Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 10 of 25
Found at i:1574153 original size:23 final size:20
Alignment explanation
Indices: 1574105--1574153 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
1574095 TTGTACCATA
*
1574105 CATTATAATAATAATTTTAT
1 CATTATAATAATAATATTAT
1574125 CA-TATAATATATAATAAATTAT
1 CATTATAATA-ATAAT--ATTAT
1574147 CATTATA
1 CATTATA
1574154 CGTGTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 7 0.29
20 7 0.29
22 6 0.25
23 4 0.17
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (20 bp):
CATTATAATAATAATATTAT
Found at i:1575876 original size:20 final size:17
Alignment explanation
Indices: 1575834--1575889 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
1575824 TGGTTAGTTC
1575834 TCTTCTTTTTTTTTTCCCTT
1 TCTTCTTTTTTTTTT---TT
* *
1575854 TCTAT-TTTATTTTTGTT
1 TCT-TCTTTTTTTTTTTT
1575871 TCTTCTTTTTTTTTTTT
1 TCTTCTTTTTTTTTTTT
1575888 TC
1 TC
1575890 AAAAATAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 1 0.03
17 17 0.57
20 11 0.37
21 1 0.03
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (17 bp):
TCTTCTTTTTTTTTTTT
Found at i:1577027 original size:160 final size:159
Alignment explanation
Indices: 1576763--1577053 Score: 564
Period size: 160 Copynumber: 1.8 Consensus size: 159
1576753 GCGTGTTTGG
1576763 TCTTGTGCAGCCTTTAACATGGTTGGAAGTGCTTAAAGAATCATCAAGGCATAATAGATATGAAA
1 TCTTGTGCAGCCTTTAACATGGTTGGAAGTGCTTAAAGAATCATCAAGGCATAATAGATATGAAA
1576828 GTCTTCAGACCTAATAAATATTATACCTAGCGATAAAGAGTAGTTTTCACCCTGGGTCCCCATCT
66 GTCTTCAGACCTAATAAATATTATACCTAGCGATAAAGAGTAGTTTTCACCCTGGGT-CCCATCT
1576893 AAAGGATGTACATCATATAAGCTTGTGGGC
130 AAAGGATGTACATCATATAAGCTTGTGGGC
*
1576923 TCTTGTGCAGCCTTTATCATGGTTGGAAGTGCTTAAAGAATCATCAAGGCATAATAGATATGAAA
1 TCTTGTGCAGCCTTTAACATGGTTGGAAGTGCTTAAAGAATCATCAAGGCATAATAGATATGAAA
1576988 GTCTTCAGACCTAATAAATATTATACCTAGCGATAAAGAGTAGTTTTCACCCTGGGTCCCATCTA
66 GTCTTCAGACCTAATAAATATTATACCTAGCGATAAAGAGTAGTTTTCACCCTGGGTCCCATCTA
1577053 A
131 A
1577054 TTTTGTAGTA
Statistics
Matches: 130, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
159 9 0.07
160 121 0.93
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (159 bp):
TCTTGTGCAGCCTTTAACATGGTTGGAAGTGCTTAAAGAATCATCAAGGCATAATAGATATGAAA
GTCTTCAGACCTAATAAATATTATACCTAGCGATAAAGAGTAGTTTTCACCCTGGGTCCCATCTA
AAGGATGTACATCATATAAGCTTGTGGGC
Found at i:1578694 original size:22 final size:22
Alignment explanation
Indices: 1578669--1578719 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1578659 ATAAATCCTC
1578669 AACATAAATCACATTTCATTTG
1 AACATAAATCACATTTCATTTG
* *
1578691 AACATATATCACCTTTCATTTG
1 AACATAAATCACATTTCATTTG
1578713 AA-ATAAA
1 AACATAAA
1578720 AGTTTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.43, C:0.18, G:0.04, T:0.35
Consensus pattern (22 bp):
AACATAAATCACATTTCATTTG
Found at i:1580768 original size:3 final size:3
Alignment explanation
Indices: 1580762--1580790 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1580752 CAGATCTTTT
1580762 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1580791 GCTGTTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1581959 original size:2 final size:2
Alignment explanation
Indices: 1581947--1581977 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1581937 TCTATTTATC
*
1581947 TA TA CA 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
1581978 TTGGCAAGCA
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1582205 original size:17 final size:18
Alignment explanation
Indices: 1582177--1582249 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 18
1582167 TAAAATTTAT
1582177 ATAAA-ATAAATTATTA-
1 ATAAATATAAATTATTAG
* *
1582193 ATAAATTTAAATT-TTAT
1 ATAAATATAAATTATTAG
*
1582210 ATAAATATAAAATATT--
1 ATAAATATAAATTATTAG
*
1582226 TTAAATAT-AATTATTAG
1 ATAAATATAAATTATTAG
1582243 ATAAATA
1 ATAAATA
1582250 AATAACATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
15 6 0.13
16 15 0.33
17 23 0.50
18 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (18 bp):
ATAAATATAAATTATTAG
Found at i:1582206 original size:32 final size:34
Alignment explanation
Indices: 1582151--1582225 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
1582141 AATATCATAA
* *
1582151 AAATATATAAATATATTAAAA-TTTATATAAA-AT
1 AAAT-TATTAATAAATTAAAATTTTATATAAATAT
*
1582184 AAATTATTAATAAATTTAAATTTTATATAAATAT
1 AAATTATTAATAAATTAAAATTTTATATAAATAT
*
1582218 AAAATATT
1 AAATTATT
1582226 TTAAATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 13 0.36
33 14 0.39
34 9 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (34 bp):
AAATTATTAATAAATTAAAATTTTATATAAATAT
Found at i:1582281 original size:22 final size:21
Alignment explanation
Indices: 1582227--1582284 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
1582217 TAAAATATTT
*
1582227 TAAATATAATTATTAGATAAA
1 TAAATATAATTATTAAATAAA
*
1582248 TAAATA-ACATTATGTAAATATA
1 TAAATATA-ATTAT-TAAATAAA
*
1582270 TAAATATTATTATTA
1 TAAATATAATTATTA
1582285 TGTATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 13 0.42
22 17 0.55
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (21 bp):
TAAATATAATTATTAAATAAA
Found at i:1582723 original size:13 final size:14
Alignment explanation
Indices: 1582707--1582735 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1582697 CATTTCAAAT
1582707 AATTAT-TTTTTAA
1 AATTATATTTTTAA
1582720 AATTATATTTTTAA
1 AATTATATTTTTAA
1582734 AA
1 AA
1582736 AATTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTATATTTTTAA
Found at i:1592083 original size:23 final size:22
Alignment explanation
Indices: 1592027--1592084 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 22
1592017 TATTATTTTT
*
1592027 TATTATAATTT-TA-TTAAAAA
1 TATTATAATTTATATTTTAAAA
1592047 TATTAT-ATTTATATTTTAAAA
1 TATTATAATTTATATTTTAAAA
1592068 TATTAATAATTTATATT
1 TATT-ATAATTTATATT
1592085 ATATAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 4 0.12
20 8 0.24
21 10 0.30
22 2 0.06
23 9 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTATAATTTATATTTTAAAA
Found at i:1592097 original size:24 final size:23
Alignment explanation
Indices: 1592027--1592103 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 23
1592017 TATTATTTTT
1592027 TATT-ATAATTT-TATTA-AAAA
1 TATTAATAATTTATATTATAAAA
*
1592047 TATT-AT-ATTTATATTTTAAAA
1 TATTAATAATTTATATTATAAAA
1592068 TATTAATAATTTATATTATATAAA
1 TATTAATAATTTATATTATA-AAA
* *
1592092 TTTTAATTATTT
1 TATTAATAATTT
1592104 TTTATTCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.08
20 10 0.21
21 8 0.17
22 2 0.04
23 11 0.23
24 13 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTAATAATTTATATTATAAAA
Found at i:1592617 original size:2 final size:2
Alignment explanation
Indices: 1592610--1592641 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1592600 TTGGGGTCCT
1592610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1592642 AGAAATTAGC
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):
TA
Found at i:1593149 original size:18 final size:19
Alignment explanation
Indices: 1593113--1593152 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1593103 TTTAGACATC
1593113 ATATGAAAATATAATTAAA
1 ATATGAAAATATAATTAAA
1593132 ATAT-AAAA-ATAATATAAA
1 ATATGAAAATATAAT-TAAA
1593150 ATA
1 ATA
1593153 AAATACGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
ATATGAAAATATAATTAAA
Found at i:1594105 original size:23 final size:25
Alignment explanation
Indices: 1594083--1594127 Score: 69
Period size: 22 Copynumber: 1.9 Consensus size: 25
1594073 TTCGACTTAT
1594083 TTTTCA-AT-TATATA-ATATATTA
1 TTTTCATATATATATATATATATTA
1594105 TTTTCATATATATATATATATAT
1 TTTTCATATATATATATATATAT
1594128 ATTATAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 2 0.10
24 6 0.30
25 6 0.30
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTCATATATATATATATATATTA
Found at i:1596568 original size:17 final size:17
Alignment explanation
Indices: 1596548--1596586 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1596538 AGATATAAAA
1596548 TAAAT-TTTTAATAATTT
1 TAAATCTTTTAA-AATTT
*
1596565 TAAATCTTTTAAATTTT
1 TAAATCTTTTAAAATTT
1596582 TAAAT
1 TAAAT
1596587 AATAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATCTTTTAAAATTT
Found at i:1596584 original size:8 final size:8
Alignment explanation
Indices: 1596548--1596586 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
1596538 AGATATAAAA
1596548 TAAATTTT
1 TAAATTTT
*
1596556 TAATAATTT
1 TAA-ATTTT
1596565 TAAATCTTT
1 TAAAT-TTT
1596574 TAAATTTT
1 TAAATTTT
1596582 TAAAT
1 TAAAT
1596587 AATAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (8 bp):
TAAATTTT
Found at i:1597099 original size:13 final size:13
Alignment explanation
Indices: 1597072--1597109 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1597062 AAAATAAAGT
*
1597072 AATTTAA-TGTAA
1 AATTTAATTTTAA
1597084 AATTTAATTTTAA
1 AATTTAATTTTAA
1597097 AATTTAATTTTAA
1 AATTTAATTTTAA
1597110 TAAATTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
AATTTAATTTTAA
Found at i:1597472 original size:2 final size:2
Alignment explanation
Indices: 1597465--1597490 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1597455 CTTTCGAAAT
1597465 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
1597491 ATAGAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1600207 original size:2 final size:2
Alignment explanation
Indices: 1600200--1600236 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1600190 CGATCTCCAG
1600200 AT AT 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 AT AT A
1600237 ATTGCTGCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1600587 original size:3 final size:3
Alignment explanation
Indices: 1600579--1600605 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1600569 AAGTTTAAAG
1600579 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1600606 TAGATCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1602901 original size:2 final size:2
Alignment explanation
Indices: 1602894--1602926 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1602884 TTTGCCAAGT
1602894 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 T
1602927 TTCAAATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1604049 original size:50 final size:51
Alignment explanation
Indices: 1603975--1604079 Score: 167
Period size: 50 Copynumber: 2.1 Consensus size: 51
1603965 TGTACAAATC
* *
1603975 ATATTCATGAATGATAATTAAAAATTCATGAAAGTTACTCGCATTTGTATT
1 ATATTAATGAATGATAATTAAAAATTCATAAAAGTTACTCGCATTTGTATT
* *
1604026 ATATTAATGAAT-TTAATTAAAAATTCATAAAAGTTACTCGCGTTTGTATT
1 ATATTAATGAATGATAATTAAAAATTCATAAAAGTTACTCGCATTTGTATT
1604076 ATAT
1 ATAT
1604080 CACCAAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 39 0.78
51 11 0.22
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (51 bp):
ATATTAATGAATGATAATTAAAAATTCATAAAAGTTACTCGCATTTGTATT
Found at i:1604213 original size:2 final size:2
Alignment explanation
Indices: 1604206--1604248 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1604196 CAAATGGATA
1604206 AT AT AT AT AT 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 AT AT AT AT AT
1604248 A
1 A
1604249 AAGTTACTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1606628 original size:5 final size:5
Alignment explanation
Indices: 1606618--1606645 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1606608 TAACATGCAA
1606618 AGCAC AGCAC AGCAC AGCAC AGCAC AGC
1 AGCAC AGCAC AGCAC AGCAC AGCAC AGC
1606646 TAGCTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.39, G:0.21, T:0.00
Consensus pattern (5 bp):
AGCAC
Found at i:1606758 original size:3 final size:3
Alignment explanation
Indices: 1606750--1606776 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1606740 TTGCCAGAGA
1606750 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1606777 ATGAGATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1607395 original size:16 final size:17
Alignment explanation
Indices: 1607359--1607397 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1607349 AAAGTAAGAT
*
1607359 ATATTTAATAAATAAAA
1 ATATATAATAAATAAAA
*
1607376 ATATATAATAAAT-GAA
1 ATATATAATAAATAAAA
1607392 ATATAT
1 ATATAT
1607398 TTAAAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
ATATATAATAAATAAAA
Found at i:1608406 original size:19 final size:19
Alignment explanation
Indices: 1608360--1608406 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
1608350 CAGTAATTTC
*
1608360 TATATGTAAAAAATATATA
1 TATATTTAAAAAATATATA
1608379 TATAAATTTAAAAAAT-TATCA
1 TAT--ATTTAAAAAATATAT-A
1608400 TATATTT
1 TATATTT
1608407 TTAACATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 7 0.29
20 3 0.12
21 14 0.58
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TATATTTAAAAAATATATA
Found at i:1611340 original size:2 final size:2
Alignment explanation
Indices: 1611328--1611359 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1611318 AATAACGTGG
*
1611328 AT AT AT GT 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
1611360 TTAACAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1611812 original size:5 final size:5
Alignment explanation
Indices: 1611802--1611827 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1611792 AGATCACTAA
1611802 ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT A
1611828 ACATTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:1612055 original size:19 final size:20
Alignment explanation
Indices: 1612033--1612078 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
1612023 AAATTTATTA
1612033 AATATAAA-AATTTTTAAAT
1 AATATAAATAATTTTTAAAT
*
1612052 AATAATTAAATAATTTTTAATT
1 AAT-A-TAAATAATTTTTAAAT
1612074 AATAT
1 AATAT
1612079 TTATAAACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 3 0.13
20 2 0.09
21 5 0.22
22 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATAAATAATTTTTAAAT
Found at i:1612064 original size:25 final size:26
Alignment explanation
Indices: 1612002--1612064 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
1611992 TCAAATATAC
1612002 ATAATT-AATAAAATATTTTTTAAAT
1 ATAATTAAATAAAATATTTTTTAAAT
* *
1612027 -TTATTAAATATAAA-AATTTTTAAAT
1 ATAATTAAATA-AAATATTTTTTAAAT
1612052 AATAATTAAATAA
1 -ATAATTAAATAA
1612065 TTTTTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 4 0.13
25 14 0.45
26 4 0.13
27 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATTAAATAAAATATTTTTTAAAT
Found at i:1612069 original size:22 final size:21
Alignment explanation
Indices: 1612037--1612077 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1612027 TTATTAAATA
1612037 TAAAAATTTTTAAATAATAAT
1 TAAAAATTTTTAAATAATAAT
*
1612058 TAAATAATTTTTAATTAATA
1 TAAA-AATTTTTAAATAATA
1612078 TTTATAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAAATTTTTAAATAATAAT
Found at i:1623103 original size:18 final size:18
Alignment explanation
Indices: 1623080--1623114 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1623070 AAATTATTAT
*
1623080 TTATTACATATAATATAA
1 TTATTACAAATAATATAA
*
1623098 TTATTATAAATAATATA
1 TTATTACAAATAATATA
1623115 TTTAATCAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TTATTACAAATAATATAA
Found at i:1627285 original size:23 final size:22
Alignment explanation
Indices: 1627232--1627290 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 22
1627222 CAAAAGTGAA
* *
1627232 ATAATAATAAATAAATATTTAAT
1 ATAATAA-AAATAAATAATAAAT
*
1627255 AAATATAAAAATAACATAATAAAT
1 ATA-ATAAAAATAA-ATAATAAAT
1627279 ATAATAAAAATA
1 ATAATAAAAATA
1627291 TTTAAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAATAAAAATAAATAATAAAT
Found at i:1629506 original size:2 final size:2
Alignment explanation
Indices: 1629499--1629536 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1629489 TAAGTATGTG
*
1629499 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1629537 AAAATTGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1635030 original size:19 final size:22
Alignment explanation
Indices: 1635008--1635062 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 22
1634998 TATATAAAAA
1635008 TAAATATAATATAAA-TT-A-T
1 TAAATATAATATAAATTTAAGT
* *
1635027 TAAATATATTAAAAATTTAAGTT
1 TAAATATAATATAAATTTAAG-T
1635050 TAAATATAATATA
1 TAAATATAATATA
1635063 TATCAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 13 0.46
20 2 0.07
21 1 0.04
23 12 0.43
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAATATAATATAAATTTAAGT
Found at i:1639918 original size:38 final size:38
Alignment explanation
Indices: 1639859--1639935 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 38
1639849 TAATTACTTT
1639859 TTATTTTATTTTAAATTTTATTTTATTCT-AATAAAATAA
1 TTATTTTA-TTTAAATTTTATTTTATT-TAAATAAAATAA
*
1639898 TTATTTTA-TTATATTATTATTTTATTTAAATAAAATAA
1 TTATTTTATTTAAATT-TTATTTTATTTAAATAAAATAA
1639936 ACATACAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
37 7 0.20
38 20 0.57
39 8 0.23
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (38 bp):
TTATTTTATTTAAATTTTATTTTATTTAAATAAAATAA
Found at i:1639996 original size:14 final size:14
Alignment explanation
Indices: 1639977--1640011 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1639967 TCTTACTATA
1639977 AAAATAATAATTTT
1 AAAATAATAATTTT
*
1639991 AAAATAATATTTTT
1 AAAATAATAATTTT
*
1640005 AATATAA
1 AAAATAA
1640012 AATATAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATAATAATTTT
Found at i:1640503 original size:3 final size:3
Alignment explanation
Indices: 1640495--1640532 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1640485 TTCTTTATGC
1640495 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1640533 GTGGTAAAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1640871 original size:24 final size:22
Alignment explanation
Indices: 1640824--1640873 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1640814 TATTGATGTT
* *
1640824 ATATTTTTTTATTTTTTAAAAA
1 ATATTTTTTTATATTTAAAAAA
1640846 ATATTTTTTTATATTTAAATATAA
1 ATATTTTTTTATATTTAAA-A-AA
1640870 ATAT
1 ATAT
1640874 AAAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.71
23 1 0.04
24 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTTTATATTTAAAAAA
Found at i:1641589 original size:13 final size:13
Alignment explanation
Indices: 1641533--1641677 Score: 57
Period size: 13 Copynumber: 10.9 Consensus size: 13
1641523 ATTTGAGTTC
*
1641533 AATTTAAAATTTAA
1 AATTT-AAATTTTA
*
1641547 AATTTAAATATT-
1 AATTTAAATTTTA
*
1641559 AA-TTAAATTTTG
1 AATTTAAATTTTA
**
1641571 TTTTTAAATTTTA
1 AATTTAAATTTTA
** *
1641584 AATTTAATAAAAATAA
1 AA-TT--TAAATTTTA
*
1641600 AATATAAATATTTA
1 AATTTAAAT-TTTA
*
1641614 AATTTAATTTTTA
1 AATTTAAATTTTA
* *
1641627 TATTGAAA-TTTA
1 AATTTAAATTTTA
1641639 AATTT-AATTATT-
1 AATTTAAATT-TTA
*
1641651 AATATTAAAATTTA
1 AAT-TTAAATTTTA
*
1641665 TATTTAAACTTTT
1 AATTTAAA-TTTT
1641678 TTATTATTAA
Statistics
Matches: 94, Mismatches: 25, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
11 10 0.11
12 13 0.14
13 38 0.40
14 24 0.26
15 1 0.01
16 8 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (13 bp):
AATTTAAATTTTA
Found at i:1650719 original size:30 final size:31
Alignment explanation
Indices: 1650685--1650742 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
1650675 ATTTTTTTTC
1650685 ATATTTTAAAATTATTATT-TTATTTTTAAA
1 ATATTTTAAAATTATTATTATTATTTTTAAA
* * *
1650715 ATATTTTATATTTGTTATTATTATTTTT
1 ATATTTTAAAATTATTATTATTATTTTT
1650743 GTAGTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (31 bp):
ATATTTTAAAATTATTATTATTATTTTTAAA
Found at i:1651209 original size:2 final size:2
Alignment explanation
Indices: 1651202--1651231 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1651192 CAGTGTTAAC
1651202 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1651232 GTTAGTGACG
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
Found at i:1652034 original size:33 final size:32
Alignment explanation
Indices: 1651967--1652051 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 32
1651957 TATACTAAAA
1651967 AATATATT-T-TTTATTTATATGATATAAATCAT
1 AATATATTATATTTATTT-T-TGATATAAATCAT
* *
1651999 AATATATTATATTTATGTTTTGATATATATTAT
1 AATATATTATATTTAT-TTTTGATATAAATCAT
1652032 AATATATTATATTTATTTTT
1 AATATATTATATTTATTTTT
1652052 CTCCTATCTC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
32 12 0.25
33 28 0.58
34 6 0.12
35 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.58
Consensus pattern (32 bp):
AATATATTATATTTATTTTTGATATAAATCAT
Found at i:1656106 original size:16 final size:19
Alignment explanation
Indices: 1656085--1656124 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
1656075 AGCTCTTTAT
1656085 TTTAATT-TTTTT-TAC-A
1 TTTAATTATTTTTGTACAA
1656101 TTTAATTATTTTTGTACAA
1 TTTAATTATTTTTGTACAA
1656120 TTTAA
1 TTTAA
1656125 AAAATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 5 0.24
18 3 0.14
19 6 0.29
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTAATTATTTTTGTACAA
Found at i:1656984 original size:15 final size:15
Alignment explanation
Indices: 1656960--1656991 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1656950 TTTATTAAAT
1656960 AATAAATTAAATTAA
1 AATAAATTAAATTAA
*
1656975 AATAATTTAAATTAA
1 AATAAATTAAATTAA
1656990 AA
1 AA
1656992 ATATAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAATTAAATTAA
Found at i:1657835 original size:12 final size:12
Alignment explanation
Indices: 1657811--1657858 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1657801 AGTGGAAGAA
1657811 GAAGAT-GACGAT
1 GAAGATGGA-GAT
1657823 GAAGATGGAGAT
1 GAAGATGGAGAT
* *
1657835 GGAGATGGAGAA
1 GAAGATGGAGAT
*
1657847 GAAGAAGGAGAT
1 GAAGATGGAGAT
1657859 AGCGAGCTCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 28 0.93
13 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.42, T:0.12
Consensus pattern (12 bp):
GAAGATGGAGAT
Found at i:1661458 original size:16 final size:14
Alignment explanation
Indices: 1661426--1661464 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
1661416 TTTAGATATG
1661426 ATAT-AAATATTAA
1 ATATAAAATATTAA
1661439 ATATAAAATATTTAAA
1 ATATAAAATA-TT-AA
1661455 ATATAAAATA
1 ATATAAAATA
1661465 AATATATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 5 0.22
15 2 0.09
16 12 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATAAAATATTAA
Found at i:1661509 original size:20 final size:20
Alignment explanation
Indices: 1661482--1661525 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1661472 ATGAATATGT
*
1661482 TAAT-TTTTATATA-AATATA
1 TAATATTTTAAATATAAT-TA
1661501 TAATATTTTAAATATAATTA
1 TAATATTTTAAATATAATTA
1661521 TAATA
1 TAATA
1661526 CAAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 15 0.68
21 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATATTTTAAATATAATTA
Found at i:1670866 original size:2 final size:2
Alignment explanation
Indices: 1670859--1670894 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1670849 TAACGCGCAC
1670859 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1670895 AATGTGTCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1673342 original size:16 final size:17
Alignment explanation
Indices: 1673313--1673345 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1673303 ATCACTTGAA
*
1673313 AAAATTTAATAAAAAAT
1 AAAATTTAACAAAAAAT
1673330 AAAA-TTAACAAAAAAT
1 AAAATTTAACAAAAAAT
1673346 TAATTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATTTAACAAAAAAT
Found at i:1673707 original size:4 final size:4
Alignment explanation
Indices: 1673698--1673729 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1673688 AAGAATCAAC
*
1673698 ATTT ATTT ATTT ATTT ATTT ATTT ACTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1673730 GAATGTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:1679515 original size:100 final size:99
Alignment explanation
Indices: 1679396--1679606 Score: 282
Period size: 100 Copynumber: 2.1 Consensus size: 99
1679386 ACCTCAAAAC
*
1679396 TTTTC-AAATAAATTACTACTTTAACAACCATTATTGCTAAAGTGTTTTCAACAATCAGTTAAAA
1 TTTTCAAAATAAATTACTACTTTAACAACCATTACTGCTAAAGTGTTTTCAACAATCAGTTAAAA
* *
1679460 TTAACTTCTTGCACAAATTAA-AACCTAATAATTTT
66 TCAACTTCTTACACAAATTAAGAACC-AAT-ATTTT
* ** * *
1679495 TTTTCAAAATAAATTGCTACTTTAACATTCATTACTGCTAAAGTTTTTTCAACAGTCAGTTAAAA
1 TTTTCAAAATAAATTACTACTTTAACAACCATTACTGCTAAAGTGTTTTCAACAATCAGTTAAAA
* ** *
1679560 TCAATTTCTTACATGAATTAAGATCCAATATTTT
66 TCAACTTCTTACACAAATTAAGAACCAATATTTT
1679594 TTTTCAAAATAAA
1 TTTTCAAAATAAA
1679607 ATACAAATTT
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
99 23 0.23
100 72 0.73
101 3 0.03
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (99 bp):
TTTTCAAAATAAATTACTACTTTAACAACCATTACTGCTAAAGTGTTTTCAACAATCAGTTAAAA
TCAACTTCTTACACAAATTAAGAACCAATATTTT
Found at i:1684210 original size:42 final size:42
Alignment explanation
Indices: 1684163--1684248 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
1684153 TAATCCTATC
* * * *
1684163 ATCAAAATTAAAGTGAATTCGGATAATGAATATTTCAAGTTT
1 ATCAAAATTAAAATGAATTCGGATAATAAATATTTAAAATTT
1684205 ATCAAAATTAAAATGAATTCGGATAATAAATATTTAAAATTT
1 ATCAAAATTAAAATGAATTCGGATAATAAATATTTAAAATTT
1684247 AT
1 AT
1684249 ATTTAAGATC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.36
Consensus pattern (42 bp):
ATCAAAATTAAAATGAATTCGGATAATAAATATTTAAAATTT
Found at i:1684735 original size:6 final size:6
Alignment explanation
Indices: 1684706--1684769 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
1684696 TATTAAAATT
** * * *
1684706 TATTT- TATTTA TATAGA TATTTTA TATTTA TATCTA TATTAA TTTTTA
1 TATTTA TATTTA TATTTA TA-TTTA TATTTA TATTTA TATTTA TATTTA
1684754 TATTTA TATTTA -ATTT
1 TATTTA TATTTA TATTT
1684770 TTTTAAAAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
5 9 0.19
6 34 0.72
7 4 0.09
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (6 bp):
TATTTA
Found at i:1684831 original size:35 final size:35
Alignment explanation
Indices: 1684789--1684868 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
1684779 ATTATTTAAT
* * *
1684789 AAATTAAAATATTTAACCCATATTA-TTTTTAAATC
1 AAATTAAAAT-CTAAACACATATTACTTTTTAAATC
* *
1684824 AAATTAAAATCTAAACATATATTACTTTTTAAATT
1 AAATTAAAATCTAAACACATATTACTTTTTAAATC
*
1684859 AAATTTAAAT
1 AAATTAAAAT
1684869 TCAAATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 10 0.26
35 28 0.74
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (35 bp):
AAATTAAAATCTAAACACATATTACTTTTTAAATC
Found at i:1691120 original size:3 final size:3
Alignment explanation
Indices: 1691114--1691145 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1691104 TTTGAAAATT
1691114 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1691146 GAATTGTTTT
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:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:1692733 original size:2 final size:2
Alignment explanation
Indices: 1692728--1692753 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1692718 GACATCTCTC
1692728 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
1692754 TCACGCCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:1694371 original size:3 final size:3
Alignment explanation
Indices: 1694363--1694396 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
1694353 TTTTCTATAT
1694363 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATCA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
1694397 CAAAGCATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1695694 original size:14 final size:13
Alignment explanation
Indices: 1695675--1695708 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1695665 TCAGGATACT
1695675 AATTTACATAAAAA
1 AATTTA-ATAAAAA
*
1695689 AATTTATTAAAAA
1 AATTTAATAAAAA
1695702 AATTTAA
1 AATTTAA
1695709 CCACCAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTTAATAAAAA
Found at i:1695886 original size:41 final size:40
Alignment explanation
Indices: 1695809--1695891 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 40
1695799 TATGAATCTT
* *
1695809 AATAGATAACTAAAATTTACTTAGATCTATCGATATTTATA
1 AATAGATAACTAAAATTTAATTAAATCTATCGATATTT-TA
*
1695850 AATAGATAATTAAAATTTAATTAAA-CTTATTC-ATATTTTA
1 AATAGATAACTAAAATTTAATTAAATC-TA-TCGATATTTTA
1695890 AA
1 AA
1695892 AAAATAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
40 5 0.14
41 30 0.81
42 2 0.05
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (40 bp):
AATAGATAACTAAAATTTAATTAAATCTATCGATATTTTA
Found at i:1695996 original size:18 final size:19
Alignment explanation
Indices: 1695971--1696014 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
1695961 ATTTTAAGAT
*
1695971 ATAAATTATATAATATATA
1 ATAAATTAAATAATATATA
1695990 A-AAATTAAATAATATATA
1 ATAAATTAAATAATATATA
1696008 ATAAATT
1 ATAAATT
1696015 TAGACTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAATTAAATAATATATA
Found at i:1696026 original size:50 final size:50
Alignment explanation
Indices: 1695921--1696016 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 50
1695911 TTTAATTTAA
* * * * * *
1695921 ATAAATTATATCATTTTATTAAAATTTAATATTATATAAAATTTTAAGAT
1 ATAAATTATATCAATATATAAAAATTAAATAATATATAAAAATTTAAGAT
1695971 ATAAATTATAT-AATATATAAAAATTAAATAATATATAATAAATTTA
1 ATAAATTATATCAATATATAAAAATTAAATAATATATAA-AAATTTA
1696017 GACTTTAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 22 0.56
50 17 0.44
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (50 bp):
ATAAATTATATCAATATATAAAAATTAAATAATATATAAAAATTTAAGAT
Found at i:1697379 original size:18 final size:18
Alignment explanation
Indices: 1697351--1697385 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1697341 TCTTTATTTT
1697351 TTTAAATATTTATATTAAA
1 TTTAAATATTTAT-TTAAA
1697370 TTTAAA-ATTTATTTAA
1 TTTAAATATTTATTTAA
1697386 TTATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAATATTTATTTAAA
Found at i:1697399 original size:11 final size:11
Alignment explanation
Indices: 1697356--1697402 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
1697346 ATTTTTTTAA
1697356 ATATTTATATT
1 ATATTTATATT
* *
1697367 AAATTTAAAATT
1 ATATTT-ATATT
1697379 -TATTTA-ATT
1 ATATTTATATT
1697388 ATATTTATATT
1 ATATTTATATT
1697399 ATAT
1 ATAT
1697403 ATGTATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 3 0.10
10 7 0.23
11 16 0.53
12 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATATTTATATT
Found at i:1697841 original size:13 final size:14
Alignment explanation
Indices: 1697823--1697851 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1697813 ATATAAAATT
1697823 TTTAAATTTG-TTA
1 TTTAAATTTGATTA
1697836 TTTAAATTTGATTA
1 TTTAAATTTGATTA
1697850 TT
1 TT
1697852 ATTTATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (14 bp):
TTTAAATTTGATTA
Found at i:1698501 original size:16 final size:17
Alignment explanation
Indices: 1698462--1698524 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 17
1698452 TGAAAATTCT
1698462 TTTTATAATTTATTATA
1 TTTTATAATTTATTATA
1698479 TTATTATAA--TATTATAA
1 TT-TTATAATTTATTAT-A
**
1698496 TTTTATTTTTATATTAATA
1 TTTTATAATT-TATT-ATA
1698515 TTTTATAATT
1 TTTTATAATT
1698525 AAATTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
16 10 0.28
17 5 0.14
18 6 0.17
19 13 0.36
20 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTATAATTTATTATA
Found at i:1698510 original size:27 final size:27
Alignment explanation
Indices: 1698464--1698524 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
1698454 AAAATTCTTT
1698464 TTATAA-TTTATTATATTATT-ATAATA
1 TTATAATTTTATTATATTATTAAT-ATA
* *
1698490 TTATAATTTTATT-TTTATATTAATATT
1 TTATAATTTTATTATAT-TATTAATATA
1698517 TTATAATT
1 TTATAATT
1698525 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 8 0.27
27 20 0.67
28 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TTATAATTTTATTATATTATTAATATA
Found at i:1698574 original size:16 final size:16
Alignment explanation
Indices: 1698553--1698590 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1698543 TATTTTTATT
*
1698553 ATTAAATATAAT-TTAA
1 ATTAAATA-AATCTAAA
1698569 ATTAAATAAATCTAAA
1 ATTAAATAAATCTAAA
1698585 ATTAAA
1 ATTAAA
1698591 AGATCATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTAAATAAATCTAAA
Found at i:1705710 original size:2 final size:2
Alignment explanation
Indices: 1705703--1705733 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1705693 TTAAACTTGC
1705703 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
1705734 GTTTGTATGA
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:1708488 original size:21 final size:20
Alignment explanation
Indices: 1708464--1708556 Score: 62
Period size: 19 Copynumber: 5.0 Consensus size: 20
1708454 TTTTTTTAGA
1708464 ATATAAAAATATAATATTAAT
1 ATATAAAAATATAATATT-AT
* *
1708485 ATATAAATATATTAAAATT-T
1 ATATAAAAATA-TAATATTAT
1708505 ATAT-AAAATA-AATTATTAT
1 ATATAAAAATATAA-TATTAT
*
1708524 -TAT----AT-TAAAATT-T
1 ATATAAAAATATAATATTAT
1708537 ATATAAAAATATAATATTAT
1 ATATAAAAATATAATATTAT
1708557 TACACCGCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 23
0.65 0.07 0.27
Matches are distributed among these distances:
13 1 0.02
14 6 0.11
15 4 0.07
17 2 0.04
18 8 0.15
19 12 0.22
20 6 0.11
21 10 0.18
22 6 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAAAAATATAATATTAT
Found at i:1708531 original size:32 final size:33
Alignment explanation
Indices: 1708492--1708558 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
1708482 AATATATAAA
1708492 TATATTAAAATTTATAT-AAAATA-AATTATTAT
1 TATATTAAAATTTATATAAAAATATAA-TATTAT
1708524 TATATTAAAATTTATATAAAAATATAATATTAT
1 TATATTAAAATTTATATAAAAATATAATATTAT
1708557 TA
1 TA
1708559 CACCGCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 17 0.52
33 14 0.42
34 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
TATATTAAAATTTATATAAAAATATAATATTAT
Found at i:1709133 original size:33 final size:33
Alignment explanation
Indices: 1709096--1709161 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1709086 TTAATTTGAT
1709096 TTTAATTATA-TAAAAGATAAATATTATTTTTAA
1 TTTAATTATATTAAAA-ATAAATATTATTTTTAA
1709129 TTTAATTATATTAAAAATAAATATTATTTTTAA
1 TTTAATTATATTAAAAATAAATATTATTTTTAA
1709162 AAATTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 27 0.84
34 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (33 bp):
TTTAATTATATTAAAAATAAATATTATTTTTAA
Found at i:1709173 original size:28 final size:32
Alignment explanation
Indices: 1709099--1709176 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 32
1709089 ATTTGATTTT
*
1709099 AATTATA-TAAAAGATAAATATTATTTTTAATTT
1 AATTATATTAAAA-ATAAATATTATTTTTAA-TA
1709132 AATTATATTAAAAATAAATATTATTTTTAA-A
1 AATTATATTAAAAATAAATATTATTTTTAATA
1709163 AATT-T-TTAAAAATA
1 AATTATATTAAAAATA
1709177 TGATTTTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 9 0.21
30 1 0.02
31 4 0.09
33 24 0.56
34 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
AATTATATTAAAAATAAATATTATTTTTAATA
Found at i:1710562 original size:16 final size:16
Alignment explanation
Indices: 1710541--1710572 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1710531 TGATCTATGG
1710541 AAAGCCCCATGTGACC
1 AAAGCCCCATGTGACC
1710557 AAAGCCCCATGTGACC
1 AAAGCCCCATGTGACC
1710573 CGCATTTACT
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:0.31, C:0.38, G:0.19, T:0.12
Consensus pattern (16 bp):
AAAGCCCCATGTGACC
Found at i:1710728 original size:17 final size:17
Alignment explanation
Indices: 1710706--1710741 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1710696 TTGAGTTAAG
*
1710706 TTTTAAATTT-AATTTA
1 TTTTTAATTTAAATTTA
1710722 TTTTTAATTTAAATTTA
1 TTTTTAATTTAAATTTA
1710739 TTT
1 TTT
1710742 AATAGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTAATTTAAATTTA
Found at i:1710792 original size:28 final size:27
Alignment explanation
Indices: 1710721--1710798 Score: 65
Period size: 28 Copynumber: 2.9 Consensus size: 27
1710711 AATTTAATTT
* *
1710721 ATTTTTAATTTAAATTTATTTAAT-AGAA
1 ATTTTT-ATTTAAATTTA-ATAATAAAAA
*
1710749 ATTATTATTT-AA--TAATAATAAAATA
1 ATTTTTATTTAAATTTAATAATAAAA-A
*
1710774 ATTTTTATTTAAATTTAATTATAAA
1 ATTTTTATTTAAATTTAATAATAAA
1710799 TTTTTAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
23 4 0.10
24 4 0.10
25 10 0.25
26 4 0.10
27 4 0.10
28 14 0.35
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (27 bp):
ATTTTTATTTAAATTTAATAATAAAAA
Found at i:1711614 original size:29 final size:28
Alignment explanation
Indices: 1711535--1711615 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
1711525 GGCAATCATT
* *
1711535 ATTTTTTAATATTTTTATTTAATTTTTTA
1 ATTTTTTAA-ATTTATATTTTATTTTTTA
* *
1711564 ATTCTTTAAA-ATA-ATTATTATTGTTTTA
1 ATTTTTTAAATTTATATT-TTATT-TTTTA
1711592 ATTTTTTAAATTTATATTTTATTT
1 ATTTTTTAAATTTATATTTTATTT
1711616 ATATATAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
26 3 0.07
27 5 0.12
28 16 0.38
29 15 0.36
30 3 0.07
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (28 bp):
ATTTTTTAAATTTATATTTTATTTTTTA
Found at i:1711699 original size:20 final size:18
Alignment explanation
Indices: 1711654--1711700 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
1711644 AATTTGTATG
1711654 TAAAA-AATATTAAAATA
1 TAAAATAATATTAAAATA
*
1711671 TAAATATAATAATTAAAATTT
1 TAAA-ATAAT-ATTAAAA-TA
1711692 TAAAATAAT
1 TAAAATAAT
1711701 TGATTATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.16
18 1 0.04
19 3 0.12
20 12 0.48
21 5 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAATAATATTAAAATA
Found at i:1712155 original size:27 final size:27
Alignment explanation
Indices: 1712110--1712164 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 27
1712100 TTTAATACAT
*
1712110 TATTTTAAATAAATTTAAA-AA-ATTA
1 TATTATAAATAAATTTAAATAATATTA
1712135 TATTATAAATATAATTTTAAATAATATTA
1 TATTATAAATA-AA-TTTAAATAATATTA
1712164 T
1 T
1712165 TAATATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 10 0.40
26 2 0.08
27 6 0.24
28 2 0.08
29 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTATAAATAAATTTAAATAATATTA
Found at i:1712161 original size:24 final size:25
Alignment explanation
Indices: 1712129--1712175 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1712119 TAAATTTAAA
*
1712129 AAATTATATTATAAATA-TAATTTT
1 AAATAATATTATAAATATTAATTTT
*
1712153 AAATAATATTATTAATATTAATT
1 AAATAATATTATAAATATTAATT
1712176 AACATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAATAATATTATAAATATTAATTTT
Found at i:1712165 original size:27 final size:25
Alignment explanation
Indices: 1712108--1712166 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
1712098 TATTTAATAC
*
1712108 ATTATTTTAAATAAATTTAAAAAAT
1 ATTATTATAAATAAATTTAAAAAAT
*
1712133 -TATATTATAAATATAATTTTAAATAAT
1 AT-TATTATAAATA-AA-TTTAAAAAAT
1712160 ATTATTA
1 ATTATTA
1712167 ATATTAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
24 1 0.04
25 10 0.36
26 2 0.07
27 14 0.50
28 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTATTATAAATAAATTTAAAAAAT
Found at i:1712981 original size:13 final size:14
Alignment explanation
Indices: 1712961--1712998 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1712951 ACACAAAATT
1712961 TAATTATTTTAAAA
1 TAATTATTTTAAAA
* *
1712975 T-ATTATTTTATAT
1 TAATTATTTTAAAA
1712988 TAATTATTTTA
1 TAATTATTTTA
1712999 TAAAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TAATTATTTTAAAA
Found at i:1712995 original size:14 final size:14
Alignment explanation
Indices: 1712960--1713000 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1712950 AACACAAAAT
*
1712960 TTAATTATTTTAAA
1 TTAATTATTTTATA
*
1712974 AT-ATTATTTTATA
1 TTAATTATTTTATA
1712987 TTAATTATTTTATA
1 TTAATTATTTTATA
1713001 AAATAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTAATTATTTTATA
Found at i:1713015 original size:21 final size:22
Alignment explanation
Indices: 1712991--1713041 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
1712981 TTTATATTAA
1712991 TTATTTTATAAA-ATA-ATAAAT
1 TTATTTT-TAAATATACATAAAT
1713012 TTATTTTTAAATATATCGATAAAT
1 TTATTTTTAAATATA-C-ATAAAT
1713036 TTATTT
1 TTATTT
1713042 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.15
21 10 0.38
24 12 0.46
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATTTTTAAATATACATAAAT
Found at i:1713056 original size:21 final size:19
Alignment explanation
Indices: 1713030--1713090 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 19
1713020 AAATATATCG
1713030 ATAAATTTATTTATTTTTAAA
1 ATAAATTTATTTA-TTTT-AA
* *
1713051 ATAAATTTTAATTATTTTAT
1 ATAAA-TTTATTTATTTTAA
1713071 ATAAATTTA-TT-TTTTAA
1 ATAAATTTATTTATTTTAA
1713088 ATA
1 ATA
1713091 TAATATTTCG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 8 0.22
18 2 0.06
19 4 0.11
20 6 0.17
21 9 0.25
22 7 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATAAATTTATTTATTTTAA
Found at i:1713091 original size:19 final size:19
Alignment explanation
Indices: 1713038--1713098 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
1713028 CGATAAATTT
1713038 ATTTA-TTTTTAAA-ATAA
1 ATTTATTTTTTAAATATAA
1713055 ATTTTAATTATTTT--ATATAA
1 A-TTT-ATT-TTTTAAATATAA
1713075 ATTTATTTTTTAAATATAA
1 ATTTATTTTTTAAATATAA
1713094 TATTT
1 -ATTT
1713099 CGTTCCAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
17 5 0.14
18 6 0.17
19 11 0.31
20 10 0.28
21 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTATTTTTTAAATATAA
Found at i:1713489 original size:8 final size:8
Alignment explanation
Indices: 1713478--1713510 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1713468 TTTAAATAAT
1713478 TAAAATTA
1 TAAAATTA
1713486 TAAAATGT-
1 TAAAAT-TA
1713494 TAAAATTA
1 TAAAATTA
1713502 TAAAATTA
1 TAAAATTA
1713510 T
1 T
1713511 TTTATTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.04
8 21 0.91
9 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
TAAAATTA
Found at i:1713496 original size:16 final size:16
Alignment explanation
Indices: 1713477--1713507 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1713467 TTTTAAATAA
1713477 TTAAAATTATAAAATG
1 TTAAAATTATAAAATG
1713493 TTAAAATTATAAAAT
1 TTAAAATTATAAAAT
1713508 TATTTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTAAAATTATAAAATG
Found at i:1713799 original size:28 final size:29
Alignment explanation
Indices: 1713744--1713823 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 29
1713734 ATTAGACTAG
* * *
1713744 ATTATTAAAATTTT-AATATTATTTTATTT
1 ATTATT-AAATTTTAAAAATTATTATATTA
*
1713773 TTTATTAAATTTTAAAAATTA-TATATTA
1 ATTATTAAATTTTAAAAATTATTATATTA
*
1713801 ATTATATATATTTATAAAAATTA
1 ATTAT-TAAATTT-TAAAAATTA
1713824 ATTTAATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
28 16 0.38
29 17 0.40
30 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTATTAAATTTTAAAAATTATTATATTA
Found at i:1713829 original size:28 final size:28
Alignment explanation
Indices: 1713781--1713836 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
1713771 TTTTTATTAA
1713781 ATTTTAAAAATTATATATTAATTATATAT
1 ATTTTAAAAATTATATATTAATTA-ATAT
1713810 ATTTATAAAAATTA-AT-TTAATTAATAT
1 ATTT-TAAAAATTATATATTAATTAATAT
1713837 TACTAAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 4 0.15
28 7 0.27
29 6 0.23
30 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTTTAAAAATTATATATTAATTAATAT
Found at i:1713874 original size:3 final size:3
Alignment explanation
Indices: 1713866--1713924 Score: 77
Period size: 3 Copynumber: 20.3 Consensus size: 3
1713856 TTTTCTTTCA
* * *
1713866 TAT TAT TAT T-T AAT TAT TAT TAT TAT TAT TAT TAG TAT T-C TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1713912 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
1713925 TTTAAACCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1714410 original size:3 final size:3
Alignment explanation
Indices: 1714402--1714431 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1714392 ATAAGTATTT
1714402 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1714432 GATTAAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1714418 original size:25 final size:25
Alignment explanation
Indices: 1714370--1714420 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1714360 TTTAATAACG
* *
1714370 AGTATTTTTAAAATATTAATTAATA
1 AGTATTTATAAAATAATAATTAATA
1714395 AGTATTTATAATAATAATAA-TAATA
1 AGTATTTATAA-AATAATAATTAATA
1714420 A
1 A
1714421 TAATAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
AGTATTTATAAAATAATAATTAATA
Found at i:1717374 original size:2 final size:2
Alignment explanation
Indices: 1717367--1717404 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1717357 GCATCGAAAC
1717367 AT AT AT 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 AT AT AT
1717405 TAATGGAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1718550 original size:19 final size:19
Alignment explanation
Indices: 1718528--1718570 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1718518 TTTCAGAGTG
1718528 TATTATTTGTTTAAAAAAA
1 TATTATTTGTTTAAAAAAA
*
1718547 TATTTATTTTTTTAAAAAAA
1 TA-TTATTTGTTTAAAAAAA
1718567 -ATTA
1 TATTA
1718571 AAAAATAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 3 0.14
20 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TATTATTTGTTTAAAAAAA
Found at i:1722807 original size:1 final size:1
Alignment explanation
Indices: 1722797--1722888 Score: 76
Period size: 1 Copynumber: 92.0 Consensus size: 1
1722787 TGGCAATTGG
* * * ** * * * **
1722797 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAGAAAAAAACAAAACGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1722862 AGAAAAAAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1722889 GTGAAGATTT
Statistics
Matches: 70, Mismatches: 21, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:1722820 original size:14 final size:13
Alignment explanation
Indices: 1722797--1722888 Score: 96
Period size: 14 Copynumber: 6.8 Consensus size: 13
1722787 TGGCAATTGG
1722797 AAAAAGAAAAAAAC
1 AAAAA-AAAAAAAC
*
1722811 AAAACAAAAAAAAGG
1 AAAA-AAAAAAAA-C
* *
1722826 AAAAAGAAAAAAG
1 AAAAAAAAAAAAC
*
1722839 AAAAAAACAAAAC
1 AAAAAAAAAAAAC
*
1722852 GAAAAAAAAAAGA-
1 -AAAAAAAAAAAAC
1722865 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
1722878 AAAAAAAAAAA
1 AAAAAAAAAAA
1722889 GTGAAGATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
12 11 0.17
13 22 0.33
14 28 0.42
15 5 0.08
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:1722842 original size:36 final size:34
Alignment explanation
Indices: 1722797--1722888 Score: 129
Period size: 36 Copynumber: 2.8 Consensus size: 34
1722787 TGGCAATTGG
1722797 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGA
1 AAAAAGAAAAAAACAAAACAAAAAAAA--AAAAAGA
*
1722833 AAAAAGAAAAAAACAAAAC--GAAAAAAAAAAGA
1 AAAAAGAAAAAAACAAAACAAAAAAAAAAAAAGA
1722865 AAAAA-AAAAAAACAAAA-AAAAAAA
1 AAAAAGAAAAAAACAAAACAAAAAAA
1722889 GTGAAGATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
31 12 0.23
32 16 0.31
34 5 0.10
36 19 0.37
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (34 bp):
AAAAAGAAAAAAACAAAACAAAAAAAAAAAAAGA
Found at i:1730228 original size:1 final size:1
Alignment explanation
Indices: 1730218--1730308 Score: 74
Period size: 1 Copynumber: 91.0 Consensus size: 1
1730208 TGGCAATTGG
* * * ** * * * **
1730218 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAGAAAAAAACAAAACGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
1730283 AAGAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1730309 GTGAAGATTT
Statistics
Matches: 69, Mismatches: 21, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:1730241 original size:14 final size:13
Alignment explanation
Indices: 1730218--1730308 Score: 101
Period size: 13 Copynumber: 6.8 Consensus size: 13
1730208 TGGCAATTGG
1730218 AAAAAGAAAAAAAC
1 AAAAA-AAAAAAAC
*
1730232 AAAACAAAAAAAAGG
1 AAAA-AAAAAAAA-C
* *
1730247 AAAAAGAAAAAAG
1 AAAAAAAAAAAAC
*
1730260 AAAAAAACAAAAC
1 AAAAAAAAAAAAC
* *
1730273 GAAAAAAAAAAAG
1 AAAAAAAAAAAAC
1730286 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
1730299 AAAAAAAAAA
1 AAAAAAAAAA
1730309 GTGAAGATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
13 42 0.65
14 18 0.28
15 5 0.08
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:1734834 original size:25 final size:25
Alignment explanation
Indices: 1734806--1734854 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1734796 TTTCAGCTTT
1734806 AAGGTGGCAACTATATGTATGAATA
1 AAGGTGGCAACTATATGTATGAATA
* * *
1734831 AAGGTGGCACCTGTATTTATGAAT
1 AAGGTGGCAACTATATGTATGAAT
1734855 TTTCATATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (25 bp):
AAGGTGGCAACTATATGTATGAATA
Found at i:1736344 original size:14 final size:15
Alignment explanation
Indices: 1736325--1736357 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1736315 TTTCTGATCC
1736325 ATTTAATA-ATAATG
1 ATTTAATATATAATG
*
1736339 ATTTAATATATAATT
1 ATTTAATATATAATG
1736354 ATTT
1 ATTT
1736358 GATTACAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTAATATATAATG
Found at i:1737451 original size:33 final size:33
Alignment explanation
Indices: 1737414--1737488 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
1737404 AATTACTTAT
1737414 ATATATATATATTTAAAAACATATAATTTTTAA
1 ATATATATATATTTAAAAACATATAATTTTTAA
* * *
1737447 ATATATGTATGTTTAAAAACATATAGTTTTTAA
1 ATATATATATATTTAAAAACATATAATTTTTAA
1737480 ATATATATA
1 ATATATATA
1737489 AAAGTGAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (33 bp):
ATATATATATATTTAAAAACATATAATTTTTAA
Found at i:1737487 original size:17 final size:16
Alignment explanation
Indices: 1737414--1737488 Score: 69
Period size: 17 Copynumber: 4.6 Consensus size: 16
1737404 AATTACTTAT
*
1737414 ATATATATATATTTAA
1 ATATATATATTTTTAA
* *
1737430 AAACATATAATTTTTAA
1 ATATATAT-ATTTTTAA
* *
1737447 ATATATGTATGTTTAA
1 ATATATATATTTTTAA
* *
1737463 AAACATATAGTTTTTAA
1 ATATATATA-TTTTTAA
1737480 ATATATATA
1 ATATATATA
1737489 AAAGTGAATA
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.43
17 25 0.57
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (16 bp):
ATATATATATTTTTAA
Found at i:1739214 original size:16 final size:16
Alignment explanation
Indices: 1739188--1739220 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1739178 ATAGTTCATA
1739188 ATTTAAAAATTATAATT
1 ATTTAAAAATTA-AATT
1739205 ATTT-AAAATTAAATT
1 ATTTAAAAATTAAATT
1739220 A
1 A
1739221 GAATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTAAAAATTAAATT
Found at i:1740544 original size:2 final size:2
Alignment explanation
Indices: 1740537--1740565 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1740527 ATGTAAACTC
1740537 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 A
1740566 AATAATGATC
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1741784 original size:3 final size:3
Alignment explanation
Indices: 1741776--1741810 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1741766 GGGGTGTACA
1741776 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1741811 AAAAGAATGA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1742664 original size:11 final size:10
Alignment explanation
Indices: 1742640--1742697 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
1742630 ATGGTAATTT
*
1742640 TTATATTTTT
1 TTATATTTTA
1742650 TTATATTTGTA
1 TTATATTT-TA
1742661 TTATA-TTTA
1 TTATATTTTA
1742670 -TATATTTTA
1 TTATATTTTA
*
1742679 TAATATTATTA
1 TTATATT-TTA
*
1742690 TTTTATTT
1 TTATATTT
1742698 AAATTATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
8 4 0.10
9 6 0.15
10 16 0.40
11 14 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (10 bp):
TTATATTTTA
Found at i:1742684 original size:29 final size:29
Alignment explanation
Indices: 1742636--1742710 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
1742626 AGTTATGGTA
* * *
1742636 ATTTTTATATTTTTTTATATT-TGTATTAT
1 ATTTATATATTTTATAATATTAT-TATTAT
*
1742665 ATTTATATATTTTATAATATTATTATTTT
1 ATTTATATATTTTATAATATTATTATTAT
*
1742694 ATTTAAATTATTTTATA
1 ATTTATA-TATTTTATA
1742711 TTTATATAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 29 0.74
30 10 0.26
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (29 bp):
ATTTATATATTTTATAATATTATTATTAT
Found at i:1742698 original size:20 final size:20
Alignment explanation
Indices: 1742660--1742722 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
1742650 TTATATTTGT
*
1742660 ATTATATTTATATAT-TTTATA
1 ATTAT-TTTATATTTATTTA-A
1742681 A-TATTATTAT-TTTATTTAA
1 ATTATT-TTATATTTATTTAA
*
1742700 ATTATTTTATATTTATATAA
1 ATTATTTTATATTTATTTAA
1742720 ATT
1 ATT
1742723 TTAATATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 9 0.25
20 26 0.72
21 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATTTTATATTTATTTAA
Found at i:1742730 original size:20 final size:20
Alignment explanation
Indices: 1742669--1742731 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
1742659 TATTATATTT
*
1742669 ATATATTT-TAT-AATATTA
1 ATATATTTATATAAATTTTA
* *
1742687 TTAT-TTTATTTAAATTATT-
1 ATATATTTATATAAATT-TTA
*
1742706 TTATATTTATATAAATTTTA
1 ATATATTTATATAAATTTTA
1742726 ATATAT
1 ATATAT
1742732 AAATAATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.09
18 5 0.14
19 9 0.26
20 18 0.51
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATATTTATATAAATTTTA
Found at i:1742757 original size:16 final size:16
Alignment explanation
Indices: 1742703--1742757 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
1742693 TATTTAAATT
*
1742703 ATTTTATATTTATATAA
1 ATTTTATA-TTATAAAA
1742720 ATTTTA-ATATATAAATA
1 ATTTTATAT-TATAAA-A
1742737 A-TTTATATTATAAAA
1 ATTTTATATTATAAAA
1742752 ATTTTA
1 ATTTTA
1742758 AAATATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 3 0.09
16 20 0.61
17 10 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTTATATTATAAAA
Found at i:1742764 original size:16 final size:16
Alignment explanation
Indices: 1742713--1742764 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
1742703 ATTTTATATT
* *
1742713 TATATAAATTTTAATA
1 TATAAAAATTTTAAAA
* *
1742729 TATAAATAA-TTTATAT
1 TATAAA-AATTTTAAAA
1742745 TATAAAAATTTTAAAA
1 TATAAAAATTTTAAAA
1742761 TATA
1 TATA
1742765 TATTATATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 2 0.07
16 24 0.86
17 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAAAAATTTTAAAA
Found at i:1742781 original size:34 final size:33
Alignment explanation
Indices: 1742697--1742781 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 33
1742687 TTATTTTATT
* * *
1742697 TAAATTATTTTATATTTATATAAATTTTAATATA
1 TAAATTA-TTTATAATTATAAAAATTTTAAAATA
*
1742731 TAAATAATTTAT-ATTATAAAAATTTTAAAATA
1 TAAATTATTTATAATTATAAAAATTTTAAAATA
*
1742763 TATATTATATTATAATTAT
1 TAAATTAT-TTATAATTAT
1742782 TTAATCTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
32 23 0.53
33 9 0.21
34 11 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TAAATTATTTATAATTATAAAAATTTTAAAATA
Found at i:1743927 original size:13 final size:14
Alignment explanation
Indices: 1743911--1743939 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1743901 TATTAGTATC
1743911 AATTTTAT-TTTAA
1 AATTTTATATTTAA
1743924 AATTTTATATTTAA
1 AATTTTATATTTAA
1743938 AA
1 AA
1743940 AATTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTTATATTTAA
Found at i:1743934 original size:15 final size:16
Alignment explanation
Indices: 1743911--1743946 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1743901 TATTAGTATC
1743911 AATTTTAT-TTT--AA
1 AATTTTATATTTAAAA
1743924 AATTTTATATTTAAAA
1 AATTTTATATTTAAAA
1743940 AATTTTA
1 AATTTTA
1743947 AAAATGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 8 0.40
14 3 0.15
16 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTTATATTTAAAA
Found at i:1744060 original size:16 final size:16
Alignment explanation
Indices: 1744039--1744069 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1744029 ATTTATTTTA
1744039 TATTATATAGTTAAAG
1 TATTATATAGTTAAAG
*
1744055 TATTATATATTTAAA
1 TATTATATAGTTAAA
1744070 TATAAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
TATTATATAGTTAAAG
Found at i:1744139 original size:11 final size:11
Alignment explanation
Indices: 1744125--1744173 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1744115 TGATATAATT
1744125 TTATATTTATA
1 TTATATTTATA
1744136 TTATATTTATA
1 TTATATTTATA
* *
1744147 TTATTTTTCCTA
1 TTATATTT-ATA
*
1744159 TTA-ATTTGTA
1 TTATATTTATA
1744169 TTATA
1 TTATA
1744174 ATTTTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 5 0.16
11 22 0.69
12 5 0.16
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATATTTATA
Done.