTGG
1255082 ATAGTTGCAGTGGCAAGGGGTCGGATTTTGTTTCAGATAAGAATGAACAGGGGAGGACAGAAGCT
1 ATAGTTGCAGTGGCAAGGGGTCGGATTTTGTTTCAGATAAGAATGAACAGGGGAGGACAGAAGCT
1255147 TTGG
66 TTGG
1255151 A
1 A
1255152 ATGTTGGAAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.29, C:0.09, G:0.36, T:0.25
Consensus pattern (69 bp):
ATAGTTGCAGTGGCAAGGGGTCGGATTTTGTTTCAGATAAGAATGAACAGGGGAGGACAGAAGCT
TTGG
Found at i:1263338 original size:21 final size:21
Alignment explanation
Indices: 1263312--1263370 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
1263302 ATTTACCGTG
1263312 ATTGCGGCTGTCGCGGGCGCT
1 ATTGCGGCTGTCGCGGGCGCT
* *
1263333 ATTGCGG-TCATCGCGGACGCT
1 ATTGCGGCT-GTCGCGGGCGCT
1263354 ATTGCGGCTGTCGCGGG
1 ATTGCGGCTGTCGCGGG
1263371 TAACTCGGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.08, C:0.27, G:0.41, T:0.24
Consensus pattern (21 bp):
ATTGCGGCTGTCGCGGGCGCT
Found at i:1278057 original size:227 final size:228
Alignment explanation
Indices: 1277653--1278616 Score: 873
Period size: 227 Copynumber: 4.2 Consensus size: 228
1277643 CTCACGAATA
* * * * *
1277653 TTTGTCAAAACTCTCACCTGAAAGACAATTACCTTGGAGGTTGAAAGCTCTGACACTATTGATAA
1 TTTGTCAAGACTCTCACCGGAAAGACAATTACCTTGGAGGTTGAAAGTTCAGACACCATTGATAA
* * * * * **
1277718 TGTCAAGTCTAAGATCCAAGACAAGGAAGGGATCCCACCAGATCAGCAAAGGCTCATCTTTGCTG
66 TGTCAAGGCTAAGATCCAAGACAAAGAAGGAATCCCACCAGATCAACAAAGGCTTATCTTTGCCA
* * * * * * *
1277783 GCAAATAACTTGAAGATGGTAGTACACTAGCTGACTATAACATCCAGAAGGAATCCACTCTTCAC
131 GAAAACAGCTTGAAGATGGCAGTACACTAGCTGACTATAACATCCAAAAGGAATCCACCCTCCAC
* * * * * *
1277848 TTGGTTCTTCGACTTCGTGGTGGCATGCAAATC
196 CTAGTGCTCCGCCTTCGTGGTGGTATGCAAATC
* * *
1277881 TTTGT-AAGACTCTCACCGGAAAGACAATTACCTTGGAGGTTGAAAGCTCGGACACTATTGATAA
1 TTTGTCAAGACTCTCACCGGAAAGACAATTACCTTGGAGGTTGAAAGTTCAGACACCATTGATAA
* * * ** * *
1277945 TGTCAAGGCTAAGATCCAAGATAAATAAGGAATACGTCCAGACCAACAGAGGCTTATCTTTGCCA
66 TGTCAAGGCTAAGATCCAAGACAAAGAAGGAATCCCACCAGATCAACAAAGGCTTATCTTTGCCA
* * * * * *
1278010 GAAAGCAGCTTGAAGATGGCCGTACATTGGCTGACTATAACATCCAGAAGGAGTCCACCCTCCAC
131 GAAAACAGCTTGAAGATGGCAGTACACTAGCTGACTATAACATCCAAAAGGAATCCACCCTCCAC
* *
1278075 CTAGTGCTTCGTCTTCGTGGTGGTTATGCAAATC
196 CTAGTGCTCCGCCTTCGTGGTGG-TATGCAAATC
* * * * * * * * * * * *
1278109 TTTGTCAAAACCCTGACTGGGAAGACTATTACCCTCGAGGTTGAGAGTTCTGACACCATCGACAA
1 TTTGTCAAGACTCTCACCGGAAAGACAATTACCTTGGAGGTTGAAAGTTCAGACACCATTGATAA
* * * * * * * * * *
1278174 CGTAAAGGCAAAGATTCAAGACTAGGAAAGG-ATCCCACCTGATCAGCAAAGGCTTATTTTTGCT
66 TGTCAAGGCTAAGATCCAAGACAAAG-AAGGAATCCCACCAGATCAACAAAGGCTTATCTTTGCC
* * * * * * * *
1278238 GGAAAACAGCTGGAAGATGGCCGTACCCTAGCTGATTACAACATTCAAAAGGAATCTACCCTCCA
130 AGAAAACAGCTTGAAGATGGCAGTACACTAGCTGACTATAACATCCAAAAGGAATCCACCCTCCA
* * *
1278303 CCTAGTGCTCCGCCTTCGAGGTTGTATGCAAATA
195 CCTAGTGCTCCGCCTTCGTGGTGGTATGCAAATC
* * *
1278337 TTTGTCAAGACTCTCACTGGAAAGAC----ACCTTGGAGGTTGAGAGTTCAGATACCATTGATAA
1 TTTGTCAAGACTCTCACCGGAAAGACAATTACCTTGGAGGTTGAAAGTTCAGACACCATTGATAA
* * * * * * * *
1278398 TGTGAAAGCCAAAATTCAGGACAAAGAAGGAATCCCACCAGATCAACAAA-GATTGATTTTTG-C
66 TGTCAAGGCTAAGATCCAAGACAAAGAAGGAATCCCACCAGATCAACAAAGGCTT-ATCTTTGCC
* * * * * * * * *
1278461 AGGAAAACAGCTTGAAGATGGAAGAACTCTGGCCGATTATAATATCCAAAAGGAGTCTACCCTCC
130 A-GAAAACAGCTTGAAGATGGCAGTACACTAGCTGACTATAACATCCAAAAGGAATCCACCCTCC
** * * *
1278526 ATTTGGTTCTCCGCCTTCGTGGTGGTATGCAGATC
194 ACCTAGTGCTCCGCCTTCGTGGTGGTATGCAAATC
* * * * * *
1278561 TTTGTGAAGACTCTTACCGGGAAGACCATTACATTGGAAGTTGAAAGTTCAGACAC
1 TTTGTCAAGACTCTCACCGGAAAGACAATTACCTTGGAGGTTGAAAGTTCAGACAC
1278617 AATAAGAACT
Statistics
Matches: 595, Mismatches: 131, Indels: 20
0.80 0.18 0.03
Matches are distributed among these distances:
223 7 0.01
224 172 0.29
227 180 0.30
228 72 0.12
229 160 0.27
230 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (228 bp):
TTTGTCAAGACTCTCACCGGAAAGACAATTACCTTGGAGGTTGAAAGTTCAGACACCATTGATAA
TGTCAAGGCTAAGATCCAAGACAAAGAAGGAATCCCACCAGATCAACAAAGGCTTATCTTTGCCA
GAAAACAGCTTGAAGATGGCAGTACACTAGCTGACTATAACATCCAAAAGGAATCCACCCTCCAC
CTAGTGCTCCGCCTTCGTGGTGGTATGCAAATC
Found at i:1278730 original size:138 final size:138
Alignment explanation
Indices: 1278482--1278757 Score: 552
Period size: 138 Copynumber: 2.0 Consensus size: 138
1278472 TTGAAGATGG
1278482 AAGAACTCTGGCCGATTATAATATCCAAAAGGAGTCTACCCTCCATTTGGTTCTCCGCCTTCGTG
1 AAGAACTCTGGCCGATTATAATATCCAAAAGGAGTCTACCCTCCATTTGGTTCTCCGCCTTCGTG
1278547 GTGGTATGCAGATCTTTGTGAAGACTCTTACCGGGAAGACCATTACATTGGAAGTTGAAAGTTCA
66 GTGGTATGCAGATCTTTGTGAAGACTCTTACCGGGAAGACCATTACATTGGAAGTTGAAAGTTCA
1278612 GACACAAT
131 GACACAAT
1278620 AAGAACTCTGGCCGATTATAATATCCAAAAGGAGTCTACCCTCCATTTGGTTCTCCGCCTTCGTG
1 AAGAACTCTGGCCGATTATAATATCCAAAAGGAGTCTACCCTCCATTTGGTTCTCCGCCTTCGTG
1278685 GTGGTATGCAGATCTTTGTGAAGACTCTTACCGGGAAGACCATTACATTGGAAGTTGAAAGTTCA
66 GTGGTATGCAGATCTTTGTGAAGACTCTTACCGGGAAGACCATTACATTGGAAGTTGAAAGTTCA
1278750 GACACAAT
131 GACACAAT
1278758 TGACAATGTG
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 138 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (138 bp):
AAGAACTCTGGCCGATTATAATATCCAAAAGGAGTCTACCCTCCATTTGGTTCTCCGCCTTCGTG
GTGGTATGCAGATCTTTGTGAAGACTCTTACCGGGAAGACCATTACATTGGAAGTTGAAAGTTCA
GACACAAT
Found at i:1278915 original size:123 final size:123
Alignment explanation
Indices: 1278696--1278948 Score: 479
Period size: 123 Copynumber: 2.1 Consensus size: 123
1278686 TGGTATGCAG
*
1278696 ATCTTTGTGAAGACTCTTACCGGGAAGACCATTACATTGGAAGTTGAAAGTTCAGACACAATTGA
1 ATCTTTGTGAAGACTCTTACCGGAAAGACCATTACATTGGAAGTTGAAAGTTCAGACACAATTGA
*
1278761 CAATGTGAAGGCGAAGATTCAAGACAAGGAGGGTATACCCCCAGACCAGCGAAGGCTC
66 CAATGTGAAGGCGAAGATTCAAGACAAGGAGGGTATACCCCCAGACCAGCAAAGGCTC
1278819 ATCTTTGTGAAGACTCTTACCGGAAAGACCATTACATTGGAAGTTGAAAGTTCAGACACAATTGA
1 ATCTTTGTGAAGACTCTTACCGGAAAGACCATTACATTGGAAGTTGAAAGTTCAGACACAATTGA
*
1278884 CAATGTGAAGGCGAAGATTTAAGACAAGGAGGGTATACCCCCAGACCAGCAAAGGCTC
66 CAATGTGAAGGCGAAGATTCAAGACAAGGAGGGTATACCCCCAGACCAGCAAAGGCTC
1278942 ATCTTTG
1 ATCTTTG
1278949 CCGGCAAGCA
Statistics
Matches: 127, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 127 1.00
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (123 bp):
ATCTTTGTGAAGACTCTTACCGGAAAGACCATTACATTGGAAGTTGAAAGTTCAGACACAATTGA
CAATGTGAAGGCGAAGATTCAAGACAAGGAGGGTATACCCCCAGACCAGCAAAGGCTC
Found at i:1279218 original size:228 final size:226
Alignment explanation
Indices: 1278819--1279388 Score: 810
Period size: 228 Copynumber: 2.5 Consensus size: 226
1278809 GCGAAGGCTC
* * * *
1278819 ATCTTTGTGAAGACTCTTACCGGAAAGACCATTACATTGGAAGTTGAAAGTTCAGACACAATTGA
1 ATCTTTGTGAAGACTCTTACTGGAAA-ACCATCACATTGGAGGTTGAAAGTTCAGACACCATTGA
* *
1278884 CAATGTGAAGGCGAAGATTTAAGACAAGGAGGGTATACCCCCAGACCAGCAAAGGCTCATCTTTG
65 CAATGTGAAGGCAAAGATTCAAGACAAGGAGGGTAT-CCCCCAGACCAGCAAAGGCTCATCTTTG
* * *
1278949 CCGGCAAGCAGCTTGAAGATGGAAGGACATTGGCTGACTATAATATCCAAAAGGAGTCAACCCTT
129 CCGGAAAGCAGCTTGAAGATGGAAGGACATTGGCCGACTATAATATCCAAAAGGAATCAACCCTT
*
1279014 CACTTGGTGCTGCGTCTT-CGTGGTGGGATGCAG
194 CACTTAGTGCTGCG-CTTGCGTGGTGGGATGCAG
* *
1279047 ATCTTTGTGAAGACTCTTACTGGTAAAACCGTCACTTTGGAGGTTGAAAGTTCAGACACCATTGA
1 ATCTTTGTGAAGACTCTTACTGG-AAAACCATCACATTGGAGGTTGAAAGTTCAGACACCATTGA
* * *
1279112 CAACGTGAAGGCAAAGATCCAGGACAAGGAGGGTATCGCCCCAGACCAGCAAAGGCTCATCTTTG
65 CAATGTGAAGGCAAAGATTCAAGACAAGGAGGGTATC-CCCCAGACCAGCAAAGGCTCATCTTTG
*
1279177 CCGGAAAGCAGCTTGAAGATAGG-CGGACATTGGCCGACTATAATATCCAAAAGGAATCAACCCT
129 CCGGAAAGCAGCTTGAAGAT-GGAAGGACATTGGCCGACTATAATATCCAAAAGGAATCAACCCT
*
1279241 TCACTTAGTGTTGCGCTTGCGTGGTGGGATGCAG
193 TCACTTAGTGCTGCGCTTGCGTGGTGGGATGCAG
* * *
1279275 ATCTTTGTGAAGAC-CTTAACTGGGAAGA-CAACAACATTGGAGGTTGAAAGTTCAGACACCATA
1 ATCTTTGTGAAGACTCTT-ACT-GGAAAACCATC-ACATTGGAGGTTGAAAGTTCAGACACCATT
* *
1279338 GACAATGTTAAGGCAAAGATTCAAGACAAGG-GGG-ATCCCACCTGACCAGCA
63 GACAATGTGAAGGCAAAGATTCAAGACAAGGAGGGTATCCC-CCAGACCAGCA
1279389 GAGGTTGGTT
Statistics
Matches: 307, Mismatches: 27, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
225 2 0.01
226 13 0.04
227 12 0.04
228 273 0.89
229 7 0.02
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (226 bp):
ATCTTTGTGAAGACTCTTACTGGAAAACCATCACATTGGAGGTTGAAAGTTCAGACACCATTGAC
AATGTGAAGGCAAAGATTCAAGACAAGGAGGGTATCCCCCAGACCAGCAAAGGCTCATCTTTGCC
GGAAAGCAGCTTGAAGATGGAAGGACATTGGCCGACTATAATATCCAAAAGGAATCAACCCTTCA
CTTAGTGCTGCGCTTGCGTGGTGGGATGCAG
Found at i:1286786 original size:2 final size:2
Alignment explanation
Indices: 1286774--1286804 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1286764 AACGGGGATT
*
1286774 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1286805 CAAAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1288512 original size:16 final size:18
Alignment explanation
Indices: 1288491--1288525 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1288481 TTAACTAAAA
1288491 AAAATT-ATT-GAGTATC
1 AAAATTAATTAGAGTATC
1288507 AAAATTAATTAGAGTATC
1 AAAATTAATTAGAGTATC
1288525 A
1 A
1288526 TAGTCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (18 bp):
AAAATTAATTAGAGTATC
Found at i:1290607 original size:15 final size:15
Alignment explanation
Indices: 1290587--1290615 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1290577 CATTATCAAA
1290587 TAAAATAATATTTTC
1 TAAAATAATATTTTC
1290602 TAAAATAATATTTT
1 TAAAATAATATTTT
1290616 TCATATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATAATATTTTC
Found at i:1290672 original size:63 final size:61
Alignment explanation
Indices: 1290559--1290679 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 61
1290549 TGTAGGGGCG
*
1290559 TTTAGTTTACTAAAAGATCATTATCAAATAAAATAATATTTTCTAAAATAATATTTTTCATA
1 TTTAGTTTACTAAAAGATCATTATCAAAT-AAATAATATTTTCTAAAATAACATTTTTCATA
* * *
1290621 TTTAGTTTGCATAAAAGATCATTATCAAGT-AATAAT-TTATTACTAGCAATAACATTTTT
1 TTTAGTTTAC-TAAAAGATCATTATCAAATAAATAATATT-TT-CTA-AAATAACATTTTT
1290680 ATTTTGTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
60 2 0.04
61 8 0.16
62 12 0.24
63 29 0.57
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (61 bp):
TTTAGTTTACTAAAAGATCATTATCAAATAAATAATATTTTCTAAAATAACATTTTTCATA
Found at i:1291077 original size:17 final size:16
Alignment explanation
Indices: 1291049--1291084 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1291039 ACCAACACAT
*
1291049 TATTATTTTTATATTA
1 TATTATTTTTATATAA
1291065 TATTATATTTTATATAA
1 TATTAT-TTTTATATAA
1291082 TAT
1 TAT
1291085 ACTTTCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATTTTTATATAA
Found at i:1291080 original size:19 final size:19
Alignment explanation
Indices: 1291047--1291085 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1291037 AGACCAACAC
*
1291047 ATTATTATTTTTATATTAT
1 ATTATTATTTTTATAATAT
1291066 ATTA-TATTTTATATAATAT
1 ATTATTATTTT-TATAATAT
1291085 A
1 A
1291086 CTTTCTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTATTTTTATAATAT
Found at i:1292241 original size:14 final size:15
Alignment explanation
Indices: 1292145--1292279 Score: 103
Period size: 15 Copynumber: 8.5 Consensus size: 15
1292135 TAATAAGGTT
1292145 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1292160 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1292175 ATTTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
1292190 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
1292209 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
1292227 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* * *
1292241 ATTTATTAGTATGAATTG
1 ATTTATT--T-TAAAATA
1292259 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1292273 ATTTATT
1 ATTTATT
1292280 AGTATGGATT
Statistics
Matches: 97, Mismatches: 12, Indels: 23
0.73 0.09 0.17
Matches are distributed among these distances:
14 22 0.23
15 42 0.43
16 6 0.06
17 3 0.03
18 11 0.11
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1292264 original size:18 final size:18
Alignment explanation
Indices: 1292241--1292295 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
1292231 ATTTTAAATA
1292241 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
1292259 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
1292273 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
1292291 ATTTA
1 ATTTA
1292296 ATTTAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
14 10 0.36
15 1 0.04
16 2 0.07
17 1 0.04
18 14 0.50
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:1292266 original size:32 final size:32
Alignment explanation
Indices: 1292227--1292302 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
1292217 TTTTAAAATA
1292227 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
1292259 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
1292291 ATTTAATTTAAA
1 ATTTATTTTAAA
1292303 ATATGGATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:1292358 original size:14 final size:14
Alignment explanation
Indices: 1292339--1292391 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1292329 GTGTGGATTG
1292339 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1292353 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
1292371 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1292385 ATTTATT
1 ATTTATT
1292392 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 16 0.52
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1292375 original size:32 final size:32
Alignment explanation
Indices: 1292332--1292764 Score: 264
Period size: 32 Copynumber: 14.6 Consensus size: 32
1292322 TGTAGTTGTG
1292332 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
*
1292364 TAGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
1292396 TGGATTGATTTATTTT-AA-AA--TA-T-G-A
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
*
1292421 ---ATTGATTTATTTTAAAA----------TA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
1292440 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
1292472 TGGATTGATTTA-TTT---TAA---A--A-TA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
1292494 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
*
1292526 TGGATTGATTTATTTTAAATAATTTATTTGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
* *
1292558 TGGATTGATTTATTTTAAAATATGAATTGATTTATTA
1 TGGATTGATTTATTTT--AA-AT-AATTTA-TTAGTA
* * * *
1292595 TTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAATA
1 -TGGA-TTG-AT--TTA------TTTTAAATAATTTATTAGTA
1292638 TGGATTGATTTATTTT-AA-AA--TA-T-G-A
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
*
1292663 ---ATTGATTTATTTTAAAA----------TA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
1292682 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
* *
1292714 TAGATTGATTTATTTTAAATAATTTATTTGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
1292746 TGGATTGATTTATTTTAAA
1 TGGATTGATTTATTTTAAA
1292765 ATATGGATTG
Statistics
Matches: 323, Mismatches: 20, Indels: 116
0.70 0.04 0.25
Matches are distributed among these distances:
19 2 0.01
22 72 0.22
23 8 0.02
25 3 0.01
26 4 0.01
27 2 0.01
28 7 0.02
29 1 0.00
30 4 0.01
31 8 0.02
32 163 0.50
34 2 0.01
35 2 0.01
36 5 0.02
37 4 0.01
38 4 0.01
39 3 0.01
40 4 0.01
41 3 0.01
42 4 0.01
43 5 0.02
44 5 0.02
45 2 0.01
46 2 0.01
48 4 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
TGGATTGATTTATTTTAAATAATTTATTAGTA
Found at i:1292376 original size:18 final size:18
Alignment explanation
Indices: 1292353--1292409 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
1292343 ATTTTAAATA
1292353 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAGATTG
* *
1292371 ATTTATT--T-TA-AATA
1 ATTTATTAGTATAGATTG
*
1292385 ATTTATTAGTATGGATTG
1 ATTTATTAGTATAGATTG
1292403 ATTTATT
1 ATTTATT
1292410 TTAAAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATAGATTG
Found at i:1292419 original size:22 final size:22
Alignment explanation
Indices: 1292394--1292458 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
1292384 AATTTATTAG
1292394 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
1292416 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1292438 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1292459 TAATTTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1292495 original size:22 final size:22
Alignment explanation
Indices: 1292470--1292512 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1292460 AATTTATTAG
1292470 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1292492 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1292513 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1292581 original size:22 final size:22
Alignment explanation
Indices: 1292556--1292700 Score: 101
Period size: 22 Copynumber: 6.0 Consensus size: 22
1292546 AATTTATTTG
*
1292556 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
***
1292578 TATGAATTGATTTATTATTGTAGTTG
1 TATGAATTGATTTA-T-TT-TA-AAA
*
1292604 TATGGATTGATTTATTTTAAATAA
1 TATGAATTGATTTATTTT-AA-AA
*
1292628 TTTATTAATATGGATTGATTTATTTTAAAA
1 --TATGAAT-T-GA-T---TTATTTTAAAA
1292658 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
1292680 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1292701 TAATTTATTA
Statistics
Matches: 97, Mismatches: 12, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
22 44 0.45
23 2 0.02
24 5 0.05
25 4 0.04
26 20 0.21
27 2 0.02
28 8 0.08
29 1 0.01
30 2 0.02
31 2 0.02
32 7 0.07
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1292615 original size:188 final size:185
Alignment explanation
Indices: 1292416--1292925 Score: 691
Period size: 188 Copynumber: 2.7 Consensus size: 185
1292406 TATTTTAAAA
* * * * *
1292416 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTT-AAATAT--ATTGATTAATTTGAATTAATTTATTAATATGGATTGAT
1292481 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAT
63 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAT
1292546 AATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTG
128 AATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTG
* * * * *
1292604 TATGGATTGATTTATTTTAAATA-ATTTATTAATATGGATTGATTTATTTTAAAATATGAATTGA
1 TATGGATTGATTTATTTTAAATATATTGATTAATTTGAATTAATTTA--TT--AATATGGATTGA
*
1292668 TTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAA
62 TTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
*
1292733 TAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
127 TAATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTG
* * * *
1292792 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGAATTGATTTATTTTAAAATATGGATTG
1 TATGGATTGATTTATTTTAAATATATTGATTAAT-TTGAATTAATTTA--TT--AATATGGATTG
***
1292856 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
61 ATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
1292921 TTAAA
122 TTAAA
1292926 ATATGGATTG
Statistics
Matches: 292, Mismatches: 21, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
184 16 0.05
186 2 0.01
187 5 0.02
188 181 0.62
189 31 0.11
190 1 0.00
191 2 0.01
192 2 0.01
193 52 0.18
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (185 bp):
TATGGATTGATTTATTTTAAATATATTGATTAATTTGAATTAATTTATTAATATGGATTGATTTA
TTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAAT
TTATTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTG
Found at i:1292708 original size:14 final size:14
Alignment explanation
Indices: 1292689--1292742 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1292679 ATATGGATTG
1292689 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1292703 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
1292721 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1292735 ATTTATTT
1 ATTTATTT
1292743 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1292722 original size:274 final size:264
Alignment explanation
Indices: 1292394--1292947 Score: 879
Period size: 269 Copynumber: 2.1 Consensus size: 264
1292384 AATTTATTAG
*
1292394 TATGGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA
1292459 TAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
66 TAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
* *
1292524 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTGAT
131 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
1292589 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAATATGGATTGATTTATTTT
196 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
1292654 AAAA
261 AAAA
*
1292658 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGAT
1 TATGAATTGATTTATTTTAAAATATGAATTGATTTATTTT-AA-AA--TA-T-G----GATTGAT
*
1292723 TTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT
56 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAT
*
1292784 --TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGAATTGATTTATTTTAAA
121 AATTTA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGG-ATTGATTTATTTTAAA
1292846 ATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
184 ATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGA
1292911 TTGATTTATTTTAAAA
249 TTGATTTATTTTAAAA
*
1292927 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1292948 TAATTTATTA
Statistics
Matches: 270, Mismatches: 8, Indels: 19
0.91 0.03 0.06
Matches are distributed among these distances:
264 38 0.14
265 2 0.01
266 2 0.01
268 42 0.16
269 118 0.44
270 3 0.01
272 2 0.01
274 63 0.23
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (264 bp):
TATGAATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA
TAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAG
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
AAAA
Found at i:1292795 original size:26 final size:25
Alignment explanation
Indices: 1292741--1292888 Score: 101
Period size: 26 Copynumber: 5.8 Consensus size: 25
1292731 AATAATTTAT
1292741 TTGTATGGATTGATTTA-T-TT-TA
1 TTGTATGGATTGATTTATTATTGTA
***
1292763 AAATATGGATTGATTTATTATTGTA
1 TTGTATGGATTGATTTATTATTGTA
*
1292788 GTTGTATGGATTGATTTATTTTAAATAATTTA
1 -TTGTATGGATTGATTTA--TT--AT--TGTA
1292820 TTAGTATGGAATTGATTTA-T-TT-TA
1 TT-GTATGG-ATTGATTTATTATTGTA
***
1292844 AAATATGGATTGATTTATTATTGTA
1 TTGTATGGATTGATTTATTATTGTA
1292869 GTTGTATGGATTGATTTATT
1 -TTGTATGGATTGATTTATT
1292889 TTAAATAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 28
0.70 0.09 0.20
Matches are distributed among these distances:
22 23 0.24
23 7 0.07
24 6 0.06
25 5 0.05
26 30 0.31
27 1 0.01
28 2 0.02
30 3 0.03
31 2 0.02
32 9 0.09
33 9 0.09
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.53
Consensus pattern (25 bp):
TTGTATGGATTGATTTATTATTGTA
Found at i:1292862 original size:81 final size:80
Alignment explanation
Indices: 1292658--1292942 Score: 455
Period size: 81 Copynumber: 3.5 Consensus size: 80
1292648 TATTTTAAAA
* * *
1292658 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATAGATTGA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGA
*
1292722 TTTATTTTAAATAATTTATTTG
59 TTTATTTTAAATAATTTATTAG
1292744 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTT
1292809 TAAATAATTTATTAG
66 TAAATAATTTATTAG
1292824 TATGGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
1 TATGG-ATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
1292889 TTAAATAATTTATTAG
65 TTAAATAATTTATTAG
1292905 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1292943 TTAAATAATT
Statistics
Matches: 193, Mismatches: 4, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
80 72 0.37
81 82 0.42
82 2 0.01
84 2 0.01
86 35 0.18
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTT
TAAATAATTTATTAG
Found at i:1292930 original size:22 final size:22
Alignment explanation
Indices: 1292905--1292947 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1292895 AATTTATTAG
1292905 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1292927 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1292948 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1293007 original size:31 final size:31
Alignment explanation
Indices: 1292972--1293030 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1292962 AGTTGTATGG
* *
1292972 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
1293003 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
1293031 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:1293069 original size:16 final size:16
Alignment explanation
Indices: 1293048--1293090 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1293038 GTTTAAAAAA
1293048 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
1293064 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
* *
1293080 TTAGTTCATTT
1 TCAGTTTATTT
1293091 TAGCAGTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (16 bp):
TCAGTTTATTTATATT
Found at i:1293569 original size:30 final size:31
Alignment explanation
Indices: 1293542--1293623 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
1293532 TTTGATAATA
*
1293542 TAATAATTATTTTATAGTATTTAGATAAATT
1 TAATAATTATTTTATAATATTTAGATAAATT
* *
1293573 TATTAATAATTTTATAATATTTA-ATAAATT
1 TAATAATTATTTTATAATATTTAGATAAATT
*
1293603 TAATAAGTATTTTATAA-ATTT
1 TAATAATTATTTTATAATATTT
1293624 TTTAACTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 4 0.09
30 21 0.47
31 20 0.44
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (31 bp):
TAATAATTATTTTATAATATTTAGATAAATT
Found at i:1293619 original size:20 final size:19
Alignment explanation
Indices: 1293575--1293623 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
1293565 GATAAATTTA
*
1293575 TTAAT-AATTTTATAATAT
1 TTAATAAATTTAATAATAT
1293593 TTAATAAATTTAATAAGTAT
1 TTAATAAATTTAATAA-TAT
*
1293613 TTTATAAATTT
1 TTAATAAATTT
1293624 TTTAACTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 5 0.19
19 9 0.33
20 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTAATAAATTTAATAATAT
Found at i:1295678 original size:14 final size:15
Alignment explanation
Indices: 1295653--1295681 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1295643 CCCATGAAAA
1295653 TAAAAAATTAAATAC
1 TAAAAAATTAAATAC
1295668 TAAAAAA-TAAATAC
1 TAAAAAATTAAATAC
1295682 ATACTGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAAATTAAATAC
Found at i:1296994 original size:18 final size:17
Alignment explanation
Indices: 1296957--1296991 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1296947 AGTAAATTTA
1296957 TATTTTATATTAATAAT
1 TATTTTATATTAATAAT
1296974 TATTTTATTATTAA-AAT
1 TATTTTA-TATTAATAAT
1296991 T
1 T
1296992 TATAAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTTATATTAATAAT
Found at i:1302783 original size:23 final size:23
Alignment explanation
Indices: 1302753--1302796 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1302743 CAAGCCAAAC
1302753 ATGATCTTTTATTTGATCCTAGA
1 ATGATCTTTTATTTGATCCTAGA
1302776 ATGATCTTTTATTTGATCCTA
1 ATGATCTTTTATTTGATCCTA
1302797 TAGTGTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (23 bp):
ATGATCTTTTATTTGATCCTAGA
Found at i:1305280 original size:25 final size:26
Alignment explanation
Indices: 1305239--1305294 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
1305229 AACTTCTAAG
1305239 AAAAAAAATCTAAAGCTTGAATACAT
1 AAAAAAAATCTAAAGCTTGAATACAT
* *
1305265 AAAAAAAA-CTAGAGCTTGAATACCT
1 AAAAAAAATCTAAAGCTTGAATACAT
1305290 AAAAA
1 AAAAA
1305295 CCTTGCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 20 0.71
26 8 0.29
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.20
Consensus pattern (26 bp):
AAAAAAAATCTAAAGCTTGAATACAT
Found at i:1313106 original size:3 final size:3
Alignment explanation
Indices: 1313091--1313122 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1313081 GAGGAGTCAA
*
1313091 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1313123 GAGAGATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1320598 original size:18 final size:18
Alignment explanation
Indices: 1320575--1320622 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1320565 TGTTCCAATC
1320575 TTAAAAAAATAAAAAATT
1 TTAAAAAAATAAAAAATT
* * * *
1320593 TTAAAATAATTATAATTT
1 TTAAAAAAATAAAAAATT
1320611 TTAATAAAAATA
1 TTAA-AAAAATA
1320623 TAAATTAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAAAAAATAAAAAATT
Found at i:1324292 original size:17 final size:16
Alignment explanation
Indices: 1324272--1324305 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1324262 GTACTTTAAG
1324272 TTATGGTTAATTAAAAA
1 TTAT-GTTAATTAAAAA
*
1324289 TTATTTTAATTAAAAA
1 TTATGTTAATTAAAAA
1324305 T
1 T
1324306 ATTATCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TTATGTTAATTAAAAA
Found at i:1327891 original size:21 final size:21
Alignment explanation
Indices: 1327841--1327882 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1327831 TTTCACAGCC
1327841 TAAGCTCTAGAGAGCTTGGCT
1 TAAGCTCTAGAGAGCTTGGCT
1327862 TAAGCTCTAGAGAGCTTGGCT
1 TAAGCTCTAGAGAGCTTGGCT
1327883 CTGGCTCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TAAGCTCTAGAGAGCTTGGCT
Found at i:1345668 original size:2 final size:2
Alignment explanation
Indices: 1345656--1345685 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1345646 GGGATTTAAT
1345656 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1345686 TTCTTTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.