Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 10 of 20
Found at i:1581422 original size:25 final size:26
Alignment explanation
Indices: 1581369--1581488 Score: 81
Period size: 23 Copynumber: 4.6 Consensus size: 26
1581359 TTAAAAAATA
* *
1581369 TATTTATATTTAAATTATAAATTATAATT
1 TATTTAAATATAAATTA-AAA-T-TAATT
* * *
1581398 T-TTTTAGTATAATTTAAAATTAATT
1 TATTTAAATATAAATTAAAATTAATT
1581423 TATTTAAATATAAATT-AAA--AATT
1 TATTTAAATATAAATTAAAATTAATT
*
1581446 TATTTAAATAT-AATAAAAATATAAAAATT
1 TATTTAAATATAAATTAAAAT-T---AATT
1581475 TATTTAAATA-AAAT
1 TATTTAAATATAAAT
1581489 AATAAAATAT
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
22 3 0.04
23 18 0.25
25 9 0.12
26 12 0.16
27 3 0.04
28 10 0.14
29 18 0.25
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
TATTTAAATATAAATTAAAATTAATT
Found at i:1581478 original size:29 final size:29
Alignment explanation
Indices: 1581428--1581499 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
1581418 TAATTTATTT
*
1581428 AAATATAAAT-TAAAAATTTATTTAAATA
1 AAATAAAAATATAAAAATTTATTTAAATA
*
1581456 TAATAAAAATATAAAAATTTATTTAAATA
1 AAATAAAAATATAAAAATTTATTTAAATA
1581485 AAATAATAAAATATA
1 AAAT-A-AAAATATA
1581500 TTATTTCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.21
29 21 0.55
30 1 0.03
31 8 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AAATAAAAATATAAAAATTTATTTAAATA
Found at i:1581495 original size:23 final size:24
Alignment explanation
Indices: 1581419--1581501 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 24
1581409 ATTTAAAATT
*
1581419 AATTTATTTAAATATAAATTA-AA
1 AATTTATTTAAATATAAATAATAA
*
1581442 AATTTATTTAAATATAATAAAAATATAAA
1 AATTTATTT-AA-AT-ATAAATA-AT-AA
1581471 AATTTATTTAAATA-AAATAATAA
1 AATTTATTTAAATATAAATAATAA
*
1581494 AATATATT
1 AATTTATT
1581502 ATTTCTTTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
23 18 0.36
24 4 0.08
25 6 0.12
26 6 0.12
27 3 0.06
28 2 0.04
29 11 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AATTTATTTAAATATAAATAATAA
Found at i:1588148 original size:2 final size:2
Alignment explanation
Indices: 1588141--1588182 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1588131 AGGCTATAAA
*
1588141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1588182 A
1 A
1588183 AAAGATGAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1588473 original size:18 final size:17
Alignment explanation
Indices: 1588446--1588487 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1588436 AAATTATTTA
*
1588446 TTTTATATTTTTATAAG
1 TTTTATATTTTAATAAG
1588463 TTTTGATATTTTAATAA-
1 TTTT-ATATTTTAATAAG
1588480 -TTTATATT
1 TTTTATATT
1588488 ATATAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
16 3 0.13
17 4 0.17
18 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (17 bp):
TTTTATATTTTAATAAG
Found at i:1588893 original size:5 final size:5
Alignment explanation
Indices: 1588883--1588962 Score: 72
Period size: 5 Copynumber: 15.2 Consensus size: 5
1588873 AATTTTAAAA
* * *
1588883 ATAAT ATAAT AAAAAT ATAAA ATAAT ATAAAAT ATAAT -TAAA ATATAT
1 ATAAT ATAAT -ATAAT ATAAT ATAAT AT--AAT ATAAT ATAAT ATA-AT
*
1588931 ATAAT ATAAT ATAAA ATAAT ATAAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT A
1588963 AAAGTATATA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
4 3 0.05
5 40 0.66
6 13 0.21
7 5 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:1588901 original size:11 final size:11
Alignment explanation
Indices: 1588885--1588975 Score: 65
Period size: 11 Copynumber: 9.1 Consensus size: 11
1588875 TTTTAAAAAT
1588885 AATATAATAAA
1 AATATAATAAA
1588896 AATAT-A-AAA
1 AATATAATAAA
*
1588905 TA-AT-AT-AA
1 AATATAATAAA
*
1588913 AATATAATTAA
1 AATATAATAAA
*
1588924 AATAT-AT-AT
1 AATATAATAAA
*
1588933 AATATAATATA
1 AATATAATAAA
*
1588944 AA-ATAATATA
1 AATATAATAAA
1588954 AATATAATAAA
1 AATATAATAAA
*
1588965 AGTAT-ATAAA
1 AATATAATAAA
1588975 A
1 A
1588976 TATTAAAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
8 6 0.09
9 12 0.18
10 23 0.35
11 25 0.38
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (11 bp):
AATATAATAAA
Found at i:1588911 original size:10 final size:10
Alignment explanation
Indices: 1588880--1588977 Score: 103
Period size: 10 Copynumber: 9.6 Consensus size: 10
1588870 GATAATTTTA
1588880 AAAATAATAT
1 AAAATAATAT
*
1588890 AATAAAAATAT
1 AA-AATAATAT
1588901 AAAATAATAT
1 AAAATAATAT
1588911 AAAAT-ATAATT
1 AAAATAAT-A-T
1588922 AAAATATATAT
1 AAAATA-ATAT
*
1588933 AATATAATAT
1 AAAATAATAT
1588943 AAAATAATAT
1 AAAATAATAT
1588953 AAATATAATA-
1 AAA-ATAATAT
*
1588963 AAAGT-ATAT
1 AAAATAATAT
1588972 AAAATA
1 AAAATA
1588978 TTAAAATTTA
Statistics
Matches: 74, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
8 3 0.04
9 7 0.09
10 34 0.46
11 27 0.36
12 1 0.01
13 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (10 bp):
AAAATAATAT
Found at i:1589001 original size:21 final size:20
Alignment explanation
Indices: 1588880--1589001 Score: 103
Period size: 21 Copynumber: 6.0 Consensus size: 20
1588870 GATAATTTTA
*
1588880 AAAATAATATAATAAAAATAT
1 AAAATAATATAATATAAAT-T
*
1588901 AAAATAATATAAAATATAATT
1 AAAATAATATAATATA-AATT
1588922 AAAATATATATAATAT-AATAT
1 AAAATA-ATATAATATAAAT-T
1588943 AAAATAATATAA-ATATAA-T
1 AAAATAATATAATATA-AATT
*
1588962 AAAAGT-ATATAA-A-ATATT
1 AAAA-TAATATAATATAAATT
*
1588980 AAAATTTATATAATATAAATT
1 AAAA-TAATATAATATAAATT
1589001 A
1 A
1589002 TTATTATATT
Statistics
Matches: 85, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
17 1 0.01
18 7 0.08
19 20 0.24
20 11 0.13
21 35 0.41
22 11 0.13
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (20 bp):
AAAATAATATAATATAAATT
Found at i:1589005 original size:17 final size:16
Alignment explanation
Indices: 1588955--1589039 Score: 57
Period size: 17 Copynumber: 5.1 Consensus size: 16
1588945 AATAATATAA
* *
1588955 ATATAATA-AAAGTAT
1 ATATAATATAAATTTT
* *
1588970 ATAAAATATTAAAATTT
1 ATATAATA-TAAATTTT
1588987 ATATAATATAAATTATT
1 ATATAATATAAATT-TT
*
1589004 ATTATATTA-AAATTTAT
1 A-TATAATATAAATTT-T
1589021 ATATATATATAATATTTT
1 ATATA-ATATAA-ATTTT
1589039 A
1 A
1589040 AAAACAATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
15 7 0.13
16 10 0.18
17 24 0.44
18 10 0.18
19 4 0.07
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (16 bp):
ATATAATATAAATTTT
Found at i:1589020 original size:15 final size:15
Alignment explanation
Indices: 1588975--1589026 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
1588965 AGTATATAAA
1588975 ATATTAAAATTTA-T
1 ATATTAAAATTTATT
*
1588989 ATAATATAAATTATTATT
1 AT-AT-TAAAAT-TTATT
1589007 ATATTAAAATTTATAT
1 ATATTAAAATTTAT-T
1589023 ATAT
1 ATAT
1589027 ATATAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 2 0.06
15 6 0.19
16 15 0.48
17 5 0.16
18 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTAAAATTTATT
Found at i:1589892 original size:17 final size:17
Alignment explanation
Indices: 1589868--1589912 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1589858 TAATTTTGAT
* *
1589868 AATTATTAAATATTTGA
1 AATTATTAAATATCTAA
*
1589885 ATTTATTAAATATCTAA
1 AATTATTAAATATCTAA
1589902 AATTATTAAAT
1 AATTATTAAAT
1589913 TAATAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
AATTATTAAATATCTAA
Found at i:1591228 original size:19 final size:18
Alignment explanation
Indices: 1591203--1591242 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1591193 AATTAAATTT
*
1591203 TAAAAATATTTAATA-AAA
1 TAAAAA-ATATAATATAAA
1591221 TAAAAAATATAATATAAA
1 TAAAAAATATAATATAAA
1591239 TAAA
1 TAAA
1591243 GTTAAACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAAATATAATATAAA
Found at i:1591504 original size:15 final size:15
Alignment explanation
Indices: 1591456--1591506 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1591446 ATGGTAATTG
* *
1591456 AATTTAATATATGTA
1 AATTTAAAATATTTA
*
1591471 ATTTTAAAATATTTA
1 AATTTAAAATATTTA
*
1591486 AATTTAAATTAGTTT-
1 AATTTAAAATA-TTTA
1591501 AATTTA
1 AATTTA
1591507 TTCAGTATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 27 0.90
16 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
AATTTAAAATATTTA
Found at i:1591655 original size:17 final size:18
Alignment explanation
Indices: 1591625--1591679 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
1591615 CTAAATTATT
* *
1591625 AAATTAATTTTTAAAC-A
1 AAATTAAATATTAAACAA
*
1591642 AAATATAAA-ATTAAATAA
1 AAAT-TAAATATTAAACAA
1591660 AAATTAAATATGTAAACAA
1 AAATTAAATAT-TAAACAA
1591679 A
1 A
1591680 TATCAAGTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 13 0.43
18 10 0.33
19 7 0.23
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATTAAATATTAAACAA
Found at i:1591662 original size:11 final size:12
Alignment explanation
Indices: 1591642--1591670 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1591632 TTTTTAAACA
1591642 AAATATAAAATT
1 AAATATAAAATT
1591654 AAATA-AAAATT
1 AAATATAAAATT
1591665 AAATAT
1 AAATAT
1591671 GTAAACAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATAAAATT
Found at i:1592010 original size:20 final size:20
Alignment explanation
Indices: 1591968--1592011 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1591958 GTAAAGTAAT
** *
1591968 AAATAATTTAAAAATCTTTA
1 AAATAATTTAAAAAAATTAA
1591988 AAATAATTTAAAAAAATTAA
1 AAATAATTTAAAAAAATTAA
1592008 AAAT
1 AAAT
1592012 TAAGCAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAATTTAAAAAAATTAA
Found at i:1596803 original size:22 final size:22
Alignment explanation
Indices: 1596775--1596825 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1596765 GTGCATATTA
1596775 TTTTTAATTATATTTTAAATAT
1 TTTTTAATTATATTTTAAATAT
1596797 TTTTTAATTATATTTTAAATAT
1 TTTTTAATTATATTTTAAATAT
1596819 TTTTTAA
1 TTTTTAA
1596826 AATATCGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTAATTATATTTTAAATAT
Found at i:1596830 original size:12 final size:11
Alignment explanation
Indices: 1596775--1596826 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
1596765 GTGCATATTA
*
1596775 TTTTTAATTAT
1 TTTTTAAATAT
*
1596786 ATTTTAAATAT
1 TTTTTAAATAT
*
1596797 TTTTTAATTAT
1 TTTTTAAATAT
*
1596808 ATTTTAAATAT
1 TTTTTAAATAT
1596819 TTTTTAAA
1 TTTTTAAA
1596827 ATATCGTGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:1596916 original size:8 final size:9
Alignment explanation
Indices: 1596899--1596967 Score: 52
Period size: 10 Copynumber: 7.2 Consensus size: 9
1596889 TATTTATTTA
1596899 TTTATTATAT
1 TTTA-TATAT
1596909 TTTA-ATAT
1 TTTATATAT
1596917 ATTTATATAT
1 -TTTATATAT
*
1596927 TCATATAATAT
1 T-TTAT-ATAT
*
1596938 TTATATTATGT
1 TT-TA-TATAT
1596949 TTTA-ATAT
1 TTTATATAT
1596957 TTTATATAT
1 TTTATATAT
1596966 TT
1 TT
1596968 ATTTTAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
8 11 0.23
9 11 0.23
10 13 0.27
11 12 0.25
12 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTATATAT
Found at i:1596919 original size:19 final size:19
Alignment explanation
Indices: 1596897--1596983 Score: 72
Period size: 19 Copynumber: 4.3 Consensus size: 19
1596887 GTTATTTATT
1596897 TATTTATTATATTTTAATA
1 TATTTATTATATTTTAATA
1596916 TATTTA-TATATTCATATAATA
1 TATTTATTATATT--T-TAATA
*
1596937 T-TTATATTATGTTTTAATA
1 TATT-TATTATATTTTAATA
1596956 T-TTTATATATTTATTTTAAATA
1 TATTTAT-TA--TATTTT-AATA
1596978 TATTTA
1 TATTTA
1596984 AAATGAGTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
18 9 0.16
19 16 0.29
20 4 0.07
21 13 0.23
22 10 0.18
23 4 0.07
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (19 bp):
TATTTATTATATTTTAATA
Found at i:1596968 original size:8 final size:8
Alignment explanation
Indices: 1596889--1596969 Score: 54
Period size: 8 Copynumber: 8.9 Consensus size: 8
1596879 TTTTACACGT
*
1596889 TATTTATT
1 TATTTATA
1596897 TATTTATTA
1 TATTTA-TA
1596906 TATTTTAATA
1 TA-TTT-ATA
1596916 TATTTATA
1 TATTTATA
1596924 TATTCATATAA
1 TATT--TAT-A
1596935 TATTTATA
1 TATTTATA
*
1596943 TTATGTTTTAA
1 -TAT-TTAT-A
1596954 TATTTTATA
1 TA-TTTATA
1596963 TATTTAT
1 TATTTAT
1596970 TTTAAATATA
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
8 19 0.32
9 15 0.25
10 18 0.30
11 8 0.13
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (8 bp):
TATTTATA
Found at i:1597218 original size:24 final size:24
Alignment explanation
Indices: 1597191--1597259 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 24
1597181 ATGTTTGCAT
1597191 TTATAATTTTTTATATTTAAAATA
1 TTATAATTTTTTATATTTAAAATA
*
1597215 TTAT-ATTTTTATATATTTTTTAAATA
1 TTATAATTTTT-TATA--TTTAAAATA
1597241 TTAATAATTTATTT-TATTT
1 TT-ATAATTT-TTTATATTT
1597260 TATATATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
23 6 0.16
24 8 0.21
25 3 0.08
26 10 0.26
27 4 0.11
28 5 0.13
29 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATAATTTTTTATATTTAAAATA
Found at i:1597264 original size:34 final size:33
Alignment explanation
Indices: 1597190--1597271 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 33
1597180 TATGTTTGCA
*
1597190 TTTATAATTTTTTATATTTAAAATATTATATTTT
1 TTTAT-ATTTTTTAAATTTAAAATATTATATTTT
*
1597224 TATATATTTTTTAAATATTAATAAT-TTAT-TTTAT
1 TTTATATTTTTTAAAT-TTAA-AATATTATATTT-T
1597258 TTTATATATTTTTA
1 TTTATAT-TTTTTA
1597272 TGTATATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
33 13 0.32
34 19 0.46
35 9 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (33 bp):
TTTATATTTTTTAAATTTAAAATATTATATTTT
Found at i:1597268 original size:18 final size:18
Alignment explanation
Indices: 1597221--1597270 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1597211 AATATTATAT
1597221 TTTTATATATTTTTTAAA
1 TTTTATATATTTTTTAAA
* *
1597239 TATTA-ATAATTTATTT-TA
1 TTTTATAT-ATTT-TTTAAA
1597257 TTTTATATATTTTT
1 TTTTATATATTTTT
1597271 ATGTATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
17 4 0.15
18 17 0.65
19 5 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATATATTTTTTAAA
Found at i:1597269 original size:14 final size:14
Alignment explanation
Indices: 1597250--1597292 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1597240 ATTAATAATT
1597250 TATTTTATTTTATA
1 TATTTTATTTTATA
* *
1597264 TA-TTT-TTATGTA
1 TATTTTATTTTATA
1597276 TATTTTATTTTATA
1 TATTTTATTTTATA
1597290 TAT
1 TAT
1597293 GGGAGAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 7 0.30
13 6 0.26
14 10 0.43
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TATTTTATTTTATA
Found at i:1597341 original size:12 final size:12
Alignment explanation
Indices: 1597311--1597335 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1597301 AAAATTTAAG
1597311 TATTTATATTTT
1 TATTTATATTTT
1597323 TATTTATATTTT
1 TATTTATATTTT
1597335 T
1 T
1597336 TATTATTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:1597591 original size:23 final size:22
Alignment explanation
Indices: 1597549--1597592 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1597539 CAGATATTCG
*
1597549 TATAATGTTTATGTTATTTTTT
1 TATAATGTTTATATTATTTTTT
1597571 TATAATGTTT-TAATTATTTTTT
1 TATAATGTTTAT-ATTATTTTTT
1597593 ATTTATGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (22 bp):
TATAATGTTTATATTATTTTTT
Found at i:1598229 original size:21 final size:21
Alignment explanation
Indices: 1598205--1598249 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1598195 GGTGGAAAAG
1598205 AAAGAAAGAAAGAAAA-AACAA
1 AAAGAAAG-AAGAAAAGAACAA
*
1598226 AAAGAAAGAAGAAAAGAAGAA
1 AAAGAAAGAAGAAAAGAACAA
1598247 AAA
1 AAA
1598250 AATTTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAGAAAAGAACAA
Found at i:1598233 original size:25 final size:26
Alignment explanation
Indices: 1598200--1598248 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
1598190 TACGTGGTGG
1598200 AAAAGAAAGAA-AGAAAGAA-AAAACA
1 AAAAGAAAGAAGA-AAAGAAGAAAACA
1598225 AAAAGAAAGAAGAAAAGAAGAAAA
1 AAAAGAAAGAAGAAAAGAAGAAAA
1598249 AAATTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAAGAAAGAAGAAAAGAAGAAAACA
Found at i:1600330 original size:7 final size:8
Alignment explanation
Indices: 1600308--1600334 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1600298 TGATAATTTG
1600308 ATTAAAAA
1 ATTAAAAA
1600316 ATTAAAAA
1 ATTAAAAA
1600324 ATTAAAAA
1 ATTAAAAA
1600332 ATT
1 ATT
1600335 TAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
ATTAAAAA
Found at i:1601284 original size:3 final size:3
Alignment explanation
Indices: 1601276--1601317 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1601266 GTATCTTTCC
*
1601276 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTG CTT C-T CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1601318 GCAGTGTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:1601968 original size:41 final size:41
Alignment explanation
Indices: 1601914--1602013 Score: 130
Period size: 43 Copynumber: 2.4 Consensus size: 41
1601904 ACATATTTTA
*
1601914 TTATTTTTAGGTTTTTTTAAACCAA-TAGCAATTTGTTAATT
1 TTATTTTTGGGTTTTTTTAAACCAATTA-CAATTTGTTAATT
* *
1601955 TTATTTTTGGGTTTTTTTTTAAATCAATTATAATTTGTTAATT
1 TTATTTTTGGG--TTTTTTTAAACCAATTACAATTTGTTAATT
*
1601998 TTATTTTTGAGTTTTT
1 TTATTTTTGGGTTTTT
1602014 AGTTTTAATC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
41 15 0.29
43 35 0.67
44 2 0.04
ACGTcount: A:0.25, C:0.04, G:0.10, T:0.61
Consensus pattern (41 bp):
TTATTTTTGGGTTTTTTTAAACCAATTACAATTTGTTAATT
Found at i:1601990 original size:43 final size:43
Alignment explanation
Indices: 1601925--1602013 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 43
1601915 TATTTTTAGG
*
1601925 TTTTTTTAAACCAATAGCAATTTGTTAATTTTATTTTTGGGTT
1 TTTTTTTAAACCAATAGCAATTTGTTAATTTTATTTTTGAGTT
* *
1601968 TTTTTTTAAATCAATTA-TAATTTGTTAATTTTATTTTTGAGTT
1 TTTTTTTAAACCAA-TAGCAATTTGTTAATTTTATTTTTGAGTT
1602011 TTT
1 TTT
1602014 AGTTTTAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
43 40 0.95
44 2 0.05
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (43 bp):
TTTTTTTAAACCAATAGCAATTTGTTAATTTTATTTTTGAGTT
Found at i:1602204 original size:10 final size:9
Alignment explanation
Indices: 1602164--1602223 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
1602154 TTTATTTCAA
*
1602164 TTTTATTTT
1 TTTTAATTT
*
1602173 TTTTTATTT
1 TTTTAATTT
*
1602182 TTTAAAATTT
1 TTT-TAATTT
1602192 TTTTAATTAT
1 TTTTAATT-T
1602202 TTTT-A-TT
1 TTTTAATTT
1602209 TTTTAATTT
1 TTTTAATTT
*
1602218 TCTTAA
1 TTTTAA
1602224 ATCTTCTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
7 5 0.12
8 2 0.05
9 22 0.54
10 12 0.29
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTAATTT
Found at i:1609586 original size:15 final size:15
Alignment explanation
Indices: 1609568--1609605 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1609558 TTAAATTAAA
*
1609568 AAAATTATAAATTTT
1 AAAATTATAAATTCT
*
1609583 AAAATTTTAAATTCT
1 AAAATTATAAATTCT
1609598 AAAATTAT
1 AAAATTAT
1609606 TATTATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTATAAATTCT
Found at i:1610881 original size:16 final size:16
Alignment explanation
Indices: 1610862--1610912 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1610852 TTTTAATTAA
1610862 TAAAATATTTAATTTT
1 TAAAATATTTAATTTT
**
1610878 T-AAATATATTAAAATT
1 TAAAATAT-TTAATTTT
* *
1610894 TAAAAAATTGAATTTT
1 TAAAATATTTAATTTT
1610910 TAA
1 TAA
1610913 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 6 0.22
16 16 0.59
17 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TAAAATATTTAATTTT
Found at i:1611074 original size:84 final size:84
Alignment explanation
Indices: 1610933--1611098 Score: 296
Period size: 84 Copynumber: 2.0 Consensus size: 84
1610923 AAAGGGGAGT
* * *
1610933 TTCTAGGCCTTATGGGCCATGGACAAATCCACCGTCACTGTCCAAGGGATAGACCGTAAGATTGG
1 TTCTAGGCCTTATGGGCCATGGACAAATCCACCGTCACCGTCCAAGAGATAGACCGTAAGATTGA
1610998 TTTGTTCGGTTGAATTCCA
66 TTTGTTCGGTTGAATTCCA
1611017 TTCTAGGCCTTATGGGCCATGGACAAATCCACCGTCACCGTCCAAGAGATAGACCGTAAGATTGA
1 TTCTAGGCCTTATGGGCCATGGACAAATCCACCGTCACCGTCCAAGAGATAGACCGTAAGATTGA
*
1611082 TTTGTTTGGTTGAATTC
66 TTTGTTCGGTTGAATTC
1611099 AATAATTTAG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (84 bp):
TTCTAGGCCTTATGGGCCATGGACAAATCCACCGTCACCGTCCAAGAGATAGACCGTAAGATTGA
TTTGTTCGGTTGAATTCCA
Found at i:1616215 original size:2 final size:2
Alignment explanation
Indices: 1616210--1616240 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1616200 TTTTTTACTC
1616210 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1616241 CATGGATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1620829 original size:16 final size:18
Alignment explanation
Indices: 1620793--1620829 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1620783 TTTCGTACTT
*
1620793 AAATTAGTTTGAAATTAA
1 AAATTAGTTTGAAATAAA
1620811 AAATTA-TTT-AAATAAA
1 AAATTAGTTTGAAATAAA
1620827 AAA
1 AAA
1620830 AAAACCACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 3 0.17
18 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
AAATTAGTTTGAAATAAA
Found at i:1623793 original size:22 final size:22
Alignment explanation
Indices: 1623762--1623808 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1623752 TTAAATTTAA
* *
1623762 TAATTAATTAATTAATTAATTT
1 TAATTAATTAATAAAATAATTT
* *
1623784 TAATTTATTAGTAAAATAATTT
1 TAATTAATTAATAAAATAATTT
1623806 TAA
1 TAA
1623809 AAGTATCTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TAATTAATTAATAAAATAATTT
Found at i:1623856 original size:17 final size:17
Alignment explanation
Indices: 1623834--1623867 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1623824 ACTCGTTAAT
1623834 TTTTTTAAAATTTATAA
1 TTTTTTAAAATTTATAA
* *
1623851 TTTTTTTAATTTTATAA
1 TTTTTTAAAATTTATAA
1623868 GTTAAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTAAAATTTATAA
Found at i:1626080 original size:3 final size:3
Alignment explanation
Indices: 1626072--1626119 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
1626062 ATTTAAGTAG
*
1626072 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CGT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1626120 TTTTTCAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:1627762 original size:20 final size:20
Alignment explanation
Indices: 1627739--1627778 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1627729 ATATAAATAT
*
1627739 AAATATTTAATAAAATTAAA
1 AAATATATAATAAAATTAAA
* *
1627759 AAATATATATTAATATTAAA
1 AAATATATAATAAAATTAAA
1627779 TACACTCTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATAATAAAATTAAA
Found at i:1628497 original size:31 final size:31
Alignment explanation
Indices: 1628462--1628532 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
1628452 TGATATTATG
*
1628462 TTATTTTTATTTAAAAATATATAAATTATTT
1 TTATTTTTATTTAAAAATATATAAATTATTA
*
1628493 TTATTTTTATTTACAAATATATAAATTATTA
1 TTATTTTTATTTAAAAATATATAAATTATTA
1628524 TTATTTTTA
1 TTATTTTTA
1628533 AAATTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
TTATTTTTATTTAAAAATATATAAATTATTA
Found at i:1629032 original size:21 final size:22
Alignment explanation
Indices: 1628992--1629037 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1628982 TTTAAAATTA
*
1628992 AAAGTTATATAATAAGTTTTTCT
1 AAAGTTATATAATAAATTTTT-T
1629015 AAAGTTAT-T-ATAAATTTTTT
1 AAAGTTATATAATAAATTTTTT
1629035 AAA
1 AAA
1629038 AAAATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 9 0.41
22 1 0.05
23 8 0.36
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (22 bp):
AAAGTTATATAATAAATTTTTT
Found at i:1629051 original size:17 final size:16
Alignment explanation
Indices: 1629027--1629060 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1629017 AGTTATTATA
1629027 AATTTTTTAAAAAAAT
1 AATTTTTTAAAAAAAT
*
1629043 AATTATTTTTAAAAAAT
1 AATT-TTTTAAAAAAAT
1629060 A
1 A
1629061 TATAAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTTTTAAAAAAAT
Found at i:1634692 original size:23 final size:20
Alignment explanation
Indices: 1634646--1634685 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1634636 GCAGCAGCAG
1634646 CAGCAAAGATCGTAGTACCA
1 CAGCAAAGATCGTAGTACCA
1634666 CAGCAAAGATCGTAGTACCA
1 CAGCAAAGATCGTAGTACCA
1634686 TTCCAGCAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (20 bp):
CAGCAAAGATCGTAGTACCA
Found at i:1637146 original size:19 final size:20
Alignment explanation
Indices: 1637124--1637164 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1637114 ATATAAATAA
* *
1637124 ATAATTTAA-ATTTTATTTT
1 ATAATTAAACATTTAATTTT
1637143 ATAATTAAACATTTAATTTT
1 ATAATTAAACATTTAATTTT
1637163 AT
1 AT
1637165 CTATTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATAATTAAACATTTAATTTT
Found at i:1637288 original size:19 final size:19
Alignment explanation
Indices: 1637250--1637286 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1637240 AAATAATTAA
1637250 ATAATAAATATTTATTTTT
1 ATAATAAATATTTATTTTT
1637269 ATAATAAATA-TTATTTTT
1 ATAATAAATATTTATTTTT
1637287 TAAAAGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATAATAAATATTTATTTTT
Found at i:1641807 original size:2 final size:2
Alignment explanation
Indices: 1641802--1641834 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1641792 GAAGATAAAC
*
1641802 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1641835 CACTTTCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1644221 original size:17 final size:16
Alignment explanation
Indices: 1644199--1644254 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 16
1644189 TTATAAAAAA
1644199 TAAATTTTTATTAATT
1 TAAATTTTTATTAATT
* *
1644215 TATAA--TTAATAAATT
1 TA-AATTTTTATTAATT
1644230 TAAATTTTTAAGTTAATT
1 TAAATTTTT-A-TTAATT
1644248 TAAATTT
1 TAAATTT
1644255 AAATAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 2 0.06
15 10 0.32
16 4 0.13
17 3 0.10
18 12 0.39
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TAAATTTTTATTAATT
Found at i:1644417 original size:8 final size:8
Alignment explanation
Indices: 1644391--1644438 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
1644381 TGGTAAAGTG
1644391 AAATATAAA
1 AAATAT-AA
1644400 AAATAATAA
1 AAAT-ATAA
*
1644409 AAATTTAA
1 AAATATAA
*
1644417 ATATATAA
1 AAATATAA
1644425 AAATA-AA
1 AAATATAA
1644432 AAATATA
1 AAATATA
1644439 TTTTATAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
7 7 0.21
8 14 0.42
9 10 0.30
10 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AAATATAA
Found at i:1645529 original size:33 final size:33
Alignment explanation
Indices: 1645490--1645563 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 33
1645480 AATATGACAC
*
1645490 AATATAATATGAATACATTT-TTAAAATTTATAT-
1 AATATAA-ATGAATA-ATTTATTAAAATTAATATA
* *
1645523 AATATAAATTATTAATTTATTAAAATTAATATA
1 AATATAAATGAATAATTTATTAAAATTAATATA
1645556 AATATAAA
1 AATATAAA
1645564 ATATTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 4 0.11
32 17 0.47
33 15 0.42
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (33 bp):
AATATAAATGAATAATTTATTAAAATTAATATA
Found at i:1645555 original size:32 final size:32
Alignment explanation
Indices: 1645506--1645568 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1645496 ATATGAATAC
* *
1645506 ATTTTTAAAATTTATAT-AATATAAATTATTA
1 ATTTTTAAAATTAATATAAATATAAAATATTA
1645537 ATTTATTAAAATTAATATAAATATAAAATATT
1 ATTT-TTAAAATTAATATAAATATAAAATATT
1645569 TTAAATACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 12 0.43
33 12 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
ATTTTTAAAATTAATATAAATATAAAATATTA
Found at i:1645614 original size:27 final size:28
Alignment explanation
Indices: 1645549--1645619 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
1645539 TTATTAAAAT
*
1645549 TAATATAAAT-ATAAAATATTTTAAATAC
1 TAATATAAATAATAAAATA-TATAAATAC
*
1645577 TAATAT-TATAATAAAATATATAAATA-
1 TAATATAAATAATAAAATATATAAATAC
1645603 TAATATAAATAAATAAA
1 TAATATAAAT-AATAAA
1645620 TTATCAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 6 0.16
27 11 0.30
28 20 0.54
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (28 bp):
TAATATAAATAATAAAATATATAAATAC
Found at i:1645620 original size:27 final size:26
Alignment explanation
Indices: 1645519--1645633 Score: 76
Period size: 27 Copynumber: 4.3 Consensus size: 26
1645509 TTTAAAATTT
* * *
1645519 ATATAATATAAATTATTAATTTATTAA
1 ATATAATATAAATAATAAATATA-TAA
*
1645546 A-ATTAATATAAAT-ATAAAATATTTTAA
1 ATA-TAATATAAATAAT-AAATA-TATAA
*
1645573 ATACTAATAT-TATAATAAAATATATAA
1 ATA-TAATATAAATAAT-AAATATATAA
1645600 ATATAATATAAATAAATAAAT-TATCAA
1 ATATAATATAAAT-AATAAATATAT-AA
*
1645627 ATTTAAT
1 ATATAAT
1645634 TTTTTATTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
26 12 0.17
27 41 0.57
28 19 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATAATATAAATAATAAATATATAA
Found at i:1648220 original size:3 final size:3
Alignment explanation
Indices: 1648214--1648241 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1648204 TGTTGTTGCG
1648214 GCT GCT GCT GCT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT G
1648242 ATGATGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.36, T:0.32
Consensus pattern (3 bp):
GCT
Found at i:1649096 original size:3 final size:3
Alignment explanation
Indices: 1649088--1649112 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1649078 AACTTGATAA
1649088 AGC AGC AGC AGC AGC AGC AGC AGC A
1 AGC AGC AGC AGC AGC AGC AGC AGC A
1649113 ACAACCCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:1650233 original size:2 final size:2
Alignment explanation
Indices: 1650228--1650259 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1650218 ACAGACACAC
1650228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1650260 TTCCTTGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1653636 original size:24 final size:24
Alignment explanation
Indices: 1653609--1653662 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
1653599 GTTAAATGTA
*
1653609 TTATATTATATTTAATAATATT-T-T
1 TTATATT-TATTAAAT-ATATTATAT
1653633 TTATATTTATTAAATATATTATAT
1 TTATATTTATTAAATATATTATAT
1653657 TTATAT
1 TTATAT
1653663 CGTATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 5 0.19
23 8 0.30
24 14 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATATTTATTAAATATATTATAT
Found at i:1653656 original size:18 final size:19
Alignment explanation
Indices: 1653610--1653660 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1653600 TTAAATGTAT
*
1653610 TATATTATATTTAATAATA
1 TATATTATATTTATTAATA
* *
1653629 TTTTTTATATTTATTAA-A
1 TATATTATATTTATTAATA
1653647 TATATTATATTTAT
1 TATATTATATTTAT
1653661 ATCGTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTATATTTATTAATA
Found at i:1654293 original size:13 final size:13
Alignment explanation
Indices: 1654277--1654335 Score: 68
Period size: 13 Copynumber: 4.6 Consensus size: 13
1654267 ATTTGATTTT
1654277 TTTATTATTAATA
1 TTTATTATTAATA
* *
1654290 TTTATAATTAAAA
1 TTTATTATTAATA
1654303 TTTATTA-TAATTA
1 TTTATTATTAA-TA
*
1654316 TTTA-TAATAATA
1 TTTATTATTAATA
1654328 TTTATTAT
1 TTTATTAT
1654336 GTATGTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 11 0.29
13 27 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTATTATTAATA
Found at i:1654307 original size:26 final size:26
Alignment explanation
Indices: 1654277--1654335 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
1654267 ATTTGATTTT
1654277 TTTATTATTAA-TATTTATAATTAAAA
1 TTTATTATTAATTATTTATAA-TAAAA
*
1654303 TTTATTA-TAATTATTTATAATAATA
1 TTTATTATTAATTATTTATAATAAAA
1654328 TTTATTAT
1 TTTATTAT
1654336 GTATGTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTATTATTAATTATTTATAATAAAA
Found at i:1654818 original size:6 final size:7
Alignment explanation
Indices: 1654800--1654826 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1654790 AATATAATAA
1654800 ATTTTTT
1 ATTTTTT
1654807 ATTTTTT
1 ATTTTTT
1654814 ATTTTTT
1 ATTTTTT
1654821 ATTTTT
1 ATTTTT
1654827 GAACTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:1658288 original size:2 final size:2
Alignment explanation
Indices: 1658281--1658319 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1658271 TAGCCCTCCT
1658281 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1658320 TTTTAAGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1663882 original size:11 final size:11
Alignment explanation
Indices: 1663866--1663890 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1663856 TGTTTGTCAT
1663866 TTTCTCTCCTG
1 TTTCTCTCCTG
1663877 TTTCTCTCCTG
1 TTTCTCTCCTG
1663888 TTT
1 TTT
1663891 TTTGTTCACC
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:0.00, C:0.32, G:0.08, T:0.60
Consensus pattern (11 bp):
TTTCTCTCCTG
Found at i:1667707 original size:44 final size:48
Alignment explanation
Indices: 1667659--1667768 Score: 122
Period size: 52 Copynumber: 2.3 Consensus size: 48
1667649 AAATTCATTA
1667659 ATTTATATATTTATTATATT-ATAA-TTATATT-TA-AAATATTTA-AT
1 ATTTATATATTTATTATATTAATAATTTATATTATATAAAT-TTTATAT
*
1667703 ATTTATATAAATTTTAATATATTAATAATTTATATTATATTAAATTTTATAT
1 ATTTATAT--A-TTTATTATATTAATAATTTATATTATA-TAAATTTTATAT
*
1667755 AATTATATATTTAT
1 ATTTATATATTTAT
1667769 ATTATTTTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
44 8 0.15
46 1 0.02
47 10 0.19
48 4 0.07
49 11 0.20
50 3 0.06
51 4 0.07
52 13 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (48 bp):
ATTTATATATTTATTATATTAATAATTTATATTATATAAATTTTATAT
Found at i:1667720 original size:18 final size:18
Alignment explanation
Indices: 1667692--1667763 Score: 64
Period size: 19 Copynumber: 4.1 Consensus size: 18
1667682 ATTATATTTA
1667692 AAATATTTAATATTTATAT
1 AAAT-TTTAATATTTATAT
1667711 AAATTTTAATATATTA-AT
1 AAATTTTAATAT-TTATAT
1667729 -AA-TTT-ATA-TTATATT
1 AAATTTTAATATTTATA-T
*
1667744 AAATTTTATATAATTATAT
1 AAATTTTA-ATATTTATAT
1667763 A
1 A
1667764 TTTATATTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.07
14 1 0.02
15 4 0.09
16 5 0.11
17 5 0.11
18 10 0.22
19 12 0.27
20 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AAATTTTAATATTTATAT
Found at i:1667738 original size:33 final size:34
Alignment explanation
Indices: 1667664--1667771 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 34
1667654 CATTAATTTA
* * *
1667664 TATATTTAT-TATATTATAATTATATTTAAAATATT
1 TATATTTATATAAATTTTAA-TATA-TTAATATATT
1667699 TAATATTTATATAAATTTTAATATATTAATA-ATT
1 T-ATATTTATATAAATTTTAATATATTAATATATT
1667733 TATA-TTATATTAAATTTT-ATATAATT-ATATATT
1 TATATTTATA-TAAATTTTAATAT-ATTAATATATT
1667766 TATATT
1 TATATT
1667772 ATTTTTATAT
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
32 12 0.19
33 21 0.33
34 5 0.08
35 6 0.09
36 12 0.19
37 8 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TATATTTATATAAATTTTAATATATTAATATATT
Found at i:1667780 original size:17 final size:16
Alignment explanation
Indices: 1667672--1667788 Score: 57
Period size: 17 Copynumber: 7.4 Consensus size: 16
1667662 TATATATTTA
*
1667672 TTATATTATAATTATAT
1 TTATATTAT-TTTATAT
* * *
1667689 TTAAAATATTTAATAT
1 TTATATTATTTTATAT
*
1667705 TTATATAAATTTTA-A-
1 TTATAT-TATTTTATAT
*
1667720 -TATATTA--ATA-AT
1 TTATATTATTTTATAT
* *
1667732 TTATATTATATTAAATT
1 TTATATTATTTTATA-T
* *
1667749 TTATATAATTATATAT
1 TTATATTATTTTATAT
1667765 TTATATTATTTTTATAT
1 TTATATTA-TTTTATAT
1667782 TATATAT
1 T-TATAT
1667789 CATATTATAA
Statistics
Matches: 74, Mismatches: 17, Indels: 17
0.69 0.16 0.16
Matches are distributed among these distances:
11 3 0.04
13 8 0.11
14 5 0.07
15 2 0.03
16 19 0.26
17 32 0.43
18 5 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATTATTTTATAT
Found at i:1668061 original size:18 final size:19
Alignment explanation
Indices: 1668040--1668089 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1668030 TATAATATAT
1668040 ATTTTATTTATATTTAA-A
1 ATTTTATTTATATTTAATA
*
1668058 ATTTTA-ATATA-TTAATA
1 ATTTTATTTATATTTAATA
*
1668075 ATTTTTTTTAT-TTTA
1 ATTTTATTTATATTTA
1668090 TGTTTCATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.15
17 10 0.38
18 12 0.46
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTATTTATATTTAATA
Found at i:1669019 original size:6 final size:6
Alignment explanation
Indices: 1669008--1669042 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1668998 GTAGTCCCTC
1669008 CTTTTT CTTTTT CTTTTT CTTTTT -TTTTT -TTTTT C
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C
1669043 AGTGCATGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
CTTTTT
Found at i:1669174 original size:13 final size:14
Alignment explanation
Indices: 1669131--1669190 Score: 63
Period size: 13 Copynumber: 4.4 Consensus size: 14
1669121 ATATTATTAA
1669131 TATATAAATTATCA-
1 TATATAAATTAT-AT
*
1669145 TATATAAATATAAAT
1 TATATAAAT-TATAT
1669160 TATAT-AATTATAT
1 TATATAAATTATAT
1669173 TATAT-AATTATAT
1 TATATAAATTATAT
*
1669186 CATAT
1 TATAT
1669191 TTAATAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
13 21 0.51
14 13 0.32
15 7 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATAAATTATAT
Found at i:1673996 original size:16 final size:18
Alignment explanation
Indices: 1673970--1674002 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1673960 TTTAATTAAT
1673970 ATAATTATTT-ATAAAAA
1 ATAATTATTTAATAAAAA
1673987 ATAA-TATTTAATAAAA
1 ATAATTATTTAATAAAA
1674003 TTAAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATTATTTAATAAAAA
Found at i:1674716 original size:22 final size:22
Alignment explanation
Indices: 1674690--1674732 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1674680 AATTAATTAA
1674690 ATTTGAATAATTT-TAATATTTT
1 ATTTGAATAATTTATAA-ATTTT
*
1674712 ATTTGAGTAATTTATAAATTT
1 ATTTGAATAATTTATAAATTT
1674733 AATTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
ATTTGAATAATTTATAAATTTT
Found at i:1675833 original size:38 final size:37
Alignment explanation
Indices: 1675773--1675845 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
1675763 ATTTTTTTAT
* **
1675773 TAATTTATATATTTTATTATA-TTATAATTATATTTAAA
1 TAATTTATAAATTTTAAAATATTTAT-A-TATATTTAAA
1675811 TAATTTATAAATTTTAAAATATTTATATATATTTA
1 TAATTTATAAATTTTAAAATATTTATATATATTTA
1675846 TGTTATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 8 0.26
38 19 0.61
39 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (37 bp):
TAATTTATAAATTTTAAAATATTTATATATATTTAAA
Found at i:1675842 original size:10 final size:10
Alignment explanation
Indices: 1675775--1675846 Score: 57
Period size: 9 Copynumber: 7.6 Consensus size: 10
1675765 TTTTTTATTA
1675775 ATTTATATAT
1 ATTTATATAT
1675785 -TTTAT-TAT
1 ATTTATATAT
1675793 A-TTATAATTAT
1 ATTTAT-A-TAT
*
1675804 ATTTAAATA-
1 ATTTATATAT
*
1675813 ATTTATAAAT
1 ATTTATATAT
*
1675823 -TTTA-AAAT
1 ATTTATATAT
1675831 ATTTATATAT
1 ATTTATATAT
1675841 ATTTAT
1 ATTTAT
1675847 GTTATTTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
8 11 0.22
9 20 0.40
10 11 0.22
11 5 0.10
12 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTATATAT
Found at i:1676535 original size:10 final size:10
Alignment explanation
Indices: 1676520--1676602 Score: 53
Period size: 10 Copynumber: 8.2 Consensus size: 10
1676510 TCTGAATTAG
1676520 ATTTTAAATA
1 ATTTTAAATA
*
1676530 ATTTTATATA
1 ATTTTAAATA
*
1676540 A-TTTAAGTA
1 ATTTTAAATA
* *
1676549 AATTTAATTTA
1 ATTTTAA-ATA
*
1676560 A-TTTAAATT
1 ATTTTAAATA
*
1676569 ATTATTTAATA
1 ATT-TTAAATA
* *
1676580 ATTTTTATTA
1 ATTTTAAATA
1676590 ATTTATAAATA
1 ATTT-TAAATA
1676601 AT
1 AT
1676603 AATTTAATTT
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
9 9 0.16
10 31 0.54
11 17 0.30
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (10 bp):
ATTTTAAATA
Found at i:1676653 original size:10 final size:11
Alignment explanation
Indices: 1676612--1676650 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1676602 TAATTTAATT
1676612 TTTAAATTAAA
1 TTTAAATTAAA
1676623 -TTAAATTAAA
1 TTTAAATTAAA
* *
1676633 TTCAATTTAAA
1 TTTAAATTAAA
1676644 TTTAAAT
1 TTTAAAT
1676651 AAAAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:1676794 original size:12 final size:13
Alignment explanation
Indices: 1676762--1676794 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1676752 TATATATTAT
1676762 CTTATTAATTTTA
1 CTTATTAATTTTA
1676775 CTTA-TAATTTTA
1 CTTATTAATTTTA
1676787 -TTATTAAT
1 CTTATTAAT
1676795 ATATCTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 12 0.63
13 4 0.21
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (13 bp):
CTTATTAATTTTA
Found at i:1677526 original size:18 final size:17
Alignment explanation
Indices: 1677505--1677566 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
1677495 TATATATTTT
1677505 AAAATTTCTATAAATATA
1 AAAATTT-TATAAATATA
* *
1677523 AAAATTATTA-ATATATT
1 AAAATT-TTATAAATATA
1677540 AAAATTTATATAAAT-TA
1 AAAATTT-TATAAATATA
1677557 AAATATTTTA
1 AAA-ATTTTA
1677567 ATATTATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
16 1 0.03
17 19 0.53
18 15 0.42
19 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTTTATAAATATA
Found at i:1677552 original size:35 final size:34
Alignment explanation
Indices: 1677498--1677575 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 34
1677488 ACATGAATAT
* *
1677498 ATATTTTAAAATTTCTATAAATATAAAA-ATTATTA
1 ATATATTAAAATTTATATAAAT-TAAAATATT-TTA
1677533 ATATATTAAAATTTATATAAATTAAAATATTTTA
1 ATATATTAAAATTTATATAAATTAAAATATTTTA
1677567 ATATTATTA
1 ATA-TATTA
1677576 TAACGAGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
34 11 0.28
35 28 0.72
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (34 bp):
ATATATTAAAATTTATATAAATTAAAATATTTTA
Found at i:1677572 original size:16 final size:17
Alignment explanation
Indices: 1677503--1677572 Score: 51
Period size: 16 Copynumber: 4.2 Consensus size: 17
1677493 AATATATATT
*
1677503 TTAAAATTTCTATAA-A
1 TTAAAATTTATATAATA
*
1677519 TATAAAAATTAT-TAATATA
1 T-TAAAATTTATAT-A-ATA
1677538 TTAAAATTTATATAA-A
1 TTAAAATTTATATAATA
1677554 TTAAAATATT-T-TAATA
1 TTAAAAT-TTATATAATA
1677570 TTA
1 TTA
1677573 TTATAACGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
15 3 0.07
16 15 0.34
17 12 0.27
18 11 0.25
19 3 0.07
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAAATTTATATAATA
Found at i:1679615 original size:4 final size:4
Alignment explanation
Indices: 1679579--1679630 Score: 50
Period size: 4 Copynumber: 13.0 Consensus size: 4
1679569 CTGAAACTTG
* * * * * *
1679579 ATAT ATGT ATAT GTAT GTAT GTAT GTAT GTAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1679627 ATAT
1 ATAT
1679631 TATTATTTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:1687726 original size:26 final size:25
Alignment explanation
Indices: 1687667--1687727 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 25
1687657 CATAAAAAAT
*
1687667 ATATATTATATTTTTAAATATTTATT
1 ATATATT-TATTTTTAAATATTTATC
*
1687693 ATTTTATTTATTTTTAAAT-TTATAATC
1 A-TATATTTATTTTTAAATATT-T-ATC
1687720 ATATATTT
1 ATATATTT
1687728 TAAAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 2 0.07
26 19 0.66
27 8 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
ATATATTTATTTTTAAATATTTATC
Found at i:1688225 original size:3 final size:3
Alignment explanation
Indices: 1688217--1688251 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1688207 TCCAAAACGA
1688217 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1688252 CCTTTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1700346 original size:6 final size:6
Alignment explanation
Indices: 1700337--1700371 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1700327 GGGATTGGGC
*
1700337 CTGGAA CTGGAA CTGGAA CTGGAA CTAGAA CTGGA
1 CTGGAA CTGGAA CTGGAA CTGGAA CTGGAA CTGGA
1700372 TCGTACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (6 bp):
CTGGAA
Found at i:1700681 original size:18 final size:18
Alignment explanation
Indices: 1700627--1700683 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
1700617 AATTTAATTA
* *
1700627 ATTAAATTAATCATATAA-
1 ATTAAATAAAT-ATTTAAT
*
1700645 ATTAATATAAAAAATTTAAT
1 ATTAA-AT-AAATATTTAAT
1700665 ATTAAATAAATATTTAAT
1 ATTAAATAAATATTTAAT
1700683 A
1 A
1700684 AAAATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 16 0.50
19 9 0.28
20 7 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTAAATAAATATTTAAT
Found at i:1700694 original size:17 final size:18
Alignment explanation
Indices: 1700658--1700695 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1700648 AATATAAAAA
*
1700658 ATTTAATATTAAATAAAT
1 ATTTAATATAAAATAAAT
*
1700676 ATTTAATA-AAAATATAT
1 ATTTAATATAAAATAAAT
1700693 ATT
1 ATT
1700696 CAGTTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTAATATAAAATAAAT
Found at i:1702071 original size:87 final size:88
Alignment explanation
Indices: 1701952--1702126 Score: 325
Period size: 87 Copynumber: 2.0 Consensus size: 88
1701942 TCCAGTTAAA
*
1701952 AGATGAGACTAGGCACTGATTTAACATTTCCCTTAAAATAAATACTCTTTTGAATCATCTTGTAG
1 AGATGAGACTAGGCACTGATCTAACATTTCCCTTAAAATAAATACTCTTTTGAATCATCTTGTAG
1702017 TCAATAAAACAGCTTTTAAAAGC
66 TCAATAAAACAGCTTTTAAAAGC
*
1702040 AGATGAGACTAGGCACTGA-CTAACATTTCCCTTAAAATAAATACTCTTTTGCATCATCTTGTAG
1 AGATGAGACTAGGCACTGATCTAACATTTCCCTTAAAATAAATACTCTTTTGAATCATCTTGTAG
1702104 TCAATAAAACAGCTTTTAAAAGC
66 TCAATAAAACAGCTTTTAAAAGC
1702127 GCATGCATGC
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
87 66 0.78
88 19 0.22
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (88 bp):
AGATGAGACTAGGCACTGATCTAACATTTCCCTTAAAATAAATACTCTTTTGAATCATCTTGTAG
TCAATAAAACAGCTTTTAAAAGC
Found at i:1703540 original size:76 final size:76
Alignment explanation
Indices: 1703414--1703568 Score: 301
Period size: 76 Copynumber: 2.0 Consensus size: 76
1703404 AAAATGCACA
1703414 CTCCTACAATGTAATTAAAATTTCCAAAGGCTTAACATCTCTAGCAGAGATGATAATTCTTCCAT
1 CTCCTACAATGTAATTAAAATTTCCAAAGGCTTAACATCTCTAGCAGAGATGATAATTCTTCCAT
*
1703479 TACATCAAAGG
66 TACATCAAAAG
1703490 CTCCTACAATGTAATTAAAATTTCCAAAGGCTTAACATCTCTAGCAGAGATGATAATTCTTCCAT
1 CTCCTACAATGTAATTAAAATTTCCAAAGGCTTAACATCTCTAGCAGAGATGATAATTCTTCCAT
1703555 TACATCAAAAG
66 TACATCAAAAG
1703566 CTC
1 CTC
1703569 GAACATGAAG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (76 bp):
CTCCTACAATGTAATTAAAATTTCCAAAGGCTTAACATCTCTAGCAGAGATGATAATTCTTCCAT
TACATCAAAAG
Found at i:1706852 original size:73 final size:73
Alignment explanation
Indices: 1706733--1706870 Score: 267
Period size: 73 Copynumber: 1.9 Consensus size: 73
1706723 CTGTTTGTAG
1706733 TTTAATGCTTACCTTGTTTAATGTTCTTATTCCATGCAGTGGGGTTAAGTTGTGATTTCAACTCC
1 TTTAATGCTTACCTTGTTTAATGTTCTTATTCCATGCAGTGGGGTTAAGTTGTGATTTCAACTCC
1706798 ATTTATAA
66 ATTTATAA
*
1706806 TTTAATGCTTACCTTGTTTAATGTTCTTATTCCATGCAGTGGGGTTATGTTGTGATTTCAACTCC
1 TTTAATGCTTACCTTGTTTAATGTTCTTATTCCATGCAGTGGGGTTAAGTTGTGATTTCAACTCC
1706871 GGATGGTATT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.46
Consensus pattern (73 bp):
TTTAATGCTTACCTTGTTTAATGTTCTTATTCCATGCAGTGGGGTTAAGTTGTGATTTCAACTCC
ATTTATAA
Found at i:1713474 original size:16 final size:16
Alignment explanation
Indices: 1713453--1713486 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1713443 TTTTTATAAT
1713453 TATATTTA-AAATATTA
1 TATATTTATAAA-ATTA
1713469 TATATTTATAAAATTA
1 TATATTTATAAAATTA
1713485 TA
1 TA
1713487 AATAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATTTATAAAATTA
Found at i:1713524 original size:34 final size:33
Alignment explanation
Indices: 1713469--1713533 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
1713459 TAAAATATTA
1713469 TATATTTATAAAATTATAAATAATTT-TATAATT
1 TATATTTATAAAATTATAAAT-ATTTATATAATT
*
1713502 TATATTATATTAAATT-TAAAATATTTATATAA
1 TATATT-TATAAAATTAT-AAATATTTATATAA
1713534 CATTTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 11 0.39
34 17 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TATATTTATAAAATTATAAATATTTATATAATT
Found at i:1713531 original size:20 final size:19
Alignment explanation
Indices: 1713506--1713558 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1713496 ATAATTTATA
1713506 TTATATTAAATTTAAAATAT
1 TTATATTAAATTTAAAAT-T
*
1713526 TTATA-TAACATTTATAATT
1 TTATATTAA-ATTTAAAATT
*
1713545 TTATATTATATTTA
1 TTATATTAAATTTA
1713559 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATATTAAATTTAAAATT
Found at i:1713549 original size:19 final size:18
Alignment explanation
Indices: 1713498--1713564 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
1713488 ATAATTTTAT
*
1713498 AATTTAT-ATTATAT-TA
1 AATTTATAATTTTATATA
*
1713514 AATTTAAAATATTTATATA
1 AATTTATAAT-TTTATATA
1713533 ACATTTATAATTTTATATTA
1 A-ATTTATAATTTTATA-TA
*
1713553 TATTTAT-ATTTT
1 AATTTATAATTTT
1713565 TTATTTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
16 6 0.14
17 2 0.05
18 9 0.21
19 15 0.36
20 10 0.24
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTATAATTTTATATA
Found at i:1713568 original size:20 final size:19
Alignment explanation
Indices: 1713506--1713569 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
1713496 ATAATTTATA
* *
1713506 TTATATTAAATTTAAAATAT
1 TTATATTAAATTT-ATATTT
*
1713526 TTATA-TAACATTTATAATT
1 TTATATTAA-ATTTATATTT
*
1713545 TTATATTATATTTATATTT
1 TTATATTAAATTTATATTT
1713564 TT-TATT
1 TTATATT
1713570 TTAAAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 4 0.11
19 22 0.59
20 11 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATATTAAATTTATATTT
Found at i:1714128 original size:22 final size:21
Alignment explanation
Indices: 1714080--1714128 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 21
1714070 ATTTATAATT
1714080 AAATTTAAATTTATATAAATA
1 AAATTTAAATTTATATAAATA
1714101 AGAATTTAAATTTA-ACTAAATCA
1 A-AATTTAAATTTATA-TAAAT-A
1714124 AAATT
1 AAATT
1714129 AAAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (21 bp):
AAATTTAAATTTATATAAATA
Found at i:1715895 original size:12 final size:12
Alignment explanation
Indices: 1715878--1715907 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1715868 TGGAATCGGC
*
1715878 GAAGACGATGAT
1 GAAGACGAAGAT
1715890 GAAGACGAAGAT
1 GAAGACGAAGAT
1715902 GAAGAC
1 GAAGAC
1715908 AAATGTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.33, T:0.10
Consensus pattern (12 bp):
GAAGACGAAGAT
Found at i:1719687 original size:2 final size:2
Alignment explanation
Indices: 1719680--1719711 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1719670 CTTCTATGTG
*
1719680 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1719712 ATACTTTACA
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):
TA
Found at i:1720586 original size:19 final size:19
Alignment explanation
Indices: 1720538--1720587 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
1720528 TATTAAAATT
1720538 TAAAATTTATTTAATATACA
1 TAAAATTTA-TTAATATACA
* *
1720558 -ATAATATATTAAGTA-ACA
1 TAAAATTTATTAA-TATACA
1720576 TAAAATTTATTA
1 TAAAATTTATTA
1720588 TTTCTATCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAAATTTATTAATATACA
Found at i:1724656 original size:12 final size:12
Alignment explanation
Indices: 1724641--1724666 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1724631 TCTAATAATA
1724641 AAAATATTTTAT
1 AAAATATTTTAT
1724653 AAAATATTTTAT
1 AAAATATTTTAT
1724665 AA
1 AA
1724667 TATAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAAATATTTTAT
Found at i:1724656 original size:13 final size:13
Alignment explanation
Indices: 1724638--1724666 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1724628 AAATCTAATA
1724638 ATAAAAATATTTT
1 ATAAAAATATTTT
1724651 AT-AAAATATTTT
1 ATAAAAATATTTT
1724663 ATAA
1 ATAA
1724667 TATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAAAAATATTTT
Found at i:1724989 original size:52 final size:52
Alignment explanation
Indices: 1724911--1725009 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
1724901 TTCATGAGCC
1724911 ACGTGGGTTGATCTAAACCCCCCGGACCCCGACCCAATCAGCTGTTGGTGCT
1 ACGTGGGTTGATCTAAACCCCCCGGACCCCGACCCAATCAGCTGTTGGTGCT
* *
1724963 ACGTGGGTTGATCTAAACCGCCCGGACCCCGACCCAGTCAGCTGTTG
1 ACGTGGGTTGATCTAAACCCCCCGGACCCCGACCCAATCAGCTGTTG
1725010 ACTTTTGACT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.19, C:0.34, G:0.26, T:0.20
Consensus pattern (52 bp):
ACGTGGGTTGATCTAAACCCCCCGGACCCCGACCCAATCAGCTGTTGGTGCT
Found at i:1726796 original size:20 final size:20
Alignment explanation
Indices: 1726747--1726796 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1726737 AAGTAATAAC
*
1726747 ATTATTAAAATTATATTAAAA
1 ATTATT-AAATTATACTAAAA
*
1726768 ATTACTAAATTATACTAAAA
1 ATTATTAAATTATACTAAAA
*
1726788 GTTATTAAA
1 ATTATTAAA
1726797 ACTAAAAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTATTAAATTATACTAAAA
Found at i:1727009 original size:21 final size:21
Alignment explanation
Indices: 1726985--1727165 Score: 66
Period size: 21 Copynumber: 8.7 Consensus size: 21
1726975 AAAGTCTACC
*
1726985 AAAAGTTATCAAATTAATATT
1 AAAAGTTATCAAAATAATATT
* * *
1727006 AAAAGCTATTAAAATCATATT
1 AAAAGTTATCAAAATAATATT
*
1727027 AAAAGTT-TGACAAAATTATACTT
1 AAAAGTTAT--CAAAATAATA-TT
* ** * *
1727050 -AACGGCATCAAAATTATATA
1 AAAAGTTATCAAAATAATATT
* * *
1727070 AAAAATTATTAAAATTATA-T
1 AAAAGTTATCAAAATAATATT
* * * *
1727090 AAAA-ATATTAAAATTATATC
1 AAAAGTTATCAAAATAATATT
* *
1727110 AAAAGTTA-CTAAAATTATATC
1 AAAAGTTATC-AAAATAATATT
* * * * *
1727131 ATAACTTATTAAAATCATATC
1 AAAAGTTATCAAAATAATATT
*
1727152 AAAAGTGATCAAAA
1 AAAAGTTATCAAAA
1727166 CTATACTAAA
Statistics
Matches: 122, Mismatches: 29, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
19 13 0.11
20 10 0.08
21 85 0.70
22 11 0.09
23 3 0.02
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (21 bp):
AAAAGTTATCAAAATAATATT
Found at i:1727102 original size:8 final size:9
Alignment explanation
Indices: 1727071--1727127 Score: 60
Period size: 9 Copynumber: 5.9 Consensus size: 9
1727061 AATTATATAA
1727071 AAAATTATT
1 AAAATTATT
1727080 AAAATTATAT
1 AAAATTAT-T
*
1727090 AAAAATATT
1 AAAATTATT
1727099 AAAATTATAT
1 AAAATTAT-T
*
1727109 CAAAAGTTACT
1 -AAAA-TTATT
1727120 AAAATTAT
1 AAAATTAT
1727128 ATCATAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 19 0.47
10 13 0.32
11 5 0.12
12 3 0.08
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAATTATT
Found at i:1727123 original size:40 final size:42
Alignment explanation
Indices: 1727059--1727157 Score: 130
Period size: 40 Copynumber: 2.4 Consensus size: 42
1727049 TAACGGCATC
* * *
1727059 AAAATTATATAAAAAATTATTAAAATTATAT-A-AAAATATT
1 AAAATTATATCAAAAGTTACTAAAATTATATCATAAAATATT
**
1727099 AAAATTATATCAAAAGTTACTAAAATTATATCATAACTTATT
1 AAAATTATATCAAAAGTTACTAAAATTATATCATAAAATATT
*
1727141 AAAATCATATCAAAAGT
1 AAAATTATATCAAAAGT
1727158 GATCAAAACT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 28 0.55
41 1 0.02
42 22 0.43
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (42 bp):
AAAATTATATCAAAAGTTACTAAAATTATATCATAAAATATT
Found at i:1727151 original size:42 final size:42
Alignment explanation
Indices: 1727012--1727157 Score: 129
Period size: 42 Copynumber: 3.5 Consensus size: 42
1727002 TATTAAAAGC
* * *
1727012 TATTAAAATCATATTAAAAGTTTGAC-AAAATTATA-CTTAACGG
1 TATTAAAATCATATCAAAAG-TT-ACTAAAATTATATCATAAC-A
* * * * * * *
1727055 CATCAAAATTATATAAAAAATTATTAAAATTATAT-A-AAAA
1 TATTAAAATCATATCAAAAGTTACTAAAATTATATCATAACA
* *
1727095 TATTAAAATTATATCAAAAGTTACTAAAATTATATCATAACT
1 TATTAAAATCATATCAAAAGTTACTAAAATTATATCATAACA
1727137 TATTAAAATCATATCAAAAGT
1 TATTAAAATCATATCAAAAGT
1727158 GATCAAAACT
Statistics
Matches: 82, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
40 30 0.37
41 4 0.05
42 33 0.40
43 15 0.18
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (42 bp):
TATTAAAATCATATCAAAAGTTACTAAAATTATATCATAACA
Found at i:1727743 original size:15 final size:15
Alignment explanation
Indices: 1727723--1727757 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1727713 TTAATTGACT
1727723 TCCAAATGGTTGGTA
1 TCCAAATGGTTGGTA
1727738 TCCAAATGGTTGGTA
1 TCCAAATGGTTGGTA
1727753 TCCAA
1 TCCAA
1727758 TTTGATTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (15 bp):
TCCAAATGGTTGGTA
Found at i:1727938 original size:2 final size:2
Alignment explanation
Indices: 1727931--1727963 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1727921 AAATTTAGTG
1727931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1727964 ATTTATAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1731646 original size:40 final size:40
Alignment explanation
Indices: 1731602--1731681 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
1731592 AAAGATAATA
*
1731602 ATTAATGACAGAATTAAA-AGTAAACTTTATTCTTTGAACT
1 ATTAATGACAGAATTAAATAGTAAACCTTATTC-TTGAACT
1731642 ATTAATGACAGAATTAAATAGTAAACCTTATTCTTGAACT
1 ATTAATGACAGAATTAAATAGTAAACCTTATTCTTGAACT
1731682 TGCAGCTGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 25 0.66
41 13 0.34
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.36
Consensus pattern (40 bp):
ATTAATGACAGAATTAAATAGTAAACCTTATTCTTGAACT
Found at i:1732025 original size:29 final size:29
Alignment explanation
Indices: 1731992--1732073 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 29
1731982 TGCAGTTACA
1731992 ATAAAAATTATAATTTAAAATAAAAATAT
1 ATAAAAATTATAATTTAAAATAAAAATAT
* * ** *
1732021 ATAAAAATTA-ATTTTAAATTTTAAATTT
1 ATAAAAATTATAATTTAAAATAAAAATAT
*
1732049 ATAAAATATTATATATTAAAAATAA
1 ATAAAA-ATTATA-ATTTAAAATAA
1732074 TTTTATAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
28 19 0.47
29 14 0.35
30 1 0.03
31 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
ATAAAAATTATAATTTAAAATAAAAATAT
Found at i:1732448 original size:15 final size:15
Alignment explanation
Indices: 1732424--1732473 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1732414 CTTAGATTAG
*
1732424 AAAACGAAAAAAAAA
1 AAAACAAAAAAAAAA
*
1732439 AAAACAAAAAAAAAG
1 AAAACAAAAAAAAAA
* *
1732454 AAAAGAAAAGAAAAA
1 AAAACAAAAAAAAAA
*
1732469 GAAAC
1 AAAAC
1732474 TAAGATTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAACAAAAAAAAAA
Found at i:1732969 original size:10 final size:10
Alignment explanation
Indices: 1732950--1733044 Score: 65
Period size: 10 Copynumber: 9.8 Consensus size: 10
1732940 AATTAATTAA
1732950 ATAT-TATTT
1 ATATATATTT
1732959 ATATATATTT
1 ATATATATTT
*
1732969 ATA-AAATTT
1 ATATATATTT
*
1732978 AT-TAAATTT
1 ATATATATTT
*
1732987 -TAAAT-TTT
1 ATATATATTT
*
1732995 AATATAAATTT
1 -ATATATATTT
* *
1733006 TTATAGTATAT
1 ATATA-TATTT
*
1733017 ATATATATAT
1 ATATATATTT
*
1733027 ATATATATAT
1 ATATATATTT
1733037 ATATATAT
1 ATATATAT
1733045 ATGAGATTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
8 4 0.06
9 18 0.26
10 38 0.54
11 10 0.14
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (10 bp):
ATATATATTT
Found at i:1733018 original size:56 final size:51
Alignment explanation
Indices: 1732920--1733025 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 51
1732910 TTACAAAAAA
*
1732920 AAAATTATATTTAAATTTTAAATTAATTAAATATTATTTATATATATTTAT
1 AAAATTATATTTAAATTTTAAATTAATTAAATATTATTTATATATATATAT
* *
1732971 AAAATT-TA-TTAAATTTTAAATTTTAATATAAATTTTTATAGTATATATATATAT
1 AAAATTATATTTAAATTTTAAA--TTAAT-TAAA-TATTAT-TTATATATATATAT
1733025 A
1 A
1733026 TATATATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
49 12 0.26
50 2 0.04
51 11 0.23
52 4 0.09
53 5 0.11
54 13 0.28
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (51 bp):
AAAATTATATTTAAATTTTAAATTAATTAAATATTATTTATATATATATAT
Found at i:1733019 original size:2 final size:2
Alignment explanation
Indices: 1733007--1733046 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
1732997 TATAAATTTT
1733007 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1733047 GAGATTATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1735090 original size:2 final size:2
Alignment explanation
Indices: 1735083--1735110 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1735073 TTTTTACATC
1735083 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
1735111 ACACTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1741244 original size:3 final size:3
Alignment explanation
Indices: 1741236--1741267 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1741226 CGTTGTCTTA
1741236 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1741268 CTAGGCAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.