Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 9 of 27
Found at i:1180989 original size:15 final size:15
Alignment explanation
Indices: 1180960--1180992 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1180950 AAAGCTCAAA
1180960 ATAAATATACTGTAT
1 ATAAATATACTGTAT
1180975 ATAAACTATAC-GTAT
1 ATAAA-TATACTGTAT
1180990 ATA
1 ATA
1180993 TACGATATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (15 bp):
ATAAATATACTGTAT
Found at i:1184919 original size:1 final size:1
Alignment explanation
Indices: 1184915--1184949 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
1184905 ACCCCCTCCT
* *
1184915 CCCCCCCCCCCACCCACCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1184950 AAAAAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.06, C:0.94, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1187587 original size:6 final size:6
Alignment explanation
Indices: 1187578--1187609 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1187568 TGGTGTTAAC
1187578 AAGATG AAGATG AAGATG AAGATG AAGATG AA
1 AAGATG AAGATG AAGATG AAGATG AAGATG AA
1187610 AGAAGGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.31, T:0.16
Consensus pattern (6 bp):
AAGATG
Found at i:1187987 original size:22 final size:21
Alignment explanation
Indices: 1187940--1187988 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1187930 AAAGTGACTA
* *
1187940 ATTTTTTTAAGTAAAAATTTG
1 ATTTTTTTAAGTAAAAAGTGG
1187961 ATTTTTTTAAGTGAAAAAGTGG
1 ATTTTTTTAAGT-AAAAAGTGG
1187983 -TTTTTT
1 ATTTTTT
1187989 CAAAATAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (21 bp):
ATTTTTTTAAGTAAAAAGTGG
Found at i:1188314 original size:25 final size:25
Alignment explanation
Indices: 1188282--1188329 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1188272 CATTTTTAAC
*
1188282 AAATAATTATT-TTATTTTAATTTTT
1 AAATAATT-TTGTTATTTAAATTTTT
1188307 AAATAATTTTGTTATTTAAATTT
1 AAATAATTTTGTTATTTAAATTT
1188330 ATATTCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
AAATAATTTTGTTATTTAAATTTTT
Found at i:1189633 original size:20 final size:20
Alignment explanation
Indices: 1189586--1189636 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1189576 ATTTTGATTT
*
1189586 TTAAATTTTTAAATGTAAAA
1 TTAAAATTTTAAATGTAAAA
* * * *
1189606 ATATAATTTTAAATTTTAAA
1 TTAAAATTTTAAATGTAAAA
1189626 TTAAAATTTTA
1 TTAAAATTTTA
1189637 GTGTCGAAAG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTAAAATTTTAAATGTAAAA
Found at i:1190336 original size:17 final size:17
Alignment explanation
Indices: 1190294--1190345 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1190284 AAAAAAACTC
1190294 TTTAATTATATATTTATTT
1 TTTAATT-TAT-TTTATTT
*
1190313 TAATAATTTATTTTATTT
1 T-TTAATTTATTTTATTT
*
1190331 TTTAATTTACTTTAT
1 TTTAATTTATTTTAT
1190346 AAAATTTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 12 0.41
18 8 0.28
19 4 0.14
20 5 0.17
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAATTTATTTTATTT
Found at i:1191006 original size:13 final size:14
Alignment explanation
Indices: 1190988--1191016 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1190978 TAAATAAAAA
1190988 TTTTTAAAA-TTTT
1 TTTTTAAAAGTTTT
1191001 TTTTTAAAAGTTTT
1 TTTTTAAAAGTTTT
1191015 TT
1 TT
1191017 AATATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTTAAAAGTTTT
Found at i:1191014 original size:23 final size:24
Alignment explanation
Indices: 1190982--1191030 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1190972 CAATGATAAA
*
1190982 TAAAAA-TTTTTAAAATTTTTTTT
1 TAAAAATTTTTTAAAATTTTATTT
* *
1191005 TAAAAGTTTTTTAATATTTTATTT
1 TAAAAATTTTTTAAAATTTTATTT
1191029 TA
1 TA
1191031 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TAAAAATTTTTTAAAATTTTATTT
Found at i:1191492 original size:19 final size:19
Alignment explanation
Indices: 1191451--1191497 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1191441 AAAGCATTTT
* * *
1191451 TTTTAATTTTGTTTTAACA
1 TTTTAAATTTATTTTAAAA
1191470 -TTTAAATTTATTTTAAAA
1 TTTTAAATTTATTTTAAAA
*
1191488 TTTTATATTT
1 TTTTAAATTT
1191498 TAAAATTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTAAATTTATTTTAAAA
Found at i:1197028 original size:28 final size:28
Alignment explanation
Indices: 1196995--1197063 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
1196985 ACGACATGAT
*
1196995 ATGAATTATATGAAAGCATGTTTAGGAC
1 ATGAATTATATGAAAACATGTTTAGGAC
*
1197023 ATGAATTATACGAAAACATGTTTAGGAC
1 ATGAATTATATGAAAACATGTTTAGGAC
*
1197051 ATGAATTAGATGA
1 ATGAATTATATGA
1197064 CTATTATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.30
Consensus pattern (28 bp):
ATGAATTATATGAAAACATGTTTAGGAC
Found at i:1197388 original size:20 final size:18
Alignment explanation
Indices: 1197355--1197391 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
1197345 ACTTATTTAT
1197355 AAAATAAAAAAATTTAAC
1 AAAATAAAAAAATTTAAC
1197373 AAAATCAAATAAAATTTAA
1 AAAAT-AAA-AAAATTTAA
1197392 TAGTTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATAAAAAAATTTAAC
Found at i:1201942 original size:15 final size:16
Alignment explanation
Indices: 1201895--1201943 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
1201885 GTTATACGAT
1201895 TATAATATAAAATATA
1 TATAATATAAAATATA
*
1201911 -ATTATATAAAATTTATA
1 TATAATATAAAA--TATA
1201928 TATAAT-TAAAATATA
1 TATAATATAAAATATA
1201943 T
1 T
1201944 TGTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 15 0.54
17 9 0.32
18 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATATAAAATATA
Found at i:1202867 original size:19 final size:20
Alignment explanation
Indices: 1202832--1202887 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
1202822 TTTAAATAAT
1202832 ATTAATAAAATATATATTTA
1 ATTAATAAAATATATATTTA
*
1202852 ATTATTAAAA-ATATATTTA
1 ATTAATAAAATATATATTTA
*
1202871 AATAA-AAAATATGATAT
1 ATTAATAAAATAT-ATAT
1202888 GAGTAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 4 0.13
19 14 0.45
20 13 0.42
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTAATAAAATATATATTTA
Found at i:1207854 original size:2 final size:2
Alignment explanation
Indices: 1207849--1207884 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1207839 TGTGTGTGTG
1207849 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1207885 AATGTTCCCT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1209689 original size:17 final size:16
Alignment explanation
Indices: 1209667--1209700 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1209657 TTTCCGATTA
*
1209667 TTTTAATATAATTATAT
1 TTTTAAT-TAAATATAT
1209684 TTTTAATTAAATATAT
1 TTTTAATTAAATATAT
1209700 T
1 T
1209701 CGAGTGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAATTAAATATAT
Found at i:1209802 original size:20 final size:20
Alignment explanation
Indices: 1209747--1209802 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1209737 GTTTTGACTT
* *
1209747 AATATTTTAAATTTATTTAA
1 AATATTTTAAATTTAATAAA
* *
1209767 ATTATTATTTAA-TTAATAAA
1 AATATT-TTAAATTTAATAAA
1209787 AATATTTTAAATTTAA
1 AATATTTTAAATTTAA
1209803 ATATAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 4 0.14
20 20 0.71
21 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AATATTTTAAATTTAATAAA
Found at i:1209824 original size:35 final size:37
Alignment explanation
Indices: 1209761--1209830 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 37
1209751 TTTTAAATTT
1209761 ATTTAAATTATTATTTAATTAATAAAAAT-ATTTTAA
1 ATTTAAATTATTATTTAATTAATAAAAATAATTTTAA
1209797 ATTTAAATATAATTA-TTAA-T-ATAAAAATAATTTT
1 ATTTAAAT-T-ATTATTTAATTAATAAAAATAATTTT
1209831 TAATATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
35 8 0.26
36 14 0.45
37 5 0.16
38 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAAATTATTATTTAATTAATAAAAATAATTTTAA
Found at i:1209826 original size:18 final size:17
Alignment explanation
Indices: 1209782--1209836 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
1209772 TATTTAATTA
1209782 ATAAAAAT-ATTTTAAAT
1 ATAAAAATAATTTT-AAT
* *
1209799 TTAAATATAATTATTAAT
1 ATAAAAATAATT-TTAAT
1209817 ATAAAAATAATTTTTAAT
1 ATAAAAATAA-TTTTAAT
1209835 AT
1 AT
1209837 TATATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 6 0.19
18 21 0.68
19 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAAAAATAATTTTAAT
Found at i:1210155 original size:11 final size:11
Alignment explanation
Indices: 1210141--1210166 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1210131 TTTAAAAATT
1210141 AAATAAATTTA
1 AAATAAATTTA
1210152 AAATAAATTTA
1 AAATAAATTTA
1210163 AAAT
1 AAAT
1210167 TTAAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATAAATTTA
Found at i:1210368 original size:18 final size:19
Alignment explanation
Indices: 1210336--1210387 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1210326 ATAAATATAT
*
1210336 ATAATATATTTATTT-TTAA
1 ATAA-ATATTAATTTATTAA
*
1210355 ATAAATATTAATTTATTTA
1 ATAAATATTAATTTATTAA
*
1210374 ATTAAT-TTAATTTA
1 ATAAATATTAATTTA
1210388 AAAAATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATAAATATTAATTTATTAA
Found at i:1210382 original size:29 final size:31
Alignment explanation
Indices: 1210317--1210383 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
1210307 TTAGATACGG
*
1210317 TTAATATAAATAAATATATATAATATATTTA
1 TTAATTTAAATAAATATATATAATATATTTA
*
1210348 TT--TTTAAAT-AA-ATAT-TAATTTATTTAA
1 TTAATTTAAATAAATATATATAATATATTT-A
1210375 TTAATTTAA
1 TTAATTTAA
1210384 TTTAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
26 9 0.29
27 7 0.23
28 2 0.06
29 11 0.35
31 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAATTTAAATAAATATATATAATATATTTA
Found at i:1211324 original size:31 final size:32
Alignment explanation
Indices: 1211268--1211339 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 32
1211258 GGTAATTTCT
*
1211268 AAATTAAAAAATAACTACAAATTTTAA-AATA
1 AAATTAATAAATAACTACAAATTTTAATAATA
*
1211299 AAATTAATAAA-AA-TACATAATTTTTAATATTA
1 AAATTAATAAATAACTACA-AA-TTTTAATAATA
1211331 AATATTAAT
1 AA-ATTAAT
1211340 TTTATGTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 4 0.11
30 4 0.11
31 16 0.46
32 5 0.14
33 6 0.17
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (32 bp):
AAATTAATAAATAACTACAAATTTTAATAATA
Found at i:1211639 original size:12 final size:12
Alignment explanation
Indices: 1211624--1211649 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1211614 TAGAATTTAT
1211624 TTTTTAAATTAA
1 TTTTTAAATTAA
1211636 TTTTTAAATTAA
1 TTTTTAAATTAA
1211648 TT
1 TT
1211650 CAATGATACT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTAAATTAA
Found at i:1211785 original size:2 final size:2
Alignment explanation
Indices: 1211778--1211809 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1211768 AATCGAATTA
*
1211778 AT AT AT AT AT AT TT 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
1211810 GTGTGTGTGT
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:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1214209 original size:2 final size:2
Alignment explanation
Indices: 1214202--1214237 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1214192 GCAATTATGT
1214202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1214238 GGGTGGAAAT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1214925 original size:33 final size:31
Alignment explanation
Indices: 1214887--1214964 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 31
1214877 ACAAATAATG
* *
1214887 TAAAATATATTTAAAATAGATATAAATAAAATA
1 TAAAATATAATAAAAATAGA-ATAAA-AAAATA
* *
1214920 TAAAATATAATAAAAATATAATAAAACAATA
1 TAAAATATAATAAAAATAGAATAAAAAAATA
1214951 TATAAATATAATAA
1 TA-AAATATAATAA
1214965 GTATACGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.17
32 16 0.40
33 17 0.43
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (31 bp):
TAAAATATAATAAAAATAGAATAAAAAAATA
Found at i:1214943 original size:21 final size:21
Alignment explanation
Indices: 1214879--1214964 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 21
1214869 TTACTATAAC
* *
1214879 AAATAATGT-AAAATATATTTA
1 AAATAATATAAAAATATA-ATA
*
1214900 AAATAGATATAAATAAAAT-ATA
1 AAATA-ATATAAA-AATATAATA
1214922 AAAT-ATAATAAAAATATAATA
1 AAATAAT-ATAAAAATATAATA
* *
1214943 AAACAATATATAAATATAATA
1 AAATAATATAAAAATATAATA
1214964 A
1 A
1214965 GTATACGAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
20 6 0.11
21 30 0.57
22 11 0.21
23 2 0.04
24 4 0.08
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (21 bp):
AAATAATATAAAAATATAATA
Found at i:1214952 original size:13 final size:12
Alignment explanation
Indices: 1214910--1214956 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
1214900 AAATAGATAT
* *
1214910 AAATAAAATATA
1 AAATATAATAAA
1214922 AAATATAAT-AA
1 AAATATAATAAA
1214933 AAATATAATAAA
1 AAATATAATAAA
1214945 ACAATAT-ATAAA
1 A-AATATAATAAA
1214957 TATAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 10 0.32
12 16 0.52
13 5 0.16
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATATAATAAA
Found at i:1237046 original size:13 final size:12
Alignment explanation
Indices: 1237028--1237057 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1237018 ATATATAATA
1237028 TTATTTTTATTAT
1 TTATTTTTATT-T
1237041 TTATTTTTATTT
1 TTATTTTTATTT
1237053 TTATT
1 TTATT
1237058 AAAATGGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTATTTTTATTT
Found at i:1237049 original size:6 final size:6
Alignment explanation
Indices: 1237028--1237057 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1237018 ATATATAATA
1237028 TTATTT TTATTAT TTATTT TTATTT TTATT
1 TTATTT TTATT-T TTATTT TTATTT TTATT
1237058 AAAATGGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:1237251 original size:13 final size:13
Alignment explanation
Indices: 1237229--1237260 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1237219 AATTTGAAAC
1237229 TAAA-TTAGAATG
1 TAAATTTAGAATG
1237241 TAAATTTAGAATG
1 TAAATTTAGAATG
1237254 TAAATTT
1 TAAATTT
1237261 CACTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (13 bp):
TAAATTTAGAATG
Found at i:1246297 original size:25 final size:25
Alignment explanation
Indices: 1246265--1246314 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1246255 GTAAGAGTTA
1246265 AAATCATAGTTTATATAAATCCCTT
1 AAATCATAGTTTATATAAATCCCTT
1246290 AAATCATAGTTTATATAAATCCCTT
1 AAATCATAGTTTATATAAATCCCTT
1246315 GTTGCAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATCATAGTTTATATAAATCCCTT
Found at i:1263338 original size:36 final size:36
Alignment explanation
Indices: 1263291--1263362 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1263281 GGGGAAATGT
*
1263291 AGTATCTTGGAGAAGTAAGAAACAAACTATTGTTGC
1 AGTATCTTGGAGAAGTAAAAAACAAACTATTGTTGC
1263327 AGTATCTTGGAGAAGTAAAAAACAAACTATTGTTGC
1 AGTATCTTGGAGAAGTAAAAAACAAACTATTGTTGC
1263363 CAGGAGCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (36 bp):
AGTATCTTGGAGAAGTAAAAAACAAACTATTGTTGC
Found at i:1269504 original size:29 final size:28
Alignment explanation
Indices: 1269449--1269505 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
1269439 AATATTTTAA
*
1269449 AAAAATTATAATTTTAAATAATTAAAAAT
1 AAAAATCATAATTTTAAATAA-TAAAAAT
*
1269478 AAAAATCATAAATTTTAAATTA-AAAAAT
1 AAAAATCAT-AATTTTAAATAATAAAAAT
1269506 CTGCACACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.24
29 8 0.32
30 11 0.44
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAAATCATAATTTTAAATAATAAAAAT
Found at i:1271588 original size:14 final size:13
Alignment explanation
Indices: 1271547--1271617 Score: 63
Period size: 14 Copynumber: 5.2 Consensus size: 13
1271537 GTTTAATTTT
*
1271547 TAATTTAATCAATA
1 TAATTTAA-AAATA
*
1271561 TAATTTAATTAATA
1 TAATTTAA-AAATA
1271575 TATATTTAAAAATA
1 TA-ATTTAAAAATA
*
1271589 -AATATAAAAATA
1 TAATTTAAAAATA
*
1271601 TAATTTTTAAAATA
1 TAA-TTTAAAAATA
1271615 TAA
1 TAA
1271618 AAAAAATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
12 10 0.20
13 3 0.06
14 30 0.61
15 6 0.12
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATTTAAAAATA
Found at i:1272017 original size:19 final size:19
Alignment explanation
Indices: 1271979--1272036 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
1271969 TCATGTGGTC
*
1271979 AAAAAAATTAAAATACATAAT
1 AAAATAATTAAAAT--ATAAT
1272000 AAAATAATTAAAATATAAT
1 AAAATAATTAAAATATAAT
*
1272019 ATAAT-ATTAAAAATATAA
1 AAAATAATT-AAAATATAA
1272037 ATATATCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.09
19 18 0.53
21 13 0.38
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAATTAAAATATAAT
Found at i:1272127 original size:26 final size:24
Alignment explanation
Indices: 1272078--1272129 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
1272068 ATAAATTAAC
*
1272078 ATTTAAATAAATATATATATAATA
1 ATTTAAATAAATATATATAAAATA
1272102 ATTTAAATATAAT-TATTATTAAAATA
1 ATTTAAATA-AATATA-TA-TAAAATA
1272128 AT
1 AT
1272130 ATTATAAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 11 0.46
25 5 0.21
26 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAAATAAATATATATAAAATA
Found at i:1272349 original size:12 final size:12
Alignment explanation
Indices: 1272328--1272371 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1272318 GATAGCTTTG
*
1272328 AATATCATATAA
1 AATATAATATAA
1272340 AATATAATATGAA
1 AATATAATAT-AA
1272353 AA-ATAATATAA
1 AATATAATATAA
1272364 ATATATAA
1 A-ATATAA
1272372 ATTTATCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 3 0.11
12 17 0.61
13 8 0.29
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (12 bp):
AATATAATATAA
Found at i:1272956 original size:14 final size:15
Alignment explanation
Indices: 1272937--1272965 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1272927 GGACTGACAT
1272937 CTATAATT-TATAAC
1 CTATAATTATATAAC
1272951 CTATAATTATATAAC
1 CTATAATTATATAAC
1272966 ATCTATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (15 bp):
CTATAATTATATAAC
Found at i:1273028 original size:2 final size:2
Alignment explanation
Indices: 1273021--1273047 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1273011 TTCAACGCTC
1273021 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 A
1273048 GTGTCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1273295 original size:11 final size:11
Alignment explanation
Indices: 1273281--1273306 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1273271 TAATAAAATT
1273281 ATAAAATAAAA
1 ATAAAATAAAA
1273292 ATAAAATAAAA
1 ATAAAATAAAA
1273303 ATAA
1 ATAA
1273307 TTATGTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:1275713 original size:3 final size:3
Alignment explanation
Indices: 1275707--1275740 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1275697 TAACGACGAC
1275707 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1275741 TAAAACCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1283032 original size:2 final size:2
Alignment explanation
Indices: 1283025--1283061 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1283015 CATTAAAACC
1283025 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
1283062 CTTTTTCTTT
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:1283245 original size:2 final size:2
Alignment explanation
Indices: 1283238--1283267 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1283228 TACTACTTGC
1283238 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
1283268 TCAAAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1286328 original size:2 final size:2
Alignment explanation
Indices: 1286321--1286345 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1286311 GTAAAACTCA
1286321 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 A
1286346 CATGATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1286709 original size:15 final size:15
Alignment explanation
Indices: 1286689--1286720 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1286679 TTTAATAAGA
1286689 AATATTAATTTAAAT
1 AATATTAATTTAAAT
*
1286704 AATATTATTTTAAAT
1 AATATTAATTTAAAT
1286719 AA
1 AA
1286721 CAAAAAATAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTAATTTAAAT
Found at i:1288682 original size:23 final size:22
Alignment explanation
Indices: 1288656--1288715 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 22
1288646 TAATAAAGAT
*
1288656 AGTTTATAATTTTATCTTACAAA
1 AGTTTATAATTTTATATT-CAAA
*
1288679 AG-TTATTAATTATT-TATTGAAA
1 AGTTTA-TAATT-TTATATTCAAA
*
1288701 AGTTTATTATTTTAT
1 AGTTTATAATTTTAT
1288716 TTGTATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
21 2 0.07
22 13 0.43
23 13 0.43
24 2 0.07
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (22 bp):
AGTTTATAATTTTATATTCAAA
Found at i:1288740 original size:22 final size:25
Alignment explanation
Indices: 1288703--1288772 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 25
1288693 TATTGAAAAG
* *
1288703 TTTATTATTTTATTTGTATAAAA-A
1 TTTATAATATTATTTGTATAAAATA
1288727 -TTATAA-ATTATTTGTGA-AAAATA
1 TTTATAATATTATTTGT-ATAAAATA
* *
1288750 TTTATAATTTTATTTGCATAAAA
1 TTTATAATATTATTTGTATAAAA
1288773 GTGATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
22 12 0.32
23 7 0.19
24 7 0.19
25 11 0.30
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (25 bp):
TTTATAATATTATTTGTATAAAATA
Found at i:1288760 original size:47 final size:46
Alignment explanation
Indices: 1288658--1288772 Score: 126
Period size: 46 Copynumber: 2.5 Consensus size: 46
1288648 ATAAAGATAG
* * * * * *
1288658 TTTATAATTTTATCT-TACAAAAGTTATTAATTATTTATTGAAAAG
1 TTTATAATTTTATTTGTATAAAAATTATAAATTATTTAGTGAAAAA
*
1288703 TTTATTATTTTATTTGTATAAAAATTATAAATTATTT-GTGAAAAATA
1 TTTATAATTTTATTTGTATAAAAATTATAAATTATTTAGTG-AAAA-A
*
1288750 TTTATAATTTTATTTGCATAAAA
1 TTTATAATTTTATTTGTATAAAA
1288773 GTGATAATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
45 15 0.26
46 22 0.38
47 21 0.36
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (46 bp):
TTTATAATTTTATTTGTATAAAAATTATAAATTATTTAGTGAAAAA
Found at i:1289083 original size:20 final size:20
Alignment explanation
Indices: 1289057--1289108 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1289047 ATATCGTAAA
*
1289057 AATTTAATTTTTTAATTTTT
1 AATTTAATTTTTTAAATTTT
* * *
1289077 TATTTAAATTATTAAATTTT
1 AATTTAATTTTTTAAATTTT
1289097 AATTTTAATTTT
1 AA-TTTAATTTT
1289109 AAAAATTAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
AATTTAATTTTTTAAATTTT
Found at i:1289972 original size:24 final size:22
Alignment explanation
Indices: 1289915--1289972 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
1289905 TATATATATG
1289915 TAAATATAAAT-TTTAAAATTA
1 TAAATATAAATATTTAAAATTA
* * *
1289936 TAAATATTTAATATCTTAAATTTT
1 TAAATA-TAAATAT-TTAAAATTA
1289960 TAAATATCAAATA
1 TAAATAT-AAATA
1289973 AATAAGTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 6 0.21
22 4 0.14
23 2 0.07
24 17 0.59
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATATAAATATTTAAAATTA
Found at i:1290516 original size:22 final size:20
Alignment explanation
Indices: 1290482--1290521 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1290472 ATATATTAAT
1290482 ATATTTAATTATTTTAAAATA
1 ATATTTAATTA-TTTAAAATA
*
1290503 ATATTTTATATATTTAAAA
1 ATATTTAAT-TATTTAAAA
1290522 GATTTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTTAATTATTTAAAATA
Found at i:1290818 original size:19 final size:18
Alignment explanation
Indices: 1290794--1290846 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
1290784 ATTTAAAAGT
1290794 TTTAAATAAAAATATTAAA
1 TTTAAATAAAAA-ATTAAA
1290813 -TT---TAAAAAA-TAAA
1 TTTAAATAAAAAATTAAA
1290826 TTTAAATAAAAAAATTAAA
1 TTTAAAT-AAAAAATTAAA
1290845 TT
1 TT
1290847 AATTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
13 4 0.14
14 3 0.11
15 6 0.21
17 1 0.04
18 8 0.29
19 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAAATAAAAAATTAAA
Found at i:1290856 original size:18 final size:18
Alignment explanation
Indices: 1290807--1290858 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
1290797 AAATAAAAAT
*
1290807 ATTAAATTTAAAAAATAA
1 ATTAAATTTAAAAATTAA
**
1290825 ATTTAAATAAAAAAATTAA
1 A-TTAAATTTAAAAATTAA
*
1290844 ATTAATTTTAAAAAT
1 ATTAAATTTAAAAAT
1290859 GAGTCGAAGC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTAAATTTAAAAATTAA
Found at i:1290856 original size:19 final size:17
Alignment explanation
Indices: 1290811--1290858 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1290801 AAAAATATTA
1290811 AATTTAAAAAATAAATTT
1 AATTTAAAAAATAAA-TT
* *
1290829 AAATAAAAAAATTAAATT
1 AATTTAAAAAA-TAAATT
*
1290847 AATTTTAAAAAT
1 AATTTAAAAAAT
1290859 GAGTCGAAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 1 0.04
18 19 0.79
19 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTTAAAAAATAAATT
Found at i:1291000 original size:29 final size:31
Alignment explanation
Indices: 1290968--1291040 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 31
1290958 AAAATATATT
*
1290968 AAATAATTTAAATTTTTA-AACTTAA-TAAA
1 AAATAATTTAAATTTTTACAAATTAACTAAA
* * *
1290997 AAATTA-TTAATTTTTTTACAAATTAACTTAA
1 AAATAATTTAA-ATTTTTACAAATTAACTAAA
1291028 AAATATATTTAAA
1 AAATA-ATTTAAA
1291041 AAATAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
28 4 0.12
29 11 0.33
30 6 0.18
31 7 0.21
32 1 0.03
33 4 0.12
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (31 bp):
AAATAATTTAAATTTTTACAAATTAACTAAA
Found at i:1291055 original size:12 final size:13
Alignment explanation
Indices: 1291026--1291060 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
1291016 AAATTAACTT
*
1291026 AAAAATATATTTA
1 AAAAATATAATTA
1291039 AAAAATA-AATTA
1 AAAAATATAATTA
1291051 AAAAATATAA
1 AAAAATATAA
1291061 AACAAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAAATATAATTA
Found at i:1301968 original size:2 final size:2
Alignment explanation
Indices: 1301961--1301985 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1301951 ATAATGGGAA
1301961 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1301986 TCAATGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1302426 original size:21 final size:22
Alignment explanation
Indices: 1302402--1302445 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1302392 TTTATATTTT
*
1302402 TTTATAATTTTA-ATAATTATA
1 TTTATAATATTATATAATTATA
*
1302423 TTTATAATATTATATATTTATA
1 TTTATAATATTATATAATTATA
1302445 T
1 T
1302446 AAATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTATAATATTATATAATTATA
Found at i:1302632 original size:16 final size:16
Alignment explanation
Indices: 1302613--1302659 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1302603 TTAATATATC
1302613 ATAAAATTATTTTTAT
1 ATAAAATTATTTTTAT
1302629 AT--AA--A-TTTTA-
1 ATAAAATTATTTTTAT
1302639 ATAAAATTATTTTTAT
1 ATAAAATTATTTTTAT
1302655 ATAAA
1 ATAAA
1302660 TTTAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
10 2 0.08
11 5 0.20
12 3 0.12
14 3 0.12
15 5 0.20
16 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAAAATTATTTTTAT
Found at i:1302660 original size:15 final size:15
Alignment explanation
Indices: 1302616--1302661 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 15
1302606 ATATATCATA
1302616 AAATTATTTTTATAT
1 AAATTATTTTTATAT
*
1302631 -AA--ATTTTAATA-
1 AAATTATTTTTATAT
1302642 AAATTATTTTTATAT
1 AAATTATTTTTATAT
1302657 AAATT
1 AAATT
1302662 TAATAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
12 10 0.40
14 10 0.40
15 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AAATTATTTTTATAT
Found at i:1302663 original size:25 final size:26
Alignment explanation
Indices: 1302613--1302681 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
1302603 TTAATATATC
1302613 ATAAAATTATTTTTATATAAATTTTA
1 ATAAAATTATTTTTATATAAATTTTA
1302639 ATAAAATTATTTTTATATAAA-TTTA
1 ATAAAATTATTTTTATATAAATTTTA
*
1302664 AT-AAATTATATATTATAT
1 ATAAAATTAT-TTTTATAT
1302682 TATATTTATA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
24 7 0.17
25 13 0.32
26 21 0.51
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATAAAATTATTTTTATATAAATTTTA
Found at i:1302682 original size:5 final size:5
Alignment explanation
Indices: 1302672--1302727 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
1302662 TAATAAATTA
* * * * *
1302672 TATAT TATAT TATATT TATAT TAAAT TTTAT TTTAT TTTA- TATTT TATAT
1 TATAT TATAT TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1302722 TATAT T
1 TATAT T
1302728 TTAAATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
4 2 0.05
5 36 0.84
6 5 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATAT
Found at i:1302696 original size:28 final size:28
Alignment explanation
Indices: 1302616--1302723 Score: 95
Period size: 26 Copynumber: 4.0 Consensus size: 28
1302606 ATATATCATA
* *
1302616 AAATTAT-TTTTATA-TAAATTT-TAATA
1 AAATTATATTTTATATTATATTTAT-ATT
*
1302642 AAATTAT-TTTTATA-TAAATTTA-A-T
1 AAATTATATTTTATATTATATTTATATT
*
1302666 AAATTATATATTATATTATATTTATATT
1 AAATTATATTTTATATTATATTTATATT
* *
1302694 AAATTTTATTTTATTTTATATTTTATATT
1 AAATTATATTTTATATTATA-TTTATATT
1302723 A
1 A
1302724 TATTTTAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.10
25 7 0.10
26 28 0.40
27 1 0.01
28 18 0.26
29 9 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
AAATTATATTTTATATTATATTTATATT
Found at i:1302728 original size:12 final size:12
Alignment explanation
Indices: 1302668--1302745 Score: 68
Period size: 12 Copynumber: 6.2 Consensus size: 12
1302658 AATTTAATAA
*
1302668 ATTATATATTAT
1 ATTATATTTTAT
1302680 ATTATATTTATATT
1 ATTATATTT-TA-T
*
1302694 AAATTTTATTTTAT
1 --ATTATATTTTAT
*
1302708 TTTATATTTTAT
1 ATTATATTTTAT
*
1302720 ATTATATTTTAA
1 ATTATATTTTAT
*
1302732 ATT-TTTTTTAT
1 ATTATATTTTAT
1302743 ATT
1 ATT
1302746 GTATAGTCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
11 9 0.17
12 31 0.57
13 2 0.04
14 2 0.04
15 2 0.04
16 8 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTATATTTTAT
Found at i:1303112 original size:22 final size:22
Alignment explanation
Indices: 1303084--1303156 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
1303074 AATTCAAACG
*
1303084 TTTTTAATTTATTTATATTATA
1 TTTTTAATTTATTTATAATATA
1303106 TTTTTAAAATTT-TTTA-AATATA
1 TTTTT--AATTTATTTATAATATA
* *
1303128 TTTTTAATTTAATTTTTAATAAA
1 TTTTTAATTT-ATTTATAATATA
1303151 TTTTTA
1 TTTTTA
1303157 TTAATATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
20 5 0.12
22 18 0.42
23 15 0.35
24 5 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTTAATTTATTTATAATATA
Found at i:1303133 original size:12 final size:12
Alignment explanation
Indices: 1303102--1303172 Score: 60
Period size: 12 Copynumber: 6.0 Consensus size: 12
1303092 TTATTTATAT
1303102 TATATTTTTAAA
1 TATATTTTTAAA
1303114 -AT-TTTTTAAA
1 TATATTTTTAAA
1303124 TATATTTTT-AA
1 TATATTTTTAAA
*
1303135 TTTAATTTTT-AA
1 TAT-ATTTTTAAA
*
1303147 TAAATTTTTATTAA
1 TATATTTTTA--AA
*
1303161 TATTTTTTTAAA
1 TATATTTTTAAA
1303173 ATTATCCAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
10 8 0.17
11 14 0.29
12 16 0.33
14 10 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTTTTAAA
Found at i:1303143 original size:23 final size:22
Alignment explanation
Indices: 1303084--1303156 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
1303074 AATTCAAACG
*
1303084 TTTTTAATTTA-TTTATATTATA
1 TTTTTAATTTATTTTA-AATATA
*
1303106 TTTTTAAAATT-TTTTAAATATA
1 TTTTT-AATTTATTTTAAATATA
* *
1303128 TTTTTAATTTAATTTTTAATAAA
1 TTTTTAATTT-ATTTTAAATATA
1303151 TTTTTA
1 TTTTTA
1303157 TTAATATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 4 0.10
22 15 0.36
23 23 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTTAATTTATTTTAAATATA
Found at i:1303165 original size:23 final size:24
Alignment explanation
Indices: 1303116--1303167 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1303106 TTTTTAAAAT
* *
1303116 TTTTTAAATATATTTTTAATTTAA
1 TTTTTAAATAAATTTTTAATTAAA
1303140 TTTTT-AATAAATTTTT-ATTAATA
1 TTTTTAAATAAATTTTTAATTAA-A
1303163 TTTTT
1 TTTTT
1303168 TTAAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 4 0.16
23 16 0.64
24 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTTAAATAAATTTTTAATTAAA
Found at i:1303276 original size:12 final size:11
Alignment explanation
Indices: 1303253--1303299 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
1303243 CAATTAATAA
*
1303253 AATAAAATTAT
1 AATAATATTAT
1303264 AATAAGTATTAT
1 AATAA-TATTAT
1303276 AA-AATATATAT
1 AATAATAT-TAT
*
1303287 AATTATATTAT
1 AATAATATTAT
1303298 AA
1 AA
1303300 AAATTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 3 0.10
11 17 0.55
12 11 0.35
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AATAATATTAT
Found at i:1303409 original size:26 final size:27
Alignment explanation
Indices: 1303373--1303424 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
1303363 CAAAAATTAA
*
1303373 TTTATTTTTTAAATAAAT-TTTATTTT
1 TTTACTTTTTAAATAAATATTTATTTT
*
1303399 TTTACTTTTTAAATTAATATTTATTT
1 TTTACTTTTTAAATAAATATTTATTT
1303425 AACTTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTACTTTTTAAATAAATATTTATTTT
Found at i:1303462 original size:18 final size:20
Alignment explanation
Indices: 1303428--1303466 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
1303418 TTTATTTAAC
1303428 TTTTTAAAATATTAAATAAA
1 TTTTTAAAATATTAAATAAA
1303448 TTTTT-AAAT-TTAAATAAA
1 TTTTTAAAATATTAAATAAA
1303466 T
1 T
1303467 AACTGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 4 0.21
20 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTTAAAATATTAAATAAA
Found at i:1304512 original size:2 final size:2
Alignment explanation
Indices: 1304505--1304534 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1304495 TTTTAGAAGA
*
1304505 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1304535 TCAATGTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1305148 original size:27 final size:24
Alignment explanation
Indices: 1305118--1305183 Score: 60
Period size: 27 Copynumber: 2.6 Consensus size: 24
1305108 ATTAATATAA
1305118 AAATAATAAAAATAAATAAATAAATTT
1 AAATAATAAAAATAAAT--AT-AATTT
** *
1305145 AAATTTTAAATATAAATATAATTT
1 AAATAATAAAAATAAATATAATTT
*
1305169 ATATAATTAAAAATA
1 AAATAA-TAAAAATA
1305184 TCATATTAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
24 8 0.26
25 9 0.29
27 14 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAATAAAAATAAATATAATTT
Found at i:1305229 original size:19 final size:18
Alignment explanation
Indices: 1305186--1305220 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1305176 TAAAAATATC
1305186 ATATTA-ATTATATTTAA
1 ATATTATATTATATTTAA
1305203 ATATTTATATTATATTTA
1 ATA-TTATATTATATTTA
1305221 TTATATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 3 0.19
19 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTATATTATATTTAA
Found at i:1306416 original size:8 final size:8
Alignment explanation
Indices: 1306334--1306417 Score: 59
Period size: 8 Copynumber: 10.9 Consensus size: 8
1306324 ATTTCAAGTC
1306334 ATATATTT
1 ATATATTT
* *
1306342 ATTTATAT
1 ATATATTT
*
1306350 ATATATAT
1 ATATATTT
*
1306358 ATATATGT
1 ATATATTT
1306366 ATAT-TTT
1 ATATATTT
* *
1306373 AATAAATTA
1 -ATATATTT
1306382 ATA-ATTT
1 ATATATTT
*
1306389 ATAT-TAT
1 ATATATTT
1306396 ATAT-TTT
1 ATATATTT
*
1306403 AAATATTT
1 ATATATTT
1306411 ATATATT
1 ATATATT
1306418 AAAATTATAT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
7 19 0.32
8 39 0.65
9 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (8 bp):
ATATATTT
Found at i:1306425 original size:30 final size:30
Alignment explanation
Indices: 1306365--1306427 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1306355 TATATATATG
* *
1306365 TATATTTTAATAAATTAATAATTTATATTA
1 TATATTTTAATAAATTAATAATTAAAATTA
* *
1306395 TATATTTTAA-ATATTTATATATTAAAATTA
1 TATATTTTAATAAATTAATA-ATTAAAATTA
1306425 TAT
1 TAT
1306428 TATAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TATATTTTAATAAATTAATAATTAAAATTA
Found at i:1306426 original size:35 final size:35
Alignment explanation
Indices: 1306378--1306476 Score: 98
Period size: 33 Copynumber: 2.9 Consensus size: 35
1306368 ATTTTAATAA
1306378 ATTAATAATTTATATTATATATTTTAAATATTTATAT
1 ATTAATAATTTATATTATA-A-TTTAAATATTTATAT
* *
1306415 ATTAA-AA-TTATATTATAATTTAATTATTTTTAT
1 ATTAATAATTTATATTATAATTTAAATATTTATAT
* * *
1306448 A-T-ATTATTTATATAATAATATTTAATATT
1 ATTAATAATTTATATTATAAT-TTAAATATT
1306477 AAAAAGTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
31 1 0.02
32 2 0.04
33 25 0.47
34 8 0.15
35 10 0.19
36 2 0.04
37 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (35 bp):
ATTAATAATTTATATTATAATTTAAATATTTATAT
Found at i:1306459 original size:33 final size:32
Alignment explanation
Indices: 1306383--1306476 Score: 91
Period size: 35 Copynumber: 2.8 Consensus size: 32
1306373 AATAAATTAA
1306383 TAATTTATATTATATATTTTAAATATTTATATAT
1 TAATTTATATTATA-A-TTTAAATATTTATATAT
* *
1306417 TAAAATTATATTATAATTTAATTATTTTTATATAT
1 T-AATTTATATTATAATTTAA--ATATTTATATAT
* *
1306452 T-ATTTATATAATAATATTTAATATT
1 TAATTTATATTATAAT-TTAAATATT
1306477 AAAAAGTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
32 4 0.08
33 17 0.34
34 5 0.10
35 24 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TAATTTATATTATAATTTAAATATTTATATAT
Found at i:1320884 original size:16 final size:17
Alignment explanation
Indices: 1320858--1320889 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1320848 GTCGAGGTTG
1320858 AAATATTTTTATTTTTA
1 AAATATTTTTATTTTTA
1320875 AAAT-TTTTTATTTTT
1 AAATATTTTTATTTTT
1320890 TTATAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
AAATATTTTTATTTTTA
Found at i:1320901 original size:19 final size:18
Alignment explanation
Indices: 1320869--1320904 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1320859 AATATTTTTA
*
1320869 TTTTTAAAATTTTTTATT
1 TTTTTAAAAGTTTTTATT
1320887 TTTTTATAAAGTTTTTAT
1 TTTTTA-AAAGTTTTTAT
1320905 AATAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTAAAAGTTTTTATT
Found at i:1320998 original size:19 final size:18
Alignment explanation
Indices: 1320963--1320998 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1320953 TTTGTTATTT
1320963 ATATAAATATAAAATATA
1 ATATAAATATAAAATATA
*
1320981 ATATAAATTATTAAATAT
1 ATATAAA-TATAAAATAT
1320999 GTAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAATATAAAATATA
Found at i:1321773 original size:23 final size:25
Alignment explanation
Indices: 1321725--1321777 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
1321715 ATGAAGGTAT
*
1321725 AAAATAAAGAGAAAATAAAATGATA
1 AAAATAAAGAGAAAATAAAATAATA
1321750 AAAATAAA-A-AAAATAAACA-AATA
1 AAAATAAAGAGAAAATAAA-ATAATA
1321773 AAAAT
1 AAAAT
1321778 TATATATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 16 0.62
24 2 0.08
25 8 0.31
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (25 bp):
AAAATAAAGAGAAAATAAAATAATA
Found at i:1323058 original size:14 final size:15
Alignment explanation
Indices: 1323034--1323070 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1323024 GATAAAATAA
1323034 AAAATTATAAATATT
1 AAAATTATAAATATT
1323049 AAAATT-TAAATATT
1 AAAATTATAAATATT
*
1323063 AAACTTAT
1 AAAATTAT
1323071 TCGATATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:1324995 original size:22 final size:21
Alignment explanation
Indices: 1324965--1325047 Score: 75
Period size: 22 Copynumber: 4.0 Consensus size: 21
1324955 TTGATGTATA
*
1324965 TATATATATATATATATATTT
1 TATAAATATATATATATATTT
*
1324986 GTATAAATATAAATATATAATATT
1 -TATAAATATATATATAT-AT-TT
1325010 T-TAAATATATA-A-ATATTT
1 TATAAATATATATATATATTT
* *
1325028 TAAAAATAAAT-TATATATTT
1 TATAAATATATATATATATTT
1325048 AAAATTAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
18 3 0.06
19 10 0.20
20 8 0.16
21 1 0.02
22 24 0.47
23 3 0.06
24 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (21 bp):
TATAAATATATATATATATTT
Found at i:1325019 original size:18 final size:18
Alignment explanation
Indices: 1324996--1325051 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
1324986 GTATAAATAT
1324996 AAATATATAATATTTTAA
1 AAATATATAATATTTTAA
*
1325014 ATATATA-AATATTTTAA
1 AAATATATAATATTTTAA
* *
1325031 AAATAAATTATATATTTAA
1 AAATATATAATAT-TTTAA
1325050 AA
1 AA
1325052 TTAATTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
17 15 0.47
18 10 0.31
19 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATATAATATTTTAA
Found at i:1325020 original size:2 final size:2
Alignment explanation
Indices: 1324961--1325008 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
1324951 AGACTTGATG
* * * *
1324961 TA TA TA TA TA TA TA TA TA TA TA TT TG TA TA AA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1325003 TA -A TA T
1 TA TA TA T
1325009 TTTAAATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1325052 original size:18 final size:18
Alignment explanation
Indices: 1324989--1325059 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 18
1324979 TATATTTGTA
1324989 TAAATATAAATATATAATATT
1 TAAA-ATAAAT-TAT-ATATT
* * *
1325010 TTAAATATA-TAAATATTT
1 TAAAATAAATTATATA-TT
1325028 TAAAAATAAATTATATATT
1 T-AAAATAAATTATATATT
*
1325047 TAAAATTAATTAT
1 TAAAATAAATTAT
1325060 TTATATTTGA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
17 3 0.08
18 16 0.40
19 9 0.22
20 9 0.22
21 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAATAAATTATATATT
Found at i:1325972 original size:17 final size:17
Alignment explanation
Indices: 1325954--1325987 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1325944 TTTAAAGGAA
1325954 TTAATAAATTTAAAAAAT
1 TTAA-AAATTTAAAAAAT
*
1325972 TTAAGAATTTAAAAAA
1 TTAAAAATTTAAAAAA
1325988 CATAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TTAAAAATTTAAAAAAT
Found at i:1326607 original size:21 final size:22
Alignment explanation
Indices: 1326569--1326610 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1326559 TTTAATTTTA
* *
1326569 ATCAAAAATGCATTTAATAAAC
1 ATCAAAAATGAATATAATAAAC
1326591 ATCAAAAAT-AATATAATAAA
1 ATCAAAAATGAATATAATAAA
1326611 AATAATACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (22 bp):
ATCAAAAATGAATATAATAAAC
Found at i:1332983 original size:27 final size:27
Alignment explanation
Indices: 1332934--1333008 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 27
1332924 TTTATTAAAA
*
1332934 TATATATAATAAATAGTTAAAAT-ATATT
1 TATAT-TAA-AAATAATTAAAATAATATT
1332962 TATATTAAATAATAATTAAAATAATATT
1 TATATTAAA-AATAATTAAAATAATATT
1332990 TATATTAAAAATAAATTAA
1 TATATTAAAAAT-AATTAA
1333009 TAAAAAAAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
26 1 0.02
27 17 0.40
28 25 0.58
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
TATATTAAAAATAATTAAAATAATATT
Found at i:1333808 original size:40 final size:41
Alignment explanation
Indices: 1333764--1333851 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 41
1333754 TTAAAATATT
* *
1333764 ATATTTACTATTTATA-TGATTTATAGA-AAAAA-ATTGTTTA
1 ATATTTACTATTTAAATTGATTT-TA-ATAAAAATATTATTTA
* *
1333804 ATATTTATTATTTAAATTTATTTTAATAAAAATATTATTTA
1 ATATTTACTATTTAAATTGATTTTAATAAAAATATTATTTA
1333845 ATATTTA
1 ATATTTA
1333852 AATTTATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
39 1 0.02
40 21 0.51
41 19 0.46
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (41 bp):
ATATTTACTATTTAAATTGATTTTAATAAAAATATTATTTA
Found at i:1333847 original size:41 final size:39
Alignment explanation
Indices: 1333783--1333877 Score: 111
Period size: 41 Copynumber: 2.4 Consensus size: 39
1333773 ATTTATATGA
* * * *
1333783 TTTATAGAAAAAAATTGTTTAATATTTATTATTTAAATTTAT
1 TTTATATAAAAATATTATTTAATATTTA-AATTT--ATTTAT
1333825 TTTA-ATAAAAATATTATTTAATATTTAAATTTATTTAT
1 TTTATATAAAAATATTATTTAATATTTAAATTTATTTAT
1333863 TTTATATAAATAATA
1 TTTATATAAA-AATA
1333878 AAATTAATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
38 10 0.21
39 5 0.11
40 8 0.17
41 20 0.43
42 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (39 bp):
TTTATATAAAAATATTATTTAATATTTAAATTTATTTAT
Found at i:1333888 original size:21 final size:21
Alignment explanation
Indices: 1333864--1333920 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1333854 TTTATTTATT
1333864 TTATATAAATAATAAAATTAA
1 TTATATAAATAATAAAATTAA
1333885 TTAT-TATAATAATAAAATTAA
1 TTATATA-AATAATAAAATTAA
*
1333906 --A-ATAAATGATAAAAT
1 TTATATAAATAATAAAAT
1333921 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 10 0.30
19 3 0.09
20 2 0.06
21 18 0.55
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TTATATAAATAATAAAATTAA
Found at i:1333951 original size:33 final size:30
Alignment explanation
Indices: 1333904--1333993 Score: 90
Period size: 33 Copynumber: 2.8 Consensus size: 30
1333894 TAATAAAATT
* *
1333904 AAAATAAATGATAAAATATTTTTTAAATGTAAA
1 AAAAT-AATAATAAAATATTTTAT-AATG-AAA
**
1333937 AAAAGTAATAATAAAATAAATTATAATGAAA
1 AAAA-TAATAATAAAATATTTTATAATGAAA
1333968 AAAATAATAATTAAAATATTTATATA
1 AAAATAATAA-TAAAATATTT-TATA
1333994 TAATAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
30 6 0.12
31 15 0.31
32 8 0.17
33 18 0.38
34 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAATAATAATAAAATATTTTATAATGAAA
Found at i:1333962 original size:15 final size:15
Alignment explanation
Indices: 1333933--1333985 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
1333923 TTTTTAAATG
1333933 TAAAA-AAAGTAATAA
1 TAAAATAAA-TAATAA
*
1333948 TAAAATAAATTATAA
1 TAAAATAAATAATAA
1333963 TGAAAA-AAATAATAA
1 T-AAAATAAATAATAA
1333978 TTAAAATA
1 -TAAAATA
1333986 TTTATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 23 0.72
16 9 0.28
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (15 bp):
TAAAATAAATAATAA
Found at i:1334020 original size:25 final size:25
Alignment explanation
Indices: 1333973--1334044 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
1333963 TGAAAAAAAT
* *
1333973 AATAATTAAAATATTTATATATAATA
1 AATAATTAAAA-ATATATTTATAATA
*
1333999 AATAATTAAAAATATATTTATATTA
1 AATAATTAAAAATATATTTATAATA
*
1334024 AATAA-TAAAATTATATTTATA
1 AATAATTAAAAATATATTTATA
1334045 TTAGAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.36
25 16 0.38
26 11 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATAATTAAAAATATATTTATAATA
Found at i:1334405 original size:19 final size:20
Alignment explanation
Indices: 1334382--1334431 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1334372 ATTATAATTT
1334382 AATTAATAAAATATAT-AAA
1 AATTAATAAAATATATAAAA
* * * *
1334401 TATTAATATAATTTTTAAAA
1 AATTAATAAAATATATAAAA
1334421 AATTAATAAAA
1 AATTAATAAAA
1334432 ATTTAATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTAATAAAATATATAAAA
Found at i:1334436 original size:19 final size:19
Alignment explanation
Indices: 1334382--1334437 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
1334372 ATTATAATTT
*
1334382 AATTAAT-AAAATATATAAA
1 AATTAATAAAAATTTA-AAA
* **
1334401 TATTAATATAATTTTTAAAA
1 AATTAATA-AAAATTTAAAA
1334421 AATTAATAAAAATTTAA
1 AATTAATAAAAATTTAA
1334438 TTATTTAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 13 0.46
20 10 0.36
21 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTAATAAAAATTTAAAA
Found at i:1334493 original size:16 final size:16
Alignment explanation
Indices: 1334472--1334502 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1334462 AATCTTAATT
1334472 TAATTTAAAATTTAAA
1 TAATTTAAAATTTAAA
*
1334488 TAATTTTAAATTTAA
1 TAATTTAAAATTTAA
1334503 GATACGATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTTAAAATTTAAA
Found at i:1334929 original size:21 final size:19
Alignment explanation
Indices: 1334892--1334943 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1334882 TATATAAAGA
* *
1334892 AATTAATATTTATTTTTTTT
1 AATTTATATTTA-ATTTTTT
1334912 AATTTATAGTTTAATTTTTT
1 AATTTATA-TTTAATTTTTT
1334932 AATTTTATATTT
1 AA-TTTATATTT
1334944 TTAGGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
AATTTATATTTAATTTTTT
Found at i:1335281 original size:24 final size:24
Alignment explanation
Indices: 1335254--1335324 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
1335244 ATAATTTCAA
1335254 TAATAATTAATATTTTAATAAAAT
1 TAATAATTAATATTTTAATAAAAT
*
1335278 TAATTATTAA-ATTTAATAATAAAAT
1 TAATAATTAATATTT--TAATAAAAT
* * *
1335303 T-ATAATTATTTTTTTTATAAAA
1 TAATAATTAATATTTTAATAAAA
1335325 GTTTAAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 11 0.28
24 15 0.38
25 13 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATAATTAATATTTTAATAAAAT
Found at i:1335285 original size:18 final size:18
Alignment explanation
Indices: 1335247--1335281 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1335237 TATATTTATA
1335247 ATTTCAATAATAATTAAT
1 ATTTCAATAATAATTAAT
*
1335265 ATTTTAATAA-AATTAAT
1 ATTTCAATAATAATTAAT
1335282 TATTAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTCAATAATAATTAAT
Found at i:1335452 original size:28 final size:26
Alignment explanation
Indices: 1335421--1335480 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 26
1335411 AATATTGATG
1335421 ATAATTAAATTAAATAAATATAAATAAT
1 ATAATTAAATT--ATAAATATAAATAAT
*
1335449 ATAA--AAATTATAAATATATATAAT
1 ATAATTAAATTATAAATATAAATAAT
1335473 -TAAATTAA
1 AT-AATTAA
1335481 TTTTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
23 1 0.04
24 16 0.57
26 7 0.25
28 4 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATAATTAAATTATAAATATAAATAAT
Found at i:1341447 original size:1 final size:1
Alignment explanation
Indices: 1341441--1341474 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
1341431 AAAATGTAAG
1341441 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1341475 CCTTTTCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1343217 original size:21 final size:22
Alignment explanation
Indices: 1343186--1343227 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
1343176 GGAAATATGC
1343186 AAAAATGGAAAAAAATAAAAGT
1 AAAAATGGAAAAAAATAAAAGT
1343208 AAAAAT-GAAAAAAATAAAAG
1 AAAAATGGAAAAAAATAAAAG
1343228 AGTTTCTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (22 bp):
AAAAATGGAAAAAAATAAAAGT
Found at i:1343555 original size:20 final size:20
Alignment explanation
Indices: 1343530--1343570 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1343520 GATTCACATT
*
1343530 TGTTTGTAGCTTTGTGGTTG
1 TGTTTGTAGCTTTCTGGTTG
1343550 TGTTTGTAGCTTTCTGGTTG
1 TGTTTGTAGCTTTCTGGTTG
1343570 T
1 T
1343571 CTGTTAGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.07, G:0.32, T:0.56
Consensus pattern (20 bp):
TGTTTGTAGCTTTCTGGTTG
Found at i:1345406 original size:24 final size:24
Alignment explanation
Indices: 1345371--1345418 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1345361 TAAGTGTAAT
*
1345371 TGTGCTGCCATGACTGCTTCTTCC
1 TGTGCTGACATGACTGCTTCTTCC
*
1345395 TGTGCTGACATGACTGTTTCTTCC
1 TGTGCTGACATGACTGCTTCTTCC
1345419 AGATGAGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.10, C:0.29, G:0.21, T:0.40
Consensus pattern (24 bp):
TGTGCTGACATGACTGCTTCTTCC
Found at i:1347310 original size:54 final size:54
Alignment explanation
Indices: 1347246--1347354 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
1347236 AATAGTGTTG
1347246 AAGTTGGATTTAAAGAATTTCAATTTGCTGGTAGCAATTGGATCCACTTTATAT
1 AAGTTGGATTTAAAGAATTTCAATTTGCTGGTAGCAATTGGATCCACTTTATAT
*
1347300 AAGTTGGATTTAAAGAATTTCAATTTGCTGGTAGCAATTGGATCCGCTTTATAT
1 AAGTTGGATTTAAAGAATTTCAATTTGCTGGTAGCAATTGGATCCACTTTATAT
1347354 A
1 A
1347355 CCCTGGTATT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (54 bp):
AAGTTGGATTTAAAGAATTTCAATTTGCTGGTAGCAATTGGATCCACTTTATAT
Found at i:1351458 original size:2 final size:2
Alignment explanation
Indices: 1351451--1351486 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1351441 TTGATATGTT
1351451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1351487 GATAGAGAGA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1351495 original size:2 final size:2
Alignment explanation
Indices: 1351490--1351529 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1351480 ATATATAGAT
1351490 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1351530 TGTTTATGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1351941 original size:3 final size:3
Alignment explanation
Indices: 1351933--1351965 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1351923 GCCAACCAAA
1351933 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1351966 GGAACTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1356070 original size:150 final size:150
Alignment explanation
Indices: 1355795--1356162 Score: 408
Period size: 150 Copynumber: 2.5 Consensus size: 150
1355785 GAATTCTAAC
* * * * *
1355795 TTCTAAGGAGCAAAAAC--CAGATAAAGTTCATCACATCATTCACCCAAAATTGGGAAA-ATATC
1 TTCTAAGCAGCAAAAACTGCA-TTAAA-TTCATCACATCATTCACCAAAAATTTGGAAACAAATC
* ** * * * *
1355857 ATACATAGTGAAAGAATTTTAGGGTTTTCTTAATAAATAGAACATGAACAATATAAAAACAACTA
64 ATACATAGTGAAAGAACTGCAGGGTTGTCTTAATAAACAAAACATGAACAACATAAAAACAACTA
*
1355922 -GTTAGCCGACACTGATGACATG
129 CG-TAGCCGACACTGATGACATA
* *
1355944 TTCTAAGCAGCAAAAACTGCATTAAATTCATCATATCGTTCACCAAAAATTTGGAAACAAATCAT
1 TTCTAAGCAGCAAAAACTGCATTAAATTCATCACATCATTCACCAAAAATTTGGAAACAAATCAT
* * * *
1356009 ACATAGT-ATAAGAACTGCGGGGTTGTCTTAATAAACAAAATATGAACCACATAAAAGCAACTAC
66 ACATAGTGA-AAGAACTGCAGGGTTGTCTTAATAAACAAAACATGAACAACATAAAAACAACTAC
* * **
1356073 GTAGCTGATACTGATGATGTA
130 GTAGCCGACACTGATGACATA
* * *
1356094 TTCTAAGCGGCAAAAACTAG-ATAAAATTCATCACATCATTCACCAATAA-TTGGAAACAAATCA
1 TTCTAAGCAGCAAAAACT-GCATTAAATTCATCACATCATTCACCAAAAATTTGGAAACAAATCA
1356157 TACATA
65 TACATA
1356163 TTACATAGTG
Statistics
Matches: 185, Mismatches: 28, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
149 64 0.35
150 117 0.63
151 4 0.02
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (150 bp):
TTCTAAGCAGCAAAAACTGCATTAAATTCATCACATCATTCACCAAAAATTTGGAAACAAATCAT
ACATAGTGAAAGAACTGCAGGGTTGTCTTAATAAACAAAACATGAACAACATAAAAACAACTACG
TAGCCGACACTGATGACATA
Found at i:1362521 original size:31 final size:32
Alignment explanation
Indices: 1362462--1362529 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
1362452 ACTAATAAAA
* * *
1362462 TAAAATTAAAAAAATAACTAATACAAAATTTT
1 TAAAAATAAAAAAATAACTAAAACAAAATTAT
*
1362494 TAAAAATAAAAAAATAAC-AAAATAAAATTAT
1 TAAAAATAAAAAAATAACTAAAACAAAATTAT
1362525 TAAAA
1 TAAAA
1362530 GGAAAAGGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.26
Consensus pattern (32 bp):
TAAAAATAAAAAAATAACTAAAACAAAATTAT
Found at i:1362963 original size:27 final size:29
Alignment explanation
Indices: 1362932--1362985 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
1362922 TTACTCATGC
*
1362932 ATTTATTTTATTA-AT-TTTAAAATATAT
1 ATTTATATTATTATATATTTAAAATATAT
*
1362959 ATTTATATTATTATATATTTTAAATAT
1 ATTTATATTATTATATATTTAAAATAT
1362986 CTTACGTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 2 0.09
29 9 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
ATTTATATTATTATATATTTAAAATATAT
Found at i:1364608 original size:41 final size:44
Alignment explanation
Indices: 1364545--1364635 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 44
1364535 AGCTCTATTG
*
1364545 ATATTTAAAATTTGATAGATAT-ATTTTATTATAAT-ATAA-TT
1 ATATTTAAAATTTGATAGATATAATTTTAATATAATAATAATTT
* *
1364586 ATATTTAAAATATT-ATATATATAAATTTTAATATATTAATAATTT
1 ATATTTAAAAT-TTGATAGATAT-AATTTTAATATAATAATAATTT
1364631 ATATT
1 ATATT
1364636 ATATGAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 18 0.43
42 2 0.05
43 11 0.26
44 4 0.10
45 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (44 bp):
ATATTTAAAATTTGATAGATATAATTTTAATATAATAATAATTT
Found at i:1364657 original size:30 final size:29
Alignment explanation
Indices: 1364585--1364662 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 29
1364575 ATAATATAAT
*
1364585 TATATTTAA-AATATTATATATATAAATTT
1 TATATTTAATAAT-TTATATATATAAATTA
*
1364614 TAATATATTAATAATTTATATTATATGAATTA
1 T-ATAT-TTAATAATTTATA-TATATAAATTA
1364646 TATATTTAATAATTTAT
1 TATATTTAATAATTTAT
1364663 TTTTATTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
29 1 0.02
30 16 0.37
31 13 0.30
32 13 0.30
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
TATATTTAATAATTTATATATATAAATTA
Found at i:1364662 original size:16 final size:16
Alignment explanation
Indices: 1364585--1364662 Score: 60
Period size: 16 Copynumber: 5.1 Consensus size: 16
1364575 ATAATATAAT
1364585 TATATTTAA-AATATTA
1 TATATTTAATAAT-TTA
* *
1364601 TATATATAA-ATTTTA
1 TATATTTAATAATTTA
1364616 -ATATATTAATAATTTA
1 TATAT-TTAATAATTTA
*
1364632 TAT-TAT-ATGAA-TTA
1 TATATTTAAT-AATTTA
1364646 TATATTTAATAATTTA
1 TATATTTAATAATTTA
1364662 T
1 T
1364663 TTTTATTATA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 12 0.24
15 13 0.27
16 22 0.45
17 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (16 bp):
TATATTTAATAATTTA
Found at i:1364692 original size:23 final size:23
Alignment explanation
Indices: 1364590--1364693 Score: 56
Period size: 23 Copynumber: 4.5 Consensus size: 23
1364580 ATAATTATAT
*
1364590 TTAAAATATTATATATATAAATT-
1 TTAAAATATTATATTTA-AAATTA
* *
1364613 TTAATATATTAATAATTT-ATATTA
1 TTAAAATATT-AT-ATTTAAAATTA
* *
1364637 TATGAATTA-TATATTTAATAATTTA
1 T-TAAAATATTATATTTAA-AA-TTA
**
1364662 TT--TTTATTATATTTAAAATTA
1 TTAAAATATTATATTTAAAATTA
1364683 TTAAAATATTA
1 TTAAAATATTA
1364694 AATTAATTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
21 5 0.08
22 9 0.15
23 30 0.49
24 6 0.10
25 11 0.18
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
TTAAAATATTATATTTAAAATTA
Done.