Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 161 of 186
Found at i:53554424 original size:21 final size:22
Alignment explanation
Indices: 53554400--53554461 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 22
53554390 TTAATAATCA
*
53554400 AATTTAACT-AAAAAATAAATT
1 AATTAAACTGAAAAAATAAATT
*
53554421 AATTAAAGTGAAAAAATAAATAAT
1 AATTAAACTGAAAAAATAAAT--T
* *
53554445 AATTAAATTGACAAAAT
1 AATTAAACTGAAAAAAT
53554462 TTATCATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.21
22 11 0.32
24 16 0.47
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (22 bp):
AATTAAACTGAAAAAATAAATT
Found at i:53554447 original size:24 final size:22
Alignment explanation
Indices: 53554409--53554461 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
53554399 AAATTTAACT
53554409 AAAAAATAAATTAATTAAAGTG
1 AAAAAATAAATTAATTAAAGTG
*
53554431 AAAAAATAAATAATAATTAAATTG
1 AAAAAATAAAT--TAATTAAAGTG
*
53554455 ACAAAAT
1 AAAAAAT
53554462 TTATCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 11 0.41
24 16 0.59
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (22 bp):
AAAAAATAAATTAATTAAAGTG
Found at i:53561084 original size:80 final size:79
Alignment explanation
Indices: 53561000--53561171 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
53560990 GGACTAAGAT
*
53561000 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
53561064 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
53561080 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
53561145 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
53561159 CCGAAGGCATTTG
1 CCGAAGGCATTTG
53561172 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:53561151 original size:39 final size:39
Alignment explanation
Indices: 53560947--53561169 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
53560937 TTGAATGCTG
* * * * *
53560947 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
53560987 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
53561026 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
53561067 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
53561107 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
53561146 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
53561170 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:53561189 original size:79 final size:80
Alignment explanation
Indices: 53561027--53561204 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
53561017 AGATACAAAT
* * * *
53561027 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
53561092 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
53561107 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
53561171 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
53561186 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
53561205 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:53566658 original size:28 final size:29
Alignment explanation
Indices: 53566604--53566658 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
53566594 TAAATACACT
* * *
53566604 TCAAGATTCAAGAGAGAGATGTCCAAACA
1 TCAAGATTCAAGAGAAAAATATCCAAACA
*
53566633 TCAAGATT-AAGAGAAAAATATTCAAA
1 TCAAGATTCAAGAGAAAAATATCCAAA
53566659 TATTTTTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 14 0.64
29 8 0.36
ACGTcount: A:0.51, C:0.13, G:0.16, T:0.20
Consensus pattern (29 bp):
TCAAGATTCAAGAGAAAAATATCCAAACA
Found at i:53572928 original size:16 final size:17
Alignment explanation
Indices: 53572896--53572935 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
53572886 AATCATTATC
53572896 AAATAATTACTAAAATAA
1 AAATAATTAC-AAAATAA
53572914 AAATAATTA-AAAATAA
1 AAATAATTACAAAATAA
*
53572930 TAATAA
1 AAATAA
53572936 ATGGTAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
18 9 0.43
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAATTACAAAATAA
Found at i:53573874 original size:16 final size:16
Alignment explanation
Indices: 53573853--53573887 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
53573843 TTGAAGAGAT
*
53573853 AAAAATAAATAACGAA
1 AAAAATAAATAAAGAA
53573869 AAAAATAAATAAAGAA
1 AAAAATAAATAAAGAA
53573885 AAA
1 AAA
53573888 TAAACAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAAATAAATAAAGAA
Found at i:53576331 original size:21 final size:21
Alignment explanation
Indices: 53576307--53576389 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 21
53576297 CATAAGTGCT
*
53576307 AACAAAAACCCGTAAGGGTTG
1 AACAGAAACCCGTAAGGGTTG
* *
53576328 AACAGAAGCCTGTAAGGGTTG
1 AACAGAAACCCGTAAGGGTTG
* * * *
53576349 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAACCCGTAAGGGTTG
* *
53576370 AACAGAAACACATAAGGGTT
1 AACAGAAACCCGTAAGGGTT
53576390 AAATTGAAGC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.41, C:0.17, G:0.27, T:0.16
Consensus pattern (21 bp):
AACAGAAACCCGTAAGGGTTG
Found at i:53576386 original size:42 final size:42
Alignment explanation
Indices: 53576340--53576435 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
53576330 CAGAAGCCTG
* ** *
53576340 TAAGGGTTGAACAGAAGCTCGTAAGAGCTGAACAGAAACACA
1 TAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACAGAAACACA
** *
53576382 TAAGGGTTAAATTGAAGCTCAAAAGAGCTAAACAGAAACCCA
1 TAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACAGAAACACA
53576424 -ATAGGGTTAAAC
1 TA-AGGGTTAAAC
53576436 TGAAACTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 1 0.02
42 44 0.98
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.17
Consensus pattern (42 bp):
TAAGGGTTAAACAGAAGCTCAAAAGAGCTAAACAGAAACACA
Found at i:53576453 original size:21 final size:21
Alignment explanation
Indices: 53576429--53576481 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
53576419 ACCCAATAGG
*
53576429 GTTAAACTGAAACTTAT-ATGA
1 GTTAAACTGAAACTCATGA-GA
*
53576450 GTTAAA-TGAAGCTCATGAGA
1 GTTAAACTGAAACTCATGAGA
*
53576470 GCTAAACTGAAA
1 GTTAAACTGAAA
53576482 GTAAAAACGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.26
Consensus pattern (21 bp):
GTTAAACTGAAACTCATGAGA
Found at i:53577974 original size:37 final size:37
Alignment explanation
Indices: 53577915--53578016 Score: 168
Period size: 37 Copynumber: 2.8 Consensus size: 37
53577905 AGCTCAGACG
* * *
53577915 AAATCTCCACACGAAGTTATCGGGTCTTACTCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
53577952 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
53577989 TAATCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTT
53578017 TAGAGCTCGG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:53578278 original size:49 final size:49
Alignment explanation
Indices: 53578135--53578308 Score: 234
Period size: 47 Copynumber: 3.7 Consensus size: 49
53578125 CCCTTCGGGA
* * * * *
53578135 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
53578182 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGG--ATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
53578227 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCGTTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
53578276 CTTATCACATATATATACACTTTCACATTCATC
1 CTTATCACATATATATACACTTTCACATTCATC
53578309 CAAATATACT
Statistics
Matches: 111, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
45 11 0.10
46 1 0.01
47 60 0.54
49 39 0.35
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:53581745 original size:17 final size:17
Alignment explanation
Indices: 53581723--53581764 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
53581713 TACTATAATG
53581723 GCAAAAGAACGAAGAGT
1 GCAAAAGAACGAAGAGT
*
53581740 GCAAAAGAACGAATAGT
1 GCAAAAGAACGAAGAGT
*
53581757 ACAAAAGA
1 GCAAAAGA
53581765 TGGAGATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.57, C:0.12, G:0.24, T:0.07
Consensus pattern (17 bp):
GCAAAAGAACGAAGAGT
Found at i:53582741 original size:27 final size:27
Alignment explanation
Indices: 53582707--53582760 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
53582697 GCTCGGAACA
53582707 ATCGCTTGCTGACACTAACAAGAAATC
1 ATCGCTTGCTGACACTAACAAGAAATC
*
53582734 ATCGCTTGCTGACATTAACAAGAAATC
1 ATCGCTTGCTGACACTAACAAGAAATC
53582761 TTCACTGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (27 bp):
ATCGCTTGCTGACACTAACAAGAAATC
Found at i:53586615 original size:34 final size:34
Alignment explanation
Indices: 53586572--53586641 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
53586562 AATTTAATCA
53586572 TGGATTTGGATATTGGAATAATTTAAATGTATTT
1 TGGATTTGGATATTGGAATAATTTAAATGTATTT
53586606 TGGATTTGGATATTGGAATAATTTAAATGTATTT
1 TGGATTTGGATATTGGAATAATTTAAATGTATTT
53586640 TG
1 TG
53586642 CTGTATGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.47
Consensus pattern (34 bp):
TGGATTTGGATATTGGAATAATTTAAATGTATTT
Found at i:53590526 original size:111 final size:111
Alignment explanation
Indices: 53590332--53590553 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
53590322 AGATGTGTTA
* * *
53590332 CTATAAGGAAATTGAAGAGATATTAAGGGAGAGGACAAAGAAGTCTTATAAGTCTCCAACTTCTC
1 CTATAAGGAAATTGAAGAGATATTAAGGGAGAGGACAAAGAAGCCTTATAAGGCTCCAACTCCTC
53590397 CTCCCAAGCTTGATTCCTTTATGCATTTCTCTGATAAGGGTTTATG
66 CTCCCAAGCTTGATTCCTTTATGCATTTCTCTGATAAGGGTTTATG
*
53590443 CTATAAGGAAATTGAAGAGATTTTAAGGGAGAGGACAAAGAAGCCTTATAAGGCTCCAACTCCTC
1 CTATAAGGAAATTGAAGAGATATTAAGGGAGAGGACAAAGAAGCCTTATAAGGCTCCAACTCCTC
53590508 CTCCCAAGCTTGATTCCTTTATGCATTTCTCTGATAAGGGTTTATG
66 CTCCCAAGCTTGATTCCTTTATGCATTTCTCTGATAAGGGTTTATG
53590554 TACTACTTTT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (111 bp):
CTATAAGGAAATTGAAGAGATATTAAGGGAGAGGACAAAGAAGCCTTATAAGGCTCCAACTCCTC
CTCCCAAGCTTGATTCCTTTATGCATTTCTCTGATAAGGGTTTATG
Found at i:53592901 original size:18 final size:20
Alignment explanation
Indices: 53592875--53592913 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
53592865 ATCTTGTCTG
*
53592875 TGATGAAAAT-TTTA-ATCT
1 TGATCAAAATATTTATATCT
53592893 TGATCAAAATATTTATATCT
1 TGATCAAAATATTTATATCT
53592913 T
1 T
53592914 CTCTTCCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 4 0.22
20 5 0.28
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (20 bp):
TGATCAAAATATTTATATCT
Found at i:53597767 original size:7 final size:8
Alignment explanation
Indices: 53597723--53597772 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
53597713 ATATAAAAAT
53597723 AATTTATA
1 AATTTATA
53597731 AATTTATA
1 AATTTATA
*
53597739 AATTTCTA
1 AATTTATA
*
53597747 ACATATATA
1 A-ATTTATA
53597756 AATTTA-A
1 AATTTATA
53597763 AATTTA-A
1 AATTTATA
53597770 AAT
1 AAT
53597773 ATCAAAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
7 11 0.30
8 20 0.54
9 6 0.16
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (8 bp):
AATTTATA
Found at i:53597901 original size:18 final size:17
Alignment explanation
Indices: 53597870--53597917 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
53597860 TATTCTAAAC
*
53597870 ATTTTTTCATAAATTTT
1 ATTTTTTCAAAAATTTT
*
53597887 ATTTTTTCAAAAAATTT
1 ATTTTTTCAAAAATTTT
**
53597904 AAATTTT-AAAAATT
1 ATTTTTTCAAAAATT
53597918 CAAAACAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTTTCAAAAATTTT
Found at i:53597983 original size:31 final size:29
Alignment explanation
Indices: 53597941--53598009 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 29
53597931 CTAGTTTAAA
*
53597941 AAAAATTAAGTTTTTTCTAGAATATATTTTT
1 AAAATTTAAGTTTTTTCTAGAA-AT-TTTTT
* * *
53597972 AAAATTTAAGTTTTTTTTTGCAATTTTTT
1 AAAATTTAAGTTTTTTCTAGAAATTTTTT
53598001 AAAATTTAA
1 AAAATTTAA
53598010 ATACTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 14 0.41
30 2 0.06
31 18 0.53
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.54
Consensus pattern (29 bp):
AAAATTTAAGTTTTTTCTAGAAATTTTTT
Found at i:53598017 original size:29 final size:27
Alignment explanation
Indices: 53597967--53598065 Score: 108
Period size: 29 Copynumber: 3.5 Consensus size: 27
53597957 CTAGAATATA
* *
53597967 TTTTTAAAATTTAAGTTTTTTTTTGCAAT
1 TTTTTAAAATTTAAATATTTTTTTG--AT
*
53597996 TTTTTAAAATTTAAATACTTTTTTTTAT
1 TTTTTAAAATTTAAATA-TTTTTTTGAT
**
53598024 TTTTTATAAATTTTTATATTTATTTTGAT
1 TTTTTA-AAATTTAAATATTT-TTTTGAT
53598053 TTTTTAAAATTTA
1 TTTTTAAAATTTA
53598066 TATTTACATA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
28 17 0.28
29 36 0.60
30 7 0.12
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTTTAAAATTTAAATATTTTTTTGAT
Found at i:53598756 original size:43 final size:42
Alignment explanation
Indices: 53598695--53598778 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 42
53598685 AATCACTTTC
* *
53598695 CCTTTTAAAAACTTTTAAGTATTTTTTAAAAAAATTGTTTTTTT
1 CCTTTTAAAAACTTTTAAG--TTATTTAAAAAAATAGTTTTTTT
53598739 CCTTTTAAAAAC-TTTAAGTTATTTAAAAAAATAGTTTTTT
1 CCTTTTAAAAACTTTTAAGTTATTTAAAAAAATAGTTTTTT
53598779 AAATTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 20 0.53
43 6 0.16
44 12 0.32
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (42 bp):
CCTTTTAAAAACTTTTAAGTTATTTAAAAAAATAGTTTTTTT
Found at i:53598892 original size:9 final size:9
Alignment explanation
Indices: 53598878--53598903 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
53598868 TAATTTTTTG
53598878 AAAATATTT
1 AAAATATTT
53598887 AAAATATTT
1 AAAATATTT
53598896 AAAATATT
1 AAAATATT
53598904 AATCTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAATATTT
Found at i:53603477 original size:34 final size:34
Alignment explanation
Indices: 53603405--53603477 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
53603395 ACAACTCAGT
* * **
53603405 ATGGAAACACCATACCTACATTTCACAGATCGGT
1 ATGGAAACACCATAACTACATTTCACACATCGCC
* * *
53603439 ATGGAAATACCATAACTACATTTCACACTTTGCC
1 ATGGAAACACCATAACTACATTTCACACATCGCC
53603473 ATGGA
1 ATGGA
53603478 TTAACCATGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.26
Consensus pattern (34 bp):
ATGGAAACACCATAACTACATTTCACACATCGCC
Found at i:53603550 original size:27 final size:27
Alignment explanation
Indices: 53603533--53603585 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
53603523 TTTACTATGT
* *
53603533 TTGGCACACTATATCACTTTTCCATAA
1 TTGGAACACTATATCACTTTACCATAA
* *
53603560 TTGGAACACTTTATCACTTTGCCATA
1 TTGGAACACTATATCACTTTACCATA
53603586 GTTCAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (27 bp):
TTGGAACACTATATCACTTTACCATAA
Found at i:53603685 original size:33 final size:31
Alignment explanation
Indices: 53603648--53603733 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 31
53603638 AGTGTAGCTA
*
53603648 AAGCTACCACTTATCACTTGTCACTTGTAGCCG
1 AAGCTACCACTTATCACTTGTCA--AGTAGCCG
53603681 AAGCTACCAC-TATTCAC-TGATCAAGTAGCCG
1 AAGCTACCACTTA-TCACTTG-TCAAGTAGCCG
*
53603712 AAGCTACCACTTTTCACATTGT
1 AAGCTACCACTTATCAC-TTGT
53603734 ACACACAAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
31 21 0.46
32 6 0.13
33 19 0.41
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (31 bp):
AAGCTACCACTTATCACTTGTCAAGTAGCCG
Found at i:53603769 original size:32 final size:32
Alignment explanation
Indices: 53603721--53603833 Score: 149
Period size: 33 Copynumber: 3.5 Consensus size: 32
53603711 GAAGCTACCA
53603721 CTTTTCACA-TTGTACACACAAGGTGTACATTTC
1 CTTTTCA-AGTTGTACACACAA-GTGTACATTTC
*
53603754 CTTTTCAAG-TGTACACACAAAGTGTACGTTTC
1 CTTTTCAAGTTGTACACAC-AAGTGTACATTTC
*
53603786 CTTTTTAAGTTGTACACACACAGTGTACATTTC
1 CTTTTCAAGTTGTACACACA-AGTGTACATTTC
*
53603819 CTTTTCTAGTTGTAC
1 CTTTTCAAGTTGTAC
53603834 CTTTTAGGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
32 29 0.41
33 42 0.59
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (32 bp):
CTTTTCAAGTTGTACACACAAGTGTACATTTC
Found at i:53608279 original size:23 final size:23
Alignment explanation
Indices: 53608236--53608280 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
53608226 ATTCCACATT
**
53608236 CATATATCAATGTCTCACATTTC
1 CATATATCAATAACTCACATTTC
53608259 CATATATCAATAAC-CATCATTT
1 CATATATCAATAACTCA-CATTT
53608281 TTCTTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (23 bp):
CATATATCAATAACTCACATTTC
Found at i:53608538 original size:21 final size:21
Alignment explanation
Indices: 53608514--53608578 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 21
53608504 AAGTCTAGGT
53608514 GAAGCACATAAGTGCTAAATG
1 GAAGCACATAAGTGCTAAATG
*
53608535 GAAGC-C-TGAAG-GCTAACT-
1 GAAGCACAT-AAGTGCTAAATG
* *
53608553 GAAGCACATAAGTGTTAAACG
1 GAAGCACATAAGTGCTAAATG
53608574 GAAGC
1 GAAGC
53608579 CCGAAGGCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
20 9 0.26
21 10 0.29
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAATG
Found at i:53608556 original size:39 final size:39
Alignment explanation
Indices: 53608496--53608596 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
53608486 ATCATGATCT
* ** *
53608496 GAAGCCCGAAGTCTAGGTGAAGCACATAAGTGCTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
53608535 GAAGCCTGAAGGCTAACTGAAGCACATAAGTGTTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
53608574 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
53608597 TCATCAGAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.37, C:0.20, G:0.28, T:0.16
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:53609834 original size:16 final size:18
Alignment explanation
Indices: 53609803--53609837 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
53609793 CAATTAACCC
53609803 CTCAATTAAGATAATTTT
1 CTCAATTAAGATAATTTT
53609821 CTCAATT-A-ATAATTTT
1 CTCAATTAAGATAATTTT
53609837 C
1 C
53609838 CTAAACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (18 bp):
CTCAATTAAGATAATTTT
Found at i:53611001 original size:62 final size:62
Alignment explanation
Indices: 53610904--53611029 Score: 218
Period size: 62 Copynumber: 2.0 Consensus size: 62
53610894 AAGGCACATA
53610904 TAACTATCTTTCAAAAATTAATGTCTTCTAACACAAAACACACACAGTTGGCATCCCAATTT
1 TAACTATCTTTCAAAAATTAATGTCTTCTAACACAAAACACACACAGTTGGCATCCCAATTT
* *
53610966 TAACTATCTTT-AACAAATTAATGTCTTCTAACACAAAGCACATACAGTTGGCATCCCAATTT
1 TAACTATCTTTCAA-AAATTAATGTCTTCTAACACAAAACACACACAGTTGGCATCCCAATTT
53611028 TA
1 TA
53611030 CTTTCACTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 2 0.03
62 59 0.97
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.32
Consensus pattern (62 bp):
TAACTATCTTTCAAAAATTAATGTCTTCTAACACAAAACACACACAGTTGGCATCCCAATTT
Found at i:53633331 original size:21 final size:21
Alignment explanation
Indices: 53633302--53633341 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53633292 GAGCATTTGG
*
53633302 GAGCAAAATGAG-CAAAAAAC
1 GAGCAAAATCAGACAAAAAAC
53633322 GAGCTAAAATCAGACAAAAA
1 GAGC-AAAATCAGACAAAAA
53633342 GCGTAGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.60, C:0.15, G:0.17, T:0.07
Consensus pattern (21 bp):
GAGCAAAATCAGACAAAAAAC
Found at i:53635258 original size:21 final size:21
Alignment explanation
Indices: 53635229--53635305 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
53635219 AATGATTAAT
*
53635229 TAAGTTCAAGTGGTAAGACCC
1 TAAGGTCAAGTGGTAAGACCC
*
53635250 TAAGGTCAAGTGATAAGACCC
1 TAAGGTCAAGTGGTAAGACCC
53635271 TAAGGTCAAGTGGTAAGACCC
1 TAAGGTCAAGTGGTAAGACCC
53635292 TAAGGTCAAGTGGT
1 TAAGGTCAAGTGGT
53635306 TTTAGAAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (21 bp):
TAAGGTCAAGTGGTAAGACCC
Found at i:53636997 original size:25 final size:25
Alignment explanation
Indices: 53636969--53637049 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
53636959 AGACCATACG
53636969 TTTTCTCCCTACTTATTGGTTAATT
1 TTTTCTCCCTACTTATTGGTTAATT
* * *** *
53636994 TTTTC-CCATTTAGTTA-TGACCATATG
1 TTTTCTCC--CTACTTATTGGTTA-ATT
53637020 TTTTCTCCCTACTTATTGGTTAATT
1 TTTTCTCCCTACTTATTGGTTAATT
53637045 TTTTC
1 TTTTC
53637050 CCATTTAGTT
Statistics
Matches: 39, Mismatches: 12, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
24 2 0.05
25 20 0.51
26 15 0.38
27 2 0.05
ACGTcount: A:0.17, C:0.20, G:0.09, T:0.54
Consensus pattern (25 bp):
TTTTCTCCCTACTTATTGGTTAATT
Found at i:53637036 original size:51 final size:51
Alignment explanation
Indices: 53636960--53637061 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
53636950 GTACTAGAAA
53636960 GACCATACGTTTTCTCCCTACTTATTGGTTAATTTTTTCCCATTTAGTTAT
1 GACCATACGTTTTCTCCCTACTTATTGGTTAATTTTTTCCCATTTAGTTAT
*
53637011 GACCATATGTTTTCTCCCTACTTATTGGTTAATTTTTTCCCATTTAGTTAT
1 GACCATACGTTTTCTCCCTACTTATTGGTTAATTTTTTCCCATTTAGTTAT
53637062 CTTTAGCATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.50
Consensus pattern (51 bp):
GACCATACGTTTTCTCCCTACTTATTGGTTAATTTTTTCCCATTTAGTTAT
Found at i:53642112 original size:17 final size:17
Alignment explanation
Indices: 53642090--53642125 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
53642080 TAATTTAAAA
53642090 TTAATTAAAATAA-ATTT
1 TTAATTAAAA-AATATTT
53642107 TTAATTAAAAAATATTT
1 TTAATTAAAAAATATTT
53642124 TT
1 TT
53642126 GAACTACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAATTAAAAAATATTT
Found at i:53645731 original size:33 final size:33
Alignment explanation
Indices: 53645689--53645757 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
53645679 TTTGTGACTC
*
53645689 TTTCTCGTTTTATTGACTCCCTTCTTGTCAAGA
1 TTTCCCGTTTTATTGACTCCCTTCTTGTCAAGA
53645722 TTTCCCGTTTTATTGACTCCCTTCTTGTCAAGA
1 TTTCCCGTTTTATTGACTCCCTTCTTGTCAAGA
53645755 TTT
1 TTT
53645758 GATTTGTTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.14, C:0.25, G:0.12, T:0.49
Consensus pattern (33 bp):
TTTCCCGTTTTATTGACTCCCTTCTTGTCAAGA
Found at i:53647464 original size:18 final size:19
Alignment explanation
Indices: 53647441--53647479 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
53647431 TCTAAGTAGA
53647441 TTCTTTC-CTGGGTATTAT
1 TTCTTTCACTGGGTATTAT
* *
53647459 TTCTTTCATTGGTTATTAT
1 TTCTTTCACTGGGTATTAT
53647478 TT
1 TT
53647480 GATTATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.62
Consensus pattern (19 bp):
TTCTTTCACTGGGTATTAT
Found at i:53664620 original size:21 final size:21
Alignment explanation
Indices: 53664595--53664644 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
53664585 GTTGTTTAGA
*
53664595 AGGAAGTTGCTACTGCAGAAG
1 AGGAAGTTGCTACTGAAGAAG
*
53664616 AGGAAGTTGTTACTGAAGAAG
1 AGGAAGTTGCTACTGAAGAAG
*
53664637 AAGAAGTT
1 AGGAAGTT
53664645 ACTGAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.22
Consensus pattern (21 bp):
AGGAAGTTGCTACTGAAGAAG
Found at i:53664971 original size:22 final size:20
Alignment explanation
Indices: 53664946--53664990 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
53664936 CCAAGGATAA
*
53664946 AAAATAAAAGAAGGAAGAGAAG
1 AAAAGAAAAGAAGG-AGA-AAG
53664968 AAAAGAAAAGAAGGAGAAAG
1 AAAAGAAAAGAAGGAGAAAG
53664988 AAA
1 AAA
53664991 CATCATGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 3 0.14
22 13 0.59
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAGAAGGAGAAAG
Found at i:53666196 original size:66 final size:66
Alignment explanation
Indices: 53666078--53666207 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
53666068 CTTATTGCAT
* *
53666078 TAATGCCACTGCATGAGTTAATCCCAGATTGGGTCTAGAATTGTCACTGCACCTGA-TAGTTGTC
1 TAATGCCACTGCATGAGTTAATCCCAGATTGCGTCCAGAATTGTCACTGCACCTGACT-GTTGTC
53666142 TA
65 TA
* * * * **
53666144 TAATGCCATTGCATGAGTTAATTCTAGATTGCGTCCAGACTTGT-TGTCGCACCTGACTGTTGTC
1 TAATGCCACTGCATGAGTTAATCCCAGATTGCGTCCAGAATTGTCACT-GCACCTGACTGTTGTC
53666208 CGAATACGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 1 0.02
66 52 0.96
67 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (66 bp):
TAATGCCACTGCATGAGTTAATCCCAGATTGCGTCCAGAATTGTCACTGCACCTGACTGTTGTCT
A
Found at i:53669614 original size:23 final size:24
Alignment explanation
Indices: 53669571--53669620 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
53669561 TGTATTAACC
53669571 TCATTTTAACATACATATCACAAA
1 TCATTTTAACATACATATCACAAA
* * *
53669595 TCATTTTCACA-ACATTTCACACA
1 TCATTTTAACATACATATCACAAA
53669618 TCA
1 TCA
53669621 CAAGTATAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (24 bp):
TCATTTTAACATACATATCACAAA
Found at i:53671526 original size:28 final size:28
Alignment explanation
Indices: 53671494--53671563 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
53671484 ATAGTAAGTC
53671494 CGCACACTTAGTGCT-TA-ATAGTCAAACT
1 CGCACACTTAGTGCTATACA-A-TCAAACT
*
53671522 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
53671550 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53671564 CAATCTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 35 0.90
29 3 0.08
30 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:53675710 original size:273 final size:273
Alignment explanation
Indices: 53675209--53675761 Score: 1007
Period size: 273 Copynumber: 2.0 Consensus size: 273
53675199 AACAGAGCTC
* * **
53675209 TCAACTTTGCCATCGACTTCCTACTCAAAGCATCAAAAATTACATTTTCCTTGCCAGTATAATAC
1 TCAACTGTGCCATCAACTTCCTACTCAAAGCATCAAAAATTACATTCGCCTTGCCAGTATAATAC
53675274 TCTATCACACAATCATAATCCTTTAACAACTCAATCCAATGTCACTGTCTTAAATTCAACTCCTT
66 TCTATCACACAATCATAATCCTTTAACAACTCAATCCAATGTCACTGTCTTAAATTCAACTCCTT
*
53675339 TTGGGTAATGAGGTACTTAAGGCTCTTATGATCCATATAGATAACACACCTTTCCCCATACAAAT
131 TTGGGTAATGAGATACTTAAGGCTCTTATGATCCATATAGATAACACACCTTTCCCCATACAAAT
* *
53675404 AATGACGCCAAATCTTGAGTGCAAAAACCACAGCAGCTAACTCCAAATCATGAGTAGGGTTGTTT
196 AATGACGCCAAATCTTAAGTGCAAAAACCACAGCAGCTAACTCCAAATCATGAGTAGGGTAGTTT
53675469 CACCCATGTATCT
261 CACCCATGTATCT
53675482 TCAACTGTGCCATCAACTTCCTACTCAAAGCATCAAAAATTACATTCGCCTTGCCAGTATAATAC
1 TCAACTGTGCCATCAACTTCCTACTCAAAGCATCAAAAATTACATTCGCCTTGCCAGTATAATAC
*
53675547 TCTATCACACAATCATAATCCTTTAACAACTCAATCCAATGTCATTGTCTTAAATTCAACTCCTT
66 TCTATCACACAATCATAATCCTTTAACAACTCAATCCAATGTCACTGTCTTAAATTCAACTCCTT
* *
53675612 TTGGGTAATGAGATACTTAAGGCTCTTATGATCTATATAGATAACACACCTTTCCCTATACAAAT
131 TTGGGTAATGAGATACTTAAGGCTCTTATGATCCATATAGATAACACACCTTTCCCCATACAAAT
*
53675677 AATGACGCCAAATCTTAAGTGCAAAACCCACAGCAGCTAACTCCAAATCATGAGTAGGGTAGTTT
196 AATGACGCCAAATCTTAAGTGCAAAAACCACAGCAGCTAACTCCAAATCATGAGTAGGGTAGTTT
53675742 CACCCATGTATCT
261 CACCCATGTATCT
53675755 TCAACTG
1 TCAACTG
53675762 CCTTGAAGCA
Statistics
Matches: 269, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
273 269 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.30
Consensus pattern (273 bp):
TCAACTGTGCCATCAACTTCCTACTCAAAGCATCAAAAATTACATTCGCCTTGCCAGTATAATAC
TCTATCACACAATCATAATCCTTTAACAACTCAATCCAATGTCACTGTCTTAAATTCAACTCCTT
TTGGGTAATGAGATACTTAAGGCTCTTATGATCCATATAGATAACACACCTTTCCCCATACAAAT
AATGACGCCAAATCTTAAGTGCAAAAACCACAGCAGCTAACTCCAAATCATGAGTAGGGTAGTTT
CACCCATGTATCT
Found at i:53685709 original size:14 final size:14
Alignment explanation
Indices: 53685692--53685721 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53685682 TTTGGTTTAT
53685692 TATATTTAAAAAAA
1 TATATTTAAAAAAA
*
53685706 TATATTTAATAAAA
1 TATATTTAAAAAAA
53685720 TA
1 TA
53685722 AGCTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATTTAAAAAAA
Found at i:53689947 original size:24 final size:24
Alignment explanation
Indices: 53689889--53689935 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
53689879 GTAGAAGACC
53689889 GAAAGAGAAATAAGGAGGTGAGCG
1 GAAAGAGAAATAAGGAGGTGAGCG
53689913 GAAAGAGAAATAAGGAGGTGAGC
1 GAAAGAGAAATAAGGAGGTGAGC
53689936 TTGTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.40, T:0.09
Consensus pattern (24 bp):
GAAAGAGAAATAAGGAGGTGAGCG
Found at i:53690947 original size:22 final size:22
Alignment explanation
Indices: 53690922--53690963 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
53690912 GCTATGTTGC
*
53690922 AACACAGGGAGTTA-AATGTCGT
1 AACACAGAGA-TTAGAATGTCGT
53690944 AACACAGAGATTAGAATGTC
1 AACACAGAGATTAGAATGTC
53690964 AGAATTGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (22 bp):
AACACAGAGATTAGAATGTCGT
Found at i:53692650 original size:22 final size:22
Alignment explanation
Indices: 53692625--53692669 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
53692615 CTATGAAAGT
53692625 GCAAAACCCGGACCTATTTCTA
1 GCAAAACCCGGACCTATTTCTA
53692647 GCAAAACCCGGACCTATTTCTA
1 GCAAAACCCGGACCTATTTCTA
53692669 G
1 G
53692670 TAAGATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (22 bp):
GCAAAACCCGGACCTATTTCTA
Found at i:53693806 original size:14 final size:15
Alignment explanation
Indices: 53693787--53693815 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53693777 AGGTAAGTTT
53693787 GTATTTCATT-TAAA
1 GTATTTCATTATAAA
53693801 GTATTTCATTATAAA
1 GTATTTCATTATAAA
53693816 ATTATGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
GTATTTCATTATAAA
Found at i:53694052 original size:16 final size:15
Alignment explanation
Indices: 53693984--53694075 Score: 96
Period size: 15 Copynumber: 5.9 Consensus size: 15
53693974 CAATGAAAAG
*
53693984 GATGAAAAGGTTATT
1 GATGAAAAGGTTATC
*
53693999 GACGAAAAGGTT-TAC
1 GATGAAAAGGTTAT-C
*
53694014 AATGAAAAGGTTATC
1 GATGAAAAGGTTATC
53694029 GATGAAAAGGTTATC
1 GATGAAAAGGTTATC
*
53694044 GATTGAAAAAGGTTATG
1 GA-TG-AAAAGGTTATC
*
53694061 GATTAAAAAGGTTAT
1 GA-TGAAAAGGTTAT
53694076 TCAAATAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
14 1 0.02
15 38 0.58
16 13 0.20
17 14 0.21
ACGTcount: A:0.42, C:0.04, G:0.25, T:0.28
Consensus pattern (15 bp):
GATGAAAAGGTTATC
Found at i:53694055 original size:17 final size:17
Alignment explanation
Indices: 53694018--53694075 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
53694008 GTTTACAATG
53694018 AAAAGGTTATCGA-TG-
1 AAAAGGTTATCGATTGA
53694033 AAAAGGTTATCGATTGA
1 AAAAGGTTATCGATTGA
*
53694050 AAAAGGTTATGGATT-A
1 AAAAGGTTATCGATTGA
53694066 AAAAGGTTAT
1 AAAAGGTTAT
53694076 TCAAATAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
15 13 0.32
16 13 0.32
17 14 0.35
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.29
Consensus pattern (17 bp):
AAAAGGTTATCGATTGA
Found at i:53694899 original size:25 final size:24
Alignment explanation
Indices: 53694849--53694899 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
53694839 AATTATGAAG
*
53694849 CACACGATCTGGGACACGAGCTGT
1 CACACGATCTGGGACACGAGCAGT
* * *
53694873 CACACGATCGTGTGCCACGCGCAGT
1 CACACGATC-TGGGACACGAGCAGT
53694898 CA
1 CA
53694900 ACCTACACGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.24, C:0.33, G:0.27, T:0.16
Consensus pattern (24 bp):
CACACGATCTGGGACACGAGCAGT
Found at i:53697549 original size:28 final size:28
Alignment explanation
Indices: 53697500--53697570 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
53697490 GATGTCTCGT
*
53697500 ACACTAAGTGTCATACTCAATATCTCAC
1 ACACTAAGTGCCATACTCAATATCTCAC
* * * * **
53697528 ACACCAAGTGCCATTCTTAATATTTTTC
1 ACACTAAGTGCCATACTCAATATCTCAC
53697556 ACACTAAGTGCCATA
1 ACACTAAGTGCCATA
53697571 TACATATATA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (28 bp):
ACACTAAGTGCCATACTCAATATCTCAC
Found at i:53701024 original size:22 final size:22
Alignment explanation
Indices: 53700999--53701047 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
53700989 TCCACATAGT
* *
53700999 TATGAAAGCCTTTTACGAGTAG
1 TATGAAAGCCCTTTAAGAGTAG
* *
53701021 TATGAAATCCCTTTAAGGGTAG
1 TATGAAAGCCCTTTAAGAGTAG
53701043 TATGA
1 TATGA
53701048 GACTCTACGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (22 bp):
TATGAAAGCCCTTTAAGAGTAG
Found at i:53707949 original size:46 final size:46
Alignment explanation
Indices: 53707777--53707945 Score: 223
Period size: 46 Copynumber: 3.7 Consensus size: 46
53707767 GATCAGAGTA
* * * *
53707777 TGCCATGGTGTCTTTCAACCATGGTCTTATTTATTCT-CATCTTGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTTTCCATCGTGT
* * ** *
53707822 TGCCATAGTGTCTTTCAGCCATGGTCTTATTCATTTTCTGTTGTGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTTTCCATCGTGT
*
53707868 TGCCATAGTGTCTTTCAACCATGGTCTTATTTGTTTTCCATCGTGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTTTCCATCGTGT
* *
53707914 TGCCAGAGTGTCTTTCAACCATGATCTTATTT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTT
53707946 GTTTGATTTG
Statistics
Matches: 106, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
45 33 0.31
46 73 0.69
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (46 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTTTCCATCGTGT
Found at i:53707957 original size:91 final size:91
Alignment explanation
Indices: 53707777--53707957 Score: 238
Period size: 91 Copynumber: 2.0 Consensus size: 91
53707767 GATCAGAGTA
* * * *
53707777 TGCCATGGTGTCTTTCAACCATGGTCTTATTTATTCTCATCTTGATGCCATAGTGTCTTTCAGCC
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCATCGTGATGCCAGAGTGTCTTTCAACC
* **
53707842 ATGGTCTTATTCATTTTCTGTTGTGT
66 ATGATCTTATTCATTTGATGTTGTGT
* * *
53707868 TGCCATAGTGTCTTTCAACCATGGTCTTATTTGTTTTCCATCGTGTTGCCAGAGTGTCTTTCAAC
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCT-CATCGTGATGCCAGAGTGTCTTTCAAC
**
53707933 CATGATCTTATTTGTTTGAT-TTGTG
65 CATGATCTTATTCATTTGATGTTGTG
53707958 ATCTCATAGC
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
91 39 0.51
92 38 0.49
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (91 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCATCGTGATGCCAGAGTGTCTTTCAACC
ATGATCTTATTCATTTGATGTTGTGT
Found at i:53707973 original size:91 final size:91
Alignment explanation
Indices: 53707787--53707987 Score: 217
Period size: 91 Copynumber: 2.2 Consensus size: 91
53707777 TGCCATGGTG
* * * *
53707787 TCTTTCAACCATGGTCTTATTTATTCTCATCTTGATGCCATAGTGTCTTTCAGCCATGGTCTTAT
1 TCTTTCAACCATGGTCTTATTTATTCTCATCGTGATGCCAGAGTGTCTTTCAACCATGATCTTAT
** * **
53707852 TCATTTTCTGTTGTGTTGCCATAGTG
66 TCATTTGATGTTGTGATGCCATAGCA
* * *
53707878 TCTTTCAACCATGGTCTTATTTGTTTTCCATCGTGTTGCCAGAGTGTCTTTCAACCATGATCTTA
1 TCTTTCAACCATGGTCTTATTTATTCT-CATCGTGATGCCAGAGTGTCTTTCAACCATGATCTTA
**
53707943 TTTGTTTGAT-TTGTGAT-CTCATAGCA
65 TTCATTTGATGTTGTGATGC-CATAGCA
* * *
53707969 TCTTTTAGCTATGGTCTTA
1 TCTTTCAACCATGGTCTTA
53707988 CTTGATAGAA
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
90 1 0.01
91 52 0.57
92 38 0.42
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.46
Consensus pattern (91 bp):
TCTTTCAACCATGGTCTTATTTATTCTCATCGTGATGCCAGAGTGTCTTTCAACCATGATCTTAT
TCATTTGATGTTGTGATGCCATAGCA
Found at i:53708004 original size:45 final size:45
Alignment explanation
Indices: 53707962--53708169 Score: 258
Period size: 45 Copynumber: 4.6 Consensus size: 45
53707952 TTTGTGATCT
* * *
53707962 CATAGCATCTTTTAG-CTATGGTCTTACTTGATAGAATCGTGATGC
1 CATAACATCTTTCAGTC-ATGGTCTTACTCGATAGAATCGTGATGC
* * * **
53708007 CATAACGTCTCTCAATCATGGTCTTACTTAATAGAATCGTGATGC
1 CATAACATCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGC
* *
53708052 CATAACGTCTTTCAGTCATAGTCTTACTCGATAGAATCGTGATGC
1 CATAACATCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGC
* *
53708097 CA-AACATCTTTCAGTCATGGTCTTACTCGATAGAATCATGATGT
1 CATAACATCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGC
** *
53708141 CATAATGTCTTTCCGTCATGGTCTTACTC
1 CATAACATCTTTCAGTCATGGTCTTACTC
53708170 ATTTCTGCTA
Statistics
Matches: 143, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
44 40 0.28
45 102 0.71
46 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.36
Consensus pattern (45 bp):
CATAACATCTTTCAGTCATGGTCTTACTCGATAGAATCGTGATGC
Found at i:53708049 original size:90 final size:89
Alignment explanation
Indices: 53707955--53708169 Score: 245
Period size: 89 Copynumber: 2.4 Consensus size: 89
53707945 TGTTTGATTT
* * * * *
53707955 GTGATCTCATAGCATCTTTTAG-CTATGGTCTTACTTGATAGAATCGTGATGCCATAACGTCTCT
1 GTGATCTCATAACATCTTTCAGTC-ATAGTCTTACTCGATAGAATCGTGATGCCA-AACATCTCT
*
53708019 CAATCATGGTCTTACTTAATAGAATC
64 CAATCATGGTCTTACTCAATAGAATC
* *
53708045 GTGATGC-CATAACGTCTTTCAGTCATAGTCTTACTCGATAGAATCGTGATGCCAAACATCTTTC
1 GTGAT-CTCATAACATCTTTCAGTCATAGTCTTACTCGATAGAATCGTGATGCCAAACATCTCTC
* *
53708109 AGTCATGGTCTTACTCGATAGAATC
65 AATCATGGTCTTACTCAATAGAATC
* * ** * *
53708134 ATGATGTCATAATGTCTTTCCGTCATGGTCTTACTC
1 GTGATCTCATAACATCTTTCAGTCATAGTCTTACTC
53708170 ATTTCTGCTA
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
89 60 0.56
90 45 0.42
91 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (89 bp):
GTGATCTCATAACATCTTTCAGTCATAGTCTTACTCGATAGAATCGTGATGCCAAACATCTCTCA
ATCATGGTCTTACTCAATAGAATC
Found at i:53708145 original size:89 final size:90
Alignment explanation
Indices: 53707982--53708169 Score: 270
Period size: 89 Copynumber: 2.1 Consensus size: 90
53707972 TTTAGCTATG
* * * *
53707982 GTCTTACTTGATAGAATCGTGATGCCATAACGTCTCTCAATCATGGTCTTACTTAATAGAATCGT
1 GTCTTACTCGATAGAATCGTGATGCCATAACATCTCTCAATCATGGTCTTACTCAATAGAATCAT
53708047 GATGCCATAACGTCTTTCAGTCATA
66 GATGCCATAACGTCTTTCAGTCATA
* * *
53708072 GTCTTACTCGATAGAATCGTGATGCCA-AACATCTTTCAGTCATGGTCTTACTCGATAGAATCAT
1 GTCTTACTCGATAGAATCGTGATGCCATAACATCTCTCAATCATGGTCTTACTCAATAGAATCAT
* * * *
53708136 GATGTCATAATGTCTTTCCGTCATG
66 GATGCCATAACGTCTTTCAGTCATA
53708161 GTCTTACTC
1 GTCTTACTC
53708170 ATTTCTGCTA
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
89 61 0.70
90 26 0.30
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (90 bp):
GTCTTACTCGATAGAATCGTGATGCCATAACATCTCTCAATCATGGTCTTACTCAATAGAATCAT
GATGCCATAACGTCTTTCAGTCATA
Found at i:53708243 original size:46 final size:46
Alignment explanation
Indices: 53708182--53708303 Score: 183
Period size: 46 Copynumber: 2.7 Consensus size: 46
53708172 TTCTGCTATG
*
53708182 GTGCCATAGTATCTTTCAACTATGGTCTTATTTATCCT-TCGGGATA
1 GTGCCATAGTGTCTTTCAACTATGGTCTTATTTATCCTCT-GGGATA
* * * *
53708228 GTGTCATAGTGTCTTTCAATTATGGTCTTATTTATTCTCTGGTATA
1 GTGCCATAGTGTCTTTCAACTATGGTCTTATTTATCCTCTGGGATA
53708274 GTGCCATAGTGTCTTTCAACTATGGTCTTA
1 GTGCCATAGTGTCTTTCAACTATGGTCTTA
53708304 ATCATTTTCC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 67 0.99
47 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.44
Consensus pattern (46 bp):
GTGCCATAGTGTCTTTCAACTATGGTCTTATTTATCCTCTGGGATA
Found at i:53710201 original size:24 final size:25
Alignment explanation
Indices: 53710151--53710201 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
53710141 ATTGGAATGG
**
53710151 ATAAAAAATAATATTTGACATTGTTT
1 ATAAAAAATAATATTTGA-ATAATTT
*
53710177 ATAAAAAGTAATATTTG-ATAATTT
1 ATAAAAAATAATATTTGAATAATTT
53710201 A
1 A
53710202 AAATATAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
26 16 0.73
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (25 bp):
ATAAAAAATAATATTTGAATAATTT
Found at i:53716041 original size:3 final size:3
Alignment explanation
Indices: 53716033--53716057 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
53716023 GGTGACGTAA
53716033 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
53716058 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:53716062 original size:3 final size:3
Alignment explanation
Indices: 53716056--53716086 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
53716046 ATAATAATAA
53716056 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
53716087 TGGGGGTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:53716854 original size:18 final size:17
Alignment explanation
Indices: 53716823--53716856 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53716813 TTGAGCTTTG
*
53716823 TTCTTTTTTTCAAATTA
1 TTCTTTTTTACAAATTA
53716840 TTCTTTTTTAACAAATT
1 TTCTTTTTT-ACAAATT
53716857 TGACGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (17 bp):
TTCTTTTTTACAAATTA
Found at i:53719559 original size:9 final size:9
Alignment explanation
Indices: 53719545--53719581 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
53719535 GTGCTCAATA
53719545 TTTTTTTCT
1 TTTTTTTCT
53719554 TTTTTTTCT
1 TTTTTTTCT
53719563 TTTTTTCTCT
1 TTTTTT-TCT
53719573 ATTTTTTTC
1 -TTTTTTTC
53719582 CAACAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 15 0.58
10 5 0.19
11 6 0.23
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:53724522 original size:8 final size:8
Alignment explanation
Indices: 53724511--53724538 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
53724501 GTCAACCAAT
53724511 AATTCTTC
1 AATTCTTC
53724519 AATTCTTC
1 AATTCTTC
53724527 AATTCTTC
1 AATTCTTC
53724535 AATT
1 AATT
53724539 TGGCCCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (8 bp):
AATTCTTC
Found at i:53730601 original size:8 final size:8
Alignment explanation
Indices: 53730590--53730617 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
53730580 GTCAACCAAT
53730590 AATTCTTC
1 AATTCTTC
53730598 AATTCTTC
1 AATTCTTC
53730606 AATTCTTC
1 AATTCTTC
53730614 AATT
1 AATT
53730618 TGGCCCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (8 bp):
AATTCTTC
Found at i:53731021 original size:59 final size:59
Alignment explanation
Indices: 53730929--53731049 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
53730919 TGGTGATAAG
53730929 AAGGTTGTGATCTCTGCTCCAAGCAAATGTTTGTAGTGGGTGTAAACGAGAAGGATTAC
1 AAGGTTGTGATCTCTGCTCCAAGCAAATGTTTGTAGTGGGTGTAAACGAGAAGGATTAC
*
53730988 AAGGTTGTGATCTCTGCTCCAAGCAAATGTTTGTAGTGGGTGTGAACGAGAAGGATTAC
1 AAGGTTGTGATCTCTGCTCCAAGCAAATGTTTGTAGTGGGTGTAAACGAGAAGGATTAC
53731047 AAG
1 AAG
53731050 CCAGAGCTCG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.28
Consensus pattern (59 bp):
AAGGTTGTGATCTCTGCTCCAAGCAAATGTTTGTAGTGGGTGTAAACGAGAAGGATTAC
Found at i:53735417 original size:13 final size:13
Alignment explanation
Indices: 53735399--53735423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53735389 TTCAAGTTTT
53735399 TTTTTAATTAATG
1 TTTTTAATTAATG
53735412 TTTTTAATTAAT
1 TTTTTAATTAAT
53735424 AAATATATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:53736062 original size:13 final size:13
Alignment explanation
Indices: 53736044--53736068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53736034 AAATATATTT
53736044 ATTAATTAAAAAC
1 ATTAATTAAAAAC
53736057 ATTAATTAAAAA
1 ATTAATTAAAAA
53736069 TAAAAATAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:53736211 original size:14 final size:14
Alignment explanation
Indices: 53736185--53736214 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
53736175 TCAAAGAAGC
53736185 TAATATATTAAAAA
1 TAATATATTAAAAA
53736199 TAATA-ATTAAAAA
1 TAATATATTAAAAA
53736212 TAA
1 TAA
53736215 AAGTAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATATATTAAAAA
Found at i:53738978 original size:24 final size:24
Alignment explanation
Indices: 53738946--53738995 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
53738936 TTTTATAAGA
53738946 AAAAAAATTGATATAATATATATT
1 AAAAAAATTGATATAATATATATT
53738970 AAAAAAATTGATATAATATATATT
1 AAAAAAATTGATATAATATATATT
53738994 AA
1 AA
53738996 TCATTAGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
AAAAAAATTGATATAATATATATT
Found at i:53740431 original size:29 final size:29
Alignment explanation
Indices: 53740399--53740490 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 29
53740389 ACGGGGGTAC
53740399 TAAAATTGTAACTTTTTATTTTGAATACT
1 TAAAATTGTAACTTTTTATTTTGAATACT
* *** * *** **
53740428 TAAAA-TGAAAAAACTATAACGTGGGTAC-
1 TAAAATTG-TAACTTTTTATTTTGAATACT
53740456 TAAAATTGTAACTTTTTATTTTGAATACT
1 TAAAATTGTAACTTTTTATTTTGAATACT
53740485 TAAAAT
1 TAAAAT
53740491 GAAAAAAAAT
Statistics
Matches: 40, Mismatches: 20, Indels: 6
0.61 0.30 0.09
Matches are distributed among these distances:
28 17 0.43
29 23 0.57
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (29 bp):
TAAAATTGTAACTTTTTATTTTGAATACT
Found at i:53740442 original size:57 final size:57
Alignment explanation
Indices: 53740381--53740497 Score: 225
Period size: 57 Copynumber: 2.1 Consensus size: 57
53740371 AAAAGTGACC
53740381 AAACTATAACGGGGGTACTAAAATTGTAACTTTTTATTTTGAATACTTAAAATGAAA
1 AAACTATAACGGGGGTACTAAAATTGTAACTTTTTATTTTGAATACTTAAAATGAAA
*
53740438 AAACTATAACGTGGGTACTAAAATTGTAACTTTTTATTTTGAATACTTAAAATGAAA
1 AAACTATAACGGGGGTACTAAAATTGTAACTTTTTATTTTGAATACTTAAAATGAAA
53740495 AAA
1 AAA
53740498 AATTATAATT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (57 bp):
AAACTATAACGGGGGTACTAAAATTGTAACTTTTTATTTTGAATACTTAAAATGAAA
Found at i:53743175 original size:12 final size:12
Alignment explanation
Indices: 53743160--53743184 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53743150 GTCAATATTT
53743160 TCTACTCCTAAC
1 TCTACTCCTAAC
53743172 TCTACTCCTAAC
1 TCTACTCCTAAC
53743184 T
1 T
53743185 TTGTATCACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (12 bp):
TCTACTCCTAAC
Found at i:53746633 original size:12 final size:12
Alignment explanation
Indices: 53746618--53746652 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
53746608 CTAAATTTTC
*
53746618 AGTAGTTTCAGT
1 AGTAGGTTCAGT
53746630 AGTAGGTTCAGT
1 AGTAGGTTCAGT
53746642 AGTAGGTTCAG
1 AGTAGGTTCAG
53746653 CAATTACCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.31, T:0.34
Consensus pattern (12 bp):
AGTAGGTTCAGT
Found at i:53746852 original size:31 final size:32
Alignment explanation
Indices: 53746788--53746875 Score: 133
Period size: 31 Copynumber: 2.8 Consensus size: 32
53746778 TCTGTTTCAT
*
53746788 GTTGCTGGATAGGAGCTGGAATGTGAGTGTTTG
1 GTTGCTGGACAGGAGCTGGAATGT-AGTGTTTG
*
53746821 GTTGCTGGACGGGAGCTGGAATGT-GTGTTTG
1 GTTGCTGGACAGGAGCTGGAATGTAGTGTTTG
*
53746852 GTTGCTGGACAGTAGCTGGAATGT
1 GTTGCTGGACAGGAGCTGGAATGT
53746876 CAAGAAGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 29 0.57
33 22 0.43
ACGTcount: A:0.17, C:0.09, G:0.42, T:0.32
Consensus pattern (32 bp):
GTTGCTGGACAGGAGCTGGAATGTAGTGTTTG
Found at i:53747206 original size:33 final size:33
Alignment explanation
Indices: 53747164--53747231 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
53747154 CTAAAATCAG
53747164 GAAAGAATTTTGCTAGAACTTGCATAAGACTTT
1 GAAAGAATTTTGCTAGAACTTGCATAAGACTTT
53747197 GAAAGAATTTTGCTAGAACTTGCATAAGACTTT
1 GAAAGAATTTTGCTAGAACTTGCATAAGACTTT
53747230 GA
1 GA
53747232 GATTCAAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (33 bp):
GAAAGAATTTTGCTAGAACTTGCATAAGACTTT
Found at i:53752609 original size:44 final size:45
Alignment explanation
Indices: 53752556--53752658 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 45
53752546 TGTCTTTGAC
* * *
53752556 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
** *
53752600 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAAT
*
53752646 ATGGAATTACATG
1 ATGGACTTACATG
53752659 GCTCATTTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 33 0.66
46 17 0.34
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (45 bp):
ATGGACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAAT
Found at i:53752661 original size:46 final size:44
Alignment explanation
Indices: 53752575--53752663 Score: 133
Period size: 46 Copynumber: 2.0 Consensus size: 44
53752565 CATGAATTAT
* *
53752575 TCCTGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAA
1 TCCTGTCTCCAAAGCCATATATAATATGGAATTACATGGCTCAA
*
53752619 TCCTGTCTCCAAAGCCATATTTCTAATATGGAATTACATGGCTCA
1 TCCTGTCTCCAAAGCCATA--TATAATATGGAATTACATGGCTCA
53752664 TTTCTGTTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 18 0.45
46 22 0.55
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (44 bp):
TCCTGTCTCCAAAGCCATATATAATATGGAATTACATGGCTCAA
Found at i:53766948 original size:19 final size:18
Alignment explanation
Indices: 53766923--53766969 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 18
53766913 TTGTTTGTTT
53766923 TTTTTTTAATTTCGTTCC
1 TTTTTTTAATTTCGTTCC
53766941 TCTTTTTTAATTTCGTTCC
1 T-TTTTTTAATTTCGTTCC
53766960 TTTATTTTAA
1 TTT-TTTTAA
53766970 AATAATTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.11
19 24 0.89
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.66
Consensus pattern (18 bp):
TTTTTTTAATTTCGTTCC
Found at i:53769604 original size:30 final size:30
Alignment explanation
Indices: 53769570--53769632 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
53769560 ACTTAACAAG
53769570 CAAAT-ACTTATAAAATAATAACAAAATTAA
1 CAAATGACTT-TAAAATAATAACAAAATTAA
* *
53769600 CAAATGTCTTTAAAATAATGACAAAATTAA
1 CAAATGACTTTAAAATAATAACAAAATTAA
53769630 CAA
1 CAA
53769633 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.11, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGACTTTAAAATAATAACAAAATTAA
Found at i:53769675 original size:11 final size:11
Alignment explanation
Indices: 53769661--53769720 Score: 75
Period size: 11 Copynumber: 5.3 Consensus size: 11
53769651 ATATCCAAAC
*
53769661 AATAATAACAA
1 AATAATAAAAA
53769672 AATAATAAAAA
1 AATAATAAAAA
*
53769683 AATACAGAAAAA
1 AATA-ATAAAAA
53769695 AATAATAAAAA
1 AATAATAAAAA
*
53769706 TAATATTAAAAA
1 -AATAATAAAAA
53769718 AAT
1 AAT
53769721 TAATTTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
11 23 0.53
12 20 0.47
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (11 bp):
AATAATAAAAA
Found at i:53769716 original size:23 final size:22
Alignment explanation
Indices: 53769661--53769720 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
53769651 ATATCCAAAC
*
53769661 AATAATAACAAAATAATAAAAA
1 AATAATAAAAAAATAATAAAAA
*
53769683 AATACAGAAAAAAATAATAAAAA
1 AATA-ATAAAAAAATAATAAAAA
*
53769706 TAATATTAAAAAAAT
1 -AATAATAAAAAAAT
53769721 TAATTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 4 0.12
23 24 0.75
24 4 0.12
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (22 bp):
AATAATAAAAAAATAATAAAAA
Found at i:53774979 original size:21 final size:22
Alignment explanation
Indices: 53774955--53774995 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53774945 TTATGCATAC
*
53774955 AGTCC-TAAATATGAGTTTACA
1 AGTCCTTAAAAATGAGTTTACA
*
53774976 AGTCCTTAAAAATGATTTTA
1 AGTCCTTAAAAATGAGTTTA
53774996 GAACTAAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (22 bp):
AGTCCTTAAAAATGAGTTTACA
Found at i:53775208 original size:54 final size:54
Alignment explanation
Indices: 53775150--53775256 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
53775140 TCAAAATGGG
* * *
53775150 GACACATGGCTGTGTCCCAGCCCGTCTC-CTTGCCCGTGTAACTCACTGACTTGA
1 GACACATGACTGTGTCCCAGCCCGTCTCTC-TACCCGTGTAACTCACTAACTTGA
* *
53775204 GACACATGACTGTGTCCCAGCCCGTGTCTCTACCCGTGTAACTCTCTAACTTG
1 GACACATGACTGTGTCCCAGCCCGTCTCTCTACCCGTGTAACTCACTAACTTG
53775257 GGCCACACGG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 46 0.98
55 1 0.02
ACGTcount: A:0.18, C:0.35, G:0.21, T:0.27
Consensus pattern (54 bp):
GACACATGACTGTGTCCCAGCCCGTCTCTCTACCCGTGTAACTCACTAACTTGA
Found at i:53775984 original size:12 final size:12
Alignment explanation
Indices: 53775967--53775991 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53775957 CCATACATGC
53775967 CCGTGTGCTAGG
1 CCGTGTGCTAGG
53775979 CCGTGTGCTAGG
1 CCGTGTGCTAGG
53775991 C
1 C
53775992 TGTGCCAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.28, G:0.40, T:0.24
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:53806982 original size:18 final size:18
Alignment explanation
Indices: 53806959--53806994 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53806949 CGTGATATCC
53806959 AGATTTATTTCCAATTCT
1 AGATTTATTTCCAATTCT
53806977 AGATTTATTTCCAATTCT
1 AGATTTATTTCCAATTCT
53806995 CGATCTCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (18 bp):
AGATTTATTTCCAATTCT
Found at i:53811533 original size:48 final size:48
Alignment explanation
Indices: 53811471--53811598 Score: 150
Period size: 48 Copynumber: 2.7 Consensus size: 48
53811461 AGCTCTCGTA
* * *
53811471 TAAGAGCATATCTGGGATATGGCTTTGACAGT-GACATGTGATCCCATG
1 TAAGACCATGTCTGGGACATGGCTTTGACA-TCGACATGTGATCCCATG
* ** * * *
53811519 TAAGACCATGTCTGGGACATGGCTTTGGCATCGTTATGTTATCTCGTG
1 TAAGACCATGTCTGGGACATGGCTTTGACATCGACATGTGATCCCATG
*
53811567 TAAGACCATGTCTGGGACATGGCATTGACATC
1 TAAGACCATGTCTGGGACATGGCTTTGACATC
53811599 ACAATAAGAC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
47 1 0.01
48 67 0.99
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCTTTGACATCGACATGTGATCCCATG
Found at i:53811614 original size:48 final size:48
Alignment explanation
Indices: 53811464--53811616 Score: 112
Period size: 48 Copynumber: 3.2 Consensus size: 48
53811454 ATGGATGAGC
* * * * * * **
53811464 TCTCGTATAAGAGCATATCTGGGATATGGCTTTGACAGTGAC-ATGTGA
1 TCTCGTGTAAGACCATGTCTGGGACATGGCATTGACA-TCACAATAAGA
* * * * *** ***
53811512 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCGTTATGTTA
1 TCTCGTGTAAGACCATGTCTGGGACATGGCATTGACATCACAATAAGA
53811560 TCTCGTGTAAGACCATGTCTGGGACATGGCATTGACATCACAATAAGA
1 TCTCGTGTAAGACCATGTCTGGGACATGGCATTGACATCACAATAAGA
53811608 -CATCGTGTA
1 TC-TCGTGTA
53811617 TGACAATAGC
Statistics
Matches: 82, Mismatches: 21, Indels: 4
0.77 0.20 0.04
Matches are distributed among these distances:
47 2 0.02
48 80 0.98
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (48 bp):
TCTCGTGTAAGACCATGTCTGGGACATGGCATTGACATCACAATAAGA
Found at i:53811708 original size:48 final size:48
Alignment explanation
Indices: 53811506--53811731 Score: 146
Period size: 48 Copynumber: 4.8 Consensus size: 48
53811496 TGACAGTGAC
* * * * *
53811506 ATGTGATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCATCGTT
1 ATGTGGTCTCATGTAAGACCATGTCTGGGACATGGCATCGGCATCATT
** * * * **
53811554 ATGTTATCTCGTGTAAGACCATGTCTGGGACATGGCATTGACATCACA
1 ATGTGGTCTCATGTAAGACCATGTCTGGGACATGGCATCGGCATCATT
** * * * * *
53811602 AT-AAGACATCGTGTATGACAATAG-CTGGG-CTAT--CA-C--C-TCAAT
1 ATGTGGTC-TCATGTAAGACCAT-GTCTGGGAC-ATGGCATCGGCATCATT
*
53811644 ATGTGTGATCTCATGTAAGACCATGTCTGGGACATGGCATCGGCATCGTT
1 ATGTG-G-TCTCATGTAAGACCATGTCTGGGACATGGCATCGGCATCATT
* *
53811694 ATGTGGTCTCATGTAAGACCATATCTGGGATATGGCAT
1 ATGTGGTCTCATGTAAGACCATGTCTGGGACATGGCAT
53811732 TAGCACCCCT
Statistics
Matches: 137, Mismatches: 27, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
42 5 0.04
43 2 0.01
44 19 0.14
45 2 0.01
46 4 0.03
47 3 0.02
48 91 0.66
49 3 0.02
50 8 0.06
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (48 bp):
ATGTGGTCTCATGTAAGACCATGTCTGGGACATGGCATCGGCATCATT
Found at i:53813782 original size:40 final size:39
Alignment explanation
Indices: 53813738--53813989 Score: 371
Period size: 40 Copynumber: 6.3 Consensus size: 39
53813728 GCTCCTCATT
* * *
53813738 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGTT-TAGTAACTCGCA
53813778 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
53813818 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
53813858 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
*
53813898 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCC-GGTTTAGTAACTCGCA
* * * *
53813938 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-TTTAGTAACTCGCA
53813977 CAAATGCCTTCGG
1 CAAATGCCTTCGG
53813990 ATCTTAGTCC
Statistics
Matches: 199, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
38 1 0.01
39 31 0.16
40 164 0.82
41 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGTTTAGTAACTCGCA
Found at i:53814019 original size:120 final size:120
Alignment explanation
Indices: 53813738--53814034 Score: 399
Period size: 120 Copynumber: 2.5 Consensus size: 120
53813728 GCTCCTCATT
* * * * *
53813738 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTAGCACAAATGCCTTCGGGACTTAACCCA
*
53813802 GATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
65 GATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
*
53813858 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTAGCACAAATGCCTTCGGGACTTAACCCAG
* * *
53813923 ATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
** *
53813977 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCAC-AA-GCCTTCGGGACTTA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TAGCACAAATGCCTTCGGGACTTA
53814035 GCCCGGACAT
Statistics
Matches: 161, Mismatches: 12, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
118 17 0.11
119 49 0.30
120 93 0.58
121 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (120 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTAGCACAAATGCCTTCGGGACTTAACCCAG
ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
Found at i:53814035 original size:79 final size:79
Alignment explanation
Indices: 53813738--53814041 Score: 402
Period size: 80 Copynumber: 3.8 Consensus size: 79
53813728 GCTCCTCATT
* * *
53813738 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCAC-AATGCCTTCGGGACTTAACCCG
53813802 GATTTAGTAACTCGCA
64 GATTTAGTAACTCGCA
53813818 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
53813883 ATTTAGTAACTCGCA
65 ATTTAGTAACTCGCA
* *
53813898 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA-CAATGCCTTCGGGACTTAACCCGG
* *
53813962 AATTAGTATCTCGCA
65 ATTTAGTAACTCGCA
** * * *
53813977 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCACAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TTAGTAAC-TCGCACAATGCCTTCGGGACTTAACCC
53814039 GGA
63 GGA
53814042 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
78 12 0.06
79 60 0.29
80 131 0.64
81 3 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAGTAACTCGCA
Found at i:53821910 original size:79 final size:78
Alignment explanation
Indices: 53821808--53822032 Score: 274
Period size: 79 Copynumber: 2.8 Consensus size: 78
53821798 GCTCCTCGTT
* *
53821808 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
53821873 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
53821888 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
53821952 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * * *
53821966 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-ACCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
53822030 GAA
63 GAA
53822033 ATCATTCAAA
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
78 36 0.29
79 55 0.44
80 35 0.28
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:53821925 original size:39 final size:40
Alignment explanation
Indices: 53821808--53822032 Score: 273
Period size: 40 Copynumber: 5.7 Consensus size: 40
53821798 GCTCCTCGTT
* *
53821808 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
53821848 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
53821888 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
53821927 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
53821966 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
*
53822007 CAAA-ACCTTCGGGACTTAGCCCGGAA
1 CAAATGCCTTCGGGACTTAGCCCGGAA
53822033 ATCATTCAAA
Statistics
Matches: 166, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 74 0.45
40 76 0.46
41 14 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:53830090 original size:48 final size:48
Alignment explanation
Indices: 53830030--53830211 Score: 146
Period size: 48 Copynumber: 3.9 Consensus size: 48
53830020 CCATGTAAGA
*
53830030 ACATGGCATTGGCATCGTTATGTGATCCCATGTAAGACCATGTCCGGG
1 ACATGGCATTGGCATCGTTATGTGATCCCATGTAAGACCATGTCTGGG
** * * * * *
53830078 ACATGGCATTGGCATTATAATGAGA-CATCGTGTAAGACTATAG-CTGGG
1 ACATGGCATTGGCATCGTTATGTGATC-CCATGTAAGACCAT-GTCTGGG
* * * *
53830126 -CTAT--CA---GCCTTGATATGTGATATCCCATGTAAGACCATGTCTTGG
1 AC-ATGGCATTGGCATCGTTATGTG--ATCCCATGTAAGACCATGTCTGGG
*
53830171 ACATGGCATTGGCATCGTTATGTGGTCCCATGTAAGACCAT
1 ACATGGCATTGGCATCGTTATGTGATCCCATGTAAGACCAT
53830212 ATCTAGGATA
Statistics
Matches: 100, Mismatches: 21, Indels: 26
0.68 0.14 0.18
Matches are distributed among these distances:
43 8 0.08
44 1 0.01
45 18 0.18
46 4 0.04
47 4 0.04
48 54 0.54
49 1 0.01
50 10 0.10
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (48 bp):
ACATGGCATTGGCATCGTTATGTGATCCCATGTAAGACCATGTCTGGG
Found at i:53832137 original size:38 final size:38
Alignment explanation
Indices: 53832094--53832387 Score: 203
Period size: 38 Copynumber: 7.0 Consensus size: 38
53832084 TTTCAAATTA
*
53832094 ACATGTATAACCATGGCATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* * * *
53832132 ACATGTTTAATCGTGGTATATCCACTTAGCACTACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACG-T--T
*
53832173 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
* * *
53832217 ACATGTTTAACCGTGGTATATCTACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
53832255 A-ATGATTTAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 ACATG--------TA--TAACCGTGGCATATCCACTTAGCACCACGTT
* *
53832302 ACATGTATCAATATGTGTAATCGTGGTATATCCACTTAGCACCACGTT
1 ACATG------TA----TAACCGTGGCATATCCACTTAGCACCACGTT
* *
53832350 ACACGTATAACCGTGGTATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
53832388 TTTTCATTTC
Statistics
Matches: 209, Mismatches: 25, Indels: 44
0.75 0.09 0.16
Matches are distributed among these distances:
37 3 0.01
38 91 0.44
39 1 0.00
40 3 0.01
41 2 0.01
42 3 0.01
43 1 0.00
44 2 0.01
45 4 0.02
46 5 0.02
47 56 0.27
48 38 0.18
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:53832196 original size:85 final size:85
Alignment explanation
Indices: 53832101--53832307 Score: 360
Period size: 85 Copynumber: 2.4 Consensus size: 85
53832091 TTAACATGTA
* * *
53832101 TAACCATGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
53832166 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
*
53832186 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCTACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
* *
53832251 CGTTAATGATTTAATATATG
66 CGTTAATGAATCAATATATG
53832271 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGT
53832308 ATCAATATGT
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 116 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (85 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAACCGTGGTATATCCACTTAGCACCA
CGTTAATGAATCAATATATG
Found at i:53832216 original size:47 final size:47
Alignment explanation
Indices: 53832143--53832350 Score: 254
Period size: 47 Copynumber: 4.6 Consensus size: 47
53832133 CATGTTTAAT
*
53832143 CGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATGTAAC
1 CGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* *
53832190 CGTGGCATATCCACTTAGCACCACG-T--T--A-C-ATGT-T-TAAC
1 CGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* * *
53832228 CGTGGTATATCTACTTAGCACCACGTTAATGATTTAATATATGTAAC
1 CGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* * * *
53832275 CGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAAT
1 CGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAAC
53832323 CGTGGTATATCCACTTAGCACCACGTTA
1 CGTGGTATATCCACTTAGCACCACGTTA
53832351 CACGTATAAC
Statistics
Matches: 135, Mismatches: 16, Indels: 19
0.79 0.09 0.11
Matches are distributed among these distances:
38 27 0.20
39 2 0.01
40 3 0.02
41 2 0.01
42 1 0.01
44 1 0.01
45 3 0.02
46 2 0.01
47 53 0.39
48 41 0.30
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (47 bp):
CGTGGTATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
Found at i:53832333 original size:48 final size:48
Alignment explanation
Indices: 53832219--53832357 Score: 192
Period size: 48 Copynumber: 2.9 Consensus size: 48
53832209 ACCACGTTAC
* * *
53832219 ATGTTTAACCGTGGTATATCTACTTAGCACCACGTTA-ATG-ATTTAAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGTA-TCAAT
* *
53832266 ATATGTAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT
* *
53832314 ATGTGTAATCGTGGTATATCCACTTAGCACCACGTTACACGTAT
1 ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGTAT
53832358 AACCGTGGTA
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
47 33 0.41
48 47 0.58
49 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (48 bp):
ATGTGTAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAAT
Found at i:53832341 original size:133 final size:132
Alignment explanation
Indices: 53832143--53832387 Score: 400
Period size: 133 Copynumber: 1.8 Consensus size: 132
53832133 CATGTTTAAT
* *
53832143 CGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAG
1 CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAG
* * *
53832208 CACCACGTTACATGTTTAACCGTGGTATATCTACTTAGCACCACGTTAATGATTTAATATATGTA
66 CACCACGTTACACGTATAACCGTGGTATATCCACTTAGCACCACGTTAATGATTTAATATATGTA
53832273 AC
131 AC
* * * *
53832275 CGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATCGTGGTATATCCACTTA
1 CGTGGCATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAACCGTGGCATATCCACTTA
53832340 GCACCACGTTACACGTATAACCGTGGTATATCCACTTAGCACCACGTT
65 GCACCACGTTACACGTATAACCGTGGTATATCCACTTAGCACCACGTT
53832388 TTTTCATTTC
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
132 26 0.25
133 77 0.75
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (132 bp):
CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAG
CACCACGTTACACGTATAACCGTGGTATATCCACTTAGCACCACGTTAATGATTTAATATATGTA
AC
Found at i:53835126 original size:15 final size:15
Alignment explanation
Indices: 53835103--53835144 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
53835093 GAAGCCCAGA
*
53835103 ATAAGGAAATCTAAG
1 ATAAGGAAATCCAAG
* *
53835118 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
53835133 ATAAGGAAATCC
1 ATAAGGAAATCC
53835145 CATTTACAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:53837648 original size:41 final size:40
Alignment explanation
Indices: 53837571--53837657 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 40
53837561 TCAAATACAT
*
53837571 TTAAAACAAATATTAAAATAAGAAACAAATAAAAAATTATA
1 TTAAAACAAATATTAAAACAAGAAACAAATAAAAAA-TATA
* * * **
53837612 TTAAAACAATTATTAAAACAATACACAAATTGAAAATATA
1 TTAAAACAAATATTAAAACAAGAAACAAATAAAAAATATA
*
53837652 ATAAAA
1 TTAAAA
53837658 AGTGATTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 9 0.23
41 30 0.77
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (40 bp):
TTAAAACAAATATTAAAACAAGAAACAAATAAAAAATATA
Found at i:53839010 original size:38 final size:38
Alignment explanation
Indices: 53838967--53839417 Score: 353
Period size: 38 Copynumber: 10.9 Consensus size: 38
53838957 TTTCAAATTA
* *
53838967 ACATGTATAACCATGGCATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
* * *
53839005 ACATGTTTAATCGTGGTATATCCACTTAGCACTACGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* *
53839046 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
* * *
53839090 ACATGTTTAATCGTGGTATATCCACTTAGCACTACGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* *
53839131 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
* * *
53839175 ACATGTTTAATCGTGGTATATCCACTTAGCACTACGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* *
53839216 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
* * *
53839260 ACATGTTTAATCGTGGTATATCCACTTAGCACTACGTTAAT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACG-T--T
* *
53839301 GAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGTATATCCACTTAGCACCACGTT
* *
53839345 ACATGTTTAATCGTGGTATATCCACTTAGCACCACGTT
1 ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
*
53839383 ACACGTATAACCGTGGTATATCCACTTAGCACCAC
1 ACATGTATAACCGTGGTATATCCACTTAGCACCAC
53839418 ATTTTTTCAT
Statistics
Matches: 330, Mismatches: 47, Indels: 72
0.73 0.10 0.16
Matches are distributed among these distances:
38 170 0.52
39 4 0.01
40 12 0.04
41 8 0.02
42 4 0.01
43 4 0.01
44 8 0.02
45 12 0.04
46 4 0.01
47 104 0.32
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (38 bp):
ACATGTATAACCGTGGTATATCCACTTAGCACCACGTT
Found at i:53839069 original size:85 final size:85
Alignment explanation
Indices: 53838974--53839383 Score: 802
Period size: 85 Copynumber: 4.8 Consensus size: 85
53838964 TTAACATGTA
*
53838974 TAACCATGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
53839039 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
53839059 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
53839124 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
53839144 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
53839209 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
53839229 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
53839294 CGTTAATGAATCAATATATG
66 CGTTAATGAATCAATATATG
*
53839314 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
53839379 CGTTA
66 CGTTA
53839384 CACGTATAAC
Statistics
Matches: 323, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 323 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (85 bp):
TAACCGTGGCATATCCACTTAGCACCACGTTACATGTTTAATCGTGGTATATCCACTTAGCACTA
CGTTAATGAATCAATATATG
Found at i:53839089 original size:47 final size:47
Alignment explanation
Indices: 53839016--53839345 Score: 345
Period size: 47 Copynumber: 7.6 Consensus size: 47
53839006 CATGTTTAAT
* *
53839016 CGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATGTAAC
1 CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* *
53839063 CGTGGCATATCCACTTAGCACCACG-T--T--A-C-ATGT-T-TAAT
1 CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* *
53839101 CGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATGTAAC
1 CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* *
53839148 CGTGGCATATCCACTTAGCACCACG-T--T--A-C-ATGT-T-TAAT
1 CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* *
53839186 CGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATGTAAC
1 CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* *
53839233 CGTGGCATATCCACTTAGCACCACG-T--T--A-C-ATGT-T-TAAT
1 CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
* *
53839271 CGTGGTATATCCACTTAGCACTACGTTAATGAATCAATATATGTAAC
1 CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
53839318 CGTGGCATATCCACTTAGCACCACGTTA
1 CGTGGCATATCCACTTAGCACCACGTTA
53839346 CATGTTTAAT
Statistics
Matches: 230, Mismatches: 26, Indels: 54
0.74 0.08 0.17
Matches are distributed among these distances:
38 78 0.34
39 6 0.03
40 9 0.04
41 6 0.03
42 3 0.01
43 3 0.01
44 6 0.03
45 9 0.04
46 6 0.03
47 104 0.45
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (47 bp):
CGTGGCATATCCACTTAGCACCACGTTAATGAATCAATATATGTAAC
Found at i:53840618 original size:26 final size:26
Alignment explanation
Indices: 53840535--53840670 Score: 190
Period size: 26 Copynumber: 5.3 Consensus size: 26
53840525 CTGGAGGCCT
53840535 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
* *
53840559 AGCCCTTTTCGATAAACTGGGACA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
53840584 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
53840610 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
53840636 AGCCCTTTTCAATAATCTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
53840662 AGCCCTTTT
1 AGCCCTTTT
53840671 GCACTTCCTC
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.05
24 6 0.06
25 32 0.32
26 57 0.57
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:53841549 original size:27 final size:27
Alignment explanation
Indices: 53841454--53841540 Score: 122
Period size: 27 Copynumber: 3.2 Consensus size: 27
53841444 CATACGTCAT
* *
53841454 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCTC
53841481 TTTACCCTACAGGGGCTTTACGGTCTC
1 TTTACCCTACAGGGGCTTTACGGTCTC
* *
53841508 TTTACCCTACAGGGGCTTTATGGTCTT
1 TTTACCCTACAGGGGCTTTACGGTCTC
53841535 TTTACC
1 TTTACC
53841541 TAATAGGGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 54 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCTC
Found at i:53841698 original size:27 final size:26
Alignment explanation
Indices: 53841658--53841828 Score: 98
Period size: 27 Copynumber: 6.3 Consensus size: 26
53841648 AGAAAGTTAA
*
53841658 GGGTATTTCT-GTAACTTTGTAAATCAG
1 GGGTATTT-TGGTAA-TTTATAAATCAG
*
53841685 GGGTATTTTGGTAATTTTATAAAT-TG
1 GGGTATTTTGGTAA-TTTATAAATCAG
* * * *
53841711 AGGGCATTTCGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTT-ATAAATCAG
* *
53841739 TGGTATTTTGGTAATTT-TACAAACTAG
1 GGGTATTTTGGTAATTTATA-AATC-AG
* *
53841766 GGGTATTTTGGTAATTTTACAAAT-TG
1 GGGTATTTTGGTAA-TTTATAAATCAG
* * * *
53841792 AGGGTATTTCGGTAATTTTACAAACCAA
1 -GGGTATTTTGGTAA-TTTATAAATCAG
53841820 GGGTATTTT
1 GGGTATTTT
53841829 AGCAATTTTA
Statistics
Matches: 112, Mismatches: 22, Indels: 20
0.73 0.14 0.13
Matches are distributed among these distances:
25 1 0.01
26 9 0.08
27 95 0.85
28 6 0.05
29 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTATAAATCAG
Found at i:53841772 original size:81 final size:81
Alignment explanation
Indices: 53841683--53841917 Score: 276
Period size: 81 Copynumber: 2.9 Consensus size: 81
53841673 TTTGTAAATC
*
53841683 AGGGGTATTTTGGTAATTTTATAAATTGAGGGCATTTCGGTAATTTCACAAACC-AGTGGTATTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGCATTTCGGTAATTTCACAAACCAAG-GGTATTT
* *
53841747 TGGTAATTTTACAAACT
65 TAGCAATTTTACAAACT
* *
53841764 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAACCAAGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGCATTTCGGTAATTTCACAAACCAAGGGTATTTT
*
53841829 AGCAATTTTACAGACT
66 AGCAATTTTACAAACT
** ** * * * *** * *
53841845 A-GGGTATTTTCATAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAATCGAGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGCATTTCGGTAATTTCACAAACCAAGGGTATTTT
*
53841909 AGTAATTTT
66 AGCAATTTT
53841918 GTAAATCGAG
Statistics
Matches: 136, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
80 61 0.45
81 73 0.54
82 2 0.01
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTGAGGGCATTTCGGTAATTTCACAAACCAAGGGTATTTT
AGCAATTTTACAAACT
Found at i:53841835 original size:27 final size:27
Alignment explanation
Indices: 53841685--53841931 Score: 212
Period size: 27 Copynumber: 9.2 Consensus size: 27
53841675 TGTAAATCAG
* **
53841685 GGGTATTTTGGTAATTTTATAAATTGA
1 GGGTATTTTGGTAATTTTACAAACCGA
* * *
53841712 GGGCATTTCGGTAATTTCACAAACC-A
1 GGGTATTTTGGTAATTTTACAAACCGA
*
53841738 GTGGTATTTTGGTAATTTTACAAA-CTA
1 G-GGTATTTTGGTAATTTTACAAACCGA
**
53841765 GGGGTATTTTGGTAATTTTACAAATTGA
1 -GGGTATTTTGGTAATTTTACAAACCGA
* *
53841793 GGGTATTTCGGTAATTTTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCGA
* * * *
53841820 GGGTATTTTAGCAATTTTACAGA-CTA
1 GGGTATTTTGGTAATTTTACAAACCGA
** ** *
53841846 GGGTATTTTCATAATTTTACTGATCGA
1 GGGTATTTTGGTAATTTTACAAACCGA
** *
53841873 GGGTATTTTGGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCGA
* ** *
53841900 GGGTATTTTAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCGA
53841927 GGGTA
1 GGGTA
53841932 AAACAGTAAT
Statistics
Matches: 183, Mismatches: 32, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
26 24 0.13
27 157 0.86
28 2 0.01
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCGA
Found at i:53841926 original size:54 final size:54
Alignment explanation
Indices: 53841685--53841971 Score: 233
Period size: 54 Copynumber: 5.4 Consensus size: 54
53841675 TGTAAATCAG
* * * * *
53841685 GGGTATTTTGGTAATTTTATAAATTGAGGGCATTTCGGTAATTTCACAAA-CCA
1 GGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTGGTAATTTTACAAATCGA
* * *
53841738 GTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAATTGA
1 G-GGTATTTTGGTAATTTTATAAATCGA-GGGTATTTTGGTAATTTTACAAATCGA
* * * * * * * *
53841793 GGGTATTTCGGTAATTTTACAAACCAAGGGTATTTTAGCAATTTTACAGA-CTA
1 GGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTGGTAATTTTACAAATCGA
** * **
53841846 GGGTATTTTCATAATTTTACT-GATCGAGGGTATTTTGGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTA-TAAATCGAGGGTATTTTGGTAATTTTACAAATCGA
* * ***** **
53841900 GGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTGGTAATTTTACAAATCGA
*
53841954 -GGTACTTTGGTAATTTTA
1 GGGTATTTTGGTAATTTTA
53841972 CAATTTGAAG
Statistics
Matches: 187, Mismatches: 40, Indels: 14
0.78 0.17 0.06
Matches are distributed among these distances:
53 56 0.30
54 127 0.68
55 4 0.02
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.40
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTATAAATCGAGGGTATTTTGGTAATTTTACAAATCGA
Found at i:53841939 original size:27 final size:27
Alignment explanation
Indices: 53841883--53841955 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
53841873 GGGTATTTTG
****
53841883 GTAATTTTGTAAATCGAGGGTATTTTA
1 GTAATTTTGTAAATCGAGGGTAAAACA
53841910 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTTTGTAAATCGAGGGTAAAACA
53841937 GTAATTTTGTAAATCGAGG
1 GTAATTTTGTAAATCGAGG
53841956 TACTTTGGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.37
Consensus pattern (27 bp):
GTAATTTTGTAAATCGAGGGTAAAACA
Found at i:53841995 original size:53 final size:54
Alignment explanation
Indices: 53841659--53842002 Score: 155
Period size: 54 Copynumber: 6.4 Consensus size: 54
53841649 GAAAGTTAAG
* * * * * * *
53841659 GGTATTTCTGTAACTTTGTAAATC-AGGGGTATTTTGGTAATTTTATAAATTGAG
1 GGTATTTCAGTAATTTTGTAAATCGA-GGGTACTTTAGTAATTTTACAAATCGAA
* * *** * * * * *
53841713 GGCATTTCGGTAATTTCACAAA-CCAGTGGTATTTTGGTAATTTTACAAA-CTAGG
1 GGTATTTCAGTAATTTTGTAAATCGAG-GGTACTTTAGTAATTTTACAAATCGA-A
** ** * * *
53841767 GGTATTTTGGTAATTTTACAAATTGAGGGTA-TTTCGGTAATTTTACAAA-CCAA
1 GGTATTTCAGTAATTTTGTAAATCGAGGGTACTTT-AGTAATTTTACAAATCGAA
* * ** * * * ** *
53841820 GGGTATTTTAGCAATTTTACAGA-CTAGGGTATTTTCA-TAATTTTACTGATCGAG
1 -GGTATTTCAGTAATTTTGTAAATCGAGGGTACTTT-AGTAATTTTACAAATCGAA
** * ** *
53841874 GGTATTTTGGTAATTTTGTAAATCGAGGGTATTTTAGTAATTTTGTAAATCGAG
1 GGTATTTCAGTAATTTTGTAAATCGAGGGTACTTTAGTAATTTTACAAATCGAA
*** * * *
53841928 GGTAAAACAGTAATTTTGTAAATCGA-GGTACTTTGGTAATTTTACAATTTGAA
1 GGTATTTCAGTAATTTTGTAAATCGAGGGTACTTTAGTAATTTTACAAATCGAA
*
53841981 GGTATTTCAGTAATTTGGTAAA
1 GGTATTTCAGTAATTTTGTAAA
53842003 CTAAAGTATT
Statistics
Matches: 228, Mismatches: 52, Indels: 21
0.76 0.17 0.07
Matches are distributed among these distances:
53 78 0.34
54 148 0.65
55 2 0.01
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.40
Consensus pattern (54 bp):
GGTATTTCAGTAATTTTGTAAATCGAGGGTACTTTAGTAATTTTACAAATCGAA
Found at i:53846993 original size:30 final size:29
Alignment explanation
Indices: 53846951--53847013 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 29
53846941 AAGTAGCCGG
53846951 AGCTAGTTAAATCGCACACTTAGTGCCAA
1 AGCTAGTTAAATCGCACACTTAGTGCCAA
*
53846980 AGCTAGTTTAAATCGCACATTTAGTGCCAA
1 AGCTAG-TTAAATCGCACACTTAGTGCCAA
53847010 AGCT
1 AGCT
53847014 TCCAATTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (29 bp):
AGCTAGTTAAATCGCACACTTAGTGCCAA
Found at i:53850555 original size:12 final size:12
Alignment explanation
Indices: 53850538--53850568 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
53850528 ACACGACCTA
53850538 ACACATGGCCTG
1 ACACATGGCCTG
53850550 ACACATGGCCTG
1 ACACATGGCCTG
53850562 ACACATG
1 ACACATG
53850569 AGTGTGTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.32, G:0.23, T:0.16
Consensus pattern (12 bp):
ACACATGGCCTG
Done.