Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008180.1 Hibiscus syriacus cultivar Beakdansim tig00110777_pilon, whole genome shotgun sequence
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: 2670214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2281320 original size:13 final size:13
Alignment explanation
Indices: 2281302--2281328 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2281292 CATAGTTGAA
2281302 CAGTCTTCATATG
1 CAGTCTTCATATG
2281315 CAGTCTTCATATG
1 CAGTCTTCATATG
2281328 C
1 C
2281329 GCGTCTATAA
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:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:2284982 original size:78 final size:78
Alignment explanation
Indices: 2284837--2284982 Score: 179
Period size: 78 Copynumber: 1.9 Consensus size: 78
2284827 AAAACTAGGT
* * * ** * *
2284837 GTCAAATTAACTATTTAGTCAAATATTATGAGTCTTTTTACATAAAAATTCAATGTTTAGAGTAA
1 GTCAAATTAACTATTTAATCAAATATTATGAGTATTTTTACATAAAAATTAAACATTTAAAGCAA
2284902 AATGCTCTAAAAA
66 AATGCTCTAAAAA
* *
2284915 GTCAAATTAACTATTTAATCAAATATTAT-AGGTATTTTTACCTTAAAA-TAAACATTTAAAGCC
1 GTCAAATTAACTATTTAATCAAATATTATGA-GTATTTTTACATAAAAATTAAACATTTAAAG-C
2284978 AAAAT
64 AAAAT
2284983 ATTTTTTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
77 10 0.18
78 47 0.82
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (78 bp):
GTCAAATTAACTATTTAATCAAATATTATGAGTATTTTTACATAAAAATTAAACATTTAAAGCAA
AATGCTCTAAAAA
Found at i:2290858 original size:23 final size:23
Alignment explanation
Indices: 2290830--2290873 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2290820 AATTAGGGCC
*
2290830 AGTGACTAAATTGCAAATTTTTA
1 AGTGACTAAATTACAAATTTTTA
2290853 AGTGACTAAATTACAAATTTT
1 AGTGACTAAATTACAAATTTT
2290874 AAAAACTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (23 bp):
AGTGACTAAATTACAAATTTTTA
Found at i:2293303 original size:23 final size:23
Alignment explanation
Indices: 2293273--2293332 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
2293263 ATTATTATAT
2293273 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
2293296 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
2293319 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
2293333 TTTATATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2296594 original size:22 final size:22
Alignment explanation
Indices: 2296566--2296624 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
2296556 AACTTTTTTT
2296566 GTCAAAGTCAACGGTCAGACCG
1 GTCAAAGTCAACGGTCAGACCG
* *
2296588 GTCAAAGTCAATGGTCAGACTG
1 GTCAAAGTCAACGGTCAGACCG
2296610 GTCAAAGTCAACGGT
1 GTCAAAGTCAACGGT
2296625 TGGATCGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (22 bp):
GTCAAAGTCAACGGTCAGACCG
Found at i:2297904 original size:115 final size:115
Alignment explanation
Indices: 2297702--2297916 Score: 331
Period size: 115 Copynumber: 1.9 Consensus size: 115
2297692 AAAGTTCTCT
* ** *
2297702 ACTTTTAATCAAATTAAGTTTATCACTTTTCTAATTAATTTGTGTCACTTTAAATTCGAGTCAAA
1 ACTTTTAATCAAACTAAGTTTATCACTTTTCTAATTAATTTGTACCACTTTAAATTCGAATCAAA
* *
2297767 CTTCAACATAAGAAAATAAGACAATAGACATCCTTGGCAAATACGCATAA
66 CTTCAACAGAAGAAAATAAGACAATAAACATCCTTGGCAAATACGCATAA
* * * *
2297817 ACTTTTAATCGAACTATGTTTATTATTTTTCTAATTAATTTGTACCACTTTAAATTCGAATCAAA
1 ACTTTTAATCAAACTAAGTTTATCACTTTTCTAATTAATTTGTACCACTTTAAATTCGAATCAAA
*
2297882 CTTCAACAGAAGGAAATAAGACAATAAACATCCTT
66 CTTCAACAGAAGAAAATAAGACAATAAACATCCTT
2297917 ACCACGCATG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
115 89 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (115 bp):
ACTTTTAATCAAACTAAGTTTATCACTTTTCTAATTAATTTGTACCACTTTAAATTCGAATCAAA
CTTCAACAGAAGAAAATAAGACAATAAACATCCTTGGCAAATACGCATAA
Found at i:2300437 original size:46 final size:45
Alignment explanation
Indices: 2300387--2300475 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 45
2300377 TCCGATGTTT
*
2300387 TTATTAAAATATGTTTTGTTATTTTAATTATTATTA-TATTATTATA
1 TTATTAAAATATG-TTT-TTATTTTAATTATTATTAGTAATATTATA
*
2300433 TTATTAAAATATGTTTTTATTTTAATTGTTATTAGTAATATTA
1 TTATTAAAATATGTTTTTATTTTAATTATTATTAGTAATATTA
2300476 ACTACTATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
44 17 0.43
45 10 0.25
46 13 0.32
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (45 bp):
TTATTAAAATATGTTTTTATTTTAATTATTATTAGTAATATTATA
Found at i:2309740 original size:16 final size:17
Alignment explanation
Indices: 2309703--2309740 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2309693 GGATAAAAAA
* *
2309703 TTAAATAAATTATTTGT
1 TTAAACAAATTATTTAT
2309720 TTAAACAAATTA-TTAT
1 TTAAACAAATTATTTAT
2309736 TTAAA
1 TTAAA
2309741 TTAATTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAAACAAATTATTTAT
Found at i:2309746 original size:16 final size:17
Alignment explanation
Indices: 2309703--2309746 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2309693 GGATAAAAAA
*
2309703 TTAAATAAATTATTTGT
1 TTAAATAAATTATTTAT
*
2309720 TTAAACAAATTA-TTAT
1 TTAAATAAATTATTTAT
*
2309736 TTAAATTAATT
1 TTAAATAAATT
2309747 GTAAACTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TTAAATAAATTATTTAT
Found at i:2310040 original size:125 final size:125
Alignment explanation
Indices: 2309911--2310387 Score: 483
Period size: 139 Copynumber: 3.6 Consensus size: 125
2309901 AAAAAATCGG
* * * *
2309911 TTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCAATTAACCGAACCGAATT-ATCG
1 TTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACAGAATTAACCA
2309975 ATTTTTTGCTTCGATTAATTCGGTTAATAATTTAAAAAAAAATCGGTTAATAATTTTCAAA
66 ATTTTTT-CTTCGATTAATTCGGTTAATAATTTAAAAAAAAATCGGTTAATAATTTTCAAA
* * *
2310036 TTAATTTGGTTTGGTTAATAATTTTCAAATAAATGTTGGTTCGATTAATCGAACTA-AATTAACC
1 TTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAAC-AGAATTAACC
2310100 AAATTTTTTCTTCGATTAATTCGGTTAATAATTTAAAAAAAATCGATTAATTCGGTCAGTTAATA
65 -AATTTTTTCTTCGATTAATTCGGTTAATAATTT--AAAAAA---A--AA-TC-G---GTTAATA
2310165 ATTTTCAAA
117 ATTTTCAAA
** *
2310174 TTAATTCAGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACAGAATTAACCA
1 TTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACAGAATTAACCA
* * * *
2310239 AATTTTTCTTCTATTAATTTGGTTAATAATTAAAAAAAAATCGGTTAATTCAAGTTCAGTTAATA
66 ATTTTTTCTTCGATTAATTCGGTTAATAATT-TAAAAAAA------AA-TC--G----GTTAATA
*
2310304 ATTTTAAAA
117 ATTTTCAAA
* * * * *
2310313 TTAATTTGGTTTGATTAATACTTTTCAAATAAATTTTGGTTCGATTAGCCGAACCA-AATTAATC
1 TTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAA-CAGAATTAACC
2310377 AATTTTTTCTT
65 AATTTTTTCTT
2310388 TAATCATTAA
Statistics
Matches: 300, Mismatches: 28, Indels: 34
0.83 0.08 0.09
Matches are distributed among these distances:
125 54 0.18
126 27 0.09
127 7 0.02
128 6 0.02
131 1 0.00
133 3 0.01
134 2 0.01
135 1 0.00
136 6 0.02
137 37 0.12
138 73 0.24
139 81 0.27
140 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (125 bp):
TTAATTTGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCGAACAGAATTAACCA
ATTTTTTCTTCGATTAATTCGGTTAATAATTTAAAAAAAAATCGGTTAATAATTTTCAAA
Found at i:2310052 original size:29 final size:30
Alignment explanation
Indices: 2310019--2310076 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
2310009 AAAAAAAATC
*
2310019 GGTTAATAATTTTCAAATTAAT-TTGGTTT
1 GGTTAATAATTTTCAAATAAATGTTGGTTT
2310048 GGTTAATAATTTTCAAATAAATGTTGGTT
1 GGTTAATAATTTTCAAATAAATGTTGGTT
2310077 CGATTAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (30 bp):
GGTTAATAATTTTCAAATAAATGTTGGTTT
Found at i:2310084 original size:30 final size:29
Alignment explanation
Indices: 2310021--2310084 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
2310011 AAAAAATCGG
* * *
2310021 TTAATAATTTTCAAATTAATTTGGTTTGG
1 TTAATAATTTTCAAATAAATTTGGTTCGA
2310050 TTAATAATTTTCAAATAAATGTTGGTTCGA
1 TTAATAATTTTCAAATAAAT-TTGGTTCGA
2310080 TTAAT
1 TTAAT
2310085 CGAACTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (29 bp):
TTAATAATTTTCAAATAAATTTGGTTCGA
Found at i:2310173 original size:138 final size:138
Alignment explanation
Indices: 2310020--2310387 Score: 535
Period size: 139 Copynumber: 2.7 Consensus size: 138
2310010 AAAAAAATCG
* *
2310020 GTTAATAATTTTCAAATTAATTTGGTTTGGTTAATAATTTTCAAATAAATGTTGGTTCGATTAAT
1 GTTAATAATTTTCAAATTAATTTGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAAC
*
2310085 CGAACTAAATTAACCAAATTTTTTCTTCGATTAATTCGGTTAATAATTTAAAAAAAATCGATTAA
66 CGAAC-AAATTAACCAAATTTTTTCTTCGATTAATTCGGTTAATAATTAAAAAAAAATCGATTAA
2310150 TTC-GGTCA
130 TTCAGGTCA
** **
2310158 GTTAATAATTTTCAAATTAATTCAGTTCAGTTAATAATTTTCAAATAAATTTTGGTTCGATTAAC
1 GTTAATAATTTTCAAATTAATTTGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAAC
* * *
2310223 CGAACAGAATTAACCAAA-TTTTTCTTCTATTAATTTGGTTAATAATTAAAAAAAAATCGGTTAA
66 CGAACA-AATTAACCAAATTTTTTCTTCGATTAATTCGGTTAATAATTAAAAAAAAATCGATTAA
*
2310287 TTCAAGTTCA
130 TTC-AGGTCA
* * * *
2310297 GTTAATAATTTTAAAATTAATTTGGTTTGATTAATACTTTTCAAATAAATTTTGGTTCGATTAGC
1 GTTAATAATTTTCAAATTAATTTGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAAC
*
2310362 CGAACCAAATTAATC-AATTTTTTCTT
66 CGAA-CAAATTAACCAAATTTTTTCTT
2310388 TAATCATTAA
Statistics
Matches: 205, Mismatches: 20, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
137 46 0.22
138 77 0.38
139 80 0.39
140 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (138 bp):
GTTAATAATTTTCAAATTAATTTGGTTTGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAAC
CGAACAAATTAACCAAATTTTTTCTTCGATTAATTCGGTTAATAATTAAAAAAAAATCGATTAAT
TCAGGTCA
Found at i:2310191 original size:29 final size:28
Alignment explanation
Indices: 2310145--2310208 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 28
2310135 AAAAAAATCG
2310145 ATTAATTCGGTCAGTTAATAATTTTCAA
1 ATTAATTCGGTCAGTTAATAATTTTCAA
*
2310173 ATTAATTCAGTTCAGTTAATAATTTTCAA
1 ATTAATTC-GGTCAGTTAATAATTTTCAA
*
2310202 ATAAATT
1 ATTAATT
2310209 TTGGTTCGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 8 0.24
29 25 0.76
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (28 bp):
ATTAATTCGGTCAGTTAATAATTTTCAA
Found at i:2310337 original size:29 final size:30
Alignment explanation
Indices: 2310298--2310359 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
2310288 TCAAGTTCAG
* *
2310298 TTAATAATTTTAAAATTAA-TTTGGTTTGA
1 TTAATAATTTTAAAATAAATTTTGGTTCGA
* *
2310327 TTAATACTTTTCAAATAAATTTTGGTTCGA
1 TTAATAATTTTAAAATAAATTTTGGTTCGA
2310357 TTA
1 TTA
2310360 GCCGAACCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (30 bp):
TTAATAATTTTAAAATAAATTTTGGTTCGA
Found at i:2311226 original size:30 final size:29
Alignment explanation
Indices: 2311191--2311249 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
2311181 GCCGGTAGTT
*
2311191 TGATTGAATCAATTAAATAGTTGGGTGGTC
1 TGATTGAATCAATTAAA-AGTTCGGTGGTC
* *
2311221 TGATTGATTCAATTGAAAGTTCGGTGGTC
1 TGATTGAATCAATTAAAAGTTCGGTGGTC
2311250 ACATTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.37
Consensus pattern (29 bp):
TGATTGAATCAATTAAAAGTTCGGTGGTC
Found at i:2311255 original size:29 final size:30
Alignment explanation
Indices: 2311193--2311258 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
2311183 CGGTAGTTTG
* * **
2311193 ATTGAATCAATTAAATAGTTGGGTGGTCTG
1 ATTGATTCAATTAAATAGTTCGGTGGTCAC
*
2311223 ATTGATTCAATTGAA-AGTTCGGTGGTCAC
1 ATTGATTCAATTAAATAGTTCGGTGGTCAC
2311252 ATTGATT
1 ATTGATT
2311259 TTTGACCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (30 bp):
ATTGATTCAATTAAATAGTTCGGTGGTCAC
Found at i:2312764 original size:19 final size:18
Alignment explanation
Indices: 2312737--2312787 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
2312727 ATTATACTTT
2312737 AATTA-TTAATATATAAC
1 AATTATTTAATATATAAC
* * *
2312754 ATTTAATTTAAAATATTAC
1 AATT-ATTTAATATATAAC
2312773 AATTATTTAATATAT
1 AATTATTTAATATAT
2312788 TTTCATTCGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 3 0.11
18 11 0.41
19 13 0.48
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTATTTAATATATAAC
Found at i:2313314 original size:25 final size:25
Alignment explanation
Indices: 2313286--2313336 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2313276 GAGGATTACG
2313286 AAATTATCTT-TCCAGAGGTATAACA
1 AAATTA-CTTCTCCAGAGGTATAACA
* *
2313311 AAATTACTTCTCCGGATGTATAACA
1 AAATTACTTCTCCAGAGGTATAACA
2313336 A
1 A
2313337 GAAACAGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (25 bp):
AAATTACTTCTCCAGAGGTATAACA
Found at i:2317581 original size:18 final size:18
Alignment explanation
Indices: 2317545--2317580 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2317535 ATAGATATAC
2317545 ACATAAAAAAAATTTAAA
1 ACATAAAAAAAATTTAAA
*
2317563 ACAT-AAAAGAATTTAAA
1 ACATAAAAAAAATTTAAA
2317580 A
1 A
2317581 ATTTTAGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (18 bp):
ACATAAAAAAAATTTAAA
Found at i:2317663 original size:6 final size:6
Alignment explanation
Indices: 2317652--2317677 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2317642 TGCTGCCTCA
2317652 CTTTGT CTTTGT CTTTGT CTTTGT CT
1 CTTTGT CTTTGT CTTTGT CTTTGT CT
2317678 CAAATTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.15, T:0.65
Consensus pattern (6 bp):
CTTTGT
Found at i:2322867 original size:320 final size:320
Alignment explanation
Indices: 2322285--2322924 Score: 1262
Period size: 320 Copynumber: 2.0 Consensus size: 320
2322275 CCCATTTGGC
2322285 CTTTGATTTCTTCCTCATCATCTCAGCCATTGCCTGGATCCCTACAGCTTTTCTGATATTCACCA
1 CTTTGATTTCTTCCTCATCATCTCAGCCATTGCCTGGATCCCTACAGCTTTTCTGATATTCACCA
2322350 AAACAGTTGCTCTCAGTCGGATGTTTATGGGAAGATTTTGGGTATCAACTTCACCTGCTCAATTA
66 AAACAGTTGCTCTCAGTCGGATGTTTATGGGAAGATTTTGGGTATCAACTTCACCTGCTCAATTA
*
2322415 ATAACATTCTACATATCAATAATTCTTTACTTCACACCAAATTAAAAAAACTCACCATATTTTCG
131 ATAACATTCTAAATATCAATAATTCTTTACTTCACACCAAATTAAAAAAACTCACCATATTTTCG
2322480 ATTTAGATATCGTGAGAGACCAGCTTGAGTTATTCCCAACATGACATCGTTAACTGTCTAGTAAA
196 ATTTAGATATCGTGAGAGACCAGCTTGAGTTATTCCCAACATGACATCGTTAACTGTCTAGTAAA
*
2322545 TATCAAGCCTATCATCTTCAAGATATGTACTTGGTAATCATTTAATACAAGTGAAGGTTA
261 TATCAAGCCTATCATCTTCAAGATATGTACTTGGAAATCATTTAATACAAGTGAAGGTTA
2322605 CTTTGATTTCTTCCTCATCATCTCAGCCATTGCCTGGATCCCTACAGCTTTTCTGATATTCACCA
1 CTTTGATTTCTTCCTCATCATCTCAGCCATTGCCTGGATCCCTACAGCTTTTCTGATATTCACCA
2322670 AAACAGTTGCTCTCAGTCGGATGTTTATGGGAAGATTTTGGGTATCAACTTCACCTGCTCAATTA
66 AAACAGTTGCTCTCAGTCGGATGTTTATGGGAAGATTTTGGGTATCAACTTCACCTGCTCAATTA
2322735 ATAACATTCTAAATATCAATAATTCTTTACTTCACACCAAATTAAAAAAACTCACCATATTTTCG
131 ATAACATTCTAAATATCAATAATTCTTTACTTCACACCAAATTAAAAAAACTCACCATATTTTCG
2322800 ATTTAGATATCGTGAGAGACCAGCTTGAGTTATTCCCAACATGACATCGTTAACTGTCTAGTAAA
196 ATTTAGATATCGTGAGAGACCAGCTTGAGTTATTCCCAACATGACATCGTTAACTGTCTAGTAAA
2322865 TATCAAGCCTATCATCTTCAAGATATGTACTTGGAAATCATTTAATACAAGTGAAGGTTA
261 TATCAAGCCTATCATCTTCAAGATATGTACTTGGAAATCATTTAATACAAGTGAAGGTTA
2322925 ATTAGAGTGA
Statistics
Matches: 318, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
320 318 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (320 bp):
CTTTGATTTCTTCCTCATCATCTCAGCCATTGCCTGGATCCCTACAGCTTTTCTGATATTCACCA
AAACAGTTGCTCTCAGTCGGATGTTTATGGGAAGATTTTGGGTATCAACTTCACCTGCTCAATTA
ATAACATTCTAAATATCAATAATTCTTTACTTCACACCAAATTAAAAAAACTCACCATATTTTCG
ATTTAGATATCGTGAGAGACCAGCTTGAGTTATTCCCAACATGACATCGTTAACTGTCTAGTAAA
TATCAAGCCTATCATCTTCAAGATATGTACTTGGAAATCATTTAATACAAGTGAAGGTTA
Found at i:2329259 original size:32 final size:32
Alignment explanation
Indices: 2329198--2329260 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
2329188 TTAAATGTTG
* *
2329198 ATGTAAAATTTTAATATATTTTACATAAAATT
1 ATGTAAAATTTTAATATATATTAAATAAAATT
2329230 ATGTAAAA-TTTAATAT-TAATTAAATTAAAAT
1 ATGTAAAATTTTAATATAT-ATTAAA-TAAAAT
2329261 AATACATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 1 0.04
31 12 0.44
32 14 0.52
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (32 bp):
ATGTAAAATTTTAATATATATTAAATAAAATT
Found at i:2329329 original size:15 final size:15
Alignment explanation
Indices: 2329309--2329339 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2329299 CAACAAATAG
2329309 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
2329324 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
2329339 A
1 A
2329340 TTTAGAATTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:2331388 original size:14 final size:14
Alignment explanation
Indices: 2331369--2331396 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2331359 AATATGACAC
2331369 TTATTTGTTATCAT
1 TTATTTGTTATCAT
2331383 TTATTTGTTATCAT
1 TTATTTGTTATCAT
2331397 GTTGATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (14 bp):
TTATTTGTTATCAT
Found at i:2338216 original size:16 final size:14
Alignment explanation
Indices: 2338187--2338221 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
2338177 TGTTCATTTA
2338187 ATAAATAAACGAAC
1 ATAAATAAACGAAC
2338201 ATAAATGAACACGAAC
1 ATAAAT-AA-ACGAAC
2338217 ATAAA
1 ATAAA
2338222 CGAATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 2 0.11
16 11 0.58
ACGTcount: A:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (14 bp):
ATAAATAAACGAAC
Found at i:2338305 original size:16 final size:16
Alignment explanation
Indices: 2338284--2338344 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
2338274 TGTTCGTTAA
2338284 ACGAACATAAATGAAC
1 ACGAACATAAATGAAC
*
2338300 ACGAACATAAACGAAC
1 ACGAACATAAATGAAC
2338316 ACGAACATAAATGAAC
1 ACGAACATAAATGAAC
*
2338332 ACAAACATAAATG
1 ACGAACATAAATG
2338345 TTGGAGACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.11
Consensus pattern (16 bp):
ACGAACATAAATGAAC
Found at i:2339279 original size:24 final size:24
Alignment explanation
Indices: 2339252--2339326 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
2339242 TATTAGGTTA
**
2339252 AACATAAATGAATGAACATAAACG
1 AACATAACCGAATGAACATAAACG
**
2339276 AACATAACCGAACAAACATAAACG
1 AACATAACCGAATGAACATAAACG
* *
2339300 AACATAACCAAATGAACATAACCG
1 AACATAACCGAATGAACATAAACG
2339324 AAC
1 AAC
2339327 GTTCACGAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.57, C:0.21, G:0.09, T:0.12
Consensus pattern (24 bp):
AACATAACCGAATGAACATAAACG
Found at i:2341337 original size:21 final size:21
Alignment explanation
Indices: 2341313--2341359 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2341303 ACCGAAAACA
2341313 TTATTATTTCTACCGATTTTG
1 TTATTATTTCTACCGATTTTG
* * *
2341334 TTATTTTTTCTAGCGGTTTTG
1 TTATTATTTCTACCGATTTTG
2341355 TTATT
1 TTATT
2341360 GTTTGGTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.11, G:0.13, T:0.62
Consensus pattern (21 bp):
TTATTATTTCTACCGATTTTG
Found at i:2343078 original size:24 final size:21
Alignment explanation
Indices: 2343046--2343102 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 21
2343036 TGCATGGTAG
*
2343046 TGCATCGATGCACCTGTTAAAGAA
1 TGCACCGATGCACCTG-T--AGAA
2343070 TGCACCGATGCA-CTGTAGAA
1 TGCACCGATGCACCTGTAGAA
2343090 TGCACCGATGCAC
1 TGCACCGATGCAC
2343103 TTCAATGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 3 0.10
24 11 0.35
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (21 bp):
TGCACCGATGCACCTGTAGAA
Found at i:2343091 original size:20 final size:20
Alignment explanation
Indices: 2343066--2343103 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2343056 CACCTGTTAA
2343066 AGAATGCACCGATGCACTGT
1 AGAATGCACCGATGCACTGT
2343086 AGAATGCACCGATGCACT
1 AGAATGCACCGATGCACT
2343104 TCAATGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (20 bp):
AGAATGCACCGATGCACTGT
Found at i:2343188 original size:2 final size:2
Alignment explanation
Indices: 2343181--2343206 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2343171 TACTGATAGC
2343181 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
2343207 GAATGTGTAG
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:2349809 original size:15 final size:15
Alignment explanation
Indices: 2349789--2349819 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2349779 TGGAAAGGCT
*
2349789 GCGGCATCATATATG
1 GCGGCATCATAAATG
2349804 GCGGCATCATAAATG
1 GCGGCATCATAAATG
2349819 G
1 G
2349820 TTGCGGTGGC
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:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (15 bp):
GCGGCATCATAAATG
Found at i:2351521 original size:17 final size:18
Alignment explanation
Indices: 2351501--2351541 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2351491 AAATTATATT
2351501 AGTAAAAT-AATAAATAA
1 AGTAAAATGAATAAATAA
*
2351518 AGTAAAATGATTAAATAA
1 AGTAAAATGAATAAATAA
*
2351536 ATTAAA
1 AGTAAA
2351542 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (18 bp):
AGTAAAATGAATAAATAA
Found at i:2358706 original size:2 final size:2
Alignment explanation
Indices: 2358694--2358729 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
2358684 ACTCTATTTG
2358694 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2358730 ATTACATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2360475 original size:17 final size:18
Alignment explanation
Indices: 2360455--2360488 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2360445 TATAATTTTT
*
2360455 TTAAAA-TATATGAAAAC
1 TTAAAATTATAAGAAAAC
2360472 TTAAAATTATAAGAAAA
1 TTAAAATTATAAGAAAA
2360489 TGACTGCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
TTAAAATTATAAGAAAAC
Found at i:2377752 original size:2 final size:2
Alignment explanation
Indices: 2377747--2377799 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2377737 CCACGGTGTG
2377747 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
2377789 TA TA TA TA TA T
1 TA TA TA TA TA T
2377800 GACGCCAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2382282 original size:18 final size:20
Alignment explanation
Indices: 2382261--2382299 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
2382251 ATTACAAATA
*
2382261 ACATTTA-AACAT-AATAAT
1 ACATTTATAAAATGAATAAT
2382279 ACATTTATAAAATGAATAAT
1 ACATTTATAAAATGAATAAT
2382299 A
1 A
2382300 TTAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (20 bp):
ACATTTATAAAATGAATAAT
Found at i:2382354 original size:23 final size:24
Alignment explanation
Indices: 2382304--2382354 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
2382294 ATAATATTAA
* *
2382304 AATATTAATTATAAATAATTTATT
1 AATATAAATTATAAATAATATATT
2382328 -ATATAAATTATAAA-AATATATT
1 AATATAAATTATAAATAATATATT
2382350 AATAT
1 AATAT
2382355 TTATGTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AATATAAATTATAAATAATATATT
Found at i:2382573 original size:32 final size:32
Alignment explanation
Indices: 2382537--2382637 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 32
2382527 ATTCAGGTTG
2382537 TAATATAATAATATATTTGTATATTGTTGATT
1 TAATATAATAATATATTTGTATATTGTTGATT
***** **
2382569 TAATA-ATATCCGCCATTTGTAATATAAATT-A-T
1 TAATATA-ATAATATATTTGT-ATAT-TGTTGATT
*
2382601 TAATATAATAATATATTTATATATTGTTGATT
1 TAATATAATAATATATTTGTATATTGTTGATT
2382633 TAATA
1 TAATA
2382638 ACATAAAAAA
Statistics
Matches: 48, Mismatches: 15, Indels: 12
0.64 0.20 0.16
Matches are distributed among these distances:
30 2 0.04
31 6 0.12
32 32 0.67
33 6 0.12
34 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.49
Consensus pattern (32 bp):
TAATATAATAATATATTTGTATATTGTTGATT
Found at i:2387420 original size:2 final size:2
Alignment explanation
Indices: 2387406--2387453 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2387396 ATGTTATAAT
*
2387406 TA TA TA -A TG 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
2387447 TA TA TA T
1 TA TA TA T
2387454 CATTACACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2388527 original size:5 final size:5
Alignment explanation
Indices: 2388517--2388555 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
2388507 TATATATATA
*
2388517 TATTT TATTT TA-TT TGTTT TATTT TATTT TA-TT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT T
2388556 TTTACCTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 7 0.23
5 23 0.77
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:2388536 original size:14 final size:13
Alignment explanation
Indices: 2388519--2388555 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
2388509 TATATATATA
2388519 TTTTATTTTATTT
1 TTTTATTTTATTT
2388532 GTTTTATTTTATTT
1 -TTTTATTTTATTT
2388546 TATTTATTTT
1 T-TTTATTTT
2388556 TTTACCTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 1 0.05
14 21 0.95
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:2388538 original size:9 final size:9
Alignment explanation
Indices: 2388520--2388559 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
2388510 ATATATATAT
2388520 TTTATTTTA
1 TTTATTTTA
*
2388529 TTTGTTTTA
1 TTTATTTTA
2388538 TTTTATTTTA
1 -TTTATTTTA
2388548 TTTATTTT-
1 TTTATTTTA
2388556 TTTA
1 TTTA
2388560 CCTAACATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 4 0.14
9 16 0.57
10 8 0.29
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2388541 original size:19 final size:19
Alignment explanation
Indices: 2388517--2388555 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2388507 TATATATATA
*
2388517 TATTTTATTTTATTTGTTT
1 TATTTTATTTTATTTATTT
2388536 TATTTTATTTTATTTATTT
1 TATTTTATTTTATTTATTT
2388555 T
1 T
2388556 TTTACCTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (19 bp):
TATTTTATTTTATTTATTT
Found at i:2388654 original size:23 final size:22
Alignment explanation
Indices: 2388626--2388701 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 22
2388616 TAAATACTTA
2388626 TATATTTTTTTAGTTTTTTTATT
1 TATATTTTTTTA-TTTTTTTATT
*
2388649 TCTATTCTTTTTTACTATTTATTTATT
1 TATA-T-TTTTTTA-T-TTT-TTTATT
* *
2388676 TATTTTTATTTTATTTTTTTACT
1 TATATTT-TTTTATTTTTTTATT
2388699 TAT
1 TAT
2388702 TAAATACTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
23 11 0.26
24 4 0.09
25 11 0.26
26 9 0.21
27 8 0.19
ACGTcount: A:0.18, C:0.05, G:0.01, T:0.75
Consensus pattern (22 bp):
TATATTTTTTTATTTTTTTATT
Found at i:2388696 original size:27 final size:28
Alignment explanation
Indices: 2388628--2388702 Score: 71
Period size: 31 Copynumber: 2.6 Consensus size: 28
2388618 AATACTTATA
*
2388628 TATTTTTTTAGTTTTTTTATTTCTATTCT
1 TATTTTTTTA-TTTATTTATTTCTATTCT
* *
2388657 TTTTTACTATTTATTTATTTATTTTTATT-T
1 TATTT--T-TTTATTTATTTATTTCTATTCT
*
2388687 TATTTTTTTACTTATT
1 TATTTTTTTATTTATT
2388703 AAATACTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
27 9 0.24
28 1 0.03
29 4 0.11
30 5 0.13
31 15 0.39
32 4 0.11
ACGTcount: A:0.17, C:0.05, G:0.01, T:0.76
Consensus pattern (28 bp):
TATTTTTTTATTTATTTATTTCTATTCT
Found at i:2388911 original size:2 final size:2
Alignment explanation
Indices: 2388904--2388936 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2388894 ATTTTATCTA
2388904 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2388937 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2388941 original size:2 final size:2
Alignment explanation
Indices: 2388936--2388963 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2388926 ACACACACAC
2388936 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
2388964 TATTTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2390433 original size:65 final size:63
Alignment explanation
Indices: 2390361--2390520 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 63
2390351 AATTAAATTG
* *
2390361 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
2390425 A
63 A
* * * *
2390426 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
*
2390490 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
2390521 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 50 0.58
66 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:2397906 original size:21 final size:21
Alignment explanation
Indices: 2397863--2397906 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2397853 ACTCCGGGAG
**
2397863 CTAGCTTTTCACGAGCTGTTC
1 CTAGCTTTTCACGAGCTCCTC
* *
2397884 CTAGCTTTTCTCGTGCTCCTC
1 CTAGCTTTTCACGAGCTCCTC
2397905 CT
1 CT
2397907 CCTCCTACGG
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:0.09, C:0.34, G:0.16, T:0.41
Consensus pattern (21 bp):
CTAGCTTTTCACGAGCTCCTC
Found at i:2399013 original size:65 final size:64
Alignment explanation
Indices: 2398944--2399085 Score: 198
Period size: 65 Copynumber: 2.2 Consensus size: 64
2398934 AATTAAATTG
*
2398944 AACATCGAATGCATTTCATGCATCGATGCACATA-CCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCAC-TAGCCATGCACCGATGCACTCAGGATATTT-TG
2399007 AA
64 -A
* * * *
2399009 AACATCGAATGCATTTGATGCATCGATGCACTAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACTAGCCATGCACCGATGCACTCAGGATATTTTGA
2399073 AACATCGAATGCA
1 AACATCGAATGCA
2399086 CTCTTAGTGC
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
64 16 0.23
65 51 0.73
66 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACTAGCCATGCACCGATGCACTCAGGATATTTTGA
Found at i:2402883 original size:47 final size:47
Alignment explanation
Indices: 2402814--2402916 Score: 181
Period size: 47 Copynumber: 2.2 Consensus size: 47
2402804 TTAACAGGAG
* *
2402814 TTGTATTTTTAATTACTACACAGTTCTTATCACAGTGACCAAAGACA
1 TTGTATTTCTAATTACTACACAGTTCTTATAACAGTGACCAAAGACA
2402861 TTGTATTTCTAATTACTACACAGTTCTTATAACAGTGACCAAAGACA
1 TTGTATTTCTAATTACTACACAGTTCTTATAACAGTGACCAAAGACA
2402908 TT-TATTTCT
1 TTGTATTTCT
2402917 TGCAACGAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
46 7 0.13
47 47 0.87
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (47 bp):
TTGTATTTCTAATTACTACACAGTTCTTATAACAGTGACCAAAGACA
Found at i:2418718 original size:31 final size:31
Alignment explanation
Indices: 2418680--2418911 Score: 235
Period size: 31 Copynumber: 7.6 Consensus size: 31
2418670 TTATTAAATC
* *
2418680 ATTATTATTAAATAATTAAAGTTAAATTATT
1 ATTATTATTAAATCATTAAAGTTAAATTATA
2418711 ATTATTATTAAATCATTAAAGTT-AATT-T-
1 ATTATTATTAAATCATTAAAGTTAAATTATA
* **
2418739 ATTA-AAGTTAAATCATTAAAGTT-AACCACTA
1 ATTATTA-TTAAATCATTAAAGTTAAATTA-TA
* *
2418770 ATTATTATTAAATCATTAAAGTTAACTAATA
1 ATTATTATTAAATCATTAAAGTTAAATTATA
* * *
2418801 ATTAGTATCAAATCATTAAAGTT-AACTACTA
1 ATTATTATTAAATCATTAAAGTTAAATTA-TA
* *
2418832 ATTATTATTAAATCATTAAAGTTAACTAATA
1 ATTATTATTAAATCATTAAAGTTAAATTATA
* *
2418863 ATTAGTATCAAATCATTAAAGTTAAAATT-TA
1 ATTATTATTAAATCATTAAAGTT-AAATTATA
* *
2418894 ATAATCATTAAATCATTA
1 ATTATTATTAAATCATTA
2418912 TTATTAAATC
Statistics
Matches: 166, Mismatches: 26, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.01
28 22 0.13
29 1 0.01
30 7 0.04
31 127 0.77
32 8 0.05
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.41
Consensus pattern (31 bp):
ATTATTATTAAATCATTAAAGTTAAATTATA
Found at i:2418720 original size:45 final size:45
Alignment explanation
Indices: 2418669--2418818 Score: 124
Period size: 45 Copynumber: 3.3 Consensus size: 45
2418659 TATCATTACC
* *
2418669 ATTATTAAATCATTATTATTAAATAATTAAAGTTAAATTATTATT
1 ATTATCAAATCATTATTATTAAATAATTAAAGTTAAATAATTATT
* * * * * *
2418714 ATTATTAAATCATTA-AAGTTAATTTATTAAAGTTAAATCATTA-A
1 ATTATCAAATCATTATTA-TTAAATAATTAAAGTTAAATAATTATT
* * * * * * *
2418758 AGTTAACCACTAATTATTATTAAATCATTAAAGTTAACTAATAATT
1 A-TTATCAAATCATTATTATTAAATAATTAAAGTTAAATAATTATT
*
2418804 AGTATCAAATCATTA
1 ATTATCAAATCATTA
2418819 AAGTTAACTA
Statistics
Matches: 79, Mismatches: 22, Indels: 8
0.72 0.20 0.07
Matches are distributed among these distances:
44 2 0.03
45 75 0.95
46 2 0.03
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (45 bp):
ATTATCAAATCATTATTATTAAATAATTAAAGTTAAATAATTATT
Found at i:2418735 original size:14 final size:14
Alignment explanation
Indices: 2418673--2418888 Score: 84
Period size: 14 Copynumber: 14.4 Consensus size: 14
2418663 ATTACCATTA
*
2418673 TTAAATCATTATTA-
1 TTAAATCATTA-AAG
*
2418687 TTAAATAATTAAAG
1 TTAAATCATTAAAG
*
2418701 TTAAATTATTATTATTA-
1 TTAAATCATTA--A--AG
2418718 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
2418732 TTAATTTATTAAAG
1 TTAAATCATTAAAG
2418746 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
2418760 TTAACCACTAATTATTA-
1 TTAA--A-TCATTA-AAG
2418777 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
2418791 TTAACT-AATAATTAG
1 TTAAATCATTAA--AG
2418806 TATCAAATCATTAAAG
1 T-T-AAATCATTAAAG
* *
2418822 TTAACTACTAATTATTA-
1 TTAA--A-TCATTA-AAG
2418839 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
2418853 TTAACT-AATAATTAG
1 TTAAATCATTAA--AG
2418868 TATCAAATCATTAAAG
1 T-T-AAATCATTAAAG
2418884 TTAAA
1 TTAAA
2418889 ATTTAATAAT
Statistics
Matches: 152, Mismatches: 24, Indels: 52
0.67 0.11 0.23
Matches are distributed among these distances:
13 12 0.08
14 73 0.48
15 11 0.07
16 11 0.07
17 34 0.22
18 11 0.07
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:2418819 original size:62 final size:62
Alignment explanation
Indices: 2418711--2418887 Score: 290
Period size: 62 Copynumber: 2.9 Consensus size: 62
2418701 TTAAATTATT
* *
2418711 ATTATTATTAAATCATTAAAGTTAATTTATTAA--AGT-T-AAATCATTAAAGTTAACCACTA
1 ATTATTATTAAATCATTAAAGTTAA-CTAATAATTAGTATCAAATCATTAAAGTTAACCACTA
*
2418770 ATTATTATTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAACTACTA
1 ATTATTATTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAACCACTA
2418832 ATTATTATTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAA
1 ATTATTATTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAA
2418888 AATTTAATAA
Statistics
Matches: 111, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
58 5 0.05
59 25 0.23
60 3 0.03
61 1 0.01
62 77 0.69
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (62 bp):
ATTATTATTAAATCATTAAAGTTAACTAATAATTAGTATCAAATCATTAAAGTTAACCACTA
Found at i:2418904 original size:62 final size:61
Alignment explanation
Indices: 2418680--2418911 Score: 278
Period size: 62 Copynumber: 3.8 Consensus size: 61
2418670 TTATTAAATC
* * * * *
2418680 ATTATTATTAAATAATTAAAGTTAAAT-TATTATTATTATTAAATCATTAAAGTTAATTTATTA
1 ATTAGTATCAAATCATTAAAGTTAAATCTA--ATTATTATTAAATCATTAAAGTTAA-CTAATA
2418743 A--AGT-T-AAATCATTAAAGTTAACCA-CTAATTATTATTAAATCATTAAAGTTAACTAATA
1 ATTAGTATCAAATCATTAAAGTTAA--ATCTAATTATTATTAAATCATTAAAGTTAACTAATA
*
2418801 ATTAGTATCAAATCATTAAAGTTAACTACTAATTATTATTAAATCATTAAAGTTAACTAATA
1 ATTAGTATCAAATCATTAAAGTTAAAT-CTAATTATTATTAAATCATTAAAGTTAACTAATA
* * *
2418863 ATTAGTATCAAATCATTAAAGTTAAAATTTAATAATCATTAAATCATTA
1 ATTAGTATCAAATCATTAAAGTT-AAATCTAATTATTATTAAATCATTA
2418912 TTATTAAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 21
0.83 0.05 0.12
Matches are distributed among these distances:
58 5 0.03
59 40 0.27
60 4 0.03
61 6 0.04
62 91 0.61
63 4 0.03
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.41
Consensus pattern (61 bp):
ATTAGTATCAAATCATTAAAGTTAAATCTAATTATTATTAAATCATTAAAGTTAACTAATA
Found at i:2421766 original size:44 final size:44
Alignment explanation
Indices: 2421712--2421818 Score: 178
Period size: 44 Copynumber: 2.4 Consensus size: 44
2421702 TTCATAATTA
* *
2421712 TAATGAATAATTAATAACCTGCAACCACCAACCTACCGGGATAT
1 TAATGGATAATTAATAACCTGCAACCACCAACCTACCAGGATAT
* *
2421756 TAATGGATAATTAATAACATGCAACCACCAACCTACCAGTATAT
1 TAATGGATAATTAATAACCTGCAACCACCAACCTACCAGGATAT
2421800 TAATGGATAATTAATAACC
1 TAATGGATAATTAATAACC
2421819 ACCAATCACT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.25
Consensus pattern (44 bp):
TAATGGATAATTAATAACCTGCAACCACCAACCTACCAGGATAT
Found at i:2422257 original size:17 final size:19
Alignment explanation
Indices: 2422237--2422272 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2422227 AAAATGTATG
2422237 CTTTGTTTT-TGCT-TTTT
1 CTTTGTTTTATGCTATTTT
2422254 CTTTGTTTTATGCTATTTT
1 CTTTGTTTTATGCTATTTT
2422273 GTGTTATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (19 bp):
CTTTGTTTTATGCTATTTT
Found at i:2422614 original size:40 final size:38
Alignment explanation
Indices: 2422538--2422614 Score: 118
Period size: 40 Copynumber: 2.0 Consensus size: 38
2422528 GACGTCGAGA
*
2422538 CCTCCATGAATTGTGTTAAAGACGCCTAGACCTCCATG
1 CCTCCATGAATTGTGTTAAAGACGCCTAGACATCCATG
*
2422576 CCTCCATGCAAATTGTGTTAAAGACGCCTAGAGATCCAT
1 CCTCCATG--AATTGTGTTAAAGACGCCTAGACATCCAT
2422615 TTTGCATGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 8 0.23
40 27 0.77
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (38 bp):
CCTCCATGAATTGTGTTAAAGACGCCTAGACATCCATG
Found at i:2427428 original size:22 final size:22
Alignment explanation
Indices: 2427398--2427444 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2427388 ATTTTTCCGG
2427398 TTTCGAATAGAAAAATAATAGC
1 TTTCGAATAGAAAAATAATAGC
* *
2427420 TTTCTAATAGGAAAATAATAGC
1 TTTCGAATAGAAAAATAATAGC
2427442 TTT
1 TTT
2427445 TGAAAACGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.34
Consensus pattern (22 bp):
TTTCGAATAGAAAAATAATAGC
Found at i:2430746 original size:22 final size:23
Alignment explanation
Indices: 2430697--2430755 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
2430687 AATTTGTATG
2430697 TTATTTTATTTCACCTTTATTATGTT
1 TTATTTTATTT-A--TTTATTATGTT
2430723 TTA-TTTATTTATTTATTCAT-TT
1 TTATTTTATTTATTTATT-ATGTT
2430745 TTATTTTATTT
1 TTATTTTATTT
2430756 GCACATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 11 0.35
23 9 0.29
24 1 0.03
25 7 0.23
26 3 0.10
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (23 bp):
TTATTTTATTTATTTATTATGTT
Found at i:2431022 original size:25 final size:25
Alignment explanation
Indices: 2430988--2431043 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
2430978 CTAAGGTAAG
2430988 TAATTTGGATCGTCATTTTACATTT
1 TAATTTGGATCGTCATTTTACATTT
2431013 TAATTTGGATCGTCATTTTACATTT
1 TAATTTGGATCGTCATTTTACATTT
2431038 TAATTT
1 TAATTT
2431044 AAATTTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.54
Consensus pattern (25 bp):
TAATTTGGATCGTCATTTTACATTT
Found at i:2442316 original size:105 final size:105
Alignment explanation
Indices: 2442130--2442902 Score: 1431
Period size: 105 Copynumber: 7.4 Consensus size: 105
2442120 GGTTTTAGCT
2442130 AGAG-CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
2442194 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTC
*
2442234 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
2442299 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCTAATTC
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTC
2442339 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
2442404 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTC
2442444 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
2442509 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTC
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTC
2442549 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
2442614 TGAAGGGACCGCTGGTTGTCACCAAACATTTCTCTAATTC
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTC
2442654 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
2442719 CGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTC
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTC
2442759 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
2442824 CGAAGGGACCGCTGGTTGTCAACAAACATGTCTCAAATTC
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTC
*
2442864 AGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTC
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
2442903 GGAACAATAC
Statistics
Matches: 653, Mismatches: 15, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
104 4 0.01
105 649 0.99
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTC
Found at i:2447184 original size:23 final size:23
Alignment explanation
Indices: 2447154--2447212 Score: 109
Period size: 23 Copynumber: 2.5 Consensus size: 23
2447144 GCAAGTGAAG
2447154 CAGAGAGAGCAGTAACGGAAGCA
1 CAGAGAGAGCAGTAACGGAAGCA
2447177 CAGAGAGAGCAGTAACGGAAGCA
1 CAGAGAGAGCAGTAACGGAAGCA
2447200 CAGAGAGAAGCAG
1 CAGAGAG-AGCAG
2447213 CGGCAGTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 30 0.86
24 5 0.14
ACGTcount: A:0.44, C:0.17, G:0.36, T:0.03
Consensus pattern (23 bp):
CAGAGAGAGCAGTAACGGAAGCA
Found at i:2453720 original size:44 final size:44
Alignment explanation
Indices: 2453672--2453777 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 44
2453662 GTTTGTAACA
* *
2453672 AAAAACACCACTATATACCATACCTTTTGCGGCATTTGCAACCT
1 AAAAACACCACTATATACCAGACCTTTTGCGGCATTTGCAACCG
* * * * *
2453716 AAAAACCCCGCTATATAGCAGACCTTTTGCGGCATTTGTATCCG
1 AAAAACACCACTATATACCAGACCTTTTGCGGCATTTGCAACCG
* *
2453760 AAAAACGCCTCTATATAC
1 AAAAACACCACTATATAC
2453778 TTACGCATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (44 bp):
AAAAACACCACTATATACCAGACCTTTTGCGGCATTTGCAACCG
Found at i:2453789 original size:44 final size:44
Alignment explanation
Indices: 2453663--2453798 Score: 114
Period size: 44 Copynumber: 3.1 Consensus size: 44
2453653 AATACCGATG
* * * * * *
2453663 TTTGTAA-CAAAAAACACCACTATATACCATACCTTTTGCGGCA
1 TTTGTAACCGAAAAACCCCGCTATATAGCAGACCATTTGCGGCA
* * *
2453706 TTTGCAACCTAAAAACCCCGCTATATAGCAGACCTTTTGCGGCA
1 TTTGTAACCGAAAAACCCCGCTATATAGCAGACCATTTGCGGCA
* * * ** *
2453750 TTTGTATCCGAAAAACGCCTCTATATA-CTTACGCATTTGCGGCG
1 TTTGTAACCGAAAAACCCCGCTATATAGCAGAC-CATTTGCGGCA
2453794 TTTGT
1 TTTGT
2453799 TGGAAAAACG
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
43 9 0.12
44 67 0.88
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (44 bp):
TTTGTAACCGAAAAACCCCGCTATATAGCAGACCATTTGCGGCA
Found at i:2453871 original size:18 final size:18
Alignment explanation
Indices: 2453848--2453885 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2453838 TTTATGGTAA
2453848 ACGCCGCTAAATCTCAAC
1 ACGCCGCTAAATCTCAAC
2453866 ACGCCGCTAAATCTCAAC
1 ACGCCGCTAAATCTCAAC
2453884 AC
1 AC
2453886 CTATTGTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.39, G:0.11, T:0.16
Consensus pattern (18 bp):
ACGCCGCTAAATCTCAAC
Found at i:2456906 original size:40 final size:38
Alignment explanation
Indices: 2456817--2456920 Score: 113
Period size: 40 Copynumber: 2.7 Consensus size: 38
2456807 TATTAAAGAT
* * * *
2456817 ATTTT-AAATTACAACTTGAAATATTACCAAACACAAC
1 ATTTTCAATTTACAACCTAAAATGTTACCAAACACAAC
* *
2456854 ATTTTCGATTTACAACAC-AAAATGTTACCAAACGTATAAC
1 ATTTTCAATTTACAAC-CTAAAATGTTACCAAAC--ACAAC
2456894 ATTTTCAATTTACAACCTAAAATGTTA
1 ATTTTCAATTTACAACCTAAAATGTTA
2456921 TATATAATGA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
37 5 0.09
38 21 0.38
39 1 0.02
40 28 0.51
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (38 bp):
ATTTTCAATTTACAACCTAAAATGTTACCAAACACAAC
Found at i:2466242 original size:23 final size:23
Alignment explanation
Indices: 2466216--2466259 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2466206 GTTCGAGTTC
*
2466216 GTTCGTTTAACATTCGCGAACTT
1 GTTCATTTAACATTCGCGAACTT
* *
2466239 GTTCATTTAATATTCTCGAAC
1 GTTCATTTAACATTCGCGAAC
2466260 ATATTGGGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (23 bp):
GTTCATTTAACATTCGCGAACTT
Found at i:2468422 original size:44 final size:44
Alignment explanation
Indices: 2468359--2468453 Score: 190
Period size: 44 Copynumber: 2.2 Consensus size: 44
2468349 TTAGACTTGG
2468359 CCTACATTAACAAGTTGGGTCCTAAAACAATATGTAGTCAAAAC
1 CCTACATTAACAAGTTGGGTCCTAAAACAATATGTAGTCAAAAC
2468403 CCTACATTAACAAGTTGGGTCCTAAAACAATATGTAGTCAAAAC
1 CCTACATTAACAAGTTGGGTCCTAAAACAATATGTAGTCAAAAC
2468447 CCTACAT
1 CCTACAT
2468454 CAAGTGGCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (44 bp):
CCTACATTAACAAGTTGGGTCCTAAAACAATATGTAGTCAAAAC
Found at i:2472790 original size:37 final size:36
Alignment explanation
Indices: 2472748--2472856 Score: 157
Period size: 35 Copynumber: 3.0 Consensus size: 36
2472738 ATATTTCAAC
*
2472748 AAACATCTACCAAACTTTGAAAAACCATTTTTCAAAG
1 AAACATTTACCAAACTTTG-AAAACCATTTTTCAAAG
* *
2472785 AAACATTTACCAAACTTTGAAAACCA-TTTTCAGAT
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
*
2472820 AAACATTTACCAAACTTTGAAAACTATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAACCA-TTTTTCAAAG
2472857 TTGGTTGCCA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
35 32 0.50
36 7 0.11
37 25 0.39
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAAAG
Found at i:2477422 original size:37 final size:36
Alignment explanation
Indices: 2477374--2477476 Score: 145
Period size: 35 Copynumber: 2.9 Consensus size: 36
2477364 ATATTTCAAC
* *
2477374 AAACATCTACCAAACTTTGAAAACCCATTTTTCATAG
1 AAACATTTACCAAACTTTGAAAA-CCATTTTTCAGAG
* *
2477411 AAATATTTACCAAACTTTGAAAACC-TTTTTCAGAT
1 AAACATTTACCAAACTTTGAAAACCATTTTTCAGAG
*
2477446 AAACATTTACCAAACTTTGAAAATCATTTTT
1 AAACATTTACCAAACTTTGAAAACCATTTTT
2477477 TCAAAGTTGG
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 31 0.53
36 7 0.12
37 21 0.36
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAACCATTTTTCAGAG
Found at i:2480574 original size:18 final size:19
Alignment explanation
Indices: 2480538--2480576 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2480528 TATTTTAACA
2480538 TTTAAAATAATAAATTATT
1 TTTAAAATAATAAATTATT
*
2480557 TTTAAAATAA-ATATTATT
1 TTTAAAATAATAAATTATT
2480575 TT
1 TT
2480577 ATATTCATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAAAATAATAAATTATT
Found at i:2485215 original size:2 final size:2
Alignment explanation
Indices: 2485210--2485296 Score: 151
Period size: 2 Copynumber: 44.5 Consensus size: 2
2485200 ATATTTAAGG
*
2485210 TA TA TA TA TA TA TA GA TA TA TA TA T- 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
2485251 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
2485292 TA TA T
1 TA TA T
2485297 CTGTCTTGAA
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 2 0.02
2 79 0.98
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2486169 original size:24 final size:24
Alignment explanation
Indices: 2486142--2486193 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2486132 AACGGATATA
*
2486142 TCAAAAATCAAAACATAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
** * *
2486166 TCAAGTATCAGATCAAAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
2486190 TCAA
1 TCAA
2486194 GTATTCGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAATCCAGG
Found at i:2486193 original size:12 final size:13
Alignment explanation
Indices: 2486158--2486242 Score: 65
Period size: 12 Copynumber: 7.0 Consensus size: 13
2486148 ATCAAAACAT
2486158 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
2486171 TAT-CAGATCAA-
1 AATCCAGGTCAAG
2486182 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
2486195 TATTC-GATC-AG
1 AATCCAGGTCAAG
2486206 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
2486219 TATCCA-ATC-AG
1 AATCCAGGTCAAG
2486230 AATCCAGGTCAAG
1 AATCCAGGTCAAG
2486243 TATTATAATA
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
11 14 0.27
12 24 0.46
13 14 0.27
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:2486194 original size:24 final size:24
Alignment explanation
Indices: 2486158--2486245 Score: 135
Period size: 24 Copynumber: 3.7 Consensus size: 24
2486148 ATCAAAACAT
*
2486158 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAG
2486182 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCAGGTCAAGTA-TCAGATCAG
2486206 AATCCAGGTCAAGTATCCA-ATCAG
1 AATCCAGGTCAAGTAT-CAGATCAG
2486230 AATCCAGGTCAAGTAT
1 AATCCAGGTCAAGTAT
2486246 TATAATAGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
23 1 0.02
24 57 0.95
25 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAG
Found at i:2486255 original size:24 final size:25
Alignment explanation
Indices: 2486158--2486255 Score: 116
Period size: 24 Copynumber: 4.1 Consensus size: 25
2486148 ATCAAAACAT
*
2486158 AATCCAGGTCAAGTA-T-CAGATCAA
1 AATCCAGGTCAAGTATTACA-ATCAG
*
2486182 AATCCAGGTCAAGTATT-CGATCAG
1 AATCCAGGTCAAGTATTACAATCAG
*
2486206 AATCCAGGTCAAGTA-TCCAATCAG
1 AATCCAGGTCAAGTATTACAATCAG
*
2486230 AATCCAGGTCAAGTATTATAAT-AG
1 AATCCAGGTCAAGTATTACAATCAG
2486254 AA
1 AA
2486256 ATCAAATCGG
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
23 1 0.02
24 59 0.89
25 6 0.09
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (25 bp):
AATCCAGGTCAAGTATTACAATCAG
Found at i:2491514 original size:24 final size:24
Alignment explanation
Indices: 2491487--2491536 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
2491477 TATATCAAAA
*
2491487 ATCAAAACATAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
2491511 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
2491535 AT
1 AT
2491537 TATAATAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:2508199 original size:24 final size:24
Alignment explanation
Indices: 2508167--2508214 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2508157 TATTCAATGA
2508167 TATTTTAGGTCTAGGTTACATCTC
1 TATTTTAGGTCTAGGTTACATCTC
*
2508191 TATTTTAGGTCTATGTTACATCTC
1 TATTTTAGGTCTAGGTTACATCTC
2508215 CTGTCCTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.48
Consensus pattern (24 bp):
TATTTTAGGTCTAGGTTACATCTC
Found at i:2514931 original size:14 final size:14
Alignment explanation
Indices: 2514920--2514954 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
2514910 AAAATGAATT
2514920 ACATTTTCTGAAAA
1 ACATTTTCTGAAAA
*
2514934 ACATTTTCTGGAAA
1 ACATTTTCTGAAAA
*
2514948 ACGTTTT
1 ACATTTT
2514955 ACGATATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (14 bp):
ACATTTTCTGAAAA
Found at i:2515177 original size:31 final size:29
Alignment explanation
Indices: 2515109--2515178 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
2515099 AATATTGTTT
*
2515109 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
2515139 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
2515172 TTATATT
1 TTATATT
2515179 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:2515256 original size:23 final size:23
Alignment explanation
Indices: 2515207--2515257 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2515197 TAGTGATATT
**
2515207 ATATTTTAAAAATAATAATTACT
1 ATATTTTAAAAATAATAATTAAA
* * *
2515230 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATAATAATTAAA
2515253 ATATT
1 ATATT
2515258 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTTTAAAAATAATAATTAAA
Found at i:2515313 original size:19 final size:19
Alignment explanation
Indices: 2515245--2515325 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
2515235 TTAAATATAT
2515245 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
2515264 TTATTAGATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
2515283 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
2515303 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
2515321 -TATTA
1 TTATTA
2515326 GTATATGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:2515414 original size:18 final size:19
Alignment explanation
Indices: 2515391--2515439 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
2515381 AAAATAAAAA
2515391 TATAATATAATAT-ATTAT
1 TATAATATAATATGATTAT
2515409 TATAATATAAT-TGATTAT
1 TATAATATAATATGATTAT
* *
2515427 TTTATTATAATAT
1 TATAATATAATAT
2515440 TAAAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TATAATATAATATGATTAT
Found at i:2515419 original size:23 final size:23
Alignment explanation
Indices: 2515389--2515439 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
2515379 TTAAAATAAA
2515389 AATATAATAT-AATATATTATTAT
1 AATATAAT-TGAATATATTATTAT
* *
2515412 AATATAATTGATTATTTTATTAT
1 AATATAATTGAATATATTATTAT
2515435 AATAT
1 AATAT
2515440 TAAAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AATATAATTGAATATATTATTAT
Found at i:2515454 original size:22 final size:22
Alignment explanation
Indices: 2515424--2515472 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2515414 TATAATTGAT
*
2515424 TATTTTATTATAATATTAAAAA
1 TATTATATTATAATATTAAAAA
* *
2515446 TATTATATTATATTATTAGAAA
1 TATTATATTATAATATTAAAAA
2515468 TATTA
1 TATTA
2515473 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTATATTATAATATTAAAAA
Found at i:2516990 original size:23 final size:24
Alignment explanation
Indices: 2516947--2516995 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
2516937 TAATATTATT
*
2516947 TTTTTAAAAATAACTTAAAAT-TG
1 TTTTAAAAAATAACTTAAAATATG
*
2516970 TTTTAAAAAATTACATT-AAATATG
1 TTTTAAAAAATAAC-TTAAAATATG
2516994 TT
1 TT
2516996 GGTAAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (24 bp):
TTTTAAAAAATAACTTAAAATATG
Found at i:2517711 original size:12 final size:12
Alignment explanation
Indices: 2517694--2517720 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2517684 AATATAAATA
2517694 AAATATAATTTT
1 AAATATAATTTT
2517706 AAATATAATTTT
1 AAATATAATTTT
2517718 AAA
1 AAA
2517721 AAAATAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATATAATTTT
Found at i:2517747 original size:23 final size:24
Alignment explanation
Indices: 2517704--2517748 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
2517694 AAATATAATT
*
2517704 TTAAATATAATTTTAAAAAAATAG
1 TTAAATATAATTTCAAAAAAATAG
2517728 TTAAA-ATAA-TTCAAATAAAAT
1 TTAAATATAATTTCAAA-AAAAT
2517749 TAAAGTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
TTAAATATAATTTCAAAAAAATAG
Found at i:2518798 original size:18 final size:17
Alignment explanation
Indices: 2518746--2518800 Score: 64
Period size: 13 Copynumber: 3.4 Consensus size: 17
2518736 ACTCGAATCG
*
2518746 ACTCAACTTGATCTAAT
1 ACTCAACTTGATTTAAT
2518763 ACTC-AC-T--TTTAAT
1 ACTCAACTTGATTTAAT
2518776 ACTCAACTTGATTTAACT
1 ACTCAACTTGATTTAA-T
2518794 ACTCAAC
1 ACTCAAC
2518801 AATATTGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
13 9 0.28
14 2 0.06
15 2 0.06
16 2 0.06
17 9 0.28
18 8 0.25
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (17 bp):
ACTCAACTTGATTTAAT
Found at i:2536813 original size:185 final size:185
Alignment explanation
Indices: 2536501--2536870 Score: 695
Period size: 185 Copynumber: 2.0 Consensus size: 185
2536491 CAAGCCAAAC
*
2536501 TTTCGGTCTTTTAGGTTGTTCTAATTTCATTTCTCTAGTTGCCCCCTCAAGTTTGGGTAAATAAA
1 TTTCGGTCCTTTAGGTTGTTCTAATTTCATTTCTCTAGTTGCCCCCTCAAGTTTGGGTAAATAAA
2536566 AAAATAGATAAACTATACAAATGATCACTAATATTTGAGTGAGTTTTCATTTTTGTCATTGAAGT
66 AAAATAGATAAACTATACAAATGATCACTAATATTTGAGTGAGTTTTCATTTTTGTCATTGAAGT
2536631 TTCAAAATTAAAAATTTGATCAATAACGTTATGAATTTATAATAAATCAGTCGCT
131 TTCAAAATTAAAAATTTGATCAATAACGTTATGAATTTATAATAAATCAGTCGCT
*
2536686 TTTCGGTCCTTTAGGTTGTTCTAATTTCATTTCTCTAGTTGCCGCCTCAAGTTTGGGTAAATAAA
1 TTTCGGTCCTTTAGGTTGTTCTAATTTCATTTCTCTAGTTGCCCCCTCAAGTTTGGGTAAATAAA
*
2536751 AAAATAGATAAACTATACAAATGATCACTAATATTTTAGTGAGTTTTCATTTTTGTCATTGAAGT
66 AAAATAGATAAACTATACAAATGATCACTAATATTTGAGTGAGTTTTCATTTTTGTCATTGAAGT
* *
2536816 TTCAAAATTAAAAATTTGATCAATAACGTTATGGATTTATAATAAATCGGTCGCT
131 TTCAAAATTAAAAATTTGATCAATAACGTTATGAATTTATAATAAATCAGTCGCT
2536871 CGCCATTAAC
Statistics
Matches: 180, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 180 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (185 bp):
TTTCGGTCCTTTAGGTTGTTCTAATTTCATTTCTCTAGTTGCCCCCTCAAGTTTGGGTAAATAAA
AAAATAGATAAACTATACAAATGATCACTAATATTTGAGTGAGTTTTCATTTTTGTCATTGAAGT
TTCAAAATTAAAAATTTGATCAATAACGTTATGAATTTATAATAAATCAGTCGCT
Found at i:2537750 original size:13 final size:13
Alignment explanation
Indices: 2537716--2537757 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2537706 TATAATAAAG
2537716 AAAAAATGAAGTA
1 AAAAAATGAAGTA
2537729 AATAAAATG-AGATA
1 AA-AAAATGAAG-TA
*
2537743 AAAAAATGGAGTA
1 AAAAAATGAAGTA
2537756 AA
1 AA
2537758 GATAAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (13 bp):
AAAAAATGAAGTA
Found at i:2537775 original size:29 final size:31
Alignment explanation
Indices: 2537743--2537813 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 31
2537733 AAATGAGATA
** *
2537743 AAAAAATGGAGTAAAGATAAA-A-AGTAAAT
1 AAAAAATAAAGTAAAGATAAAGACAATAAAT
2537772 AAAATAA-AAAGTAAAGATAAAGACAATAAAT
1 AAAA-AATAAAGTAAAGATAAAGACAATAAAT
2537803 AAATAAATAAA
1 AAA-AAATAAA
2537814 TATGAATAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 16 0.47
30 3 0.09
31 11 0.32
32 4 0.12
ACGTcount: A:0.70, C:0.01, G:0.11, T:0.17
Consensus pattern (31 bp):
AAAAAATAAAGTAAAGATAAAGACAATAAAT
Found at i:2537778 original size:16 final size:17
Alignment explanation
Indices: 2537754--2537809 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
2537744 AAAAATGGAG
2537754 TAAAGATAAAAAGTAAA
1 TAAAGATAAAAAGTAAA
2537771 TAAA-ATAAAAAGTAAAGA
1 TAAAGATAAAAAGT-AA-A
*
2537789 TAAAGACAATAAA-TAAA
1 TAAAGATAA-AAAGTAAA
2537806 TAAA
1 TAAA
2537810 TAAATATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 9 0.26
17 11 0.32
18 7 0.21
19 4 0.12
20 3 0.09
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (17 bp):
TAAAGATAAAAAGTAAA
Found at i:2537805 original size:4 final size:4
Alignment explanation
Indices: 2537796--2537913 Score: 78
Period size: 4 Copynumber: 27.5 Consensus size: 4
2537786 AGATAAAGAC
* *
2537796 AATA AATA AATA AATA AATA TGAATA AGTAA AACTA AGATA AAGAA AATA
1 AATA AATA AATA AATA AATA --AATA AAT-A AA-TA A-ATA AA-TA AATA
* * * *
2537846 AAAA AATAA AATT AATA AAGA GAA-G AA-A AATA AATA AATA AATA AATA
1 AATA AAT-A AATA AATA AATA -AATA AATA AATA AATA AATA AATA AATA
2537894 AATA AATA ATATA ATATA AA
1 AATA AATA A-ATA A-ATA AA
2537914 GAAAAATAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
3 4 0.04
4 58 0.62
5 25 0.27
6 6 0.06
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:2537920 original size:20 final size:20
Alignment explanation
Indices: 2537897--2537954 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 20
2537887 ATAAATAAAT
2537897 AAATAATATAATATAAAGAA
1 AAATAATATAATATAAAGAA
2537917 AAAT-A-ATAATAGTAAAGAA
1 AAATAATATAATA-TAAAGAA
2537936 ATAATATATATATATATAA
1 A-AATA-ATATA-ATATAA
2537955 TATTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
18 6 0.19
19 9 0.28
20 7 0.22
22 1 0.03
23 6 0.19
24 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAATAATATAATATAAAGAA
Found at i:2538246 original size:38 final size:38
Alignment explanation
Indices: 2538201--2538304 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 38
2538191 TTAGGAAAAC
* *
2538201 AAAATAAAA-AGAAATAGAAAATATATATAATA-GATAT
1 AAAATAAAATAGAAATAAAAAATATATATAAAAGGAT-T
*
2538238 AAAAATAAAATA-AACA-AAAAAATA-AAATAAAAGGATT
1 -AAAATAAAATAGAA-ATAAAAAATATATATAAAAGGATT
2538275 AAAATAAAATAGAAATAAAAAATATATATA
1 AAAATAAAATAGAAATAAAAAATATATATA
2538305 TACAATAACG
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
36 12 0.21
37 17 0.30
38 25 0.45
39 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (38 bp):
AAAATAAAATAGAAATAAAAAATATATATAAAAGGATT
Found at i:2540352 original size:80 final size:81
Alignment explanation
Indices: 2540117--2541077 Score: 1036
Period size: 80 Copynumber: 11.8 Consensus size: 81
2540107 CTGAATTTAA
* * * * *** * * *
2540117 TGTAATCGAACTCGAAGCTCTTTGATGATATAAAACCCTTCTCAACTTGAGTTATGCTGTAAATA
1 TGTAATCGAACTCGAAGGTCTTTG--GACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATG
2540182 ATGTGCCTTTGAGCTGAG
64 ATGTGCCTTTGAGCTGAG
* ** * *
2540200 TGTAATCGAACTCGAAGGTCTTTTGGA-AGATAGCTTTTCTTGCATTGAGCTAAGCTGCAAATGA
1 TGTAATCGAACTCGAAGGTC-TTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGA
*
2540264 TGTACCTTTGAGCTGAG
65 TGTGCCTTTGAGCTGAG
*
2540281 TGTAATCGAACTCGAAGGTCTTTGGA-AGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATAAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
*
2540345 GTGCCTTTGAGCTAAG
66 GTGCCTTTGAGCTGAG
* * * * *
2540361 TGTAATAGAACTTGAAGGTCTTT-GACAGATAACCCTTCTTCCCTTGAGCTATGCTGCAAATGAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
*
2540425 GTGCCTTTGAGCTAAG
66 GTGCCTTTGAGCTGAG
* * * * *
2540441 TGTAATCGAACTCGAAAGTATTTTGATAACATATAACCCTT-TTAGCCTTGAGTTATA-CTACAA
1 TGTAATCGAACTCGAAGGT-CTTTG--GACAGATAACCCTTCTT-GCCTTGAGTTA-AGCTGCAA
*
2540504 ATGATATGCCTTTGAGCTGAG
61 ATGATGTGCCTTTGAGCTGAG
* * * *
2540525 TGTAATCGAACTCGAAGGTCTTT-GACAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATAAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
2540589 GTGCCTTTGAGCTGAG
66 GTGCCTTTGAGCTGAG
** * *
2540605 TGTAATTAAACTCGAAGGTATTTGG-CAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
*
2540669 ATGCCTTTGAGCTGAG
66 GTGCCTTTGAGCTGAG
* * * * *
2540685 TGTAATAGAACTCGAAGGTCTTTTGATGACAAATAACCCTTCTAGCATTGATTTATA-CTGCAAA
1 TGTAATCGAACTCGAAGGTC-TTTG--GACAGATAACCCTTCTTGCCTTGAGTTA-AGCTGCAAA
* *
2540749 TGATGTGCCTCTGAGTTGAG
62 TGATGTGCCTTTGAGCTGAG
* * * * *
2540769 TGTAATCAAACTCGAAGGTCTTTTGATGATAAATAACCCTT-TTAGCATTGATTTATA-CTGCAA
1 TGTAATCGAACTCGAAGGTC-TTTG--GACAGATAACCCTTCTT-GCCTTGAGTTA-AGCTGCAA
*
2540832 ATGATGTGCCTCTGAGCTGAG
61 ATGATGTGCCTTTGAGCTGAG
* * *
2540853 TATAATCGAACTCGAAGGTCTTTGG-CAGATAACTCTTCTTGCCTTGAGCTAAGCTGCAAATGAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
*
2540917 GTGTCTTTGAGCTGAG
66 GTGCCTTTGAGCTGAG
* * *
2540933 TGTAATCGAACTCGAAGGTATTTTGATGACAGATAACCCTTCTAGCCTTGAGTTATGCTGC-AA-
1 TGTAATCGAACTCGAAGGT-CTTTG--GACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAAT
* *
2540996 -ATGTGCCTCTAAGCTGAG
63 GATGTGCCTTTGAGCTGAG
* ** * *
2541014 TGTAATCAAACTCGAAGGTCTTTGG-CAGATAA-CCTTCTTGCCTTGAACTATGCTACAAATGAT
1 TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
2541077 G
66 G
2541078 AGCCGATCAT
Statistics
Matches: 754, Mismatches: 98, Indels: 56
0.83 0.11 0.06
Matches are distributed among these distances:
76 20 0.03
77 9 0.01
78 1 0.00
79 6 0.01
80 337 0.45
81 110 0.15
82 2 0.00
83 33 0.04
84 236 0.31
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (81 bp):
TGTAATCGAACTCGAAGGTCTTTGGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATGAT
GTGCCTTTGAGCTGAG
Found at i:2540547 original size:164 final size:165
Alignment explanation
Indices: 2540056--2541077 Score: 1159
Period size: 164 Copynumber: 6.3 Consensus size: 165
2540046 GACAATTTTG
* * * * * * * ** * *
2540056 TTGACAAATAACCCTTATTACCTTGAGCTATGTTGTAAATTTGATTTGCCTCTGAATTTAATGTA
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTA
* * * * * * * * * *
2540121 ATCGAACTCGAAGCT-CTTTGATGATATAAAACCCTTCTCA-ACTTGAGTTATGCTGTAAATAAT
64 ATCGAACTCGAAGGTATTTTGATGACAGATAACCCTTCTTAGCCTTGAGTTATACTGCAAATGAT
2540184 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT
129 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-T
* ** * * *
2540222 TTGGA-AGATAGCTTTTCTTGCATTGAGCTAAGCTGCAAATGATGTACCTTTGAGCTGAGTGTAA
1 TT-GACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAA
* *
2540286 TCGAACTCGAAGGT-CTTTG--GA-AGATAACCCTTCTT-GCCTTGAGTTA-AGCTGCAAATAAT
65 TCGAACTCGAAGGTATTTTGATGACAGATAACCCTTCTTAGCCTTGAGTTATA-CTGCAAATGAT
* * *
2540345 GTGCCTTTGAGCTAAGTGTAATAGAACTTGAAGGTCT
129 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* *
2540382 TTGACAGATAACCCTTCTTCCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAAT
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
* * * * *
2540447 CGAACTCGAAAGTATTTTGATAACATATAACCCTT-TTAGCCTTGAGTTATACTACAAATGATAT
66 CGAACTCGAAGGTATTTTGATGACAGATAACCCTTCTTAGCCTTGAGTTATACTGCAAATGATGT
2540511 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
131 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* *
2540546 TTGACAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATAATGTGCCTTTGAGCTGAGTGTAAT
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
** * *
2540611 TAAACTCGAAGGTA-TTTG--G-CAGATAACCCTTCTT-GCCTTGAGTTATGCTGCAAATGATAT
66 CGAACTCGAAGGTATTTTGATGACAGATAACCCTTCTTAGCCTTGAGTTATACTGCAAATGATGT
*
2540671 GCCTTTGAGCTGAGTGTAATAGAACTCGAAGGTCTTT
131 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC--T
* * * ** * * *
2540708 TGATGACAAATAACCCTTCTAGCATTGATTTATACTGCAAATGATGTGCCTCTGAGTTGAGTGTA
1 T--TGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
* * * * * *
2540773 ATCAAACTCGAAGGTCTTTTGATGATAAATAACCCTT-TTAGCATTGATTTATACTGCAAATGAT
64 ATCGAACTCGAAGGTATTTTGATGACAGATAACCCTTCTTAGCCTTGAGTTATACTGCAAATGAT
* *
2540837 GTGCCTCTGAGCTGAGTATAATCGAACTCGAAGGTCT
129 GTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * * *
2540874 TTGGCAGATAACTCTTCTTGCCTTGAGCTAAGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAAT
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
*
2540939 CGAACTCGAAGGTATTTTGATGACAGATAACCCTTC-TAGCCTTGAGTTATGCTGC-AA--ATGT
66 CGAACTCGAAGGTATTTTGATGACAGATAACCCTTCTTAGCCTTGAGTTATACTGCAAATGATGT
* * *
2541000 GCCTCTAAGCTGAGTGTAATCAAACTCGAAGGTCT
131 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
* * *
2541035 TTGGCAGATAA-CCTTCTTGCCTTGAACTATGCTACAAATGATG
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATG
2541078 AGCCGATCAT
Statistics
Matches: 731, Mismatches: 104, Indels: 48
0.83 0.12 0.05
Matches are distributed among these distances:
159 2 0.00
160 163 0.22
161 116 0.16
162 4 0.01
163 9 0.01
164 336 0.46
165 5 0.01
166 28 0.04
167 5 0.01
168 63 0.09
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (165 bp):
TTGACAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
CGAACTCGAAGGTATTTTGATGACAGATAACCCTTCTTAGCCTTGAGTTATACTGCAAATGATGT
GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCT
Found at i:2540569 original size:244 final size:244
Alignment explanation
Indices: 2540162--2541059 Score: 1163
Period size: 244 Copynumber: 3.7 Consensus size: 244
2540152 CCCTTCTCAA
* * * *
2540162 CTTGAGTTATGCTGTAAATAATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG--
1 CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGAT
* ** * * * *
2540225 GA-AGATAGCTTTTCTTGCATTGAGCTA-AGCTGCAAATGATGTACCTTTGAGCTGAGTGTAATC
66 GACAGATAACCCTTCTAGCATTGAGTTATA-CTGCAAATGATGTGCCTCTGAGCTGAGTGTAATC
*
2540288 GAACTCGAAGGTCTTTGGA-AGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATAATGTGCCTT
130 AAACTCGAAGGTCTTT-GACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATAATGTGCCTT
* * * *
2540352 TGAGCTAAGTGTAATAGAACTTGAAGGTCTTTGACAGATAACCCTTCTTCC
194 TGAGCTGAGTGTAATAGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGC
* *
2540403 CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCGAAAGTATTTTGAT
1 CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGAT
* * * * * * * *
2540468 AACATATAACCCTTTTAGCCTTGAGTTATACTACAAATGATATGCCTTTGAGCTGAGTGTAATCG
66 GACAGATAACCCTTCTAGCATTGAGTTATACTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCA
* * *
2540533 AACTCGAAGGTCTTTGACAGATAACCCTTTTTGCCTTGAGCTATGCTGCAAATAATGTGCCTTTG
131 AACTCGAAGGTCTTTGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATAATGTGCCTTTG
*
2540598 AGCTGAGTGTAATTA-AACTCGAAGGTATTTGGCAGATAACCCTTCTTGC
196 AGCTGAGTGTAA-TAGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGC
* * * *
2540647 CTTGAGTTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATAGAACTCGAAGGTCTTTTGAT
1 CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGAT
* * *
2540712 GACAAATAACCCTTCTAGCATTGATTTATACTGCAAATGATGTGCCTCTGAGTTGAGTGTAATCA
66 GACAGATAACCCTTCTAGCATTGAGTTATACTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCA
* * * * *
2540777 AACTCGAAGGTCTTTTGATGATAAATAACCCTT-TTAGCATTGATTTATA-CTGCAAATGATGTG
131 AACTCGAAGGTC--TT--TGACAGATAACCCTTCTT-GCCTTGAGTTA-AGCTGCAAATAATGTG
* * * *
2540840 CCTCTGAGCTGAGTATAATCGAACTCGAAGGTCTTTGGCAGATAACTCTTCTTGC
190 CCTTTGAGCTGAGTGTAATAGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGC
* *
2540895 CTTGAGCTAAGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGAT
1 CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGAT
* * *
2540960 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGC-AA--ATGTGCCTCTAAGCTGAGTGTAATCA
66 GACAGATAACCCTTCTAGCATTGAGTTATACTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCA
*
2541022 AACTCGAAGGTCTTTGGCAGATAA-CCTTCTTGCCTTGA
131 AACTCGAAGGTCTTTGACAGATAACCCTTCTTGCCTTGA
2541060 ACTATGCTAC
Statistics
Matches: 573, Mismatches: 70, Indels: 29
0.85 0.10 0.04
Matches are distributed among these distances:
240 10 0.02
241 66 0.12
243 5 0.01
244 275 0.48
245 39 0.07
246 2 0.00
247 5 0.01
248 171 0.30
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (244 bp):
CTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGAT
GACAGATAACCCTTCTAGCATTGAGTTATACTGCAAATGATGTGCCTCTGAGCTGAGTGTAATCA
AACTCGAAGGTCTTTGACAGATAACCCTTCTTGCCTTGAGTTAAGCTGCAAATAATGTGCCTTTG
AGCTGAGTGTAATAGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGC
Found at i:2542378 original size:95 final size:95
Alignment explanation
Indices: 2542169--2542429 Score: 332
Period size: 95 Copynumber: 2.7 Consensus size: 95
2542159 GACTAGCTGG
* * *
2542169 ATCCATAAAGCCAGGACGTTTAACCAATTGCTCTAG-GGGACAGCTCAAT--ATTATTGTATAGA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTC-ATGCTTTATTG--T--A
* *
2542231 TATTACAATCGCCTTTAGCAGGCTAGCTGAATATT
61 TATTATAATCACCTTTAGCAGGCTAGCTGAATATT
* *
2542266 ATACATAAGGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCATGCTTTATTGTATATTA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCATGCTTTATTGTATATTA
* * *
2542331 TAATCACCTTTATCTGGCTAGCTGAATCTT
66 TAATCACCTTTAGCAGGCTAGCTGAATATT
* * *
2542361 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATA-TA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCATGCTTTATTGTATATTA
2542425 TAATC
66 TAATC
2542430 TGGGTATACG
Statistics
Matches: 146, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
94 7 0.05
95 88 0.60
97 36 0.25
98 9 0.06
99 6 0.04
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (95 bp):
ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCATGCTTTATTGTATATTA
TAATCACCTTTAGCAGGCTAGCTGAATATT
Found at i:2548016 original size:65 final size:63
Alignment explanation
Indices: 2547928--2548049 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
2547918 CCCATTCAAC
* * * *
2547928 AGGTATCGATACCCTCTCAAACGAAAAGAATCACAGAATGTAATGAGGGTACCGATACCCCAGTT
1 AGGTACCGATACCCTCTCAAACG-AAA-AATAACAGAATGCAATAAGGGTACCGATACCCCAGTT
** * *
2547993 AGGTACCGATACCCTCTTGAACGAAAACTAACAGAATGCAGTAAGGGTACCGATACC
1 AGGTACCGATACCCTCTCAAACGAAAAATAACAGAATGCAATAAGGGTACCGATACC
2548050 TCAAGGGGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 26 0.53
64 3 0.06
65 20 0.41
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (63 bp):
AGGTACCGATACCCTCTCAAACGAAAAATAACAGAATGCAATAAGGGTACCGATACCCCAGTT
Found at i:2553115 original size:45 final size:45
Alignment explanation
Indices: 2553031--2553118 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 45
2553021 AAAACAAATA
* *
2553031 AGATACAAAAAATAGATTAAAGAAAAAAATGAAGTAAATAAAACG
1 AGATACAAAAAATAGAGTAAAGAAAAAAATGAAATAAATAAAACG
* *
2553076 AGATA-AAAAAATGGAGTAAAGATAAAAA-GTAAATAAAATAAAA
1 AGATACAAAAAATAGAGTAAAGAAAAAAATG-AAAT-AAATAAAA
2553119 ATAACGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 1 0.03
44 23 0.62
45 13 0.35
ACGTcount: A:0.68, C:0.02, G:0.14, T:0.16
Consensus pattern (45 bp):
AGATACAAAAAATAGAGTAAAGAAAAAAATGAAATAAATAAAACG
Found at i:2553116 original size:16 final size:16
Alignment explanation
Indices: 2553092--2553139 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
2553082 AAAAATGGAG
2553092 TAAAGATAAAAAGTAAA
1 TAAA-ATAAAAAGTAAA
*
2553109 TAAAATAAAAA-TAAC
1 TAAAATAAAAAGTAAA
*
2553124 GAAAATAAAAAGTAAA
1 TAAAATAAAAAGTAAA
2553140 GATAAATACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 13 0.48
16 10 0.37
17 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (16 bp):
TAAAATAAAAAGTAAA
Found at i:2553169 original size:22 final size:22
Alignment explanation
Indices: 2553141--2553193 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2553131 AAAAGTAAAG
*
2553141 ATAAATACA-AAATAACAAATGA
1 ATAAATAAATAAATAA-AAATGA
*
2553163 ATAAATAAATAAATAAATATGA
1 ATAAATAAATAAATAAAAATGA
*
2553185 ATAAGTAAA
1 ATAAATAAA
2553194 ACGAAGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.23
Consensus pattern (22 bp):
ATAAATAAATAAATAAAAATGA
Found at i:2553245 original size:9 final size:9
Alignment explanation
Indices: 2553165--2553260 Score: 54
Period size: 9 Copynumber: 10.3 Consensus size: 9
2553155 ACAAATGAAT
2553165 AAATAAAT-
1 AAATAAATA
2553173 AAATAAATA
1 AAATAAATA
* *
2553182 TGAATAAGTA
1 -AAATAAATA
*
2553192 AAACGAAGATA
1 AAA-TAA-ATA
2553203 AAGA-AAATA
1 AA-ATAAATA
*
2553212 AAATAAAGA
1 AAATAAATA
*
2553221 GAAGAAAAAT-
1 -AA-ATAAATA
2553231 AAATAAATA
1 AAATAAATA
2553240 AAATAAATA
1 AAATAAATA
* *
2553249 AGATAAAGA
1 AAATAAATA
2553258 AAA
1 AAA
2553261 AATAATAGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
8 14 0.21
9 31 0.46
10 13 0.19
11 8 0.12
12 1 0.01
ACGTcount: A:0.72, C:0.01, G:0.10, T:0.17
Consensus pattern (9 bp):
AAATAAATA
Found at i:2553731 original size:18 final size:16
Alignment explanation
Indices: 2553685--2553779 Score: 63
Period size: 18 Copynumber: 5.9 Consensus size: 16
2553675 AATAACGTTT
2553685 AAACAAAATATTAAAATA
1 AAACAAAA-A-TAAAATA
* *
2553703 AAATAATAATAGGAAATA
1 AAACAAAAATA--AAATA
2553721 AAACAAAAATAAAAT-
1 AAACAAAAATAAAATA
2553736 AAAC--AAATAAAA-A
1 AAACAAAAATAAAATA
* *
2553749 TAATAAAAATAATAATA
1 AAACAAAAATAA-AATA
* *
2553766 AAAGAATAATAAAA
1 AAACAAAAATAAAA
2553780 GGACTAAATT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
13 10 0.16
15 10 0.16
16 10 0.16
17 11 0.18
18 20 0.33
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAACAAAAATAAAATA
Found at i:2553773 original size:11 final size:11
Alignment explanation
Indices: 2553747--2553780 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2553737 AACAAATAAA
*
2553747 AATAATAAAAAT
1 AATAAT-AAAAG
2553759 AATAATAAAAG
1 AATAATAAAAG
2553770 AATAATAAAAG
1 AATAATAAAAG
2553781 GACTAAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (11 bp):
AATAATAAAAG
Found at i:2553775 original size:14 final size:13
Alignment explanation
Indices: 2553689--2553777 Score: 60
Period size: 13 Copynumber: 6.8 Consensus size: 13
2553679 ACGTTTAAAC
*
2553689 AAAATATTAA-AA
1 AAAATAATAATAA
*
2553701 TAAAATAATAATAG
1 -AAAATAATAATAA
* *
2553715 GAAATAA-AA-CA
1 AAAATAATAATAA
2553726 AAAATAA-AATAA
1 AAAATAATAATAA
*
2553738 ACAAATAAAAATAATA
1 A-AAATAATAAT-A-A
2553754 AAAATAATAATAA
1 AAAATAATAATAA
2553767 AAGAATAATAA
1 AA-AATAATAA
2553778 AAGGACTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
11 8 0.13
12 4 0.07
13 24 0.39
14 13 0.21
15 10 0.16
16 2 0.03
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:2560258 original size:6 final size:6
Alignment explanation
Indices: 2560247--2560280 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2560237 TTTTCTTCCC
2560247 GGGGTG GGGGTG GGGGTG GGGGTG GGGGTG GGGG
1 GGGGTG GGGGTG GGGGTG GGGGTG GGGGTG GGGG
2560281 AGGAAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.85, T:0.15
Consensus pattern (6 bp):
GGGGTG
Found at i:2563758 original size:40 final size:40
Alignment explanation
Indices: 2563712--2563790 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
2563702 CCTTTTTAGT
* *
2563712 GTGGAACTTTTATGTAAATTAGGTTAACTGCATTTTCCAC
1 GTGGAACTTTTACGTAAACTAGGTTAACTGCATTTTCCAC
*
2563752 GTGGAACTTTTACGTAAACTAGGTTAACTTCATTTTCCA
1 GTGGAACTTTTACGTAAACTAGGTTAACTGCATTTTCCA
2563791 TGTAAAACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (40 bp):
GTGGAACTTTTACGTAAACTAGGTTAACTGCATTTTCCAC
Found at i:2563800 original size:40 final size:40
Alignment explanation
Indices: 2563716--2563800 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
2563706 TTTAGTGTGG
* * **
2563716 AACTTTTATGTAAATTAGGTTAACTGCATTTTCCACGTGG
1 AACTTTTACGTAAACTAGGTTAACTGCATTTTCCACGTAA
* *
2563756 AACTTTTACGTAAACTAGGTTAACTTCATTTTCCATGTAA
1 AACTTTTACGTAAACTAGGTTAACTGCATTTTCCACGTAA
2563796 AACTT
1 AACTT
2563801 AGGCTCACTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (40 bp):
AACTTTTACGTAAACTAGGTTAACTGCATTTTCCACGTAA
Found at i:2566031 original size:44 final size:44
Alignment explanation
Indices: 2565968--2566055 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
2565958 ACAATAATCT
2565968 CCCTAGCATAAACTAAGGCCCCAATTTCCCCAACCAAAGAACTA
1 CCCTAGCATAAACTAAGGCCCCAATTTCCCCAACCAAAGAACTA
2566012 CCCTAGCATAAACTAAGGCCCCAATTTCCCCAACCAAAGAACTA
1 CCCTAGCATAAACTAAGGCCCCAATTTCCCCAACCAAAGAACTA
2566056 AAAAACGAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.39, C:0.36, G:0.09, T:0.16
Consensus pattern (44 bp):
CCCTAGCATAAACTAAGGCCCCAATTTCCCCAACCAAAGAACTA
Found at i:2568281 original size:18 final size:19
Alignment explanation
Indices: 2568253--2568290 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
2568243 AACTAGTAAA
2568253 GCAGAGGAAAGATCAGAAG
1 GCAGAGGAAAGATCAGAAG
2568272 GCAG-GGAAAGATCAGAAG
1 GCAGAGGAAAGATCAGAAG
2568290 G
1 G
2568291 AAGGCATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.45, C:0.11, G:0.39, T:0.05
Consensus pattern (19 bp):
GCAGAGGAAAGATCAGAAG
Found at i:2568680 original size:3 final size:3
Alignment explanation
Indices: 2568672--2568698 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2568662 GGAACTCTTC
2568672 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
2568699 AGATAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2569637 original size:23 final size:24
Alignment explanation
Indices: 2569601--2569658 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
2569591 TTTTTCGGAT
2569601 AAAAAA-CGGTTTTTTAACCAGTA
1 AAAAAACCGGTTTTTTAACCAGTA
* *
2569624 AAAAAACCGGTTTTTTATCCGGTA
1 AAAAAACCGGTTTTTTAACCAGTA
2569648 AAAAAACCGGT
1 AAAAAACCGGT
2569659 CGTCCAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 6 0.19
24 26 0.81
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (24 bp):
AAAAAACCGGTTTTTTAACCAGTA
Found at i:2576407 original size:84 final size:84
Alignment explanation
Indices: 2576262--2576430 Score: 293
Period size: 84 Copynumber: 2.0 Consensus size: 84
2576252 CTGCCGAAAA
* *
2576262 GTGTTTGCGACACTTTGGAAAAGTTTATTCGTAGATTTGTGTGGAATGCAAATAGAAGTTCAAAT
1 GTGTTTGCGACACTTTGGAAAAGCTTATTCGTAGATTTGTGCGGAATGCAAATAGAAGTTCAAAT
2576327 AGCCTTGCGTTAATTAAAT
66 AGCCTTGCGTTAATTAAAT
* * *
2576346 GTGTTTGCGATACTTTGGAAAAGCTTATTCGTAGATTTGTGCGGAATGCAAATGGAGGTTCAAAT
1 GTGTTTGCGACACTTTGGAAAAGCTTATTCGTAGATTTGTGCGGAATGCAAATAGAAGTTCAAAT
2576411 AGCCTTGCGTTAATTAAAT
66 AGCCTTGCGTTAATTAAAT
2576430 G
1 G
2576431 GGACACAGCT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (84 bp):
GTGTTTGCGACACTTTGGAAAAGCTTATTCGTAGATTTGTGCGGAATGCAAATAGAAGTTCAAAT
AGCCTTGCGTTAATTAAAT
Done.