Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold78
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: 2238306
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 23262 characters in sequence are not A, C, G, or T
File 13 of 15
Found at i:1759899 original size:28 final size:28
Alignment explanation
Indices: 1759864--1759931 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
1759854 ATAAAACCGA
1759864 GGTTGGAGTATCCCCTCAAAAATAAT-G
1 GGTTGGAGTATCCCCTCAAAAATAATAG
*
1759891 GGATTGGAGTATCCCCTCGAAAATAATAG
1 GG-TTGGAGTATCCCCTCAAAAATAATAG
*
1759920 GGTTGAAGTATC
1 GGTTGGAGTATC
1759932 TCCGATTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 2 0.05
28 32 0.86
29 3 0.08
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCTCAAAAATAATAG
Found at i:1759917 original size:107 final size:109
Alignment explanation
Indices: 1759790--1759994 Score: 283
Period size: 107 Copynumber: 1.9 Consensus size: 109
1759780 ATTGGGGTTA
* * * * * *
1759790 GAGTATCTCTTCGAAAATAATGGGGTTGGAGTATC-CTCGATTGTGAAAAATTAG-TGTTTTGGA
1 GAGTATCCCCTCGAAAATAATAGGGTTGAAGTATCTC-CGATTATGAAAAA-TAGATGTTTTGAA
1759853 AAT-AAAACCGAGGTTGGAGTATCCCCTC-AAAAATAATGGGATTG
64 AATAAAAACCGAGGTTGGAGTATCCCCTCGAAAAATAATGGGATTG
*
1759897 GAGTATCCCCTCGAAAATAATAGGGTTGAAGTATCTCCGATTATGAAAAATCGATGTTTTGAAAA
1 GAGTATCCCCTCGAAAATAATAGGGTTGAAGTATCTCCGATTATGAAAAATAGATGTTTTGAAAA
* *
1759962 TAAAAACTGGGGTTGGAGTATCCCCTCGAAAAA
66 TAAAAACCGAGGTTGGAGTATCCCCTCGAAAAA
1759995 ACAGGGTTAG
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
106 2 0.02
107 54 0.64
108 24 0.28
109 5 0.06
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (109 bp):
GAGTATCCCCTCGAAAATAATAGGGTTGAAGTATCTCCGATTATGAAAAATAGATGTTTTGAAAA
TAAAAACCGAGGTTGGAGTATCCCCTCGAAAAATAATGGGATTG
Found at i:1760169 original size:79 final size:77
Alignment explanation
Indices: 1759889--1760220 Score: 305
Period size: 79 Copynumber: 4.2 Consensus size: 77
1759879 TCAAAAATAA
* * *
1759889 TGGGATTGGAGTATCCCCTCGAAAATAATAGGGTTGAAGTATCTCCGATTATGAAAAATCGATGT
1 TGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTG-AGTATCT-CGATTATAAAAAATCGATGT
1759954 TTTGAAAATAAAAAC
64 TTTGAAAAT-AAAAC
** * * * * *
1759969 TGGGGTTGGAGTATCCCCTCGAAAA-AACAGGGTTAGAGTATCTCTGATGGTAGAGAATTGGTAT
1 TGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTT-GAGTATCTC-GATTATAAAAAATCGATGT
1760033 TTT-AGAAATAAAAC
64 TTTGA-AAATAAAAC
* * * * *
1760047 TGGGGATT-GAGTATCCCATC-AGAAATAATAGGGTTGGAGTATCCTCGATTGTAAAAAATTGGT
1 TGGGG-TTGGAGTATCCCCTCGA-AAATAACAGGGTT-GAGTAT-CTCGATTATAAAAAATCGAT
1760110 GTTTTGAAAATAAAAC
62 GTTTTGAAAATAAAAC
* * * * *
1760126 TAGGGTTGGAGTATCCCTTCGAAAATAACAGGGTTGTAGTATCCCCAATTATAGAAAATCGATGT
1 TGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTG-AGTAT-CTCGATTATAAAAAATCGATGT
*
1760191 TTTGGAAATAAAA-
64 TTTGAAAATAAAAC
* *
1760204 TCGAGGTTAGAGTATCC
1 T-GGGGTTGGAGTATCC
1760221 TCGATTGTAG
Statistics
Matches: 210, Mismatches: 30, Indels: 25
0.79 0.11 0.09
Matches are distributed among these distances:
77 1 0.00
78 30 0.14
79 149 0.71
80 30 0.14
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (77 bp):
TGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGAGTATCTCGATTATAAAAAATCGATGTTT
TGAAAATAAAAC
Found at i:1760199 original size:158 final size:159
Alignment explanation
Indices: 1759890--1760203 Score: 395
Period size: 158 Copynumber: 2.0 Consensus size: 159
1759880 CAAAAATAAT
* *
1759890 GGGATTGGAGTATCCCCTCGAAAATAATAGGGTTGAAGTATCTCCGATTATGAAAAATCGATGTT
1 GGGATTGGAGTATCCCATCGAAAATAATAGGGTTGAAGTATCTCCGATTATAAAAAATCGATGTT
* * ** *
1759955 TTGAAAATAAAAACTGGGGTTGGAGTATCCCCTCGAAAAAACAGGGTTAGAGTATCTCTGATGGT
66 TTGAAAATAAAAACTAGGGTTGGAGTATCCCCTCGAAAAAACAGGGTTAGAGTATCCCCAATGAT
* * *
1760020 AGAGAATTGGTATTTTAGAAATAAAACTG
131 AGAAAATCGATATTTTAGAAATAAAACTG
* * * *
1760049 GGGATT-GAGTATCCCATC-AGAAATAATAGGGTTGGAGTATC-CTCGATTGTAAAAAATTGGTG
1 GGGATTGGAGTATCCCATCGA-AAATAATAGGGTTGAAGTATCTC-CGATTATAAAAAATCGATG
*
1760111 TTTTGAAAAT-AAAACTAGGGTTGGAGTATCCCTTCGAAAATAACAGGGTT-GTAGTATCCCCAA
64 TTTTGAAAATAAAAACTAGGGTTGGAGTATCCCCTCGAAAA-AACAGGGTTAG-AGTATCCCCAA
* * *
1760174 TTATAGAAAATCGATGTTTTGGAAATAAAA
127 TGATAGAAAATCGATATTTTAGAAATAAAA
1760204 TCGAGGTTAG
Statistics
Matches: 133, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
157 31 0.23
158 96 0.72
159 6 0.05
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (159 bp):
GGGATTGGAGTATCCCATCGAAAATAATAGGGTTGAAGTATCTCCGATTATAAAAAATCGATGTT
TTGAAAATAAAAACTAGGGTTGGAGTATCCCCTCGAAAAAACAGGGTTAGAGTATCCCCAATGAT
AGAAAATCGATATTTTAGAAATAAAACTG
Found at i:1760232 original size:51 final size:51
Alignment explanation
Indices: 1760163--1760273 Score: 152
Period size: 51 Copynumber: 2.2 Consensus size: 51
1760153 ACAGGGTTGT
*
1760163 AGTATCCCCAATTATAGAAAATCGATGTTTTGGAAAT-AAAATCGAGGTTAG
1 AGTATCCCCAATTATAGAAAATCGATATTTTGGAAATAAAAAT-GAGGTTAG
* * * * *
1760214 AGTATCCTCGATTGTAGAAAATCGGTATTTTGGAAATAAAAATGGGGTTAG
1 AGTATCCCCAATTATAGAAAATCGATATTTTGGAAATAAAAATGAGGTTAG
1760265 AGTATCCCC
1 AGTATCCCC
1760274 TCGAAAATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
51 47 0.90
52 5 0.10
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.30
Consensus pattern (51 bp):
AGTATCCCCAATTATAGAAAATCGATATTTTGGAAATAAAAATGAGGTTAG
Found at i:1760251 original size:130 final size:130
Alignment explanation
Indices: 1760078--1760350 Score: 395
Period size: 130 Copynumber: 2.1 Consensus size: 130
1760068 GAAATAATAG
* * * * *
1760078 GGTTGGAGTATCCTCGATTGTAAAAAATTGGTGTTTTGAAAATAAAACTAGGGTTGGAGTATCCC
1 GGTTAGAGTATCCTCGATTGTAAAAAATCGGTATTTTGAAAATAAAAATAGGGTTAGAGTATCCC
* * * * *
1760143 TTCGAAAATAACAGGGTTGTAGTATCCCCAATTAT-AGAAAATCGATGTTTTGGAAATAAAATCG
66 CTCGAAAATAACAAGATTGGAGTATCCCCAATTATGA-AAAATCGATGTTTTGGAAATAAAACCG
1760207 A
130 A
* * *
1760208 GGTTAGAGTATCCTCGATTGTAGAAAATCGGTATTTTGGAAATAAAAATGGGGTTAGAGTATCCC
1 GGTTAGAGTATCCTCGATTGTAAAAAATCGGTATTTTGAAAATAAAAATAGGGTTAGAGTATCCC
* *
1760273 CTCGAAAATAACAAGATTGGAGTATCCCTAATTGTGAAAAATCGATGTTTTGGAAATAAAACCGA
66 CTCGAAAATAACAAGATTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAACCGA
1760338 GGTTAGAGTATCC
1 GGTTAGAGTATCC
1760351 CTTCGAAAAT
Statistics
Matches: 127, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
130 126 0.99
131 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (130 bp):
GGTTAGAGTATCCTCGATTGTAAAAAATCGGTATTTTGAAAATAAAAATAGGGTTAGAGTATCCC
CTCGAAAATAACAAGATTGGAGTATCCCCAATTATGAAAAATCGATGTTTTGGAAATAAAACCGA
Found at i:1760295 original size:209 final size:209
Alignment explanation
Indices: 1759999--1760412 Score: 514
Period size: 209 Copynumber: 2.0 Consensus size: 209
1759989 GAAAAAACAG
* * *
1759999 GGTTAGAGTATCTCTGATGGTAGAGAATTGGTATTTTAGAAATAAAACTGGGGATTGAGTATCCC
1 GGTTAGAGTATCTCTGATGGTAGAAAATCGGTATTTTAGAAATAAAAATGGGGATTGAGTATCCC
* * * * * *
1760064 ATCAGAAATAATAGGGTTGGAGTAT-CCTCGATTGTAAAAAATTGGTGTTTTGAAAATAAAACTA
66 ATCAGAAATAACAAGATTGGAGTATCCCT-AATTGTAAAAAATCGATGTTTTGAAAATAAAAC-A
* * * * *
1760128 G-GGTTGGAGTATCCCTTCGAAAATAACAGGGTTGTAGTATCCCCAATTATAGAAAATCGATGTT
129 GAGGTTAGAGTATCCCTTCGAAAATAACAGAGTTGGAGTATCCCCAATGATAGAAAATCGATATT
*
1760192 TTGGAAATAAAATCGA
194 TTAGAAATAAAATCGA
* *
1760208 GGTTAGAGTATC-CTCGATTGTAGAAAATCGGTATTTTGGAAATAAAAATGGGG-TTAGAGTATC
1 GGTTAGAGTATCTCT-GATGGTAGAAAATCGGTATTTTAGAAATAAAAATGGGGATT-GAGTATC
* * *
1760271 CCCTC-GAAAATAACAAGATTGGAGTATCCCTAATTGTGAAAAATCGATGTTTTGGAAATAAAAC
64 CCATCAG-AAATAACAAGATTGGAGTATCCCTAATTGTAAAAAATCGATGTTTTGAAAATAAAAC
* * * * * *
1760335 CGAGGTTAGAGTATCCCTTCGAAAATAACCGAGTTGGGGTATCCCCGATGGTAGAAAATCGGTAT
128 AGAGGTTAGAGTATCCCTTCGAAAATAACAGAGTTGGAGTATCCCCAATGATAGAAAATCGATAT
1760400 TTTAGAAATAAAA
193 TTTAGAAATAAAA
1760413 ACATGAATGA
Statistics
Matches: 174, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
208 6 0.03
209 165 0.95
210 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (209 bp):
GGTTAGAGTATCTCTGATGGTAGAAAATCGGTATTTTAGAAATAAAAATGGGGATTGAGTATCCC
ATCAGAAATAACAAGATTGGAGTATCCCTAATTGTAAAAAATCGATGTTTTGAAAATAAAACAGA
GGTTAGAGTATCCCTTCGAAAATAACAGAGTTGGAGTATCCCCAATGATAGAAAATCGATATTTT
AGAAATAAAATCGA
Found at i:1760314 original size:79 final size:79
Alignment explanation
Indices: 1760213--1760414 Score: 237
Period size: 79 Copynumber: 2.6 Consensus size: 79
1760203 ATCGAGGTTA
* * * * *
1760213 GAGTATCCTCGATTGTAGAAAATCGGTATTTTGGAAATAAAAATGGGGTTAGAGTATCCCCTCGA
1 GAGTATCCCCAATGGTAGAAAATCGGTATTTTGGAAATAAAAACGAGGTTAGAGTATCCCCTCGA
1760278 AAATAACA-AGATTG
66 AAATAACAGAG-TTG
* * * * * *
1760292 GAGTATCCCTAATTGT-GAAAAATCGATGTTTTGGAAATAAAACCGAGGTTAGAGTATCCCTTCG
1 GAGTATCCCCAATGGTAG-AAAATCGGTATTTTGGAAATAAAAACGAGGTTAGAGTATCCCCTCG
*
1760356 AAAATAACCGAGTTG
65 AAAATAACAGAGTTG
* * *
1760371 GGGTATCCCCGATGGTAGAAAATCGGTATTTTAGAAATAAAAAC
1 GAGTATCCCCAATGGTAGAAAATCGGTATTTTGGAAATAAAAAC
1760415 ATGAATGAAA
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
78 1 0.01
79 98 0.96
80 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (79 bp):
GAGTATCCCCAATGGTAGAAAATCGGTATTTTGGAAATAAAAACGAGGTTAGAGTATCCCCTCGA
AAATAACAGAGTTG
Found at i:1760716 original size:19 final size:19
Alignment explanation
Indices: 1760692--1760741 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1760682 ATCGATACAA
*
1760692 TGTATCAATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
1760711 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
1760730 TGTATCGATACA
1 TGTATCGATACA
1760742 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:1760885 original size:37 final size:37
Alignment explanation
Indices: 1760835--1760906 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
1760825 TGTATCGATA
*
1760835 CACTATGAAATGTATCGATACATACAGGTAAATTTGC
1 CACTATGAAATGTATCGATACATACAAGTAAATTTGC
*
1760872 CACTATGAAATGTATCGATACATGCAAGTAAATTT
1 CACTATGAAATGTATCGATACATACAAGTAAATTT
1760907 TCATATTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (37 bp):
CACTATGAAATGTATCGATACATACAAGTAAATTTGC
Found at i:1780107 original size:13 final size:13
Alignment explanation
Indices: 1780089--1780114 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1780079 TACAGCAAGT
1780089 ATGTATCGATACA
1 ATGTATCGATACA
1780102 ATGTATCGATACA
1 ATGTATCGATACA
1780115 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1782366 original size:21 final size:21
Alignment explanation
Indices: 1782333--1782377 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1782323 TTGCAAGTTG
*
1782333 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1782355 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1782375 AAA
1 AAA
1782378 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1784201 original size:15 final size:15
Alignment explanation
Indices: 1784181--1784211 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1784171 TAAAAATATC
*
1784181 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1784196 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1784211 C
1 C
1784212 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1786309 original size:13 final size:13
Alignment explanation
Indices: 1786291--1786329 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1786281 CATTTTTTCT
1786291 TTGTATCGATACA
1 TTGTATCGATACA
1786304 TTGTATCGATACA
1 TTGTATCGATACA
1786317 TTGTATCGATACA
1 TTGTATCGATACA
1786330 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1788883 original size:13 final size:13
Alignment explanation
Indices: 1788865--1788890 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1788855 TACAGCAAGT
1788865 ATGTATCGATACA
1 ATGTATCGATACA
1788878 ATGTATCGATACA
1 ATGTATCGATACA
1788891 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1790057 original size:66 final size:66
Alignment explanation
Indices: 1789951--1790083 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1789941 AGTAGATTTC
*
1789951 ATCTTAATTATTTCCAATGCAAATAATGGCATGCAACTAAAATATTAATTCAATGCTATTAATTG
1 ATCTTAATTATTTCCAATGCAAATAATGGCATGCAACTAAAATATCAATTCAATGCTATTAATTG
1790016 G
66 G
*
1790017 ATCTTAATTATTTCCAATGCAAATAATGGTATGCAACTAAAATATCAATTCAATGCTATTAATTG
1 ATCTTAATTATTTCCAATGCAAATAATGGCATGCAACTAAAATATCAATTCAATGCTATTAATTG
1790082 G
66 G
1790083 A
1 A
1790084 ATTGGCAATT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.36
Consensus pattern (66 bp):
ATCTTAATTATTTCCAATGCAAATAATGGCATGCAACTAAAATATCAATTCAATGCTATTAATTG
G
Found at i:1791897 original size:17 final size:17
Alignment explanation
Indices: 1791875--1791923 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1791865 ACAAAAGTTT
*
1791875 TTCCTAAGATACGACTA
1 TTCCTAAGATACAACTA
* *
1791892 TTCCTAACATGATAACTA
1 TTCCTAAGAT-ACAACTA
*
1791910 TTCTTAAGATACAA
1 TTCCTAAGATACAA
1791924 GCATTTAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (17 bp):
TTCCTAAGATACAACTA
Found at i:1793369 original size:21 final size:20
Alignment explanation
Indices: 1793342--1793392 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
1793332 GGAAATGAAG
*
1793342 GAATTTGATGTGTTTTTAAA
1 GAATTTGATGTGTATTTAAA
* *
1793362 GAAATTTGAAGTGTATTTGAA
1 G-AATTTGATGTGTATTTAAA
1793383 GAATTTGATG
1 GAATTTGATG
1793393 ATTTGAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (20 bp):
GAATTTGATGTGTATTTAAA
Found at i:1793517 original size:13 final size:13
Alignment explanation
Indices: 1793499--1793526 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1793489 ATACAATTTT
1793499 AATGTATCAATAC
1 AATGTATCAATAC
1793512 AATGTATCAATAC
1 AATGTATCAATAC
1793525 AA
1 AA
1793527 ATTTCATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:1793764 original size:22 final size:22
Alignment explanation
Indices: 1793706--1793779 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 22
1793696 AACATCCATA
* *
1793706 AACATCAAATTCAA-GAACAATT
1 AACATCAAAATCAATCAACAA-T
1793728 AATCA-CAAAA-C-ATCAACAAT
1 AA-CATCAAAATCAATCAACAAT
* *
1793748 AACATCAAAATCAATCAAAAAC
1 AACATCAAAATCAATCAACAAT
*
1793770 AATATCAAAA
1 AACATCAAAA
1793780 GTGCAACATA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
19 2 0.05
20 9 0.21
21 7 0.17
22 22 0.52
23 2 0.05
ACGTcount: A:0.61, C:0.20, G:0.01, T:0.18
Consensus pattern (22 bp):
AACATCAAAATCAATCAACAAT
Found at i:1797704 original size:19 final size:20
Alignment explanation
Indices: 1797680--1797732 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
1797670 ATATTATGCT
**
1797680 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGGACAA
1797699 TTGTATCGATACATGGACAAA
1 TTGTATCGATACATGGAC-AA
1797720 TTGTATCGATACA
1 TTGTATCGATACA
1797733 AGAAATTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.53
21 14 0.47
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:1798588 original size:21 final size:21
Alignment explanation
Indices: 1798524--1798598 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
1798514 TATGCAATTT
**
1798524 TTTATTTTTCTTAGTTAATTCA
1 TTTA-TTTTCTTCTTTAATTCA
* *
1798546 -TTATTCTCTTCTTGCAATTCA
1 TTTATTTTCTTCTT-TAATTCA
*
1798567 TTTATTTTCTTCTTTAAATCA
1 TTTATTTTCTTCTTTAATTCA
*
1798588 TTTAATTTCTT
1 TTTATTTTCTT
1798599 TTCAAGAGTA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 7 0.16
21 24 0.56
22 12 0.28
ACGTcount: A:0.21, C:0.15, G:0.03, T:0.61
Consensus pattern (21 bp):
TTTATTTTCTTCTTTAATTCA
Found at i:1798869 original size:15 final size:16
Alignment explanation
Indices: 1798849--1798881 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1798839 TGCTTTCTTC
1798849 TTTTGCTTGTT-CATG
1 TTTTGCTTGTTCCATG
*
1798864 TTTTGCTTTTTCCATG
1 TTTTGCTTGTTCCATG
1798880 TT
1 TT
1798882 GGACAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.06, C:0.15, G:0.15, T:0.64
Consensus pattern (16 bp):
TTTTGCTTGTTCCATG
Found at i:1799073 original size:3 final size:3
Alignment explanation
Indices: 1799065--1799090 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1799055 AACTTCTTGC
1799065 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
1799091 GCTTTGGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:1800685 original size:20 final size:21
Alignment explanation
Indices: 1800657--1800710 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1800647 TGGGCCAAAG
* * *
1800657 GTATTGATATAATTCATA-AT
1 GTATCGATACAATTCAAATAT
*
1800677 GTATCGATACAATTTAAATAT
1 GTATCGATACAATTCAAATAT
1800698 GTATCGATACAAT
1 GTATCGATACAAT
1800711 CACAGGGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (21 bp):
GTATCGATACAATTCAAATAT
Found at i:1803452 original size:2 final size:2
Alignment explanation
Indices: 1803441--1803483 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1803431 TTTAAGTTGG
1803441 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1803482 AT
1 AT
1803484 TATTTTAGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1807169 original size:99 final size:99
Alignment explanation
Indices: 1807044--1807224 Score: 240
Period size: 99 Copynumber: 1.8 Consensus size: 99
1807034 GCAAACAACC
* *
1807044 TAAAAGAAAATTTTAAGTAGCGAAACCCATAACAAAACATATA-TGTGGCTAAAGCAAGCGGTCT
1 TAAAAGAAAATTTTAAGTAGCAAAACCCATAACAAAACATA-ACTATGGCTAAAGCAAGCGGTCT
*
1807108 ATATTTAGTTATATTTTTTTTCTTCAAATACAATT
65 ATATTTAGTCATATTTTTTTTCTTCAAATACAATT
* ** * * *
1807143 TAAAAGAGAATTTTGAA-TAGCAAAACCCATAATGAAACCTAACTATGGCTAGAGCAAGTGGTCT
1 TAAAAGAAAATTTT-AAGTAGCAAAACCCATAACAAAACATAACTATGGCTAAAGCAAGCGGTCT
*
1807207 ATGTTTAGTCATATTTTT
65 ATATTTAGTCATATTTTT
1807225 CCTTTATTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
98 1 0.01
99 67 0.96
100 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (99 bp):
TAAAAGAAAATTTTAAGTAGCAAAACCCATAACAAAACATAACTATGGCTAAAGCAAGCGGTCTA
TATTTAGTCATATTTTTTTTCTTCAAATACAATT
Found at i:1807815 original size:30 final size:30
Alignment explanation
Indices: 1807781--1807925 Score: 127
Period size: 30 Copynumber: 5.2 Consensus size: 30
1807771 TATGAACTCC
1807781 TTGTATTAGTAAATGTTTGTCATGATGCAT
1 TTGTATTAGTAAATGTTTGTCATGATGCAT
* * *
1807811 TTG---TA-TAAATG-TTGTTATGAATTC-C
1 TTGTATTAGTAAATGTTTGTCATG-ATGCAT
1807836 TTGTATTAGTAAATGTTTGTCATGATGCAT
1 TTGTATTAGTAAATGTTTGTCATGATGCAT
* *
1807866 TTG---TA-TAAATG-TTGTTATGAACT-C-C
1 TTGTATTAGTAAATGTTTGTCATG-A-TGCAT
1807891 TTGTATTAGTAAATGTTTGTCATGATGCAT
1 TTGTATTAGTAAATGTTTGTCATGATGCAT
1807921 TTGTA
1 TTGTA
1807926 AAGAGGACTC
Statistics
Matches: 89, Mismatches: 10, Indels: 32
0.68 0.08 0.24
Matches are distributed among these distances:
25 20 0.22
26 17 0.19
27 5 0.06
28 5 0.06
29 17 0.19
30 25 0.28
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.47
Consensus pattern (30 bp):
TTGTATTAGTAAATGTTTGTCATGATGCAT
Found at i:1807830 original size:25 final size:26
Alignment explanation
Indices: 1807790--1807925 Score: 107
Period size: 26 Copynumber: 5.0 Consensus size: 26
1807780 CTTGTATTAG
1807790 TAAATGTTTGTCATGATGCATTTGTA
1 TAAATGTTTGTCATGATGCATTTGTA
* * * *
1807816 TAAATG-TTGTTATGAATTCCTTGTATTA
1 TAAATGTTTGTCATG-ATGCATT-T-GTA
1807844 GTAAATGTTTGTCATGATGCATTTGTA
1 -TAAATGTTTGTCATGATGCATTTGTA
* * *
1807871 TAAATG-TTGTTATGAACT-CCTTGTATTA
1 TAAATGTTTGTCATG-A-TGCATT-T-GTA
1807899 GTAAATGTTTGTCATGATGCATTTGTA
1 -TAAATGTTTGTCATGATGCATTTGTA
1807926 AAGAGGACTC
Statistics
Matches: 84, Mismatches: 14, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
25 14 0.17
26 21 0.25
27 7 0.08
28 7 0.08
29 21 0.25
30 14 0.17
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.46
Consensus pattern (26 bp):
TAAATGTTTGTCATGATGCATTTGTA
Found at i:1807831 original size:55 final size:55
Alignment explanation
Indices: 1807760--1807925 Score: 314
Period size: 55 Copynumber: 3.0 Consensus size: 55
1807750 AATGTTACTA
*
1807760 ATAAGTGTTGTTATGAACTCCTTGTATTAGTAAATGTTTGTCATGATGCATTTGT
1 ATAAATGTTGTTATGAACTCCTTGTATTAGTAAATGTTTGTCATGATGCATTTGT
*
1807815 ATAAATGTTGTTATGAATTCCTTGTATTAGTAAATGTTTGTCATGATGCATTTGT
1 ATAAATGTTGTTATGAACTCCTTGTATTAGTAAATGTTTGTCATGATGCATTTGT
1807870 ATAAATGTTGTTATGAACTCCTTGTATTAGTAAATGTTTGTCATGATGCATTTGT
1 ATAAATGTTGTTATGAACTCCTTGTATTAGTAAATGTTTGTCATGATGCATTTGT
1807925 A
1 A
1807926 AAGAGGACTC
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 108 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (55 bp):
ATAAATGTTGTTATGAACTCCTTGTATTAGTAAATGTTTGTCATGATGCATTTGT
Found at i:1807848 original size:29 final size:29
Alignment explanation
Indices: 1807765--1807907 Score: 122
Period size: 29 Copynumber: 5.1 Consensus size: 29
1807755 TACTAATAAG
*
1807765 TGTTGTTATGAACTCCTTGTATTAGTAAA
1 TGTTGTTATGAATTCCTTGTATTAGTAAA
* * * *
1807794 TGTTTGTCATG-ATGCATT-T-GTA-TAAA
1 TG-TTGTTATGAATTCCTTGTATTAGTAAA
1807820 TGTTGTTATGAATTCCTTGTATTAGTAAA
1 TGTTGTTATGAATTCCTTGTATTAGTAAA
* * * *
1807849 TGTTTGTCATG-ATGCATT-T-GTA-TAAA
1 TG-TTGTTATGAATTCCTTGTATTAGTAAA
*
1807875 TGTTGTTATGAACTCCTTGTATTAGTAAA
1 TGTTGTTATGAATTCCTTGTATTAGTAAA
1807904 TGTT
1 TGTT
1807908 TGTCATGATG
Statistics
Matches: 86, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
25 14 0.16
26 21 0.24
27 6 0.07
28 6 0.07
29 25 0.29
30 14 0.16
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (29 bp):
TGTTGTTATGAATTCCTTGTATTAGTAAA
Found at i:1811581 original size:13 final size:13
Alignment explanation
Indices: 1811563--1811589 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1811553 ATAGTAACCC
1811563 ATGTATCGATACA
1 ATGTATCGATACA
1811576 ATGTATCGATACA
1 ATGTATCGATACA
1811589 A
1 A
1811590 AGAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1813224 original size:226 final size:226
Alignment explanation
Indices: 1812824--1813275 Score: 877
Period size: 226 Copynumber: 2.0 Consensus size: 226
1812814 GAAGTCCCAA
1812824 AAAGAATGCTAATTCTCCCATCATGCTCATCTCGAATTCACCTTGCATTAACTTAGAAAATTCTT
1 AAAGAATGCTAATTCTCCCATCATGCTCATCTCGAATTCACCTTGCATTAACTTAGAAAATTCTT
1812889 GACACAAGGATTCATTAGTAGCACCAAAAATAATGTCATCAACATATAATTGTACAATTAGAATG
66 GACACAAGGATTCATTAGTAGCACCAAAAATAATGTCATCAACATATAATTGTACAATTAGAATG
1812954 TCTTTTCCTTTTGATTTAATAAAAAGAGTTTTATCCACATTACCTCTATTAAAGCCTTTTACAAT
131 TCTTTTCCTTTTGATTTAATAAAAAGAGTTTTATCCACATTACCTCTATTAAAGCCTTTTACAAT
1813019 CAAAAATTTTGAAAGCCTTTCATACCATGCT
196 CAAAAATTTTGAAAGCCTTTCATACCATGCT
1813050 AAAGAATGCTAATTCTCCCATCATGCTCATCTCGAATTCACCTTGCATTAACTTAGAAAATTCTT
1 AAAGAATGCTAATTCTCCCATCATGCTCATCTCGAATTCACCTTGCATTAACTTAGAAAATTCTT
* *
1813115 GATACGAGGATTCATTAGTAGCACCAAAAATAATGTCATCAACATATAATTGTACAATTAGAATG
66 GACACAAGGATTCATTAGTAGCACCAAAAATAATGTCATCAACATATAATTGTACAATTAGAATG
*
1813180 TCTTTTCCTTTTGATTTAATAAAAAGAGTTTTATCCATATTACCTCTATTAAAGCCTTTTACAAT
131 TCTTTTCCTTTTGATTTAATAAAAAGAGTTTTATCCACATTACCTCTATTAAAGCCTTTTACAAT
1813245 CAAAAATTTTGAAAGCCTTTCATACCATGCT
196 CAAAAATTTTGAAAGCCTTTCATACCATGCT
1813276 CGAGGAGCTT
Statistics
Matches: 223, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
226 223 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (226 bp):
AAAGAATGCTAATTCTCCCATCATGCTCATCTCGAATTCACCTTGCATTAACTTAGAAAATTCTT
GACACAAGGATTCATTAGTAGCACCAAAAATAATGTCATCAACATATAATTGTACAATTAGAATG
TCTTTTCCTTTTGATTTAATAAAAAGAGTTTTATCCACATTACCTCTATTAAAGCCTTTTACAAT
CAAAAATTTTGAAAGCCTTTCATACCATGCT
Found at i:1817884 original size:19 final size:21
Alignment explanation
Indices: 1817845--1817888 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
1817835 TTTTTAACCG
*
1817845 TTTATCAAGGAGGAGAAATTT
1 TTTATCAAAGAGGAGAAATTT
1817866 TTTATCAAAG-GGA-AAATTT
1 TTTATCAAAGAGGAGAAATTT
1817885 TTTA
1 TTTA
1817889 AAGAGAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 3 0.14
21 9 0.41
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (21 bp):
TTTATCAAAGAGGAGAAATTT
Found at i:1818394 original size:20 final size:20
Alignment explanation
Indices: 1818371--1818408 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1818361 TACATAGGTA
1818371 TTTGTATCAATACATTATGC
1 TTTGTATCAATACATTATGC
*
1818391 TTTGTATCGATACATTAT
1 TTTGTATCAATACATTAT
1818409 ATTAATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (20 bp):
TTTGTATCAATACATTATGC
Found at i:1818433 original size:32 final size:32
Alignment explanation
Indices: 1818395--1818469 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
1818385 TTATGCTTTG
* *
1818395 TATCGATACATTATATTAATACATGTTCACTA
1 TATCGATACATTATATCAATACATATTCACTA
* * *
1818427 TATCGATACATTGTATCGATACATATTTACTA
1 TATCGATACATTATATCAATACATATTCACTA
1818459 TATCGATACAT
1 TATCGATACAT
1818470 GCATAATTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (32 bp):
TATCGATACATTATATCAATACATATTCACTA
Found at i:1819685 original size:46 final size:46
Alignment explanation
Indices: 1819628--1819717 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
1819618 AATAAAATGG
1819628 TTAGAAATTGAATTCATCTTAATTCTTTTAATTTTATACTTTTTGT
1 TTAGAAATTGAATTCATCTTAATTCTTTTAATTTTATACTTTTTGT
* * *
1819674 TTAGAATTTGAATTCATCTTGATTCTTTTACTTTTATACTTTTT
1 TTAGAAATTGAATTCATCTTAATTCTTTTAATTTTATACTTTTT
1819718 TGTTAGTATG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.58
Consensus pattern (46 bp):
TTAGAAATTGAATTCATCTTAATTCTTTTAATTTTATACTTTTTGT
Found at i:1823981 original size:2 final size:2
Alignment explanation
Indices: 1823974--1824039 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
1823964 AGACAGTGTC
1823974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1824016 AT TT AT TT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
1824040 GCTATGTTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:1827044 original size:2 final size:2
Alignment explanation
Indices: 1827037--1827062 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1827027 AGATTTTAAG
1827037 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
1827063 GAGGCACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1828592 original size:56 final size:57
Alignment explanation
Indices: 1828453--1828599 Score: 133
Period size: 56 Copynumber: 2.6 Consensus size: 57
1828443 ATAATTCGTG
* * **
1828453 TATTTATATTAT-TTTTATTATTTTTT-ATGTCGTA-ATCCTATTTAAAATATTATA
1 TATTTATATTATATTTAATTATTTTTTCATGTCATATATAATATTTAAAATATTATA
* * ** * ** *
1828507 TATTTATATAAAATTTAACAAATAATTCATGTCATATA-AAT-TTTAATATATTCATA
1 TATTTATATTATATTTAATTATTTTTTCATGTCATATATAATATTTAAAATATT-ATA
*
1828563 TATTTATATTATATTTAATTATTTTTTCATATCATAT
1 TATTTATATTATATTTAATTATTTTTTCATGTCATAT
1828600 TTACGTCATG
Statistics
Matches: 69, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
54 10 0.14
55 18 0.26
56 40 0.58
57 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.54
Consensus pattern (57 bp):
TATTTATATTATATTTAATTATTTTTTCATGTCATATATAATATTTAAAATATTATA
Found at i:1830837 original size:2 final size:2
Alignment explanation
Indices: 1830832--1830882 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1830822 TCTCTTTCGT
1830832 TA TA TA 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 TA TA TA
1830874 TA TA TA TA T
1 TA TA TA TA T
1830883 CATCGTTGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1831282 original size:17 final size:18
Alignment explanation
Indices: 1831248--1831290 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1831238 TTTTGTTTAA
1831248 TTTATTATTAAATAATAT
1 TTTATTATTAAATAATAT
* *
1831266 TTTATT-TTATATGATAT
1 TTTATTATTAAATAATAT
*
1831283 TTTCTTAT
1 TTTATTAT
1831291 GGGTATTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTATTATTAAATAATAT
Found at i:1832145 original size:22 final size:22
Alignment explanation
Indices: 1832117--1832187 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
1832107 AGTTAAATTT
1832117 GTGATATGTACATATAGTTATA
1 GTGATATGTACATATAGTTATA
** * *
1832139 GTGATATACACATATTGATATA
1 GTGATATGTACATATAGTTATA
* **
1832161 GTGATATGTACGTACCGTTATA
1 GTGATATGTACATATAGTTATA
1832183 GTGAT
1 GTGAT
1832188 TTTTTGTGAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (22 bp):
GTGATATGTACATATAGTTATA
Found at i:1833174 original size:21 final size:21
Alignment explanation
Indices: 1833132--1833175 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1833122 CATAACTAAA
* **
1833132 GAAAATAATCGAATCCTTAAG
1 GAAAAAAATCGAATCCCAAAG
*
1833153 GAAAAAAATCGATTCCCAAAG
1 GAAAAAAATCGAATCCCAAAG
1833174 GA
1 GA
1833176 CAAGAACTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (21 bp):
GAAAAAAATCGAATCCCAAAG
Found at i:1833215 original size:21 final size:21
Alignment explanation
Indices: 1833149--1833215 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
1833139 ATCGAATCCT
* * *
1833149 TAAGGAAAAAAATCGATTCCC
1 TAAGGAAAAGAACCAATTCCC
* * * **
1833170 AAAGGACAAGAACTAGCTCCC
1 TAAGGAAAAGAACCAATTCCC
*
1833191 TAAGGAAAAGAACCAATTCCT
1 TAAGGAAAAGAACCAATTCCC
1833212 TAAG
1 TAAG
1833216 CCTTAAAAAA
Statistics
Matches: 32, Mismatches: 14, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.16
Consensus pattern (21 bp):
TAAGGAAAAGAACCAATTCCC
Found at i:1833649 original size:21 final size:21
Alignment explanation
Indices: 1833602--1833645 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1833592 ACTTAAAGTC
*
1833602 AAGAACTAATCCCTTCAAAGA
1 AAGAACTAACCCCTTCAAAGA
1833623 AAGAACTAACCCCTT-AAAGA
1 AAGAACTAACCCCTTCAAAGA
1833643 AAG
1 AAG
1833646 GAACCGACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.50, C:0.23, G:0.11, T:0.16
Consensus pattern (21 bp):
AAGAACTAACCCCTTCAAAGA
Found at i:1834352 original size:22 final size:22
Alignment explanation
Indices: 1834311--1834380 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
1834301 ACGTATGACT
*
1834311 ATAACAATATATA-ATATCATA
1 ATAACATTATATACATATCATA
1834332 ATAACATTATATACATATCATA
1 ATAACATTATATACATATCATA
*
1834354 ATAACATTATATACATATCACA
1 ATAACATTATATACATATCATA
1834376 ATAAC
1 ATAAC
1834381 TAAAAGAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 12 0.26
22 34 0.74
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAACATTATATACATATCATA
Found at i:1834591 original size:22 final size:22
Alignment explanation
Indices: 1834566--1834635 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
1834556 TTCATGTAGA
*
1834566 ATCAATATAACAATATGTGCAT
1 ATCAATATAACAATATGTACAT
* **
1834588 ATCATTATATTAATATGTACAT
1 ATCAATATAACAATATGTACAT
* **
1834610 ATCACTATAACTGTATGTACAT
1 ATCAATATAACAATATGTACAT
1834632 ATCA
1 ATCA
1834636 TAAATTTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.37
Consensus pattern (22 bp):
ATCAATATAACAATATGTACAT
Found at i:1835480 original size:15 final size:17
Alignment explanation
Indices: 1835448--1835483 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
1835438 AATTAATATG
1835448 AATATCGAATATAAATT
1 AATATCGAATATAAATT
1835465 AATAT-GAATA-AAATT
1 AATATCGAATATAAATT
1835480 AATA
1 AATA
1835484 ATACAAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 5 0.26
17 5 0.26
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (17 bp):
AATATCGAATATAAATT
Found at i:1835484 original size:23 final size:22
Alignment explanation
Indices: 1835437--1835478 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1835427 CACAAAATCA
*
1835437 AAATTAATATGAATATCGAATAT
1 AAATTAATATGAATA-CAAATAT
1835460 AAATTAATATGAATA-AAAT
1 AAATTAATATGAATACAAAT
1835479 TAATAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
23 15 0.83
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33
Consensus pattern (22 bp):
AAATTAATATGAATACAAATAT
Found at i:1841511 original size:21 final size:23
Alignment explanation
Indices: 1841455--1841513 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
1841445 ATTCTCAAAT
*
1841455 TATTTAAATTAAATT--TTAATA
1 TATTTAAATTAATTTAATTAATA
*
1841476 TATTTTAATTAATTTAATTAATA
1 TATTTAAATTAATTTAATTAATA
1841499 -ATTTAAATT-ATTTAA
1 TATTTAAATTAATTTAA
1841514 ATTTAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 19 0.58
22 8 0.24
23 6 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTAAATTAATTTAATTAATA
Found at i:1841520 original size:32 final size:31
Alignment explanation
Indices: 1841466--1841535 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
1841456 ATTTAAATTA
* *
1841466 AATTTTAATATATTTTAATTAATTTAATTAAT
1 AATTTAAATATATTTAAATTAATTTAA-TAAT
1841498 AATTTAAAT-TATTTAAATTTAATTTAATAAT
1 AATTTAAATATATTTAAA-TTAATTTAATAAT
1841529 AACTTTA
1 AA-TTTA
1841536 TCAAATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
AATTTAAATATATTTAAATTAATTTAATAAT
Found at i:1841544 original size:32 final size:31
Alignment explanation
Indices: 1841456--1841535 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 31
1841446 TTCTCAAATT
* *
1841456 ATTTAAATTAA-ATTTTAATATATTTTAA-TTA
1 ATTT-AATTAATAATTTAA-ATATTTAAATTTA
1841487 ATTTAATTAATAATTTAAATTATTTAAATTTA
1 ATTTAATTAATAATTTAAA-TATTTAAATTTA
1841519 ATTTAA-TAATAACTTTA
1 ATTTAATTAATAA-TTTA
1841536 TCAAATTTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 7 0.16
31 23 0.53
32 13 0.30
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTTAATTAATAATTTAAATATTTAAATTTA
Found at i:1842784 original size:19 final size:18
Alignment explanation
Indices: 1842743--1842882 Score: 68
Period size: 19 Copynumber: 7.2 Consensus size: 18
1842733 TTTAGTAAAA
1842743 TAAATAATAATTTAAATT
1 TAAATAATAATTTAAATT
* **
1842761 AAAATAATAAATTTTTATT
1 TAAATAAT-AATTTAAATT
*
1842780 TAAAT-TTAATTATAAAATAT
1 TAAATAATAATT-T-AAAT-T
* * *
1842800 ATAAAAATATTAATATAAATA
1 -T--AAATAATAATTTAAATT
*
1842821 TAAAT-ATAATTTTTTAATT
1 TAAATAATAA--TTTAAATT
1842840 AAATAAATAATAATTTAAATT
1 ---TAAATAATAATTTAAATT
*
1842861 TAAATAAATAAATTAAATT
1 TAAAT-AATAATTTAAATT
1842880 TAA
1 TAA
1842883 TTAAATACGA
Statistics
Matches: 92, Mismatches: 15, Indels: 29
0.68 0.11 0.21
Matches are distributed among these distances:
17 7 0.08
18 18 0.20
19 34 0.37
20 2 0.02
21 8 0.09
22 9 0.10
23 9 0.10
24 5 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAATAATAATTTAAATT
Found at i:1842847 original size:22 final size:22
Alignment explanation
Indices: 1842820--1842889 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
1842810 TAATATAAAT
1842820 ATAAATATAATTTTTTAATTAA
1 ATAAATATAATTTTTTAATTAA
*
1842842 ATAAATAATAA--TTTAAATTTAA
1 ATAAAT-ATAATTTTTTAA-TTAA
*
1842864 ATAAATA-AATTAAATTTAATTAA
1 ATAAATATAATT--TTTTAATTAA
1842887 ATA
1 ATA
1842890 CGAATTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
20 2 0.05
21 6 0.15
22 16 0.41
23 11 0.28
24 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAAATATAATTTTTTAATTAA
Found at i:1842887 original size:19 final size:19
Alignment explanation
Indices: 1842843--1842889 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1842833 TTTAATTAAA
*
1842843 TAAAT-AATAATTTAAATT
1 TAAATAAATAAATTAAATT
1842861 TAAATAAATAAATTAAATT
1 TAAATAAATAAATTAAATT
*
1842880 TAATTAAATA
1 TAAATAAATA
1842890 CGAATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAAATAAATTAAATT
Found at i:1843257 original size:20 final size:20
Alignment explanation
Indices: 1843228--1843266 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1843218 TATTTTTATT
* *
1843228 TAAATTTAATTATATAATTA
1 TAAATATAATTAAATAATTA
1843248 TAAATATAATTAAATAATT
1 TAAATATAATTAAATAATT
1843267 TATTTTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATATAATTAAATAATTA
Found at i:1844754 original size:18 final size:20
Alignment explanation
Indices: 1844710--1844754 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
1844700 TGTATTCATT
1844710 ATCAAAATAAAATTAACTATA
1 ATCAAAAT-AAATTAACTATA
*
1844731 AT-AAAAT-AATTAA-TTTA
1 ATCAAAATAAATTAACTATA
1844748 ATCAAAA
1 ATCAAAA
1844755 ATTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 5 0.23
18 10 0.45
20 5 0.23
21 2 0.09
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
ATCAAAATAAATTAACTATA
Found at i:1845550 original size:20 final size:21
Alignment explanation
Indices: 1845508--1845550 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1845498 TTTTATAATT
*
1845508 TGTATTGATAGAACAAGTTAA
1 TGTATTGATAGAACAAGTAAA
* *
1845529 TGTATTGAT-GCATAAGTAAA
1 TGTATTGATAGAACAAGTAAA
1845549 TG
1 TG
1845551 CATCGATACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (21 bp):
TGTATTGATAGAACAAGTAAA
Found at i:1845680 original size:20 final size:20
Alignment explanation
Indices: 1845640--1845680 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1845630 CATAAGAAAA
* *
1845640 TGTATTGATACATTATTCGT
1 TGTATCGATACATTATGCGT
*
1845660 TGTATCGATACATTCTGCGT
1 TGTATCGATACATTATGCGT
1845680 T
1 T
1845681 TTTAACCCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATTATGCGT
Found at i:1848425 original size:20 final size:21
Alignment explanation
Indices: 1848383--1848435 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1848373 TTCAATAACT
1848383 TGTATCGATACAATAAGGCAA
1 TGTATCGATACAATAAGGCAA
*
1848404 TGTATCGATA-TATAAGTG-AA
1 TGTATCGATACAATAAG-GCAA
1848424 TGTATCGATACA
1 TGTATCGATACA
1848436 TGCCTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAATAAGGCAA
Found at i:1854392 original size:105 final size:105
Alignment explanation
Indices: 1854203--1854409 Score: 333
Period size: 105 Copynumber: 2.0 Consensus size: 105
1854193 TACAAATGAG
* *
1854203 TGAGACCTTGTCCATTTTCACTATATCGTATAATACTTTTTAAAAGCATAACATTAATTCTTTAT
1 TGAGACCTTGTCCATTTTCACTATACCGTATAATACTTTTTAAAAGCATAACATTAACTCTTTAT
* *
1854268 AAGAGCTATAATTCTACATCTACGAGTAAAGCTCTCAGAC
66 AAGAGCTATAATTCCACATCTACAAGTAAAGCTCTCAGAC
* * *
1854308 TGAGACCTTGTCCATTTTCACTATACCGTATAATACTTTTTAAGAGGATAACCTTAACTCTTTAT
1 TGAGACCTTGTCCATTTTCACTATACCGTATAATACTTTTTAAAAGCATAACATTAACTCTTTAT
* *
1854373 AAGAGCTATGATTCCACATCTATAAGTAAAGCTCTCA
66 AAGAGCTATAATTCCACATCTACAAGTAAAGCTCTCA
1854410 TCAAGTATAA
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 93 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (105 bp):
TGAGACCTTGTCCATTTTCACTATACCGTATAATACTTTTTAAAAGCATAACATTAACTCTTTAT
AAGAGCTATAATTCCACATCTACAAGTAAAGCTCTCAGAC
Found at i:1858708 original size:20 final size:20
Alignment explanation
Indices: 1858644--1858710 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
1858634 AAAAAGACAG
* * *
1858644 AATGCATCGATATATTGAAG
1 AATGTATCGATACATTGAAA
* *
1858664 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
*
1858684 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
1858704 AATGTAT
1 AATGTAT
1858711 TACTACATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:1859360 original size:2 final size:2
Alignment explanation
Indices: 1859302--1859344 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1859292 CATGCTTTTG
1859302 TA TA TA 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 TA TA TA
1859344 T
1 T
1859345 TATCTACACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1859476 original size:19 final size:18
Alignment explanation
Indices: 1859449--1859498 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
1859439 TTTGTAGCTT
*
1859449 TTTTAATATTTTGTTTTAAG
1 TTTT-ATATTTT-TTTTAAA
1859469 TTTTATATTTATTTTTAAA
1 TTTTATATTT-TTTTTAAA
*
1859488 TTATATATTTT
1 TTTTATATTTT
1859499 AAGGTTGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 21 0.78
20 5 0.19
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (18 bp):
TTTTATATTTTTTTTAAA
Found at i:1869981 original size:2 final size:2
Alignment explanation
Indices: 1869974--1870012 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1869964 CATGTTTATT
* *
1869974 TA TA TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1870013 AATGTACCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1871678 original size:26 final size:24
Alignment explanation
Indices: 1871649--1871696 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
1871639 ATTGTTTAAT
*
1871649 TTATTAATAATATTTAAATTTATACA
1 TTATTAAT-ATA-TTAAATATATACA
1871675 TTATTAATATATTAAATATATA
1 TTATTAATATATTAAATATATA
1871697 TTTTTATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 3 0.14
26 8 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATTAATATATTAAATATATACA
Found at i:1872711 original size:17 final size:17
Alignment explanation
Indices: 1872689--1872722 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1872679 ATTGGTTAAA
*
1872689 TTTAATTTAATTTTATT
1 TTTAATATAATTTTATT
*
1872706 TTTAATATGATTTTATT
1 TTTAATATAATTTTATT
1872723 AATCAATCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTAATATAATTTTATT
Found at i:1872845 original size:17 final size:17
Alignment explanation
Indices: 1872825--1872866 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1872815 TAATAAATAA
1872825 AAAAATTTAT-AATTATT
1 AAAAATTTATCAATT-TT
*
1872842 -AAAATTAATCAATTTT
1 AAAAATTTATCAATTTT
1872858 AAAAATTTA
1 AAAAATTTA
1872867 CATAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAATTTATCAATTTT
Found at i:1876802 original size:54 final size:54
Alignment explanation
Indices: 1876739--1876863 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 54
1876729 GATGCCATTA
* *
1876739 TGGCGATCAAAATTTGACATGAGTGACTTGGTATCACTAAGAAAGATACCACGG
1 TGGCAATCAAAATTTGACAGGAGTGACTTGGTATCACTAAGAAAGATACCACGG
* * * * * * *
1876793 TGTCAATCAAAATTTAATAGGAGTGACTTGGTGTCACTAAGAATGATGCCATGG
1 TGGCAATCAAAATTTGACAGGAGTGACTTGGTATCACTAAGAAAGATACCACGG
* *
1876847 TGGCGATCAACATTTGA
1 TGGCAATCAAAATTTGA
1876864 AGTTAGTGTT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (54 bp):
TGGCAATCAAAATTTGACAGGAGTGACTTGGTATCACTAAGAAAGATACCACGG
Found at i:1880498 original size:19 final size:19
Alignment explanation
Indices: 1880474--1880536 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1880464 TAGCCAAACT
1880474 TGTATCGATACACAAAGTA
1 TGTATCGATACACAAAGTA
1880493 TGTATCGAT--AC--A--A
1 TGTATCGATACACAAAGTA
1880506 TGTATCGATACACAAAGTA
1 TGTATCGATACACAAAGTA
1880525 TGTATCGATACA
1 TGTATCGATACA
1880537 ATGTATCAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
15 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACAAAGTA
Found at i:1880510 original size:13 final size:13
Alignment explanation
Indices: 1880492--1880549 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
1880482 TACACAAAGT
1880492 ATGTATCGATACA
1 ATGTATCGATACA
1880505 ATGTATCGATACACAAA
1 ATGTATCGAT--AC--A
1880522 GTATGTATCGATACA
1 --ATGTATCGATACA
*
1880537 ATGTATCAATACA
1 ATGTATCGATACA
1880550 CAAAAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 22 0.58
15 3 0.08
17 3 0.08
19 10 0.26
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1880515 original size:32 final size:32
Alignment explanation
Indices: 1880474--1880553 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
1880464 TAGCCAAACT
1880474 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAGTATGTATCGATACAA
1880506 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAGTATGTATCGATACAA
*
1880538 TGTATCAATACACAAA
1 TGTATCGATACACAAA
1880554 AAAATTGTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAGTATGTATCGATACAA
Found at i:1884649 original size:15 final size:15
Alignment explanation
Indices: 1884626--1884656 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1884616 TAAAAATGTC
*
1884626 CAAATTGAGGAAGCT
1 CAAAATGAGGAAGCT
1884641 CAAAATGAGGAAGCT
1 CAAAATGAGGAAGCT
1884656 C
1 C
1884657 CACAAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16
Consensus pattern (15 bp):
CAAAATGAGGAAGCT
Found at i:1886753 original size:13 final size:13
Alignment explanation
Indices: 1886735--1886773 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1886725 ACATTTTTCT
*
1886735 TTGTATTGATACA
1 TTGTATCGATACA
1886748 TTGTATCGATACA
1 TTGTATCGATACA
*
1886761 CTGTATCGATACA
1 TTGTATCGATACA
1886774 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1887131 original size:17 final size:17
Alignment explanation
Indices: 1887109--1887150 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
1887099 TTGGTTTGCA
1887109 TCAAAATCGTCCCATTT
1 TCAAAATCGTCCCATTT
1887126 TCAAAATCGTCCCATTT
1 TCAAAATCGTCCCATTT
1887143 TCAAAATC
1 TCAAAATC
1887151 TAAACCTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (17 bp):
TCAAAATCGTCCCATTT
Found at i:1889378 original size:13 final size:13
Alignment explanation
Indices: 1889360--1889385 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1889350 TACACAAAGT
1889360 ATGTATCGATACA
1 ATGTATCGATACA
1889373 ATGTATCGATACA
1 ATGTATCGATACA
1889386 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1889404 original size:34 final size:34
Alignment explanation
Indices: 1889342--1889440 Score: 166
Period size: 34 Copynumber: 3.0 Consensus size: 34
1889332 TAGCCAAACT
**
1889342 TGTATCGATACAC-AAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
1889374 TGTATCGATACACAAAAAAATTGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
1889408 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
1889441 TTGGCTTGTA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.21
33 4 0.06
34 46 0.73
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.27
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:1889413 original size:13 final size:13
Alignment explanation
Indices: 1889395--1889419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1889385 ACAAAAAAAT
1889395 TGTATCGATACAA
1 TGTATCGATACAA
1889408 TGTATCGATACA
1 TGTATCGATACA
1889420 CAAAAAAATT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1893442 original size:27 final size:25
Alignment explanation
Indices: 1893412--1893469 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 25
1893402 ACAAAATCAT
*
1893412 TAAAATTTTTTATGAATACAATTATAA
1 TAAAATATTTTAT-AATA-AATTATAA
*
1893439 TAAAATATTTTATAATAAATTAT-G
1 TAAAATATTTTATAATAAATTATAA
1893463 TAAAATA
1 TAAAATA
1893470 AAAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 7 0.24
25 6 0.21
26 4 0.14
27 12 0.41
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (25 bp):
TAAAATATTTTATAATAAATTATAA
Found at i:1894166 original size:19 final size:20
Alignment explanation
Indices: 1894142--1894193 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1894132 TGTATTGATA
*
1894142 CATTGTATCGATACAT-GTT
1 CATTGTATCGATACATACTT
1894161 CATTGTATCGATACATACTT
1 CATTGTATCGATACATACTT
*
1894181 AATTGTATCGATA
1 CATTGTATCGATA
1894194 TAAGAAACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
CATTGTATCGATACATACTT
Found at i:1894260 original size:13 final size:13
Alignment explanation
Indices: 1894242--1894272 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1894232 AATACATGGG
1894242 ACATTGTATCAAT
1 ACATTGTATCAAT
*
1894255 ACATTGTATCGAT
1 ACATTGTATCAAT
1894268 ACATT
1 ACATT
1894273 ATGCCCAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
ACATTGTATCAAT
Found at i:1906821 original size:13 final size:13
Alignment explanation
Indices: 1906803--1906833 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1906793 ATACAAAGAT
1906803 CAATGTATCGATA
1 CAATGTATCGATA
1906816 CAATGTATCGATA
1 CAATGTATCGATA
1906829 CAATG
1 CAATG
1906834 AATAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1906830 original size:33 final size:33
Alignment explanation
Indices: 1906788--1906850 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1906778 TTCCCAGATT
1906788 TATCGATACAAAG-ATCAATGTATCGATACAATG
1 TATCGATACAAAGAAT-AATGTATCGATACAATG
*
1906821 TATCGATACAATGAATAATGTATCGATACA
1 TATCGATACAAAGAATAATGTATCGATACA
1906851 TTTCCTTGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (33 bp):
TATCGATACAAAGAATAATGTATCGATACAATG
Found at i:1906908 original size:19 final size:19
Alignment explanation
Indices: 1906884--1906944 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
1906874 CGATACATTG
1906884 TATCGATACAACACTTATT
1 TATCGATACAACACTTATT
1906903 TATCGAT---ACA--T-TT
1 TATCGATACAACACTTATT
* *
1906916 TATCAATACAACACTTATG
1 TATCGATACAACACTTATT
1906935 TATCGATACA
1 TATCGATACA
1906945 TTTACTGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
13 8 0.24
14 1 0.03
16 6 0.18
18 1 0.03
19 17 0.52
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (19 bp):
TATCGATACAACACTTATT
Found at i:1906925 original size:32 final size:32
Alignment explanation
Indices: 1906869--1906947 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
1906859 GCAGTAGCTT
* * *
1906869 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTTTATCAATACAACACTTA
*
1906901 TTTATCGATACATTTTATCAATACAACACTTA
1 TGTATCGATACATTTTATCAATACAACACTTA
1906933 TGTATCGATACATTT
1 TGTATCGATACATTT
1906948 ACTGTTTGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATTTTATCAATACAACACTTA
Found at i:1907703 original size:20 final size:21
Alignment explanation
Indices: 1907680--1907730 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1907670 CAGATTGCAT
**
1907680 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1907700 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1907721 TGTATCGATA
1 TGTATCGATA
1907731 TAGGTCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:1907801 original size:13 final size:13
Alignment explanation
Indices: 1907783--1907808 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1907773 TACACACAAT
1907783 ATGTATCGATACA
1 ATGTATCGATACA
1907796 ATGTATCGATACA
1 ATGTATCGATACA
1907809 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1907825 original size:33 final size:32
Alignment explanation
Indices: 1907765--1907828 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1907755 TAGCCAAATT
*
1907765 TGTATCGATACACACAATATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1907797 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1907829 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1913739 original size:8 final size:8
Alignment explanation
Indices: 1913726--1913751 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1913716 ATTTGATTCA
1913726 ATTTTGTG
1 ATTTTGTG
1913734 ATTTTGTG
1 ATTTTGTG
1913742 ATTTTGTG
1 ATTTTGTG
1913750 AT
1 AT
1913752 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:1914438 original size:20 final size:21
Alignment explanation
Indices: 1914398--1914449 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
1914388 CCTCTAGGCA
*
1914398 GCACCCACCAAGTCGCGACC-G
1 GCACCC-CCAAGTCGCAACCGG
*
1914419 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAAGTCGCAACCGG
1914440 GCAGCCCCCA
1 GCA-CCCCCA
1914450 CACTAGCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 11 0.41
21 10 0.37
22 6 0.22
ACGTcount: A:0.21, C:0.50, G:0.25, T:0.04
Consensus pattern (21 bp):
GCACCCCCAAGTCGCAACCGG
Found at i:1915861 original size:21 final size:22
Alignment explanation
Indices: 1915821--1915865 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1915811 CGAAATTGTT
1915821 AAATTATTTTATTAAGGGGGAG
1 AAATTATTTTATTAAGGGGGAG
1915843 AAATT-TTTTGATTAAGGGGGAG
1 AAATTATTTT-ATTAAGGGGGAG
1915865 A
1 A
1915866 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (22 bp):
AAATTATTTTATTAAGGGGGAG
Found at i:1916457 original size:20 final size:21
Alignment explanation
Indices: 1916434--1916484 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1916424 CAGATTGCAT
**
1916434 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1916454 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1916475 TGTATCGATA
1 TGTATCGATA
1916485 TAGGTCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:1916555 original size:13 final size:13
Alignment explanation
Indices: 1916537--1916562 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1916527 TACACACAAT
1916537 ATGTATCGATACA
1 ATGTATCGATACA
1916550 ATGTATCGATACA
1 ATGTATCGATACA
1916563 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1916579 original size:33 final size:32
Alignment explanation
Indices: 1916519--1916582 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1916509 TAGCCAAATT
*
1916519 TGTATCGATACACACAATATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1916551 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1916583 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1918017 original size:13 final size:13
Alignment explanation
Indices: 1917999--1918055 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1917989 CATAAAGTGT
1917999 TGTATCGATACAA
1 TGTATCGATACAA
1918012 TGTATCGATACATAA
1 TGTATCGATAC--AA
1918027 GTTTTGTATCGATACAA
1 ----TGTATCGATACAA
1918044 TGTATCGATACA
1 TGTATCGATACA
1918056 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1918036 original size:19 final size:19
Alignment explanation
Indices: 1917977--1918074 Score: 94
Period size: 19 Copynumber: 5.7 Consensus size: 19
1917967 ATTTCAATGA
1917977 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACAT-AAGT
*
1917997 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1918012 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1918029 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1918044 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1918061 TTTGTATCGATACA
1 TTTGTATCGATACA
1918075 ATGTAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 25
0.71 0.01 0.27
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 23 0.35
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1918039 original size:32 final size:32
Alignment explanation
Indices: 1917979--1918079 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
1917969 TTCAATGATT
*
1917979 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1918012 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
1918044 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTTTTGTATCGATACAA
1918076 TGTA
1 TGTA
1918080 AGCTACTGCC
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 54 0.81
33 13 0.19
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTTTTGTATCGATACAA
Found at i:1918135 original size:13 final size:13
Alignment explanation
Indices: 1918117--1918141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1918107 ATTACTCAAA
1918117 TGTATCGATACAT
1 TGTATCGATACAT
1918130 TGTATCGATACA
1 TGTATCGATACA
1918142 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1922864 original size:59 final size:60
Alignment explanation
Indices: 1922759--1922875 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 60
1922749 GAGTAATGTA
* * *
1922759 GTTTTTTTTTCTTTTTTTAGACACCAACGAGACCTTCATTGGCGTGGCCATCCTACTTAG
1 GTTTTTTTTTCTTTTTATAGACACCAACGAGACCCTCACTGGCGTGGCCATCCTACTTAG
* *
1922819 GTTTTTTTTT-TTTTTATAGACACCATCGAGACCCTCACTGTCGTGGCCATCCTACTT
1 GTTTTTTTTTCTTTTTATAGACACCAACGAGACCCTCACTGGCGTGGCCATCCTACTT
1922876 GTGGTTGTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
59 42 0.81
60 10 0.19
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (60 bp):
GTTTTTTTTTCTTTTTATAGACACCAACGAGACCCTCACTGGCGTGGCCATCCTACTTAG
Found at i:1923743 original size:7 final size:7
Alignment explanation
Indices: 1923731--1923755 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1923721 AATGTTAAAT
1923731 ATAATTA
1 ATAATTA
1923738 ATAATTA
1 ATAATTA
1923745 ATAATTA
1 ATAATTA
1923752 ATAA
1 ATAA
1923756 AATATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAATTA
Found at i:1926422 original size:2 final size:2
Alignment explanation
Indices: 1926415--1926441 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1926405 ATCAGTGTCC
1926415 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1926442 CCTTTAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1928112 original size:75 final size:77
Alignment explanation
Indices: 1928003--1928155 Score: 220
Period size: 75 Copynumber: 2.0 Consensus size: 77
1927993 ATATCAAGAT
* *
1928003 TACATATAAGGATGGTGAGGAAACTCTTCAACAATCTTT-CCTGCAAAGAAGATAAT-TATAAAT
1 TACATATAAGGATGGTGAGGAAAATCTTCAACAATCTTTGCCTGCAAAAAAGATAATCTATAAAT
1928066 CTCCGAGTTGAC
66 CTCCGAGTTGAC
* ** **
1928078 TACATATAAGGATGGTGATGAAAATCTTGGACAATCTTTGCCTGCAAAAAAGATAATCTATATCT
1 TACATATAAGGATGGTGAGGAAAATCTTCAACAATCTTTGCCTGCAAAAAAGATAATCTATAAAT
*
1928143 CTCTGAGTTGAC
66 CTCCGAGTTGAC
1928155 T
1 T
1928156 GCCATTACTG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 35 0.51
76 16 0.24
77 17 0.25
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (77 bp):
TACATATAAGGATGGTGAGGAAAATCTTCAACAATCTTTGCCTGCAAAAAAGATAATCTATAAAT
CTCCGAGTTGAC
Found at i:1929991 original size:2 final size:2
Alignment explanation
Indices: 1929984--1930027 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1929974 AATTCATTTG
1929984 AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1930024 AT AT
1 AT AT
1930028 TCATTGACGC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1930253 original size:34 final size:34
Alignment explanation
Indices: 1930205--1930269 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
1930195 ACCCAAAGTT
* *
1930205 AATCAAAATTAAGTACAATTATGGAAGCATCGAA
1 AATCAAAATCAAGTACAATTATGCAAGCATCGAA
*
1930239 AATCAAAGTCAAGTACAATTATGCAAGCATC
1 AATCAAAATCAAGTACAATTATGCAAGCATC
1930270 TTTCGTTTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (34 bp):
AATCAAAATCAAGTACAATTATGCAAGCATCGAA
Found at i:1932708 original size:15 final size:15
Alignment explanation
Indices: 1932674--1932711 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1932664 TCTGGGTTGA
*
1932674 ATTTAGG-TTGGATC
1 ATTTAGGATTGAATC
*
1932688 ACTTAGGATTGAATC
1 ATTTAGGATTGAATC
1932703 ATTTAGGAT
1 ATTTAGGAT
1932712 AGAAGAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (15 bp):
ATTTAGGATTGAATC
Found at i:1932782 original size:16 final size:15
Alignment explanation
Indices: 1932762--1932806 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1932752 TTAACTTCAT
1932762 ATTATATTAAATTTAA
1 ATTAT-TTAAATTTAA
* *
1932778 GTTATTTTAAGTTTAA
1 ATTA-TTTAAATTTAA
1932794 ATTATTTAAATTT
1 ATTATTTAAATTT
1932807 GACACTTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 8 0.33
16 15 0.62
17 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (15 bp):
ATTATTTAAATTTAA
Found at i:1940648 original size:26 final size:26
Alignment explanation
Indices: 1940619--1940700 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 26
1940609 ATATTCTTAA
1940619 TAATAATTTTACCCTTTCATAATATT
1 TAATAATTTTACCCTTTCATAATATT
* *
1940645 TAATAA--TTA--C--TAATATTATT
1 TAATAATTTTACCCTTTCATAATATT
1940665 AATAATAATTTTACCCTTTCATAATATT
1 --TAATAATTTTACCCTTTCATAATATT
1940693 TAATAATT
1 TAATAATT
1940701 ACTACTACTT
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
20 8 0.18
22 7 0.16
24 6 0.14
26 15 0.34
28 8 0.18
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (26 bp):
TAATAATTTTACCCTTTCATAATATT
Found at i:1940667 original size:48 final size:48
Alignment explanation
Indices: 1940606--1940704 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
1940596 CATATTTAAT
*
1940606 CTAATATTCTTAATAATAATTTTACCCTTTCATAATATTTAATAATTA
1 CTAATATTATTAATAATAATTTTACCCTTTCATAATATTTAATAATTA
1940654 CTAATATTATTAATAATAATTTTACCCTTTCATAATATTTAATAATTA
1 CTAATATTATTAATAATAATTTTACCCTTTCATAATATTTAATAATTA
1940702 CTA
1 CTA
1940705 CTACTTTTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.47
Consensus pattern (48 bp):
CTAATATTATTAATAATAATTTTACCCTTTCATAATATTTAATAATTA
Found at i:1941333 original size:16 final size:17
Alignment explanation
Indices: 1941308--1941345 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1941298 AAGTCAAAGA
*
1941308 TGGGCACTTGG-GCACT
1 TGGGCACTTGGACCACT
*
1941324 TGGACACTTGGACCACT
1 TGGGCACTTGGACCACT
1941341 TGGGC
1 TGGGC
1941346 TTAAATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (17 bp):
TGGGCACTTGGACCACT
Found at i:1944209 original size:22 final size:22
Alignment explanation
Indices: 1944161--1944236 Score: 93
Period size: 22 Copynumber: 3.4 Consensus size: 22
1944151 TTATTGGTCA
1944161 TTATATTATT-AAA-ATTATTAT
1 TTATATTATTAAAATATTATT-T
1944182 TTATATTATTAAAATATTATTT
1 TTATATTATTAAAATATTATTT
*
1944204 TTATATTATTAAAAAATATAATTT
1 TTATATTATT--AAAATATTATTT
1944228 TTAATATTA
1 TT-ATATTA
1944237 AATAGTAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
21 10 0.20
22 14 0.29
23 6 0.12
24 13 0.27
25 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATATTATTAAAATATTATTT
Found at i:1944238 original size:22 final size:24
Alignment explanation
Indices: 1944161--1944236 Score: 83
Period size: 21 Copynumber: 3.3 Consensus size: 24
1944151 TTATTGGTCA
1944161 TTATATTATT--AAAAT-T-ATTAT
1 TTATATTATTAAAAAATATAATT-T
*
1944182 TTATATTATT--AAAATATTATTT
1 TTATATTATTAAAAAATATAATTT
1944204 TTATATTATTAAAAAATATAATTT
1 TTATATTATTAAAAAATATAATTT
1944228 TTAATATTA
1 TT-ATATTA
1944237 AATAGTAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
21 15 0.31
22 12 0.24
23 3 0.06
24 13 0.27
25 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATATTATTAAAAAATATAATTT
Found at i:1947698 original size:25 final size:25
Alignment explanation
Indices: 1947665--1947723 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
1947655 CCTATCATTT
1947665 TTTTCAATTTAAT-AGATTCAATTTAA
1 TTTT-AATTTAATAAG-TTCAATTTAA
* *
1947691 TTTTAATTTAATAAGTTTAATTTCA
1 TTTTAATTTAATAAGTTCAATTTAA
1947716 TTTTAATT
1 TTTTAATT
1947724 GTATTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 24 0.80
26 6 0.20
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (25 bp):
TTTTAATTTAATAAGTTCAATTTAA
Found at i:1947731 original size:36 final size:36
Alignment explanation
Indices: 1947690--1947759 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
1947680 ATTCAATTTA
**
1947690 ATTTTAATTTAATAAGTTTAA-TTTCAT-TTTAATTGT
1 ATTTTAATAAAATAA-TTTAAGTTT-ATGTTTAATTGT
1947726 ATTTTAATAAAATAATTTAAGTTTATGTTTAATT
1 ATTTTAATAAAATAATTTAAGTTTATGTTTAATT
1947760 CGAATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 7 0.23
36 23 0.77
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (36 bp):
ATTTTAATAAAATAATTTAAGTTTATGTTTAATTGT
Found at i:1947823 original size:26 final size:26
Alignment explanation
Indices: 1947769--1947830 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
1947759 TCGAATTATT
*
1947769 ATTTAATTTATAAAAAGTTTTATTTAA
1 ATTT-ATTTATAAAAAGTTTTATTAAA
1947796 ATTTATTTAT-AAAA-TATTTATATAAA
1 ATTTATTTATAAAAAGT-TTTAT-TAAA
1947822 ATTTTATTT
1 A-TTTATTT
1947831 TGATATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
24 1 0.03
25 9 0.29
26 10 0.32
27 11 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTATTTATAAAAAGTTTTATTAAA
Found at i:1960609 original size:14 final size:14
Alignment explanation
Indices: 1960587--1960619 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1960577 ATCGTGTTCA
*
1960587 AAATAATTATATTT
1 AAATTATTATATTT
1960601 AAATTATTATATTT
1 AAATTATTATATTT
1960615 AAATT
1 AAATT
1960620 CACCCATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTATTATATTT
Found at i:1961100 original size:2 final size:2
Alignment explanation
Indices: 1961093--1961119 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1961083 CAATTTTCAA
1961093 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
1961120 AATTGAGATA
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:1961347 original size:2 final size:2
Alignment explanation
Indices: 1961342--1961370 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1961332 ATATACATTT
1961342 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1961371 TTATCTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1961714 original size:15 final size:15
Alignment explanation
Indices: 1961689--1961728 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1961679 ATCTTGATAA
1961689 ATTTATTTATGTGTAT
1 ATTT-TTTATGTGTAT
*
1961705 ATTTTTTATGTGTGT
1 ATTTTTTATGTGTAT
*
1961720 AATTTTTAT
1 ATTTTTTAT
1961729 TTTTTATTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (15 bp):
ATTTTTTATGTGTAT
Found at i:1962086 original size:22 final size:22
Alignment explanation
Indices: 1962058--1962104 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1962048 AGATTCGAAT
1962058 TCAGCTTAATTTCTCAGTTAAA
1 TCAGCTTAATTTCTCAGTTAAA
1962080 TCAGCTTAATTTCTCAGTTAAA
1 TCAGCTTAATTTCTCAGTTAAA
1962102 TCA
1 TCA
1962105 CACATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (22 bp):
TCAGCTTAATTTCTCAGTTAAA
Done.