Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_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: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 16
Found at i:2078338 original size:42 final size:42
Alignment explanation
Indices: 2078253--2078476 Score: 154
Period size: 42 Copynumber: 5.1 Consensus size: 42
2078243 CTTGGAATAA
*
2078253 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCAACT
1 ATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCAACT
* **
2078295 ATTGCAACGAATTTGGAATAAATCGCAATGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCAACT
* * *
2078337 ATCGCAATGCGAATAT-G--TAAATCGCAATGCGATA-GTCGAAGTTCGC
1 ATCGCAA--CGAATTTGGAATAAATCGCAATGCGA-ACTTC-AA---C-T
* * * *
2078383 GTCGCGATAGTCGAATTTGGAATAAATCACAACGCGAACTTCGACT
1 ATCGC-A-A--CGAATTTGGAATAAATCGCAATGCGAACTTCAACT
* * *
2078429 ATCGCAATGCGAACTTGGACT--ATCGCAATGCGAACTTCGACT
1 ATCGCAA--CGAATTTGGAATAAATCGCAATGCGAACTTCAACT
2078471 ATCGCA
1 ATCGCA
2078477 TTGCGATTTA
Statistics
Matches: 142, Mismatches: 26, Indels: 28
0.72 0.13 0.14
Matches are distributed among these distances:
41 16 0.11
42 71 0.50
43 1 0.01
44 17 0.12
45 2 0.01
46 8 0.06
47 2 0.01
48 7 0.05
49 1 0.01
50 2 0.01
51 15 0.11
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCAACT
Found at i:2078340 original size:21 final size:21
Alignment explanation
Indices: 2078145--2078482 Score: 123
Period size: 21 Copynumber: 15.9 Consensus size: 21
2078135 CGTTGCGATT
*
2078145 TTGGACTATCGCAAT--GAAT
1 TTGGACTATCGCAATGCGAAC
*
2078164 TTGGAATAAATCGCAA--CGAAC
1 TTGGACT--ATCGCAATGCGAAC
*
2078185 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
*
2078204 TTGGAATAAATCGCAA--CGAAC
1 TTGGACT--ATCGCAATGCGAAC
*
2078225 TTGGACTATCGCAA--CAAAC
1 TTGGACTATCGCAATGCGAAC
* *
2078244 TTGGAATAAATCGCAA--CGAAT
1 TTGGACT--ATCGCAATGCGAAC
* *
2078265 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
** * *
2078288 TTCAACTATTGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
*
2078307 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
2078330 TTGGACTATCGCAATGCGAA-
1 TTGGACTATCGCAATGCGAAC
* * *
2078350 TATGTA-AATCGCAATGCGATAG
1 T-TGGACTATCGCAATGCGA-AC
* * ** * *
2078372 TCGAAGTTCGCGTCGCGATAGTCGAAT
1 TTG--G-AC-TATCGCAAT-G-CGAAC
* * *
2078399 TTGGAATAAATCACAACGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
*
2078422 TTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
2078443 TTGGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
* *
2078464 TTCGACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
2078483 TTTACATATT
Statistics
Matches: 246, Mismatches: 48, Indels: 48
0.72 0.14 0.14
Matches are distributed among these distances:
19 48 0.20
20 13 0.05
21 138 0.56
22 1 0.00
23 27 0.11
24 1 0.00
25 5 0.02
26 6 0.02
27 4 0.02
28 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:2078502 original size:134 final size:133
Alignment explanation
Indices: 2078260--2078531 Score: 354
Period size: 134 Copynumber: 2.0 Consensus size: 133
2078250 TAAATCGCAA
* * *
2078260 CGAATTTGGAATAAATCGCAACGCGAACTTCAACTATTGCAACGAATTTGGAATAAATCGCAATG
1 CGAATTTGGAATAAATCACAACGCGAACTTCAACTATCGCAACGAACTTGGAAT-AATCGCAATG
* * *
2078325 CGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTCGCGA
65 CGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAGTTCGCATCGCGA
2078390 TAGT
130 TAGT
* *
2078394 CGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAATGCGAACTTGGACT-ATCGCAAT
1 CGAATTTGGAATAAATCACAACGCGAACTTCAACTATCGCAA--CGAACTTGGAATAATCGCAAT
* * * *
2078458 GCGAACTTCGACTATCGCATTGCG-AT-T-TACATATTCGCATTGCGATAGTCCAAGTTCGTATT
64 GCGAACTTCGACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCCAAGTTCGCATC
2078520 GCGATAGT
126 GCGATAGT
2078528 CGAA
1 CGAA
2078532 GTTCGCGTTG
Statistics
Matches: 121, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
131 2 0.02
132 2 0.02
133 3 0.02
134 104 0.86
136 10 0.08
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (133 bp):
CGAATTTGGAATAAATCACAACGCGAACTTCAACTATCGCAACGAACTTGGAATAATCGCAATGC
GAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAGTTCGCATCGCGAT
AGT
Found at i:2078520 original size:21 final size:21
Alignment explanation
Indices: 2078491--2078544 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2078481 GATTTACATA
2078491 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
2078512 TTCGTATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
2078533 TTCGCGTTGCGA
1 TTCGCATTGCGA
2078545 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:2078914 original size:13 final size:12
Alignment explanation
Indices: 2078885--2078915 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2078875 TTAGGTAACT
2078885 GAAAAATTCAAA
1 GAAAAATTCAAA
2078897 GAAAAATTCAAA
1 GAAAAATTCAAA
2078909 GAAAAAT
1 GAAAAAT
2078916 AAAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.10, T:0.16
Consensus pattern (12 bp):
GAAAAATTCAAA
Found at i:2078930 original size:17 final size:17
Alignment explanation
Indices: 2078910--2078954 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2078900 AAATTCAAAG
2078910 AAAAATAAAATAAATAC
1 AAAAATAAAATAAATAC
* *
2078927 AAAATTAAAATAAATAG
1 AAAAATAAAATAAATAC
*
2078944 ATAAATAAAAT
1 AAAAATAAAAT
2078955 TAAAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAAATAAAATAAATAC
Found at i:2088374 original size:29 final size:29
Alignment explanation
Indices: 2088342--2088507 Score: 138
Period size: 29 Copynumber: 5.7 Consensus size: 29
2088332 AATTATTGTT
* * *
2088342 AGGTGATATTCTGGGAAATATTTCGATAA
1 AGGTGACATTCTGGGAATTATTTCGAAAA
* * * *
2088371 AGGTTATATTTTGGGAATTATTTTGAAAAAA
1 AGGTGACATTCTGGGAATTATTTCG--AAAA
* * * *
2088402 AAGTGACATTATGAGAAATATTTCGAAAA
1 AGGTGACATTCTGGGAATTATTTCGAAAA
* *
2088431 AGGTAACATAT-TGGGAATTATTTCGTAAA
1 AGGTGACAT-TCTGGGAATTATTTCGAAAA
* *
2088460 AGGTGACACTCTGGGAATTATTT-TAAAA
1 AGGTGACATTCTGGGAATTATTTCGAAAA
*
2088488 AGGGTGACATTTTGGGAATT
1 A-GGTGACATTCTGGGAATT
2088508 TTCAAATGTT
Statistics
Matches: 109, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
28 5 0.05
29 82 0.75
30 1 0.01
31 21 0.19
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.34
Consensus pattern (29 bp):
AGGTGACATTCTGGGAATTATTTCGAAAA
Found at i:2095165 original size:29 final size:28
Alignment explanation
Indices: 2095053--2095217 Score: 118
Period size: 29 Copynumber: 5.6 Consensus size: 28
2095043 AATTGTTGTT
* * *
2095053 AGGTGATATTCTGGGAAATATTTCGATAA
1 AGGTGACATT-TGGGAATTATTTCGAAAA
**
2095082 AGGTGACATTTTGGGAATTATTTTTAAAAAA
1 AGGTGACA-TTTGGGAATTA--TTTCGAAAA
* ** *
2095113 AAGTGACATTATAAGAAATA-TTCGAAAA
1 AGGTGACATT-TGGGAATTATTTCGAAAA
* *
2095141 AGGTAACATATTGGGAATTATTTCGTAAA
1 AGGTGACAT-TTGGGAATTATTTCGAAAA
* *
2095170 AGGTGACACTCTGGGAATTATTT-TAAAA
1 AGGTGACA-TTTGGGAATTATTTCGAAAA
2095198 AGGGTGACATTTTGGGAATT
1 A-GGTGACA-TTTGGGAATT
2095218 TTCAAATGTT
Statistics
Matches: 105, Mismatches: 23, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
28 23 0.22
29 58 0.55
30 5 0.05
31 19 0.18
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (28 bp):
AGGTGACATTTGGGAATTATTTCGAAAA
Found at i:2097151 original size:177 final size:173
Alignment explanation
Indices: 2096843--2097202 Score: 623
Period size: 177 Copynumber: 2.1 Consensus size: 173
2096833 ACAATTATGA
* *
2096843 TATACTTAAACATGCAAGACAGTCTACACTTACATAATTACAAACAATTATACCCATAAAATTTT
1 TATAATTAAACATGCAAGACAGTCTACACTTACATAATTACAAACAATTATACCCATAAAAATTT
* *
2096908 TAAATATGTATAAGAAATATGAAAGAATAAATATCTACTTGACAAATGGACTTTCTCTCAATTAC
66 AAAATATCTATAAGAAATATGAAAGAATAAATATCTACTTGACAAATGGACTTTCTCTCAATTAC
2096973 AATAGATAAATAAAAATAAATTTGAAAGTTATTATAATTAAAG
131 AATAGATAAATAAAAATAAATTTGAAAGTTATTATAATTAAAG
2097016 TATAATTAAACATGCAAGACAGTCTACACTTACATAATTACAAACAATTATACCCATAAAAATTT
1 TATAATTAAACATGCAAGACAGTCTACACTTACATAATTACAAACAATTATACCCATAAAAATTT
2097081 AAAACTCATAACCTA-AAGAAATATGAAAGAATAAATATCTACTTGACAAATGGACTTTCTCTCA
66 AAAA-T-AT---CTATAAGAAATATGAAAGAATAAATATCTACTTGACAAATGGACTTTCTCTCA
*
2097145 ATTACAATATATAAATAAAAATAAATTTGAAAGTTATTATAATTAAAG
126 ATTACAATAGATAAATAAAAATAAATTTGAAAGTTATTATAATTAAAG
2097193 TATAATTAAA
1 TATAATTAAA
2097203 ATACTCTAAA
Statistics
Matches: 177, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
173 66 0.37
174 1 0.01
175 2 0.01
177 106 0.60
178 2 0.01
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.31
Consensus pattern (173 bp):
TATAATTAAACATGCAAGACAGTCTACACTTACATAATTACAAACAATTATACCCATAAAAATTT
AAAATATCTATAAGAAATATGAAAGAATAAATATCTACTTGACAAATGGACTTTCTCTCAATTAC
AATAGATAAATAAAAATAAATTTGAAAGTTATTATAATTAAAG
Found at i:2102997 original size:24 final size:24
Alignment explanation
Indices: 2102965--2103011 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2102955 TTGATAAATT
2102965 TATAATTTAAAAATCTTTATCAAA
1 TATAATTTAAAAATCTTTATCAAA
2102989 TATAATTTAAAAATCTTTATCAA
1 TATAATTTAAAAATCTTTATCAA
2103012 TTTGATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (24 bp):
TATAATTTAAAAATCTTTATCAAA
Found at i:2103274 original size:35 final size:36
Alignment explanation
Indices: 2103228--2103310 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
2103218 TTAAAAGTTA
*
2103228 AAAGTTTGGTAACCA-ACTTTGAAAAA-ATGATTTTC
1 AAAGTTTGGTAAACATACTTTGAAAAATA-GATTTTC
* * *
2103263 AAAGTTTGGTAAATATTTCTTTGAAAAATAGTTTTTC
1 AAAGTTTGGTAAACA-TACTTTGAAAAATAGATTTTC
2103300 AAAGTTTGGTA
1 AAAGTTTGGTA
2103311 GATGCTTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 13 0.32
37 27 0.66
38 1 0.02
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (36 bp):
AAAGTTTGGTAAACATACTTTGAAAAATAGATTTTC
Found at i:2103323 original size:36 final size:36
Alignment explanation
Indices: 2103250--2103330 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 36
2103240 CCAACTTTGA
* *
2103250 AAAAATGATTTTCAAAGTTTGGTAAATATTTCTTTG
1 AAAAATGATTTTCAAAGTTTGGTAAATACTTCGTTG
* * *
2103286 AAAAATAGTTTTTCAAAGTTTGGTAGATGCTT-GTTG
1 AAAAAT-GATTTTCAAAGTTTGGTAAATACTTCGTTG
2103322 AAAAATGAT
1 AAAAATGAT
2103331 AATGGGATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 2 0.05
36 15 0.39
37 21 0.55
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (36 bp):
AAAAATGATTTTCAAAGTTTGGTAAATACTTCGTTG
Found at i:2106764 original size:21 final size:21
Alignment explanation
Indices: 2106736--2106783 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2106726 GTATATTGAT
2106736 GACATGCTTGTTGCAGGTTCA
1 GACATGCTTGTTGCAGGTTCA
*
2106757 GGCATGCTTGTTGCAGGTTCA
1 GACATGCTTGTTGCAGGTTCA
2106778 GACATG
1 GACATG
2106784 AAATAGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (21 bp):
GACATGCTTGTTGCAGGTTCA
Found at i:2109137 original size:37 final size:38
Alignment explanation
Indices: 2109092--2109174 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 38
2109082 TGGCAACCAA
* *
2109092 CTTTGAAAAAATGGTTTTT-AAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATAGTTTTTCAAAGTTTGATAAATGTTT
*
2109129 CTTTG-AAAAATAGTTTTTCAAAGTTTGATAGATGTTT
1 CTTTGAAAAAATAGTTTTTCAAAGTTTGATAAATGTTT
*
2109166 -GTTGAAAAA
1 CTTTGAAAAA
2109175 TGATAATGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
36 15 0.38
37 25 0.62
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAAATAGTTTTTCAAAGTTTGATAAATGTTT
Found at i:2109145 original size:36 final size:37
Alignment explanation
Indices: 2109092--2109175 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 37
2109082 TGGCAACCAA
* *
2109092 CTTTGAAAAAATGGTTTTT-AAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTTCAAAGTTTGATAAATGTTT
*
2109129 CTTTGAAAAATAGTTTTTCAAAGTTTGATAGATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGATAAATGTTT
*
2109166 -GTTGAAAAAT
1 CTTTGAAAAAT
2109176 GATAATGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 21 0.50
37 21 0.50
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGTTTTTCAAAGTTTGATAAATGTTT
Found at i:2111203 original size:17 final size:17
Alignment explanation
Indices: 2111162--2111194 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2111152 AGCCCAGTGG
2111162 CACACTAACAACTAAGC
1 CACACTAACAACTAAGC
2111179 CACACTAACAACTAAG
1 CACACTAACAACTAAG
2111195 TCATACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.33, G:0.06, T:0.12
Consensus pattern (17 bp):
CACACTAACAACTAAGC
Found at i:2122139 original size:22 final size:22
Alignment explanation
Indices: 2122082--2122140 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
2122072 ACGCGATTCT
2122082 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
2122104 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
2122125 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
2122141 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:2122180 original size:20 final size:20
Alignment explanation
Indices: 2122157--2122242 Score: 118
Period size: 20 Copynumber: 4.3 Consensus size: 20
2122147 AAATCGTAAT
* *
2122157 GCGATTATGACTATCACAAC
1 GCGATTCTGACTATCGCAAC
2122177 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
* *
2122197 GAGATTCTAACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
* *
2122217 GCGATGCTGACTATCGCAAT
1 GCGATTCTGACTATCGCAAC
2122237 GCGATT
1 GCGATT
2122243 TTCAAAGCGC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAC
Found at i:2122412 original size:20 final size:20
Alignment explanation
Indices: 2122389--2122474 Score: 118
Period size: 20 Copynumber: 4.3 Consensus size: 20
2122379 AAATCGTAAT
* *
2122389 GCGATTATGACTATCACAAC
1 GCGATTCTGACTATCGCAAC
2122409 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
* *
2122429 GAGATTCTAACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
* *
2122449 GCGATGCTGACTATCGCAAT
1 GCGATTCTGACTATCGCAAC
2122469 GCGATT
1 GCGATT
2122475 TTCAAAGCGC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAC
Found at i:2122532 original size:232 final size:236
Alignment explanation
Indices: 2122126--2122594 Score: 885
Period size: 232 Copynumber: 2.0 Consensus size: 236
2122116 CGATTTTCCG
2122126 ACTATCGCAATGCGAATATGTAAATCGTAATGCGATTATGACTATCACAACGCGATTCTGACTAT
1 ACTATCGCAATGCGAATATGTAAATCGTAATGCGATTATGACTATCACAACGCGATTCTGACTAT
2122191 CGCAACGAGATTCTAACTATCGCAACGCGATGCTGACTATCGCAATGCGATTTTCAAAGCGCCAT
66 CGCAACGAGATTCTAACTATCGCAACGCGATGCTGACTATCGCAATGCGATTTTCAAAGCGCCAT
2122256 TATTATCGTAACGCGTATTTTTTTTTCAAATTCCAACACGAATATT-A-ATATCGAAACACTGAA
131 TATTATCGTAACGCGTATTTTTTTTTCAAATTCCAACACGAATATTAATATATCGAAACACTGAA
2122319 CCGTCCACAG-TAT-CCGTAATCGCAACTTATAACCTAAAA
196 CCGTCCACAGATATCCCGTAATCGCAACTTATAACCTAAAA
2122358 ACTATCGCAATGCGAATATGTAAATCGTAATGCGATTATGACTATCACAACGCGATTCTGACTAT
1 ACTATCGCAATGCGAATATGTAAATCGTAATGCGATTATGACTATCACAACGCGATTCTGACTAT
2122423 CGCAACGAGATTCTAACTATCGCAACGCGATGCTGACTATCGCAATGCGATTTTCAAAGCGCCAT
66 CGCAACGAGATTCTAACTATCGCAACGCGATGCTGACTATCGCAATGCGATTTTCAAAGCGCCAT
2122488 TATTATCGTAACGCGTA-TTTTTTTTCAAATTCCAAACACGAATATTAATATATCGAAACACTGA
131 TATTATCGTAACGCGTATTTTTTTTTCAAATTCC-AACACGAATATTAATATATCGAAACACTGA
2122552 ACCGTCCACAGTATATCCCGTAATCGCAACTTATAACCTAAAA
195 ACCGTCCACAG-ATATCCCGTAATCGCAACTTATAACCTAAAA
2122595 CCCTAAATCA
Statistics
Matches: 231, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
231 16 0.07
232 159 0.69
233 1 0.00
234 26 0.11
236 3 0.01
237 26 0.11
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.28
Consensus pattern (236 bp):
ACTATCGCAATGCGAATATGTAAATCGTAATGCGATTATGACTATCACAACGCGATTCTGACTAT
CGCAACGAGATTCTAACTATCGCAACGCGATGCTGACTATCGCAATGCGATTTTCAAAGCGCCAT
TATTATCGTAACGCGTATTTTTTTTTCAAATTCCAACACGAATATTAATATATCGAAACACTGAA
CCGTCCACAGATATCCCGTAATCGCAACTTATAACCTAAAA
Found at i:2123093 original size:20 final size:20
Alignment explanation
Indices: 2123064--2123117 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
2123054 GCGATTTTAG
*
2123064 TTTCGCGTTGCGATAGTCAT
1 TTTCGTGTTGCGATAGTCAT
**
2123084 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATAGTCAT
*
2123104 TTTCGTGTTACGAT
1 TTTCGTGTTGCGAT
2123118 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (20 bp):
TTTCGTGTTGCGATAGTCAT
Found at i:2123118 original size:20 final size:20
Alignment explanation
Indices: 2123080--2123120 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2123070 GTTGCGATAG
*
2123080 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTACGATTT
2123100 TCATTTTCGTGTTACGATTT
1 TCATTTTCGTGTTACGATTT
2123120 T
1 T
2123121 AAGTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTGTTACGATTT
Found at i:2123127 original size:20 final size:20
Alignment explanation
Indices: 2123084--2123127 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2123074 CGATAGTCAT
* * *
2123084 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTACGATTTTAAG
2123104 TTTCGTGTTACGATTTTAAG
1 TTTCGTGTTACGATTTTAAG
2123124 TTTC
1 TTTC
2123128 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAG
Found at i:2123667 original size:162 final size:161
Alignment explanation
Indices: 2123351--2123673 Score: 637
Period size: 162 Copynumber: 2.0 Consensus size: 161
2123341 TCAATTGACC
2123351 TTAAGAAATAAAGTAAGCCAGGCCAAAACAATTGCGTCGAAGCTTTCACCTGCACAAAGAAAAAT
1 TTAAGAAATAAAGTAAGCCAGGCCAAAACAATTGCGTCGAAGCTTTCACCTGCACAAAGAAAAAT
2123416 AATTGAGGATACTGCTTCGGGCCATGGCTGAAAGTACACAATCCGGGTGGAGATGCTATGTTGAC
66 AATTGAGGATACTGCTTCGGGCCATGGCTGAAAGTACACAATCCGGGTGGAGATGCTATGTTGAC
2123481 CCTTCTGTTTCTTCAAACCATGACTAGCGAT
131 CCTTCTGTTTCTTCAAACCATGACTAGCGAT
2123512 TTAAGAAATAAAGTAAGCCAGGCCAAAACAATTGCGTCGAAGCTTTCACCTGCACAAAGAAAAAT
1 TTAAGAAATAAAGTAAGCCAGGCCAAAACAATTGCGTCGAAGCTTTCACCTGCACAAAGAAAAAT
2123577 AATTGAGGATACTTGCTTCGGGCCATGGCTGAAAGTACACAATCCGGGTGGAGATGCTATGTTGA
66 AATTGAGGATAC-TGCTTCGGGCCATGGCTGAAAGTACACAATCCGGGTGGAGATGCTATGTTGA
2123642 CCCTTCTGTTTCTTCAAACCATGACTAGCGAT
130 CCCTTCTGTTTCTTCAAACCATGACTAGCGAT
2123674 CTACCAGAGA
Statistics
Matches: 161, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
161 77 0.48
162 84 0.52
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (161 bp):
TTAAGAAATAAAGTAAGCCAGGCCAAAACAATTGCGTCGAAGCTTTCACCTGCACAAAGAAAAAT
AATTGAGGATACTGCTTCGGGCCATGGCTGAAAGTACACAATCCGGGTGGAGATGCTATGTTGAC
CCTTCTGTTTCTTCAAACCATGACTAGCGAT
Found at i:2125219 original size:20 final size:20
Alignment explanation
Indices: 2125190--2125255 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
2125180 TAGTTTACTT
2125190 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
2125210 TCGTAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
2125230 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
2125250 TCGCAA
1 TCGCAA
2125256 TGAAAGAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:2126488 original size:14 final size:14
Alignment explanation
Indices: 2126451--2126512 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
2126441 TTGCTTGTTT
*
2126451 AATTGATTTATAAA
1 AATTGATTTGTAAA
2126465 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* * *
2126479 AGTTGGTTTGTTTAA
1 AATTGATTTG-TAAA
* *
2126494 TATTGATGTGTAAA
1 AATTGATTTGTAAA
2126508 TAATT
1 -AATT
2126513 CTTATTTTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 24 0.67
15 12 0.33
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2126637 original size:20 final size:20
Alignment explanation
Indices: 2126612--2126665 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2126602 AGGTACACTT
*
2126612 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
2126632 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
2126652 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
2126666 TCAATTCGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:2126742 original size:20 final size:20
Alignment explanation
Indices: 2126710--2126836 Score: 146
Period size: 20 Copynumber: 6.3 Consensus size: 20
2126700 AATTTTCTCA
2126710 TTGCGATAGTCAAATACCCG
1 TTGCGATAGTCAAATACCCG
* * * *
2126730 TTACGATAATCAAATTCACG
1 TTGCGATAGTCAAATACCCG
* *
2126750 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATACCCG
2126770 TTGCGATAGTCAAATACCCG
1 TTGCGATAGTCAAATACCCG
* * *
2126790 TTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATACCCG
* * *
2126810 TTGCGATAGACAAATTCGCG
1 TTGCGATAGTCAAATACCCG
2126830 TTGCGAT
1 TTGCGAT
2126837 TTTTGCGTTG
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 93 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (20 bp):
TTGCGATAGTCAAATACCCG
Found at i:2126777 original size:40 final size:40
Alignment explanation
Indices: 2126710--2126952 Score: 231
Period size: 40 Copynumber: 6.4 Consensus size: 40
2126700 AATTTTCTCA
* * * * *
2126710 TTGCGATAGTCAAATACCCGTTACGATAATCAAATTCACG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCG
* *
2126750 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATACCCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCG
* *
2126790 TTGCGATAATCAAATTCGCGTTGCGATAGACAAATTCGCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCG
* * *
2126830 TTGCGAT--T----TTTGCGTTGCGATAGTCATATTCGTG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCG
* * * *
2126864 TTGCAATAGTCAAATTCGCGTTGCG---GT---TTTTGAG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCG
*
2126898 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCG
* *
2126938 TTACGATATTCAAAT
1 TTGCGATAGTCAAAT
2126953 GAATGTGTAA
Statistics
Matches: 165, Mismatches: 26, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
34 55 0.33
36 1 0.01
37 4 0.02
38 1 0.01
40 104 0.63
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (40 bp):
TTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCG
Found at i:2126867 original size:54 final size:54
Alignment explanation
Indices: 2126728--2126944 Score: 263
Period size: 54 Copynumber: 3.9 Consensus size: 54
2126718 GTCAAATACC
* * ***
2126728 CGTTACGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATACC
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTTG
*
2126788 CGTTGCGATAATCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* * * * *
2126842 CGTTGCGATAGTCATATTCGTGTTGCAATAGTCAAATTCGCGTTGCGGTTTTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* *
2126896 AGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACGAT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
2126945 ATTCAAATGA
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
54 91 0.66
58 1 0.01
60 46 0.33
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:2126872 original size:20 final size:20
Alignment explanation
Indices: 2126841--2126887 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2126831 TGCGATTTTT
* *
2126841 GCGTTGCGATAGTCATATTC
1 GCGTTGCAATAGTCAAATTC
*
2126861 GTGTTGCAATAGTCAAATTC
1 GCGTTGCAATAGTCAAATTC
2126881 GCGTTGC
1 GCGTTGC
2126888 GGTTTTTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
GCGTTGCAATAGTCAAATTC
Found at i:2126922 original size:20 final size:20
Alignment explanation
Indices: 2126897--2126952 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2126887 CGGTTTTTGA
2126897 GTTGCGATAATCAAATTCGC
1 GTTGCGATAATCAAATTCGC
*
2126917 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAATCAAATTCGC
* *
2126937 GTTACGATATTCAAAT
1 GTTGCGATAATCAAAT
2126953 GAATGTGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (20 bp):
GTTGCGATAATCAAATTCGC
Found at i:2126951 original size:74 final size:73
Alignment explanation
Indices: 2126749--2126952 Score: 187
Period size: 74 Copynumber: 2.8 Consensus size: 73
2126739 TCAAATTCAC
* *
2126749 GTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGC
1 GTTGCGATA-TCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGC
2126814 GATAGACAA
65 GATAGACAA
* ** * * * * *
2126823 ATTCGCG-T-TGCGATTTTTGCGTTGCGATAGTCATATTCGTGTTGCAATAGTCAAATTCGCGTT
1 GTT-GCGATAT-C-AAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTT
* *****
2126886 GCGGTTTTTGA
63 GCGATAGACAA
* *
2126897 GTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACGATATTCAAAT
1 GTTGCGAT-ATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAAT
2126953 GAATGTGTAA
Statistics
Matches: 99, Mismatches: 25, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
72 1 0.01
73 4 0.04
74 89 0.90
75 4 0.04
76 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (73 bp):
GTTGCGATATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCGCGTTGCG
ATAGACAA
Found at i:2127175 original size:140 final size:140
Alignment explanation
Indices: 2126923--2127192 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
2126913 TCGCGTTGCG
* *
2126923 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCACGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
2126988 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTATACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2127053 AATACACATA
131 AATACACATA
* * *
2127063 ATAGTCAAATTCATGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAATAGATCA
1 ATAGTCAAATTCACGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
2127128 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
2127193 TACAACGTTT
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (140 bp):
ATAGTCAAATTCACGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:2129430 original size:24 final size:24
Alignment explanation
Indices: 2129396--2129449 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2129386 CTGAAACATC
2129396 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2129420 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2129444 ATCAAA
1 ATCAAA
2129450 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2130309 original size:20 final size:20
Alignment explanation
Indices: 2130263--2130309 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2130253 AAATTCAGTG
* *
2130263 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
2130283 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCA
2130303 TTGCGAT
1 TTGCGAT
2130310 TTACATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:2132792 original size:31 final size:31
Alignment explanation
Indices: 2132756--2132814 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2132746 AACTTAAAAG
*
2132756 AGTTTTGCAATAATGAAATTTAAATAATTTT
1 AGTTTTACAATAATGAAATTTAAATAATTTT
*
2132787 AGTTTTACAATATTGAAATTTAAATAAT
1 AGTTTTACAATAATGAAATTTAAATAAT
2132815 CAATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATAATGAAATTTAAATAATTTT
Found at i:2137672 original size:21 final size:21
Alignment explanation
Indices: 2137646--2137702 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
2137636 TCAGTGCCTA
2137646 GGTTGGGTATCGATACTAAA-G
1 GGTT-GGTATCGATACTAAATG
*
2137667 GGTTGGTATTGATACTAAATG
1 GGTTGGTATCGATACTAAATG
* *
2137688 GCTTAGTATCGATAC
1 GGTTGGTATCGATAC
2137703 CATCATACTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (21 bp):
GGTTGGTATCGATACTAAATG
Found at i:2140166 original size:32 final size:32
Alignment explanation
Indices: 2140121--2140189 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
2140111 TCGGTTCAGA
* *
2140121 TTAATTTTTGTTCGAATTGCTTTTAGG-TCGGG
1 TTAAATTTGGTTCGAATTGCTTTT-GGATCGGG
*
2140153 TTAAATTTGGTTCGAGTTGCTTTTGGATCGGG
1 TTAAATTTGGTTCGAATTGCTTTTGGATCGGG
2140185 TTAAA
1 TTAAA
2140190 ATTTAGTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 2 0.06
32 31 0.94
ACGTcount: A:0.19, C:0.09, G:0.26, T:0.46
Consensus pattern (32 bp):
TTAAATTTGGTTCGAATTGCTTTTGGATCGGG
Found at i:2146424 original size:348 final size:349
Alignment explanation
Indices: 2145780--2146470 Score: 1197
Period size: 348 Copynumber: 2.0 Consensus size: 349
2145770 TAGAACTTCA
* * *
2145780 CCATCCCAGATTTATTCCATTGTTCACGTTGATCTATCTTAATTCTCACGAATTTAAGAATCACT
1 CCATCCCAGATTTATTCCATTGCTCAAGTTGATCTATCTTAATTCTCACGAATTTAAGAATCAAT
* * * * *
2145845 TATATAGATAAAAGGCTATCTCTGCGATGCTCTTACACTGCCAAGACATGTTTTATCAAAACCCA
66 TATATAGACAAAAGGCCATATCTGCGATGCTCTTACAATGCCAAGACATGTTTTACCAAAACCCA
* *
2145910 AGGTAATCTCTCGATGCTCTTACAGTGCTAAGGTAAAATATTTTAAACTATGAACAAAACAGTCA
131 AGGTAATCTCTCGATGCTCTTACAGTGCTAAGGTAAAATATTTTAAACTATGAACAAAAAAATCA
*
2145975 TAAGCAAAACATAATTCATCATTCATAAACATAAAAATATTGTTGAGGAAAAACAAAGTTTAACA
196 TAAGCAAAACATAATTCATCATTCATAAACATAAAAATATTGTTCAGGAAAAACAAAGTTTAACA
2146040 CCAAGTAAAGCATTCATGGTGCTATCAAAGATCATCCAAGATTCAACGTTTAATACAACCCCAAA
261 CCAAGTAAAGCATTCATGGTGCTATCAAAGATCATCCAAGATTCAACGTTTAATACAACCCCAAA
2146105 TAGATAAAGAGTTAAAAATTAAGG
326 TAGATAAAGAGTTAAAAATTAAGG
* * *
2146129 CCATCTCAGATTTATTCCATTGCTCAAGTTGATCTATCTTAATTCTCTCGAATTTAAGAATTAAT
1 CCATCCCAGATTTATTCCATTGCTCAAGTTGATCTATCTTAATTCTCACGAATTTAAGAATCAAT
* *
2146194 TATCTAGACAAAAGGCCATATCT-CGATGCTCTTACAATGCCAAGACATGTTTTACCAAAACCTA
66 TATATAGACAAAAGGCCATATCTGCGATGCTCTTACAATGCCAAGACATGTTTTACCAAAACCCA
*
2146258 AGGTTATCTCTCGATGCTCTTACAGTGCTAAGGTAAAATATTTTAAACTATGAACAAACAAAATC
131 AGGTAATCTCTCGATGCTCTTACAGTGCTAAGGTAAAATATTTTAAACTATGAACAAA-AAAATC
*
2146323 ATAAGCAAAACATAATTCATCATTCATAAACAT-AAAATATTGTTCAGGCAAAACAAAGTTTAAC
195 ATAAGCAAAACATAATTCATCATTCATAAACATAAAAATATTGTTCAGGAAAAACAAAGTTTAAC
2146387 ACCAAGTAAAGCATTCATGGTGCTATCAAAGATCATCCAAGATTCAACGTTTAATACAACCCCAA
260 ACCAAGTAAAGCATTCATGGTGCTATCAAAGATCATCCAAGATTCAACGTTTAATACAACCCCAA
2146452 ATAGATAAAGAGTTAAAAA
325 ATAGATAAAGAGTTAAAAA
2146471 CAAAAGAAGA
Statistics
Matches: 323, Mismatches: 18, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
348 208 0.64
349 115 0.36
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (349 bp):
CCATCCCAGATTTATTCCATTGCTCAAGTTGATCTATCTTAATTCTCACGAATTTAAGAATCAAT
TATATAGACAAAAGGCCATATCTGCGATGCTCTTACAATGCCAAGACATGTTTTACCAAAACCCA
AGGTAATCTCTCGATGCTCTTACAGTGCTAAGGTAAAATATTTTAAACTATGAACAAAAAAATCA
TAAGCAAAACATAATTCATCATTCATAAACATAAAAATATTGTTCAGGAAAAACAAAGTTTAACA
CCAAGTAAAGCATTCATGGTGCTATCAAAGATCATCCAAGATTCAACGTTTAATACAACCCCAAA
TAGATAAAGAGTTAAAAATTAAGG
Found at i:2159629 original size:41 final size:41
Alignment explanation
Indices: 2159572--2159691 Score: 204
Period size: 41 Copynumber: 2.9 Consensus size: 41
2159562 CCAACGGTGC
*
2159572 TGAACATTGATACACGAATGTACCCAAGCTGAACTGATAAT
1 TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAAT
*
2159613 TGAACATTGATACACGAATGTACCAAAGTTGAACTGATAAT
1 TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAAT
* *
2159654 TGAACATTGATACATGAATGTACCAAAGCTGAATTGAT
1 TGAACATTGATACACGAATGTACCAAAGCTGAACTGAT
2159692 GTGTACTCAC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (41 bp):
TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAAT
Found at i:2162666 original size:30 final size:30
Alignment explanation
Indices: 2162625--2162695 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
2162615 TAAAATATAT
* *
2162625 AACTCTTCAAAATTATATTTTTGGTCCTTA
1 AACTTTTCAAAATTATATTTCTGGTCCTTA
*
2162655 AACTTTTCAAAATTATATTTCTGGTCTTTA
1 AACTTTTCAAAATTATATTTCTGGTCCTTA
2162685 AACTTTTCAAA
1 AACTTTTCAAA
2162696 CTTTATACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.46
Consensus pattern (30 bp):
AACTTTTCAAAATTATATTTCTGGTCCTTA
Found at i:2166645 original size:41 final size:41
Alignment explanation
Indices: 2166588--2166667 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
2166578 CCAATGGTGC
*
2166588 TGAACATTGATACACGAATGTACCAAAGCTGAACTGATAAT
1 TGAACATTGATACACGAATGTACCAAAGCTAAACTGATAAT
*
2166629 TGAACATTGATACACGAATGTACCAAAGTTAAACTGATA
1 TGAACATTGATACACGAATGTACCAAAGCTAAACTGATA
2166668 TGTACTCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (41 bp):
TGAACATTGATACACGAATGTACCAAAGCTAAACTGATAAT
Found at i:2182585 original size:3 final size:3
Alignment explanation
Indices: 2182577--2182640 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
2182567 CATTTGTTAT
2182577 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
**
2182625 AAA TATA TTA TTA TTA
1 TTA T-TA TTA TTA TTA
2182641 CATTTCAGGC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 54 0.96
4 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:2184067 original size:29 final size:30
Alignment explanation
Indices: 2184015--2184074 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
2184005 AAGCTTTACA
* *
2184015 TTTTAATACTATGTTTTAATTTTATTTATTT
1 TTTTAATAATATG-TTTAATTTTATATATTT
*
2184046 TTTTAATAATATG-TTACTTTTATATATTT
1 TTTTAATAATATGTTTAATTTTATATATTT
2184075 ATGTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 14 0.54
31 12 0.46
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTTAATAATATGTTTAATTTTATATATTT
Found at i:2184487 original size:17 final size:16
Alignment explanation
Indices: 2184467--2184507 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2184457 ATAAATATCC
2184467 TATTTTTATATATATAT
1 TATTTTTATATATA-AT
*
2184484 TA-TTTTAT-TTTAAT
1 TATTTTTATATATAAT
2184498 TATTTTTATA
1 TATTTTTATA
2184508 GAAATGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 6 0.29
17 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTTATATATAAT
Found at i:2184513 original size:143 final size:144
Alignment explanation
Indices: 2184353--2184615 Score: 363
Period size: 144 Copynumber: 1.8 Consensus size: 144
2184343 ATAAATCTAT
* * * * *
2184353 ATTATTTTTAGATAAATG-TTCTATTAAAATTTATTTATTTTTTAATAT-TAAGAAAGGAGCTGT
1 ATTATTTTTAGAGAAATGCTTCTATTAAAATTTATTTA-CTTTTAACATCGAAGAAAAGAGCTGT
2184416 CTTAAAGCACCTAGAAGCC-ATTTTCTAATA-TTCTTAAATAAATAAATATCCTATTTTTATATA
65 CTTAAAGCACCTAGAAGCCTA-TTTCTAATATTTC-TAAATAAATAAATATCCTATTTTTATATA
2184479 TATATTATTTTATTTTA
128 TATATTATTTTATTTTA
* * *
2184496 ATTATTTTTATAGAAATGCTTTTATTAATATTTATTTACTTTTAACATCGAAGAAAAGAGCTGTC
1 ATTATTTTTAGAGAAATGCTTCTATTAAAATTTATTTACTTTTAACATCGAAGAAAAGAGCTGTC
* * * *
2184561 TTAAAGCACCTAGAAGTCTATTTCTGATATTTCTAAGTAAATAAATATCTTATTT
66 TTAAAGCACCTAGAAGCCTATTTCTAATATTTCTAAATAAATAAATATCCTATTT
2184616 ATAAAAATAT
Statistics
Matches: 104, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
143 24 0.23
144 76 0.73
145 4 0.04
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (144 bp):
ATTATTTTTAGAGAAATGCTTCTATTAAAATTTATTTACTTTTAACATCGAAGAAAAGAGCTGTC
TTAAAGCACCTAGAAGCCTATTTCTAATATTTCTAAATAAATAAATATCCTATTTTTATATATAT
ATTATTTTATTTTA
Found at i:2184629 original size:2 final size:2
Alignment explanation
Indices: 2184622--2184649 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2184612 ATTTATAAAA
2184622 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
2184650 TTTCTTAAAA
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:2194065 original size:18 final size:18
Alignment explanation
Indices: 2194026--2194065 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2194016 TGTTTACTAT
*
2194026 GATGGAGAAATTTAGGAT
1 GATGGAGAAATTTAGGAA
*
2194044 GATGGAGAAATTTGGGAA
1 GATGGAGAAATTTAGGAA
2194062 GATG
1 GATG
2194066 AAACCGGCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (18 bp):
GATGGAGAAATTTAGGAA
Found at i:2196451 original size:183 final size:183
Alignment explanation
Indices: 2196239--2196648 Score: 615
Period size: 183 Copynumber: 2.2 Consensus size: 183
2196229 CCATTCAAAT
*
2196239 ATGTATCGATACATAACAATATATCAGGTAAAAATATGATAAAACCAGGTTCAATATGACAAAAC
1 ATGTATCGATACGTAACAATATATCAGGTAAAAATATGATAAAACCAGGTTCAATATGACAAAAC
* * * *
2196304 TGGTAAAACGCTACCGGATATGTTGAAGGTATC-GATTCTATTCATATAAGTATCGATACTTACG
66 CGGTAAAACGCTACCAGATATGTTGAAGGTATCAG-TTCCATTCAAATAAGTATCGATACTTACG
***
2196368 AAATTTAAAAGAAAAGCAATAATATTGCCTATAAAATATCGATACTTTATAAAC
130 AAATTTAAAAGAAAAGCAATAATAGCACCTATAAAATATCGATACTTTATAAAC
* ** *
2196422 ATGTATCGATACGCAACAATATATCAGGTAAAAATATGATAAAACTGGGTTCAATATGATAAAAC
1 ATGTATCGATACGTAACAATATATCAGGTAAAAATATGATAAAACCAGGTTCAATATGACAAAAC
* * *
2196487 CGGTAAAGCGCTACCAGATATGTTGAAGGTATCAGTTCCATTCAAATAAGTATCGATACTTATGG
66 CGGTAAAACGCTACCAGATATGTTGAAGGTATCAGTTCCATTCAAATAAGTATCGATACTTACGA
* *
2196552 AATTTAAAAGAAGAGCAATAATAGCACCTATAAAGTATCGATACTTTATAAAC
131 AATTTAAAAGAAAAGCAATAATAGCACCTATAAAATATCGATACTTTATAAAC
* * * *
2196605 ATGTTTCAATACGTAACAATATAACAGGTAAAAATATGACAAAA
1 ATGTATCGATACGTAACAATATATCAGGTAAAAATATGATAAAA
2196649 TCGGTAATTC
Statistics
Matches: 204, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
183 203 1.00
184 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (183 bp):
ATGTATCGATACGTAACAATATATCAGGTAAAAATATGATAAAACCAGGTTCAATATGACAAAAC
CGGTAAAACGCTACCAGATATGTTGAAGGTATCAGTTCCATTCAAATAAGTATCGATACTTACGA
AATTTAAAAGAAAAGCAATAATAGCACCTATAAAATATCGATACTTTATAAAC
Found at i:2196695 original size:163 final size:162
Alignment explanation
Indices: 2196474--2196815 Score: 533
Period size: 163 Copynumber: 2.1 Consensus size: 162
2196464 AACTGGGTTC
* * *
2196474 AATATGATAAAACCGGTAAAGCGCTACCAGATATGTTGAAGGTATCAGTTCCATTCAAATAAGTA
1 AATATGACAAAATCGGTAAAGCGCTACCAGATATGTTGAAGGTATCAGTTACATTCAAATAAGTA
*
2196539 TCGATACTTATGGAATTTAAAAGAAGAGCAATAATAGCACCTATAAAGTATCGATACTTTATAAA
66 TCGATACTTATGGAATTTAAAAGAAAAGCAATAATAGCACCTATAAAGTATCGATACTTTATAAA
* * *
2196604 CATGTTTCAATACGTAACAATATAACAGGTAAA
131 CATATATCAATACATAACAATATAACAGGT-AA
** * * *
2196637 AATATGACAAAATCGGTAATTCTCTACCGGATATGTTGAAGGTATC-GATTATATTCAAATAAGT
1 AATATGACAAAATCGGTAAAGCGCTACCAGATATGTTGAAGGTATCAG-TTACATTCAAATAAGT
*
2196701 ATCGATACTTTTGGAATTTAAAAGAAAAGCAATAATAGCACCTATAAAGTATCGATACTTTATAA
65 ATCGATACTTATGGAATTTAAAAGAAAAGCAATAATAGCACCTATAAAGTATCGATACTTTATAA
*
2196766 ACATATATCGATACATAACAATATAACAGGTAA
130 ACATATATCAATACATAACAATATAACAGGTAA
2196799 AATATGACAAAATCGGT
1 AATATGACAAAATCGGT
2196816 TTCATTATGA
Statistics
Matches: 164, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
162 20 0.12
163 144 0.88
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (162 bp):
AATATGACAAAATCGGTAAAGCGCTACCAGATATGTTGAAGGTATCAGTTACATTCAAATAAGTA
TCGATACTTATGGAATTTAAAAGAAAAGCAATAATAGCACCTATAAAGTATCGATACTTTATAAA
CATATATCAATACATAACAATATAACAGGTAA
Found at i:2198562 original size:65 final size:65
Alignment explanation
Indices: 2198440--2198562 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 65
2198430 AGTGGTTGGA
* * *
2198440 AAAATAGATGGAGTGGTTAAAGAAGTTGTGAAGTTGAGGGGTGAACTTAAGATGGTGATGGGTGG
1 AAAATAGATGGAGTGGTGAAAGAAGTTGTGAAGTTAAGGGGTGAACTTAAGAGGGTGATGGGTGG
* * * *
2198505 AAAATTGATGGAGTGGTGAATGAAGTTGTGGAA-TTAAGGGGTGAACTTACGGGGGTGA
1 AAAATAGATGGAGTGGTGAAAGAAGTTGT-GAAGTTAAGGGGTGAACTTAAGAGGGTGA
2198563 AGGGAGTGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 47 0.94
66 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.40, T:0.26
Consensus pattern (65 bp):
AAAATAGATGGAGTGGTGAAAGAAGTTGTGAAGTTAAGGGGTGAACTTAAGAGGGTGATGGGTGG
Found at i:2202249 original size:19 final size:21
Alignment explanation
Indices: 2202190--2202243 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
2202180 TACAGGTAGG
2202190 AAGTATCGATACCTATGACAC
1 AAGTATCGATACCTATGACAC
2202211 AAGTATCGATACCTATGACAC
1 AAGTATCGATACCTATGACAC
*
2202232 ATGTATCGATAC
1 AAGTATCGATAC
2202244 ATGACAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (21 bp):
AAGTATCGATACCTATGACAC
Found at i:2205476 original size:118 final size:116
Alignment explanation
Indices: 2205227--2205484 Score: 311
Period size: 118 Copynumber: 2.2 Consensus size: 116
2205217 ACAAATTAAA
* * * * *
2205227 TAATTAACCTATTTTGTTATCGTCGGATTTCCAAAGTCCCATCAGCTTAAAAATACGCTACCTAT
1 TAATTAACCGATTATGTTATCGTCGAATTTCCAAAGCCCCATCAGCTTAAAAAGACGCTACCTAT
* * * * *
2205292 TACGTTATATAAATGATACTAATTTGTTATTATGCTTGATAATGTTTTCAG
66 TACGTTATATAAACGATACTAATATGTTATTATGATTAATAATGTTATCAG
* *
2205343 TAATTAACCGATTATGTTATCGTTGAATTTCCAAAGCCCCATCAGCTTTAAAAAGACGTTACCTA
1 TAATTAACCGATTATGTTATCGTCGAATTTCCAAAGCCCCATCAGC-TTAAAAAGACGCTACCTA
* * * *
2205408 TTACGTTATATAAGCGCTACCTAATATGTTATTGTGATTAATAATGTTAAT-GG
65 TTACGTTATATAAACGATA-CTAATATGTTATTATGATTAATAATGTT-ATCAG
* * *
2205461 TAATTAATCGGTTATGTTACCGTC
1 TAATTAACCGATTATGTTATCGTC
2205485 TATATTTTTT
Statistics
Matches: 119, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
116 41 0.34
117 32 0.27
118 45 0.38
119 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (116 bp):
TAATTAACCGATTATGTTATCGTCGAATTTCCAAAGCCCCATCAGCTTAAAAAGACGCTACCTAT
TACGTTATATAAACGATACTAATATGTTATTATGATTAATAATGTTATCAG
Found at i:2206590 original size:3 final size:3
Alignment explanation
Indices: 2206578--2206634 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
2206568 CACGTGATTT
2206578 TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2206625 TTC TTC TTC T
1 TTC TTC TTC T
2206635 GCTCCTCCTC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2206642 original size:3 final size:3
Alignment explanation
Indices: 2206636--2206660 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2206626 TCTTCTTCTG
2206636 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
2206661 AACTTTCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:2211259 original size:20 final size:20
Alignment explanation
Indices: 2211234--2211287 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2211224 GATCAACAAA
2211234 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
2211254 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
*
2211274 TTCCCAACGCGAAT
1 TTCGCAACGCGAAT
2211288 ATGTAAATCG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.28, C:0.33, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:2211334 original size:20 final size:20
Alignment explanation
Indices: 2211311--2211395 Score: 95
Period size: 20 Copynumber: 4.2 Consensus size: 20
2211301 TGAGATTTTC
2211311 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
2211331 CAAATTCGCAACGCGAATTTGT
1 CAAATTCGCAACGCGAA--AGT
*
2211353 -AAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGA-AAGT
*
2211371 CAAATTTGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
2211391 CAAAT
1 CAAAT
2211396 GTTTTTACGC
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.04
19 4 0.07
20 42 0.78
21 4 0.07
22 2 0.04
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:2211809 original size:13 final size:13
Alignment explanation
Indices: 2211791--2211815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2211781 TTTGCCTTTG
2211791 TTTTGTCTTTTTA
1 TTTTGTCTTTTTA
2211804 TTTTGTCTTTTT
1 TTTTGTCTTTTT
2211816 GTTAAAGAAA
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:0.04, C:0.08, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTGTCTTTTTA
Found at i:2212674 original size:20 final size:20
Alignment explanation
Indices: 2212649--2212688 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2212639 TTCCTGAGCT
2212649 GGCAAAGTCGAAGCCGAGTA
1 GGCAAAGTCGAAGCCGAGTA
2212669 GGCAAAGTCGAAGCCGAGTA
1 GGCAAAGTCGAAGCCGAGTA
2212689 TACACGTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.35, T:0.10
Consensus pattern (20 bp):
GGCAAAGTCGAAGCCGAGTA
Found at i:2213708 original size:21 final size:20
Alignment explanation
Indices: 2213684--2213723 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2213674 TGGTGCATGG
2213684 CGTGATGAGGTTCGATTTTTA
1 CGTGATGAGG-TCGATTTTTA
* *
2213705 CGTGGTGAGGTGGATTTTT
1 CGTGATGAGGTCGATTTTT
2213724 TACGCAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.07, G:0.35, T:0.42
Consensus pattern (20 bp):
CGTGATGAGGTCGATTTTTA
Found at i:2214156 original size:21 final size:21
Alignment explanation
Indices: 2214100--2214193 Score: 66
Period size: 21 Copynumber: 4.5 Consensus size: 21
2214090 CGTGTCCTAT
2214100 CGTTCAAGAGGCCCCTCTCA-
1 CGTTCAAGAGGCCCCTCTCAC
* ** *
2214120 -TTATCAAAGAACCCCCTCCCAC
1 CGT-TC-AAGAGGCCCCTCTCAC
* *
2214142 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCTCAC
* * * *
2214163 CGTTCAAGTGGTCCCGCTCGC
1 CGTTCAAGAGGCCCCTCTCAC
2214184 CGTTCAAGAG
1 CGTTCAAGAG
2214194 CCCGATTCAC
Statistics
Matches: 53, Mismatches: 17, Indels: 7
0.69 0.22 0.09
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 47 0.89
22 2 0.04
23 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.21
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCTCAC
Found at i:2216291 original size:24 final size:24
Alignment explanation
Indices: 2216236--2216281 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2216226 CGAAATTTAT
2216236 ATTGAAATTCAAACTCAAATTAAA
1 ATTGAAATTCAAACTCAAATTAAA
* *
2216260 ATTAAAATTCAAACTCCAATTA
1 ATTGAAATTCAAACTCAAATTA
2216282 CATATGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.30
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTAAA
Found at i:2216696 original size:25 final size:25
Alignment explanation
Indices: 2216659--2216708 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
2216649 ATTATTTTTC
* *
2216659 CAAATAATTTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2216684 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
2216709 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:2217137 original size:18 final size:18
Alignment explanation
Indices: 2217114--2217149 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2217104 AAGCCAGTTG
*
2217114 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2217132 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2217150 CCTTTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2219433 original size:24 final size:24
Alignment explanation
Indices: 2219399--2219452 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2219389 CCATCACATC
2219399 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* * * *
2219423 ATCAAAGTCTGGGTGTTGATCAAG
1 ATCAAAATCTGAGTATTGACCAAG
2219447 ATCAAA
1 ATCAAA
2219453 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:2219599 original size:12 final size:12
Alignment explanation
Indices: 2219578--2219611 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2219568 GGTTGTGGGT
*
2219578 TTTGAGATTGTG
1 TTTGATATTGTG
2219590 TTTGATATTGTG
1 TTTGATATTGTG
*
2219602 TTTGGTATTG
1 TTTGATATTG
2219612 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2220186 original size:16 final size:15
Alignment explanation
Indices: 2220164--2220202 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2220154 GAAATCATTG
2220164 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
2220180 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
2220195 AAAAATTA
1 AAAAATTA
2220203 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:2220393 original size:20 final size:20
Alignment explanation
Indices: 2220359--2220467 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
2220349 ACTAAAACCT
*
2220359 GTTGCGAA-ATTAAATTCGC
1 GTTGCGAATTTTAAATTCGC
*
2220378 GTTGCGAATTTTAAATTC-A
1 GTTGCGAATTTTAAATTCGC
* *
2220397 GTTGCG-ATTTACAAATTTGC
1 GTTGCGAATTT-TAAATTCGC
* **
2220417 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTTAAATTCGC
* * * *
2220437 ATTGC-AAATTTGACTATCGC
1 GTTGCGAATTTTAAAT-TCGC
2220457 GTTGCGAATTT
1 GTTGCGAATTT
2220468 GGAAAATCGC
Statistics
Matches: 67, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
18 4 0.06
19 24 0.36
20 31 0.46
21 8 0.12
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTTAAATTCGC
Found at i:2220400 original size:19 final size:19
Alignment explanation
Indices: 2220359--2220403 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2220349 ACTAAAACCT
*
2220359 GTTGCGAAATTAAATTCGC
1 GTTGCGAAATTAAATTCGA
*
2220378 GTTGCGAATTTTAAATTC-A
1 GTTGCGAA-ATTAAATTCGA
2220397 GTTGCGA
1 GTTGCGA
2220404 TTTACAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (19 bp):
GTTGCGAAATTAAATTCGA
Found at i:2220468 original size:20 final size:20
Alignment explanation
Indices: 2220415--2220468 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
2220405 TTACAAATTT
*
2220415 GCGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATC
* *
2220435 GCATTGCAAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
2220455 GCGTTGCGAATTTG
1 GCGTTGCGAATTTG
2220469 GAAAATCGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:2222045 original size:16 final size:18
Alignment explanation
Indices: 2222026--2222058 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2222016 CAACTTAAAT
2222026 CCTTT-ATA-TCTTAACC
1 CCTTTAATACTCTTAACC
2222042 CCTTTAATACTCTTAAC
1 CCTTTAATACTCTTAAC
2222059 TCAAATATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 3 0.20
18 7 0.47
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.42
Consensus pattern (18 bp):
CCTTTAATACTCTTAACC
Found at i:2224825 original size:21 final size:21
Alignment explanation
Indices: 2224801--2224844 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2224791 ATTTTGAAAC
2224801 AAATTAAAACTTTAGGTACTA
1 AAATTAAAACTTTAGGTACTA
* * *
2224822 AAATTGATAGTTTAGGTACTA
1 AAATTAAAACTTTAGGTACTA
2224843 AA
1 AA
2224845 TGCGTTAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (21 bp):
AAATTAAAACTTTAGGTACTA
Found at i:2225122 original size:30 final size:29
Alignment explanation
Indices: 2225086--2225161 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
2225076 TTTCGGCGAT
*
2225086 TTTCCCGATATATCACCGGTGAACAGTATA
1 TTTCCCGATATAACACCGGT-AACAGTATA
* * * *
2225116 TTTCCCGATTTAACACCGGTCAGATTATA
1 TTTCCCGATATAACACCGGTAACAGTATA
*
2225145 TTTCCCGATCTAACACC
1 TTTCCCGATATAACACC
2225162 CTTAGCAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 22 0.55
30 18 0.45
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.32
Consensus pattern (29 bp):
TTTCCCGATATAACACCGGTAACAGTATA
Found at i:2229072 original size:3 final size:3
Alignment explanation
Indices: 2229066--2229097 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2229056 GTCATCATCA
*
2229066 TCG TCG TCG TCA TCG TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
2229098 TTGCGCAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.28, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:2229078 original size:12 final size:12
Alignment explanation
Indices: 2229052--2229097 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
2229042 TCATCATCAC
* *
2229052 CATCGTCATCAT
1 CATCGTCGTCGT
2229064 CATCGTCGTCGT
1 CATCGTCGTCGT
2229076 CATCGTCGTCGT
1 CATCGTCGTCGT
*
2229088 CGTCGTCGTC
1 CATCGTCGTC
2229098 TTGCGCAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.11, C:0.35, G:0.22, T:0.33
Consensus pattern (12 bp):
CATCGTCGTCGT
Found at i:2231165 original size:110 final size:111
Alignment explanation
Indices: 2230971--2231191 Score: 408
Period size: 110 Copynumber: 2.0 Consensus size: 111
2230961 ATTACAAAAA
* *
2230971 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
2231036 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
2231082 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
2231146 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
2231192 ATGATTTCCA
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
110 72 0.67
111 35 0.33
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:2231579 original size:51 final size:50
Alignment explanation
Indices: 2231485--2231581 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
2231475 TATAGCGCGC
* *
2231485 TGCAGGGGCCGCGCTATACCCACGTGTATGCCAGATCACCGTATAGTGTGG
1 TGCAGGGGCCGCGCTATACCCACGTG-ACGCCAAATCACCGTATAGTGTGG
* *
2231536 TGCAGGGGGCGCGCTATACCCCACGT-AGCGCCAAATCATCGTATAG
1 TGCAGGGGCCGCGCTATA-CCCACGTGA-CGCCAAATCACCGTATAG
2231582 CGCGATGTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
50 1 0.03
51 32 0.80
52 7 0.17
ACGTcount: A:0.22, C:0.29, G:0.30, T:0.20
Consensus pattern (50 bp):
TGCAGGGGCCGCGCTATACCCACGTGACGCCAAATCACCGTATAGTGTGG
Found at i:2232362 original size:20 final size:19
Alignment explanation
Indices: 2232339--2232385 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2232329 CGATATAACA
2232339 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
2232359 GGTATCAAAATGATGAAACC
1 GGTA-AAAAATGATAAAACC
2232379 GGTAAAA
1 GGTAAAA
2232386 CGCTACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2232514 original size:181 final size:181
Alignment explanation
Indices: 2232127--2232780 Score: 1083
Period size: 181 Copynumber: 3.6 Consensus size: 181
2232117 GATCCAAATT
* * **
2232127 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * *
2232192 AAACTGGTAAAGCGGTACCGGATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
* *
2232257 GTTAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTAGATACTTTAA
130 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
*
2232309 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATG
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
2232374 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTG
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTG
* * *
2232439 TGAATTTAAAAGAGAAACTGTTTTAGCGCCTATAAACTGTCGATACTTTAA
131 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
*
2232490 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTACCAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
2232555 AAACTGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGAAACTTTA
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTG
2232620 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
131 TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * *
2232671 AAATATGTATCGATCCACAACGATATAACAGGTAAAAATATGATGAAACCGATATCAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
2232736 AAATCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT
2232781 CGTAAGTACG
Statistics
Matches: 442, Mismatches: 30, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
181 342 0.77
182 100 0.23
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTG
TGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:2232543 original size:20 final size:19
Alignment explanation
Indices: 2232520--2232566 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2232510 CGATATAACA
2232520 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
2232540 GGTACCAAAATGATAAAACT
1 GGTA-AAAAATGATAAAACC
2232560 GGTAAAA
1 GGTAAAA
2232567 CGCTACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:2234996 original size:21 final size:21
Alignment explanation
Indices: 2234970--2235033 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
2234960 AAGACAATCA
*
2234970 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
*
2234991 AGAGTCAAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2235012 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2235033 A
1 A
2235034 TGCATAAGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2235110 original size:33 final size:33
Alignment explanation
Indices: 2235068--2235133 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
2235058 AAATAGATGG
* * *
2235068 AGTGGTGAAAGAAGTAGATGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAAGGGTGA
*
2235101 AGTGGTGAAAGAAGTTGAGGTGTTAAAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAAGGGTGA
2235134 TCTTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.44, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAAGGGTGA
Found at i:2235344 original size:21 final size:21
Alignment explanation
Indices: 2235318--2235358 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2235308 GAAAAAATAT
2235318 GAAGAAGAAAAGAGGGAAGAG
1 GAAGAAGAAAAGAGGGAAGAG
* *
2235339 GAAGAAGAAGAGATGGAAGA
1 GAAGAAGAAAAGAGGGAAGA
2235359 AAAGAGGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.41, T:0.02
Consensus pattern (21 bp):
GAAGAAGAAAAGAGGGAAGAG
Found at i:2235358 original size:33 final size:33
Alignment explanation
Indices: 2235321--2235409 Score: 160
Period size: 33 Copynumber: 2.7 Consensus size: 33
2235311 AAAATATGAA
*
2235321 GAAGAAAAGAGGGAAGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
2235354 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
2235387 GAAGAAAAGAGGGAGGAAGGAAG
1 GAAGAAAAGAGGGAGG-AGGAAG
2235410 TCGATGTCAT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 48 0.89
34 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.45, T:0.02
Consensus pattern (33 bp):
GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
Found at i:2237576 original size:200 final size:200
Alignment explanation
Indices: 2237221--2238405 Score: 1948
Period size: 200 Copynumber: 5.9 Consensus size: 200
2237211 AATTTACAAT
* * *
2237221 ATGGAAAACAGGGTGCAACCATAAAGTGTAGATCCATATATAAAAAGTGTCGATCCCAGACACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
* *
2237286 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCAGTTTT
66 CGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
2237351 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2237416 AATGA
196 AATGA
* *
2237421 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCAATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
*
2237486 CGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACCGGTATCAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * *
2237551 ATGAGAGATTAGGTGTA-ATATATGTATTGATACTTTTTAATTTTGTGTCGATACTATTGGTCCA
131 ATGAGAGATTAGGTATATA-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
2237615 GAATGA
195 GAATGA
* * * *
2237621 ATGGAAAACAGGGTACAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCTAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
2237686 CGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
2237751 ATGAGAGATTAGGTATATAATATGTATCCACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2237816 AATGA
196 AATGA
* *
2237821 ATGGCAAATAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCTCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
* * *
2237886 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTTAATCTAACTGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
*
2237951 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTAGTCCAG
131 ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
2238016 AATGA
196 AATGA
*
2238021 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAATGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
* *
2238086 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATATCGGTTTT
66 CGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
* * * * *
2238151 ATGAGATAATAGGTGTA-ATATATGTATCGACACTTTTTAATTTTGTGTTGATACTATTGGTCTA
131 ATGAGAGATTAGGTATATA-ATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCA
2238215 GAATGA
195 GAATGA
* * *
2238221 ATGGCAAATAGGGTGCAACCAT-AAGCTG-C-TTCCCATATATAAAAAGTATCGATCCCAGAAAC
1 ATGGCAAACAGGGTGCAACCATAAAG-TGTCGAT-CCATATATAAAAAGTGTCGATCCCAGAAAC
* *
2238283 ATCGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACCTGTATAAGTATACCGATT
64 ATCGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTT
* * * *
2238348 TTATGAGATAATAGGTGTATAATATGTATCGACACTTTTTAATTTTGTGTCTATACTA
129 TTATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTA
2238406 ATTTAAATAT
Statistics
Matches: 926, Mismatches: 53, Indels: 13
0.93 0.05 0.01
Matches are distributed among these distances:
198 1 0.00
199 149 0.16
200 775 0.84
201 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
ATGAGAGATTAGGTATATAATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:2239906 original size:12 final size:12
Alignment explanation
Indices: 2239889--2239933 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
2239879 AAGATAAAGC
2239889 TGACGATGAAGA
1 TGACGATGAAGA
2239901 TGACGATGAAGA
1 TGACGATGAAGA
* *
2239913 TGACGACGACGA
1 TGACGATGAAGA
*
2239925 TGATGATGA
1 TGACGATGA
2239934 TGATTCAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.38, C:0.11, G:0.33, T:0.18
Consensus pattern (12 bp):
TGACGATGAAGA
Found at i:2239937 original size:6 final size:6
Alignment explanation
Indices: 2239889--2239933 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
2239879 AAGATAAAGC
* * * *
2239889 TGACGA TGAAGA TGACGA TGAAGA TGACGA CGACGA TGATGA TGA
1 TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA TGACGA TGA
2239934 TGATTCAAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.38, C:0.11, G:0.33, T:0.18
Consensus pattern (6 bp):
TGACGA
Found at i:2244547 original size:21 final size:20
Alignment explanation
Indices: 2244500--2244549 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
2244490 AAATTACATA
*
2244500 ACTTTCAAAAAAGTTTCGAT
1 ACTTTCAAAAAAGTATCGAT
* *
2244520 TCTTTTCACAAAAAGTATCTAT
1 AC-TTTCA-AAAAAGTATCGAT
2244542 ACTTTCAA
1 ACTTTCAA
2244550 CATATCAGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 10 0.42
22 12 0.50
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (20 bp):
ACTTTCAAAAAAGTATCGAT
Found at i:2244706 original size:20 final size:20
Alignment explanation
Indices: 2244681--2244719 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2244671 AATCGCTACT
2244681 GGTTTTGTTACTTTTTTACC
1 GGTTTTGTTACTTTTTTACC
*
2244701 GGTTTTGTTATTTTTTTAC
1 GGTTTTGTTACTTTTTTAC
2244720 ATGTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.10, G:0.15, T:0.64
Consensus pattern (20 bp):
GGTTTTGTTACTTTTTTACC
Found at i:2244727 original size:111 final size:111
Alignment explanation
Indices: 2244590--2244815 Score: 391
Period size: 112 Copynumber: 2.0 Consensus size: 111
2244580 TAATAAAACT
* *
2244590 GGTTTTGTCATTTTTTTACATGTTATATTGTAAAGTATCTATCC-TTTTATAAAAGGATCGATAC
1 GGTTTTGTCATTTTTTTACATGTTATATTATAAAGTATCGATCCTTTTTATAAAAGGATCGATAC
* *
2244654 TTTCAATATATCAGGTAAATCGCTACTGGTTTTGTTACTTTTTTACC
66 TTTCAATATATCAGGTAAAACGCTACCGGTTTTGTTA-TTTTTTACC
*
2244701 GGTTTTGTTATTTTTTTACATGTTATATTATAAAGTATCGATCCTTTTTATAAAAGGATCGATAC
1 GGTTTTGTCATTTTTTTACATGTTATATTATAAAGTATCGATCCTTTTTATAAAAGGATCGATAC
2244766 TTTCAATATATCAGGTAAAACGCTACCGGTTTTGTTATTTTTTACC
66 TTTCAATATATCAGGTAAAACGCTACCGGTTTTGTTATTTTTTACC
2244812 GGTT
1 GGTT
2244816 ATATTGTAAA
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
111 54 0.50
112 55 0.50
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (111 bp):
GGTTTTGTCATTTTTTTACATGTTATATTATAAAGTATCGATCCTTTTTATAAAAGGATCGATAC
TTTCAATATATCAGGTAAAACGCTACCGGTTTTGTTATTTTTTACC
Found at i:2244753 original size:20 final size:21
Alignment explanation
Indices: 2244728--2244768 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2244718 ACATGTTATA
* *
2244728 TTAT-AAAGTATCGATCCTTT
1 TTATAAAAGGATCGATACTTT
2244748 TTATAAAAGGATCGATACTTT
1 TTATAAAAGGATCGATACTTT
2244769 CAATATATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (21 bp):
TTATAAAAGGATCGATACTTT
Found at i:2244831 original size:91 final size:92
Alignment explanation
Indices: 2244697--2244907 Score: 361
Period size: 91 Copynumber: 2.3 Consensus size: 92
2244687 GTTACTTTTT
** *
2244697 TACCGGTTTTGTTATTTTTTTACATGTTATATTATAAAGTATCGATCCTTTTTATAAAAGGATCG
1 TACCGGTTTTGTTATTTTTTTACCGGTTATATTATAAAATATCGATCCTTTTTATAAAAGGATCG
2244762 ATACTTTCAATATATCAGGTAAAACGC
66 ATACTTTCAATATATCAGGTAAAACGC
*
2244789 TACCGGTTTTGTTA-TTTTTTACCGGTTATATTGTAAAATATCGATCCTTTTTATAAAAGGATCG
1 TACCGGTTTTGTTATTTTTTTACCGGTTATATTATAAAATATCGATCCTTTTTATAAAAGGATCG
* *
2244853 ATACTTTCAATATATTAGGTAAAGCGC
66 ATACTTTCAATATATCAGGTAAAACGC
2244880 TACCGGTTTTGTTATTTTTTTACCGGTT
1 TACCGGTTTTGTTATTTTTTTACCGGTT
2244908 TTGTTATTTT
Statistics
Matches: 112, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
91 85 0.76
92 27 0.24
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (92 bp):
TACCGGTTTTGTTATTTTTTTACCGGTTATATTATAAAATATCGATCCTTTTTATAAAAGGATCG
ATACTTTCAATATATCAGGTAAAACGC
Found at i:2244919 original size:19 final size:20
Alignment explanation
Indices: 2244880--2244928 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
2244870 GGTAAAGCGC
2244880 TACCGGTTTTGTTATTTTTT
1 TACCGGTTTTGTTATTTTTT
2244900 TACCGGTTTTGTTA-TTTTT
1 TACCGGTTTTGTTATTTTTT
*
2244919 TACCGATTTT
1 TACCGGTTTT
2244929 ACCGAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.61
Consensus pattern (20 bp):
TACCGGTTTTGTTATTTTTT
Found at i:2245304 original size:24 final size:24
Alignment explanation
Indices: 2245277--2245328 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
2245267 AGCATCAAAT
2245277 ACAATAA-AATAATATTATTTATTA
1 ACAATAATAATAATATTATTT-TTA
2245301 ACAA-AATAATAATATTATTTTTA
1 ACAATAATAATAATATTATTTTTA
2245324 A-AATA
1 ACAATA
2245329 TTAGAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 2 0.08
23 7 0.27
24 17 0.65
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
ACAATAATAATAATATTATTTTTA
Found at i:2245379 original size:14 final size:14
Alignment explanation
Indices: 2245360--2245432 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
2245350 TATCTATGTC
2245360 AATATTATTATTAA
1 AATATTATTATTAA
*
2245374 AATATTA-TATCTAT
1 AATATTATTAT-TAA
* * *
2245388 AATTTTATAAATAA
1 AATATTATTATTAA
* * *
2245402 AAAATTATGATTAT
1 AATATTATTATTAA
*
2245416 TATATT-TTATTAA
1 AATATTATTATTAA
2245429 AATA
1 AATA
2245433 AATTTACAAT
Statistics
Matches: 42, Mismatches: 15, Indels: 5
0.68 0.24 0.08
Matches are distributed among these distances:
13 11 0.26
14 30 0.71
15 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:2245395 original size:28 final size:28
Alignment explanation
Indices: 2245360--2245432 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
2245350 TATCTATGTC
2245360 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
2245388 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
*
2245416 TATATT-TTATTAAAATA
1 AATATTATTATTAAAATA
2245433 AATTTACAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
27 8 0.23
28 25 0.71
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:2245532 original size:23 final size:23
Alignment explanation
Indices: 2245476--2245532 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
2245466 TTTATGATAG
* *
2245476 AATATGTCAATATAAGCATTACCT
1 AATATGT-TATATAAGCACTACCT
* **
2245500 ATTACATTATATAAGCACTACCT
1 AATATGTTATATAAGCACTACCT
2245523 AATATGTTAT
1 AATATGTTAT
2245533 TATGCTTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (23 bp):
AATATGTTATATAAGCACTACCT
Found at i:2245587 original size:87 final size:87
Alignment explanation
Indices: 2245485--2245725 Score: 374
Period size: 87 Copynumber: 2.8 Consensus size: 87
2245475 GAATATGTCA
** *
2245485 ATATAAGCATTACCTATTACATTATATAAGCACTACCTAATATGTTATTATGCTTGATAATGTTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTT
*
2245550 CCAGTAATTAACATATTTTATT
66 CCAATAATTAACATATTTTATT
* * *
2245572 ATATAAGCGCTACCTATTACATTATATAAACGGTACCTAATATGTTATTGTGCTTGATAATGTTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTT
2245637 CCAATAATTAACATATTTTATT
66 CCAATAATTAACATATTTTATT
* * * * *
2245659 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATTTATTATTTTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTT
2245724 CC
66 CC
2245726 GGTTAAATAA
Statistics
Matches: 140, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 140 1.00
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATGCTTGATAATGTTT
CCAATAATTAACATATTTTATT
Found at i:2245619 original size:23 final size:23
Alignment explanation
Indices: 2245569--2245613 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2245559 AACATATTTT
* *
2245569 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
*
2245592 ATTATATAAACGGTACCTAATA
1 ATTATATAAACGCTACCTAATA
2245614 TGTTATTGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:2245676 original size:23 final size:23
Alignment explanation
Indices: 2245650--2245706 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
2245640 ATAATTAACA
2245650 TATTTTATTATATAAGCGCTACC
1 TATTTTATTATATAAGCGCTACC
**
2245673 TATTACATTATATAAGCGCTACC
1 TATTTTATTATATAAGCGCTACC
*
2245696 TAATTTATTAT
1 TATTTTATTAT
2245707 TTTACTTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (23 bp):
TATTTTATTATATAAGCGCTACC
Found at i:2250914 original size:37 final size:37
Alignment explanation
Indices: 2250832--2250933 Score: 154
Period size: 37 Copynumber: 2.8 Consensus size: 37
2250822 ATTAGAATTT
*
2250832 TACTAGGATTCAAACTCCTAAAAATATG--AGAGTTT
1 TACTAGGATTCAAACTCCTAAAAATATGATAGAGTTC
**
2250867 TACTAGGATTCAAACTTTTAAAAATATGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATATGATAGAGTTC
*
2250904 TACTATGATTCAAACTCCTAAAAATATGAT
1 TACTAGGATTCAAACTCCTAAAAATATGAT
2250934 CTACAAGTGT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 26 0.44
37 33 0.56
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATATGATAGAGTTC
Found at i:2253503 original size:25 final size:25
Alignment explanation
Indices: 2253475--2253536 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
2253465 CTGTCAGGAT
* *
2253475 ATTTTTGTCTCTTAAAAGATAAAAC
1 ATTTTTGTCCCCTAAAAGATAAAAC
2253500 ATTTTTGTCCCCTAAAAGATAAAAC
1 ATTTTTGTCCCCTAAAAGATAAAAC
*
2253525 ATTCTTGTCCCC
1 ATTTTTGTCCCC
2253537 AATAAGGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (25 bp):
ATTTTTGTCCCCTAAAAGATAAAAC
Found at i:2254769 original size:20 final size:18
Alignment explanation
Indices: 2254738--2254806 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 18
2254728 AGATCAAATC
2254738 AGAAAAAAAAGAAAAAAG
1 AGAAAAAAAAGAAAAAAG
2254756 AGAAAAAATGAAGAAAAAAG
1 AGAAAAAA--AAGAAAAAAG
2254776 CA-AAGAGAAAATA-AAAAAAG
1 -AGAA-A-AAAA-AGAAAAAAG
2254796 AGAAACAAAAA
1 AGAAA-AAAAA
2254807 TAAAGGAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
18 9 0.21
19 6 0.14
20 22 0.51
21 3 0.07
22 3 0.07
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (18 bp):
AGAAAAAAAAGAAAAAAG
Found at i:2254786 original size:14 final size:15
Alignment explanation
Indices: 2254741--2254800 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
2254731 TCAAATCAGA
* *
2254741 AAAAAAAGAAAAAAG
1 AAAAAAAGAGAAAAT
2254756 AGAAAAAATGAAGAAAA-
1 A-AAAAAA-G-AGAAAAT
**
2254773 AAGCAAAGAGAAAAT
1 AAAAAAAGAGAAAAT
2254788 AAAAAAAGAGAAA
1 AAAAAAAGAGAAA
2254801 CAAAAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
14 6 0.17
15 13 0.36
16 10 0.28
17 2 0.06
18 5 0.14
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (15 bp):
AAAAAAAGAGAAAAT
Found at i:2254806 original size:15 final size:16
Alignment explanation
Indices: 2254777--2254816 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2254767 AGAAAAAAGC
2254777 AAAGAGAAAATAAAA-
1 AAAGAGAAAATAAAAT
2254792 AAAGAGAAACA-AAAAT
1 AAAGAGAAA-ATAAAAT
2254808 AAAG-GAAAA
1 AAAGAGAAAA
2254817 AGTGAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 17 0.74
16 5 0.22
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAGAGAAAATAAAAT
Found at i:2256319 original size:20 final size:22
Alignment explanation
Indices: 2256294--2256333 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2256284 TGTTGTATAT
2256294 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
2256314 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
2256334 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:2256467 original size:20 final size:20
Alignment explanation
Indices: 2256436--2256509 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
2256426 GCAGCCTTCG
*
2256436 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* **
2256456 TTCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-CAGGA
*
2256477 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
2256497 TGCATCGATGCAC
1 TGCATCGATGCAC
2256510 TAATTGCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:2256487 original size:41 final size:41
Alignment explanation
Indices: 2256427--2256509 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
2256417 CTAGTCGTTG
* * *
2256427 CAGCCTTCGTGCATGGATGCACAGCAGGATTCATCGATGCA
1 CAGCCTTCGTGCATCGATGCACAGAAGGATGCATCGATGCA
2256468 CAGCCTT-GATGCATCGATGCACAGAAGGATGCATCGATGCA
1 CAGCCTTCG-TGCATCGATGCACAGAAGGATGCATCGATGCA
2256509 C
1 C
2256510 TAATTGCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (41 bp):
CAGCCTTCGTGCATCGATGCACAGAAGGATGCATCGATGCA
Found at i:2256603 original size:21 final size:21
Alignment explanation
Indices: 2256531--2256649 Score: 127
Period size: 21 Copynumber: 5.7 Consensus size: 21
2256521 GGTGTTTGAG
*
2256531 TGCATGGATGCACTGCA-TGA
1 TGCATGGATGCACTGCAGGGA
*
2256551 TGCATCGATGCACTAGTGCA-GG-
1 TGCATGGATGCAC---TGCAGGGA
2256573 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
* *
2256594 TGCATAGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
* *
2256615 TACATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
*
2256636 TGCATGAATGCACT
1 TGCATGGATGCACT
2256650 TTGACACCCT
Statistics
Matches: 85, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.05
20 14 0.16
21 50 0.59
22 12 0.14
23 5 0.06
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:2256750 original size:29 final size:29
Alignment explanation
Indices: 2256729--2256786 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
2256719 AAACTTTGAA
*
2256729 TAAATTCAATT-GAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
2256758 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
2256787 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 13 0.50
31 2 0.08
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:2256777 original size:30 final size:30
Alignment explanation
Indices: 2256729--2256788 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
2256719 AAACTTTGAA
*
2256729 TAAATTCAATTGAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
2256758 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
2256789 CCTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:2256979 original size:32 final size:32
Alignment explanation
Indices: 2256933--2257013 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
2256923 TGGGGGAATC
* * *
2256933 TTTGAAGATTCAACATCAAATGTTGGAGCATT
1 TTTGGAGATTCAACATCAAATATCGGAGCATT
* *
2256965 TTTGGAGATTCAACATCGAATATCGGGGCATT
1 TTTGGAGATTCAACATCAAATATCGGAGCATT
* *
2256997 TTTGGGGATCCAACATC
1 TTTGGAGATTCAACATC
2257014 CTGATGCGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (32 bp):
TTTGGAGATTCAACATCAAATATCGGAGCATT
Found at i:2257705 original size:21 final size:22
Alignment explanation
Indices: 2257664--2257711 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
2257654 GACAGTTTCC
2257664 CTTGAAACAAAGTTTTATCTCT
1 CTTGAAACAAAGTTTTATCTCT
*
2257686 CTTGAAACAAA-TTTTGTCTCT
1 CTTGAAACAAAGTTTTATCTCT
2257707 CTTGA
1 CTTGA
2257712 GACAGTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (22 bp):
CTTGAAACAAAGTTTTATCTCT
Found at i:2257708 original size:58 final size:58
Alignment explanation
Indices: 2257631--2257870 Score: 309
Period size: 58 Copynumber: 4.0 Consensus size: 58
2257621 AATTTACTCA
2257631 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCTCTTG
* * *
2257690 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATCTTTGAATATGCTTTCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-GTTT---TAT-CTCT-CTTG
* * ** * * *
2257754 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCTCTTG
* *
2257812 AAACAAATGTTGTCTCTCTTGAGGCAGTTTCCCTTGAAACAAAGTTTTATCTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCTCTTG
2257870 A
1 A
2257871 GACAGTTTCT
Statistics
Matches: 155, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
58 89 0.57
59 13 0.08
60 2 0.01
62 3 0.02
63 6 0.04
64 42 0.27
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.40
Consensus pattern (58 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTATCTCTCTTG
Found at i:2257848 original size:36 final size:37
Alignment explanation
Indices: 2257808--2257889 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
2257798 TTTTGTCTCT
* *
2257808 CTTGAAACAAA-TGTTGTCTCTCTTGAGGCAGTTTCC
1 CTTGAAACAAAGTGTTATCTCTCTTGAGACAGTTTCC
* *
2257844 CTTGAAACAAAGTTTTATCTCTCTTGAGACAGTTTCT
1 CTTGAAACAAAGTGTTATCTCTCTTGAGACAGTTTCC
2257881 CTTGAAACA
1 CTTGAAACA
2257890 CCAATCTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 11 0.27
37 30 0.73
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.37
Consensus pattern (37 bp):
CTTGAAACAAAGTGTTATCTCTCTTGAGACAGTTTCC
Found at i:2258627 original size:37 final size:37
Alignment explanation
Indices: 2258586--2258692 Score: 169
Period size: 37 Copynumber: 2.9 Consensus size: 37
2258576 AACGTTATAA
* * *
2258586 TTTTACTAGGATTCAAACTCCTAAAAATAGGTTAGAG
1 TTTTACTATGATTCAAACTCCTAAAAATAGGATAAAG
*
2258623 TTTTACTATAATTCAAACTCCTAAAAATAGGATAAAG
1 TTTTACTATGATTCAAACTCCTAAAAATAGGATAAAG
*
2258660 TTCTACTATGATTCAAACTCCTAAAAATAGGAT
1 TTTTACTATGATTCAAACTCCTAAAAATAGGAT
2258693 CCACAAACGT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (37 bp):
TTTTACTATGATTCAAACTCCTAAAAATAGGATAAAG
Found at i:2258973 original size:13 final size:13
Alignment explanation
Indices: 2258930--2259038 Score: 56
Period size: 13 Copynumber: 8.8 Consensus size: 13
2258920 ATTTTTTATG
2258930 TTTTTATTTATTA
1 TTTTTATTTATTA
* * *
2258943 TATATATATA-TA
1 TTTTTATTTATTA
*
2258955 -TATTATTT-TTA
1 TTTTTATTTATTA
2258966 TTTATTA-TTATTA
1 TTT-TTATTTATTA
*
2258979 -TTTTATTTGTT-
1 TTTTTATTTATTA
2258990 TGTTTTATTTATATA
1 T-TTTTATTTAT-TA
* *
2259005 TTTTT-CTTCTTA
1 TTTTTATTTATTA
*
2259017 TTTTTCTTTATT-
1 TTTTTATTTATTA
2259029 TTTTT-TTTAT
1 TTTTTATTTAT
2259039 CTTTTTACAT
Statistics
Matches: 72, Mismatches: 14, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
11 14 0.19
12 23 0.32
13 29 0.40
14 5 0.07
15 1 0.01
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTTTATTTATTA
Found at i:2259130 original size:26 final size:26
Alignment explanation
Indices: 2259093--2259142 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2259083 TTATCTTATC
* *
2259093 TTTTATTTAATTTGTTT-TTTCTTCG
1 TTTTATTCAATTTATTTATTTCTTCG
2259118 TTTTAATTCAATTTATTTATTTCTT
1 TTTT-ATTCAATTTATTTATTTCTT
2259143 ACCTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 11 0.52
27 6 0.29
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTATTCAATTTATTTATTTCTTCG
Found at i:2263438 original size:19 final size:19
Alignment explanation
Indices: 2263416--2263453 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2263406 ATAAGAAATG
2263416 ATATGAAT-TATATATGAGA
1 ATATGAATATAT-TATGAGA
*
2263435 ATATGTATATATTATGAGA
1 ATATGAATATATTATGAGA
2263454 TAAGACCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (19 bp):
ATATGAATATATTATGAGA
Done.