Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 14 of 22
Found at i:2176317 original size:15 final size:14
Alignment explanation
Indices: 2176214--2176313 Score: 55
Period size: 16 Copynumber: 6.9 Consensus size: 14
2176204 AATCAATATA
2176214 ATTATATCATATTTAT
1 ATTATAT-AT-TTTAT
2176230 ATTAT-T-TTTTAT
1 ATTATATATTTTAT
* * *
2176242 GTCATA-ATTATAT
1 ATTATATATTTTAT
*
2176255 -TTAAAATATTTTAT
1 ATT-ATATATTTTAT
2176269 ATTTATATAATTTTAAT
1 A-TTATAT-ATTTT-AT
* *
2176286 ATTTTAAATATTTAT
1 ATTATATAT-TTTAT
2176301 ATTATATATTTTA
1 ATTATATATTTTA
2176314 ATATGTACAT
Statistics
Matches: 64, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
12 9 0.14
13 8 0.12
14 10 0.16
15 15 0.23
16 19 0.30
17 3 0.05
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (14 bp):
ATTATATATTTTAT
Found at i:2179038 original size:23 final size:22
Alignment explanation
Indices: 2179011--2179072 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
2179001 TGTAATTATT
2179011 TTTAAAAAATAATATTTAATA-TA
1 TTTAAAAAATAATATTT--TAGTA
* *
2179034 TTT-AAAATTAAAATTTTAGTA
1 TTTAAAAAATAATATTTTAGTA
*
2179055 TTTATAAAATAATATTTT
1 TTTAAAAAATAATATTTT
2179073 TTTTTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.06
21 5 0.16
22 22 0.69
23 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTAAAAAATAATATTTTAGTA
Found at i:2179410 original size:32 final size:31
Alignment explanation
Indices: 2179356--2179416 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
2179346 AATTGAATTG
*
2179356 AATTTAAATAAATAAAATATTTATTAATATCA
1 AATTTAAAT-AATAAAATATTTATAAATATCA
2179388 AATTTAAAT-ATAAAATTAATTTATAAATA
1 AATTTAAATAATAAAA-T-ATTTATAAATA
2179417 ACCTTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 1 0.04
32 19 0.73
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (31 bp):
AATTTAAATAATAAAATATTTATAAATATCA
Found at i:2180196 original size:35 final size:35
Alignment explanation
Indices: 2180122--2180213 Score: 121
Period size: 35 Copynumber: 2.6 Consensus size: 35
2180112 TCGAATATAA
* *
2180122 AAAAATTATAATTATTATTATATAAACTAATTAAAT
1 AAAAATTATAATTACT-TTGTATAAACTAATTAAAT
* **
2180158 AAAAATTATAATTACTTTGTATGAACTAATTACGT
1 AAAAATTATAATTACTTTGTATAAACTAATTAAAT
*
2180193 AAAAATTATAATCACTTTGTA
1 AAAAATTATAATTACTTTGTA
2180214 AGATTGATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
35 35 0.70
36 15 0.30
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (35 bp):
AAAAATTATAATTACTTTGTATAAACTAATTAAAT
Found at i:2184813 original size:51 final size:51
Alignment explanation
Indices: 2184737--2184841 Score: 158
Period size: 51 Copynumber: 2.1 Consensus size: 51
2184727 TATGTTATAG
2184737 AATTTTTATTTTTTTAAAGTATTCATTTTTAAAATTTGATCAAAACATCAA
1 AATTTTTATTTTTTTAAAGTATTCATTTTTAAAATTTGATCAAAACATCAA
* * * *
2184788 AATTTTATTTTTTTTTAAA-TATTCATTTTTTAAATTTGATCAAAATATCGA
1 AATTTT-TATTTTTTTAAAGTATTCATTTTTAAAATTTGATCAAAACATCAA
2184839 AAT
1 AAT
2184842 ATAGAATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
51 38 0.78
52 11 0.22
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (51 bp):
AATTTTTATTTTTTTAAAGTATTCATTTTTAAAATTTGATCAAAACATCAA
Found at i:2199734 original size:27 final size:26
Alignment explanation
Indices: 2199648--2199739 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 26
2199638 TAGCCACAAA
* * *
2199648 TTTTGACAAATA-AACAAGCCTCCAT
1 TTTTGACAAATACAAAAAACCACCAT
* *
2199673 ATTTGACAAATACAAAGGAAACTACCAT
1 TTTTGACAAATACAAA--AAACCACCAT
2199701 TTTTGACAAATACAAAATAACCACCAT
1 TTTTGACAAATACAAAA-AACCACCAT
2199728 TTTTGACAAATA
1 TTTTGACAAATA
2199740 AATGGGTGGC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 20 0.36
28 22 0.39
ACGTcount: A:0.46, C:0.20, G:0.08, T:0.27
Consensus pattern (26 bp):
TTTTGACAAATACAAAAAACCACCAT
Found at i:2206835 original size:2 final size:2
Alignment explanation
Indices: 2206826--2206859 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2206816 ATAGTTTATC
2206826 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2206860 GTTTCCATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2207763 original size:2 final size:2
Alignment explanation
Indices: 2207756--2207787 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2207746 TCATTAATTG
2207756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2207788 TCATTTAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2208149 original size:9 final size:9
Alignment explanation
Indices: 2208135--2208173 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
2208125 CTAACTAGTT
2208135 TTCCTCAGC
1 TTCCTCAGC
2208144 TTCCTCAGC
1 TTCCTCAGC
2208153 TT-CT--GC
1 TTCCTCAGC
2208159 TTCCTCAGC
1 TTCCTCAGC
2208168 TTCCTC
1 TTCCTC
2208174 TTCCTCAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.15
7 2 0.07
8 2 0.07
9 19 0.70
ACGTcount: A:0.08, C:0.44, G:0.10, T:0.38
Consensus pattern (9 bp):
TTCCTCAGC
Found at i:2208162 original size:15 final size:16
Alignment explanation
Indices: 2208142--2208191 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 16
2208132 GTTTTCCTCA
2208142 GCTTCCTCAGCTT-CT
1 GCTTCCTCAGCTTCCT
2208157 GCTTCCTCAGCTTCCT
1 GCTTCCTCAGCTTCCT
*
2208173 -CTTCCTCAGGTTCCT
1 GCTTCCTCAGCTTCCT
2208188 -CTTC
1 GCTTC
2208192 ACTTGGCCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
15 31 0.94
16 2 0.06
ACGTcount: A:0.06, C:0.42, G:0.12, T:0.40
Consensus pattern (16 bp):
GCTTCCTCAGCTTCCT
Found at i:2208186 original size:24 final size:24
Alignment explanation
Indices: 2208135--2208188 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2208125 CTAACTAGTT
* *
2208135 TTCCTCAGCTTCCTCAGCTTCTGC
1 TTCCTCAGCTTCCTCAGCCTCAGC
** *
2208159 TTCCTCAGCTTCCTCTTCCTCAGG
1 TTCCTCAGCTTCCTCAGCCTCAGC
2208183 TTCCTC
1 TTCCTC
2208189 TTCACTTGGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.07, C:0.43, G:0.11, T:0.39
Consensus pattern (24 bp):
TTCCTCAGCTTCCTCAGCCTCAGC
Found at i:2209465 original size:25 final size:23
Alignment explanation
Indices: 2209398--2209467 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 23
2209388 CAGGTAATAC
*
2209398 ATAAATTTATATATTATTAATTAAA
1 ATAAA-TTATATA-TATTTATTAAA
* *
2209423 TTAAATAATAT-TATTTTATTAAAA
1 ATAAATTATATATA-TTTATT-AAA
2209447 ATAATATTATATATATTTATT
1 ATAA-ATTATATATATTTATT
2209468 TTTAAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
22 2 0.06
23 5 0.14
24 11 0.31
25 16 0.44
26 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAAATTATATATATTTATTAAA
Found at i:2214073 original size:34 final size:34
Alignment explanation
Indices: 2214009--2214222 Score: 193
Period size: 34 Copynumber: 6.4 Consensus size: 34
2213999 GTAAAAACCA
** *
2214009 CCATTTAATCAACAATGACAA-CTTATCAAATCTC
1 CCATTTAATCAACAATGGTAAGC-TACCAAATCTC
* * *
2214043 CCATTTAGTCAACAATGTTAAG-TCACCAAATC-A
1 CCATTTAATCAACAATGGTAAGCT-ACCAAATCTC
*
2214076 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
2214110 TCATTTAATCAATAATGGTAAGCTACCAAATTTT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * * * *
2214144 TCATTTAGTCAACAATGGCAAACCACCAAATCAC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * *
2214178 CCATTTAATCAACAATGATAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
*
2214211 CTATTTAATCAA
1 CCATTTAATCAA
2214223 TATTTTTTTT
Statistics
Matches: 149, Mismatches: 27, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
33 39 0.26
34 110 0.74
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.29
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:2219675 original size:27 final size:27
Alignment explanation
Indices: 2219644--2219711 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
2219634 AGCCACCCAT
*
2219644 TGTTTGTCAAAAATAGTGGTTACTTTG
1 TGTTTGTCAAAAATAGTGATTACTTTG
* * *
2219671 TGTTTGTCAAAAATGGTGATTTCTTTT
1 TGTTTGTCAAAAATAGTGATTACTTTG
*
2219698 TATTTGTCAAAAAT
1 TGTTTGTCAAAAAT
2219712 GATGACATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATAGTGATTACTTTG
Found at i:2220034 original size:3 final size:3
Alignment explanation
Indices: 2220026--2220050 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2220016 CAGAATTAAC
2220026 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
2220051 GTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2220058 original size:3 final size:3
Alignment explanation
Indices: 2220052--2220081 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2220042 ATAATAATAG
2220052 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2220082 ATGGTATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2221109 original size:34 final size:34
Alignment explanation
Indices: 2221066--2221216 Score: 293
Period size: 34 Copynumber: 4.4 Consensus size: 34
2221056 CTAACATATT
*
2221066 ACCTAACACACTTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
2221100 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
2221134 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
2221168 ACCTAACACACCTAACATTCTCACCAAATACATC
1 ACCTAACACACCTAACATTCTCACCAAATACATC
2221202 ACCTAACACACCTAA
1 ACCTAACACACCTAA
2221217 TATGCTTCAC
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 116 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.21
Consensus pattern (34 bp):
ACCTAACACACCTAACATTCTCACCAAATACATC
Found at i:2221137 original size:25 final size:25
Alignment explanation
Indices: 2221108--2221209 Score: 80
Period size: 25 Copynumber: 4.4 Consensus size: 25
2221098 TCACCTAACA
2221108 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
*
2221133 CACCTAACA----CACCTAACATTC-T
1 CACCTAACATTCTCACC-AA-ATACAT
* *
2221155 CACC-AA-ATACATCACC-TA-ACA-
1 CACCTAACATTC-TCACCAAATACAT
2221176 CACCTAACATTCTCACCAAATACAT
1 CACCTAACATTCTCACCAAATACAT
2221201 CACCTAACA
1 CACCTAACA
2221210 CACCTAATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 26
0.66 0.06 0.29
Matches are distributed among these distances:
20 1 0.02
21 11 0.19
22 15 0.25
23 7 0.12
24 3 0.05
25 22 0.37
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (25 bp):
CACCTAACATTCTCACCAAATACAT
Found at i:2221396 original size:24 final size:27
Alignment explanation
Indices: 2221348--2221401 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
2221338 AACTACTAAT
*
2221348 AAATTAATATATAATTATTTCTTTA-A
1 AAATTAATATACAATTATTTCTTTATA
2221374 AAATTAATATACAATT-TTT-TTTATA
1 AAATTAATATACAATTATTTCTTTATA
2221399 AAA
1 AAA
2221402 AAGTCTCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 7 0.27
26 15 0.58
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
AAATTAATATACAATTATTTCTTTATA
Found at i:2221917 original size:14 final size:15
Alignment explanation
Indices: 2221892--2221929 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2221882 TAAAAGAAGT
*
2221892 TATAAATATTAAA-A
1 TATAAATTTTAAATA
*
2221906 TTTAAATTTTAAATA
1 TATAAATTTTAAATA
2221921 TATAAATTT
1 TATAAATTT
2221930 AGTGAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAAATTTTAAATA
Found at i:2222357 original size:14 final size:14
Alignment explanation
Indices: 2222338--2222368 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2222328 ATTATATTTT
2222338 TTAAATAGATGAAG
1 TTAAATAGATGAAG
2222352 TTAAATAGATGAAG
1 TTAAATAGATGAAG
2222366 TTA
1 TTA
2222369 GCCATGCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.32
Consensus pattern (14 bp):
TTAAATAGATGAAG
Found at i:2223695 original size:37 final size:37
Alignment explanation
Indices: 2223654--2223726 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
2223644 TAGATTGGTG
* *
2223654 CTGCCACCCAAATTCTAACAATCATAGTTGATTGGCA
1 CTGCCACCCAAATACTAACAATCATAGTGGATTGGCA
*
2223691 CTGCCACCCAAATACTGACAATCATAGTGGATTGGC
1 CTGCCACCCAAATACTAACAATCATAGTGGATTGGC
2223727 CAAGCCACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (37 bp):
CTGCCACCCAAATACTAACAATCATAGTGGATTGGCA
Found at i:2223734 original size:37 final size:37
Alignment explanation
Indices: 2223656--2223741 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
2223646 GATTGGTGCT
* * *
2223656 GCCACCCAAATTCTAACAATCATAGTTGATTGGCACT
1 GCCACCCAAATACTAACAATCATAGTGGATTGGCACA
*
2223693 GCCACCCAAATACTGACAATCATAGTGGATTGGC-CAA
1 GCCACCCAAATACTAACAATCATAGTGGATTGGCAC-A
*
2223730 GCCACCTAAATA
1 GCCACCCAAATA
2223742 TTACTTGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 1 0.02
37 42 0.98
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (37 bp):
GCCACCCAAATACTAACAATCATAGTGGATTGGCACA
Found at i:2229884 original size:2 final size:2
Alignment explanation
Indices: 2229877--2229904 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2229867 CATATAATTC
2229877 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
2229905 CTATTCTTTT
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:2233928 original size:2 final size:2
Alignment explanation
Indices: 2233923--2233966 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2233913 CTTTCTTTTG
2233923 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2233965 AT
1 AT
2233967 TTATGCATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2238734 original size:19 final size:21
Alignment explanation
Indices: 2238695--2238738 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
2238685 TCTAAAAAAA
*
2238695 AAAAGAAATTATAATTTTTTT
1 AAAAGAAATTATAACTTTTTT
2238716 AAAA-AAATTA-AACTTTTTT
1 AAAAGAAATTATAACTTTTTT
2238735 AAAA
1 AAAA
2238739 TATAGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.55
20 6 0.27
21 4 0.18
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAGAAATTATAACTTTTTT
Found at i:2240447 original size:27 final size:28
Alignment explanation
Indices: 2240386--2240456 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 28
2240376 AAACAAGCCT
* *
2240386 CCATATTTGACAAATC-CAAAGTAAACCA
1 CCATTTTTGACAAA-CACAAAATAAACCA
2240414 CCATTTTTGACAAACACAAAAT-AACCA
1 CCATTTTTGACAAACACAAAATAAACCA
2240441 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
2240457 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.45, C:0.25, G:0.06, T:0.24
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAATAAACCA
Found at i:2242373 original size:21 final size:22
Alignment explanation
Indices: 2242335--2242380 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2242325 ATCTGTTGAA
* **
2242335 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
2242356 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
2242378 ACT
1 ACT
2242381 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:2255459 original size:42 final size:42
Alignment explanation
Indices: 2255400--2255517 Score: 209
Period size: 42 Copynumber: 2.8 Consensus size: 42
2255390 TAAAAATGAG
*
2255400 AGGTGTATGCATGTATATAAATGCACACATATTTAGAAGGAC
1 AGGTGTATGCATGTATATAAATGCGCACATATTTAGAAGGAC
*
2255442 AGGTGTATGCATGTATATAAATGCGCACTTATTTAGAAGGAC
1 AGGTGTATGCATGTATATAAATGCGCACATATTTAGAAGGAC
*
2255484 AGGAGTATGCATGTATATAAATGCGCACATATTT
1 AGGTGTATGCATGTATATAAATGCGCACATATTT
2255518 CCTAACGCTG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (42 bp):
AGGTGTATGCATGTATATAAATGCGCACATATTTAGAAGGAC
Found at i:2262179 original size:17 final size:17
Alignment explanation
Indices: 2262157--2262189 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2262147 TACGCAAAAA
2262157 AAAT-AATAATAATAAAT
1 AAATAAATAA-AATAAAT
2262174 AAATAAATAAAATAAA
1 AAATAAATAAAATAAA
2262190 GTCATTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAATAAAATAAAT
Found at i:2266873 original size:17 final size:17
Alignment explanation
Indices: 2266826--2266879 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2266816 TATTAATAAT
2266826 TATAAAAA-A-TAAATA
1 TATAAAAATATTAAATA
* *
2266841 TAATATAAATTATTAATTA
1 T-ATA-AAAATATTAAATA
2266860 TATAAAAATATTAAATA
1 TATAAAAATATTAAATA
2266877 TAT
1 TAT
2266880 TATATTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 17 0.55
18 4 0.13
19 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TATAAAAATATTAAATA
Found at i:2266878 original size:36 final size:35
Alignment explanation
Indices: 2266816--2266883 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
2266806 TATTTTTTTA
2266816 TATTAATAATTATAAAAAATAAATATAATATAAAT
1 TATTAATAATTATAAAAAATAAATATAATATAAAT
* *
2266851 TATTAATTA-TATAAAAATATTAAATATATTATA
1 TATTAATAATTATAAAAA-A-TAAATATAATATA
2266884 TTTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.28
35 9 0.31
36 12 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
TATTAATAATTATAAAAAATAAATATAATATAAAT
Found at i:2266899 original size:22 final size:23
Alignment explanation
Indices: 2266874--2266916 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2266864 AAAATATTAA
* *
2266874 ATATATTATATT-TTTTATTTAG
1 ATATATCATATTATATTATTTAG
2266896 ATATATCATATTATATTATTT
1 ATATATCATATTATATTATTT
2266917 TTTATATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
ATATATCATATTATATTATTTAG
Found at i:2266944 original size:30 final size:30
Alignment explanation
Indices: 2266882--2266944 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
2266872 AAATATATTA
*
2266882 TATTTTTTATTTAGATATATCATATTATAT
1 TATTTTTTATTTAGATATATCATATTAAAT
* * *
2266912 TATTTTTTATATTTG-TATATCTTTTTAAAT
1 TATTTTTTAT-TTAGATATATCATATTAAAT
2266942 TAT
1 TAT
2266945 AATGTTTACC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (30 bp):
TATTTTTTATTTAGATATATCATATTAAAT
Found at i:2267665 original size:2 final size:2
Alignment explanation
Indices: 2267658--2267698 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2267648 TAATTTCATC
2267658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2267699 ACACTTAACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2268175 original size:4 final size:4
Alignment explanation
Indices: 2268166--2268190 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2268156 GCTTACGTAA
2268166 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
2268191 TCCCAACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2268355 original size:21 final size:22
Alignment explanation
Indices: 2268328--2268373 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2268318 TTAATATATG
*
2268328 AAAAAAATATTATTAAAAT-TTT
1 AAAAAATTA-TATTAAAATATTT
*
2268350 AAAAAATTATATTAACATATTT
1 AAAAAATTATATTAAAATATTT
2268372 AA
1 AA
2268374 TTTATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAAATTATATTAAAATATTT
Found at i:2268389 original size:17 final size:18
Alignment explanation
Indices: 2268354--2268392 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
2268344 AATTTTAAAA
2268354 AATTATATTAACATATTT
1 AATTATATTAACATATTT
2268372 AATT-TATTAA-ATATTT
1 AATTATATTAACATATTT
*
2268388 TATTA
1 AATTA
2268393 AAAATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 9 0.47
17 6 0.32
18 4 0.21
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTATATTAACATATTT
Found at i:2268435 original size:18 final size:18
Alignment explanation
Indices: 2268412--2268446 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2268402 TGATAATTTT
2268412 TAAAAT-TATTTTTATTAA
1 TAAAATGTA-TTTTATTAA
2268430 TAAAATGTATTTTATTA
1 TAAAATGTATTTTATTA
2268447 TTTTTGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TAAAATGTATTTTATTAA
Found at i:2268545 original size:17 final size:19
Alignment explanation
Indices: 2268512--2268550 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
2268502 ATATGTTATT
2268512 TAATTAATTTAATTTTAAA
1 TAATTAATTTAATTTTAAA
2268531 TAATT-ATTT-ATTTTAAA
1 TAATTAATTTAATTTTAAA
2268548 TAA
1 TAA
2268551 AAATAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
18 4 0.20
19 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATTAATTTAATTTTAAA
Found at i:2268546 original size:23 final size:23
Alignment explanation
Indices: 2268519--2268576 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
2268509 ATTTAATTAA
*
2268519 TTTAATTTTAAATAAT-TATTTAT
1 TTTAATTTTAAATAATATAATT-T
* **
2268542 TTTAAATAAAAATAATATAATTT
1 TTTAATTTTAAATAATATAATTT
2268565 TTT-ATTTTAAAT
1 TTTAATTTTAAAT
2268577 TTAATATATA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
22 6 0.22
23 17 0.63
24 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAATTTTAAATAATATAATTT
Found at i:2268546 original size:28 final size:29
Alignment explanation
Indices: 2268507--2268594 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 29
2268497 AATAAATATG
* **
2268507 TTATTTA-ATTAATTTAATTTTAA-ATAA
1 TTATTTATTTTAATTTAATAATAATATAA
* *
2268534 TTATTTATTTTAA-ATAAAAATAATATAA
1 TTATTTATTTTAATTTAATAATAATATAA
* *
2268562 TTTTTTATTTTAAATT--TAAT-ATATAA
1 TTATTTATTTTAATTTAATAATAATATAA
2268588 TTATTTA
1 TTATTTA
2268595 AAAATAAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
26 12 0.24
27 16 0.33
28 20 0.41
29 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TTATTTATTTTAATTTAATAATAATATAA
Found at i:2268594 original size:26 final size:28
Alignment explanation
Indices: 2268530--2268594 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
2268520 TTAATTTTAA
2268530 ATAATTATTTATTTTAAATAAAAATAAT
1 ATAATTATTTATTTTAAATAAAAATAAT
* **
2268558 ATAATTTTTTATTTTAAAT-TTAAT-AT
1 ATAATTATTTATTTTAAATAAAAATAAT
2268584 ATAATTATTTA
1 ATAATTATTTA
2268595 AAAATAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 12 0.36
27 3 0.09
28 18 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATAATTATTTATTTTAAATAAAAATAAT
Found at i:2280816 original size:15 final size:15
Alignment explanation
Indices: 2280787--2280825 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2280777 AAATTAATTT
2280787 TTTAATTAATATTAAA
1 TTTAA-TAATATTAAA
*
2280803 TTTAATAATTTTAAA
1 TTTAATAATATTAAA
*
2280818 TATAATAA
1 TTTAATAA
2280826 AAAAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTAATAATATTAAA
Found at i:2280841 original size:12 final size:13
Alignment explanation
Indices: 2280815--2280847 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2280805 TAATAATTTT
2280815 AAATATAATAAAA
1 AAATATAATAAAA
*
2280828 AAATATAAT-TAA
1 AAATATAATAAAA
2280840 AAATATAA
1 AAATATAA
2280848 AAACAGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATATAATAAAA
Found at i:2281453 original size:2 final size:2
Alignment explanation
Indices: 2281446--2281474 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2281436 ATATTATGTC
2281446 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 A
2281475 ACTTGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2281869 original size:6 final size:6
Alignment explanation
Indices: 2281858--2281915 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
2281848 ATTAAAATAC
* * *
2281858 ATATAA ATATAA ATATAAA ATTTAA AAAT-T ATATAA ATAT-A ATATAA
1 ATATAA ATATAA ATAT-AA ATATAA ATATAA ATATAA ATATAA ATATAA
*
2281905 ATCTAA ATATA
1 ATATAA ATATA
2281916 TTAATTATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
5 8 0.20
6 28 0.68
7 5 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:2281883 original size:13 final size:12
Alignment explanation
Indices: 2281858--2281915 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 12
2281848 ATTAAAATAC
2281858 ATATAAATATAA
1 ATATAAATATAA
*
2281870 ATATAAAATTTAA
1 ATAT-AAATATAA
* *
2281883 AAAT-TATATAA
1 ATATAAATATAA
2281894 ATAT-AATATAA
1 ATATAAATATAA
*
2281905 ATCTAAATATA
1 ATATAAATATA
2281916 TTAATTATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 17 0.46
12 10 0.27
13 10 0.27
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
ATATAAATATAA
Found at i:2282580 original size:287 final size:289
Alignment explanation
Indices: 2282280--2282831 Score: 968
Period size: 289 Copynumber: 1.9 Consensus size: 289
2282270 AGTTTTTTTT
2282280 TTTTAAATTTGCAAACACTTTTTTTCCAAAAAATACTAAAATTTTTGTTTATATTTTAATTTTTT
1 TTTTAAATTTGCAAACACTTTTTTTCCAAAAAATACTAAAATTTTTGTTTATATTTTAATTTTTT
* * *
2282345 TCAATTTTCTAACATTATATTTTGTAGACATTTTAATTTTTTTTAC-A-A-TTTTTTTAATAATA
66 TCAATTTTCTAACATTATATTTTGCAAACATTTTAA-TTTTTGTACGATATTTTTTTTAATAATA
2282407 ATGTCAAAAATCTATCAATTTTATATTTTATGAGATATAAATAATTCAATAATTTAATTATTTTA
130 ATGTCAAAAATCTATCAATTTTATATTTTATGAGATATAAATAATTCAATAATTTAATTATTTTA
*
2282472 AAAATAAGAGGTGAAAAAAA-ACCCAACAATCACATAATTTATCAATAAAATATTAAATTCTTAA
195 AAAATAAGAGGTGAAAAAAATA-CCAACAACCACATAATTTATCAATAAAATATTAAATTCTTAA
2282536 ATAAAAAATATTAAAAAAAAGCTTCAAACAC
259 ATAAAAAATATTAAAAAAAAGCTTCAAACAC
*
2282567 TTTTATATTTGCAAACACTTTTTTTCCAAAAAATACTAAAATTTTTGTTTATATTTTAATTTTTT
1 TTTTAAATTTGCAAACACTTTTTTTCCAAAAAATACTAAAATTTTTGTTTATATTTTAATTTTTT
*
2282632 TGAATTTTCTAACATTATATTTTGCAAACATTTTAATTTTTGTACGATATTTTTTTTAATAATAA
66 TCAATTTTCTAACATTATATTTTGCAAACATTTTAATTTTTGTACGATATTTTTTTTAATAATAA
*
2282697 TGTCATAAATCTATCAATTTTATATTTTATGAGATATAAATAATTCAATAATTTAATTATTTTAA
131 TGTCAAAAATCTATCAATTTTATATTTTATGAGATATAAATAATTCAATAATTTAATTATTTTAA
* * *
2282762 AAATAAGAGGTGAAAAAAATACCAACAACCATATAATTTATCAGTAAAATATTAAATTTTTAAAT
196 AAATAAGAGGTGAAAAAAATACCAACAACCACATAATTTATCAATAAAATATTAAATTCTTAAAT
2282827 AAAAA
261 AAAAA
2282832 GTAAAAAGAT
Statistics
Matches: 251, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
286 8 0.03
287 98 0.39
288 1 0.00
289 143 0.57
290 1 0.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.44
Consensus pattern (289 bp):
TTTTAAATTTGCAAACACTTTTTTTCCAAAAAATACTAAAATTTTTGTTTATATTTTAATTTTTT
TCAATTTTCTAACATTATATTTTGCAAACATTTTAATTTTTGTACGATATTTTTTTTAATAATAA
TGTCAAAAATCTATCAATTTTATATTTTATGAGATATAAATAATTCAATAATTTAATTATTTTAA
AAATAAGAGGTGAAAAAAATACCAACAACCACATAATTTATCAATAAAATATTAAATTCTTAAAT
AAAAAATATTAAAAAAAAGCTTCAAACAC
Found at i:2283144 original size:3 final size:3
Alignment explanation
Indices: 2283136--2283161 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2283126 ATCCTAGGAC
2283136 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2283162 TTCACCACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2284283 original size:1 final size:1
Alignment explanation
Indices: 2284277--2284303 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2284267 AGCTCTGATC
2284277 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
2284304 GCTTGTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2284747 original size:22 final size:21
Alignment explanation
Indices: 2284706--2284747 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2284696 TATTTTTATT
2284706 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
2284727 TAAATATT-ATTATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
2284747 T
1 T
2284748 TTTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 14 0.70
22 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:2292289 original size:27 final size:27
Alignment explanation
Indices: 2292216--2292300 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
2292206 ATTAAAATTT
* * *
2292216 AATATAAAATATAAA-AATTATAATATA
1 AATATATAATATAAATTATTATATTA-A
* *
2292243 AATATGATAAAAATATATTATTATATTAA
1 AATAT-AT-AATATAAATTATTATATTAA
* *
2292272 AATATATAATATAAATTAATATGTTAA
1 AATATATAATATAAATTATTATATTAA
2292299 AA
1 AA
2292301 GTTATTTAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
27 23 0.50
28 3 0.07
29 12 0.26
30 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
AATATATAATATAAATTATTATATTAA
Found at i:2308517 original size:2 final size:2
Alignment explanation
Indices: 2308510--2308548 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2308500 TGTTTCTGGA
* * *
2308510 AT AT AT AT GT AT AC AT AC AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2308549 AGTTTAGGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2311719 original size:2 final size:2
Alignment explanation
Indices: 2311712--2311772 Score: 51
Period size: 2 Copynumber: 32.0 Consensus size: 2
2311702 TTGAGCAATA
* *
2311712 AT AT AT AT AT AT AT AT AT AT AT -T GT -T CAT A- AGC A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A-T AT AT AT AT
2311751 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2311773 TTGGTTATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
1 5 0.10
2 45 0.87
3 2 0.04
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2313460 original size:14 final size:14
Alignment explanation
Indices: 2313441--2313470 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2313431 GATATTAACC
*
2313441 TTTTTTTAATAAAT
1 TTTTTTTAAAAAAT
2313455 TTTTTTTAAAAAAT
1 TTTTTTTAAAAAAT
2313469 TT
1 TT
2313471 AAACTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTTAAAAAAT
Found at i:2313638 original size:21 final size:21
Alignment explanation
Indices: 2313601--2313641 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2313591 GCCCACAGGT
*
2313601 AAAATAAATAAATAAATTATA
1 AAAATAAATAAAAAAATTATA
2313622 AAAATAAA-AATAAAAATTAT
1 AAAATAAATAA-AAAAATTAT
2313642 CCTCAATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAATAAATAAAAAAATTATA
Found at i:2325259 original size:14 final size:13
Alignment explanation
Indices: 2325237--2325279 Score: 63
Period size: 14 Copynumber: 3.4 Consensus size: 13
2325227 AAAATAAATT
2325237 TAAATTTAAATAA
1 TAAATTTAAATAA
2325250 TAATATTTAAATAA
1 TAA-ATTTAAATAA
2325264 TAAA-TT-AATAA
1 TAAATTTAAATAA
2325275 TAAAT
1 TAAAT
2325280 AGATTTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.32
12 2 0.07
13 4 0.14
14 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATTTAAATAA
Found at i:2325963 original size:2 final size:2
Alignment explanation
Indices: 2325956--2325985 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2325946 GGGGCAAAGC
2325956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2325986 CTTCGGGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2326997 original size:17 final size:18
Alignment explanation
Indices: 2326975--2327010 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2326965 GTGCTCTTAC
2326975 ATTTTTAATATAT-TTTA
1 ATTTTTAATATATCTTTA
*
2326992 ATTTTTAATTTATCTTTA
1 ATTTTTAATATATCTTTA
2327010 A
1 A
2327011 CTTAATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTAATATATCTTTA
Found at i:2328026 original size:5 final size:5
Alignment explanation
Indices: 2328009--2328038 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2327999 ATGTTACTAC
*
2328009 ATTTT ATTCT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
2328039 CACAAACATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:2328519 original size:22 final size:23
Alignment explanation
Indices: 2328494--2328545 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2328484 TAAAGTTATT
2328494 AAATAATCAAATA-TTAAATATA
1 AAATAATCAAATATTTAAATATA
****
2328516 AAATAATTTTGTATTTAAATATA
1 AAATAATCAAATATTTAAATATA
2328539 AAATAAT
1 AAATAAT
2328546 TTTGTATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATAATCAAATATTTAAATATA
Found at i:2328537 original size:23 final size:23
Alignment explanation
Indices: 2328507--2328553 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2328497 TAATCAAATA
2328507 TTAAATATAAAATAATTTTGTAT
1 TTAAATATAAAATAATTTTGTAT
2328530 TTAAATATAAAATAATTTTGTAT
1 TTAAATATAAAATAATTTTGTAT
2328553 T
1 T
2328554 AAAAATACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TTAAATATAAAATAATTTTGTAT
Found at i:2329261 original size:19 final size:19
Alignment explanation
Indices: 2329229--2329265 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2329219 TTAAAAAGTT
2329229 ATTATATTTTTTAATTTTA
1 ATTATATTTTTTAATTTTA
2329248 ATTAT-TTTTATTAATTTT
1 ATTATATTTT-TTAATTTT
2329266 TAATACAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTATATTTTTTAATTTTA
Found at i:2330865 original size:2 final size:2
Alignment explanation
Indices: 2330858--2330887 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2330848 GACTTGGTAA
2330858 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2330888 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2330892 original size:2 final size:2
Alignment explanation
Indices: 2330887--2330922 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2330877 TCTCTCTCTC
2330887 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
2330923 AATCATTCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2332087 original size:35 final size:35
Alignment explanation
Indices: 2332041--2332107 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
2332031 CAACTTGTAC
*
2332041 ATATATATATATATAACGTATATTGCTACTTTATT
1 ATATACATATATATAACGTATATTGCTACTTTATT
*
2332076 ATATACATATATATAATGTATATTGCTACTTT
1 ATATACATATATATAACGTATATTGCTACTTT
2332108 GCTATTTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (35 bp):
ATATACATATATATAACGTATATTGCTACTTTATT
Found at i:2336257 original size:17 final size:18
Alignment explanation
Indices: 2336219--2336256 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2336209 TTTTTTTTGG
2336219 TTTTAGTTTTTATAATAT
1 TTTTAGTTTTTATAATAT
*
2336237 TTTTA-TTTTTTTAAT-T
1 TTTTAGTTTTTATAATAT
2336253 TTTT
1 TTTT
2336257 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 9 0.47
18 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTAGTTTTTATAATAT
Found at i:2337360 original size:18 final size:19
Alignment explanation
Indices: 2337337--2337372 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2337327 ATATAATACT
*
2337337 TTTAATATACTT-TAAATA
1 TTTAATAAACTTCTAAATA
2337355 TTTAATAAACTTCTAAAT
1 TTTAATAAACTTCTAAAT
2337373 CCAAATCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (19 bp):
TTTAATAAACTTCTAAATA
Found at i:2337648 original size:24 final size:24
Alignment explanation
Indices: 2337620--2337673 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
2337610 AAAAAAAAAT
2337620 TATATACAAATAA-T-AATTGCATAA
1 TATATACAAA-AATTAAATTG-ATAA
**
2337644 TATATGTAAAAATTAAATTGATAA
1 TATATACAAAAATTAAATTGATAA
2337668 TATATA
1 TATATA
2337674 GACTAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 2 0.08
24 18 0.72
25 5 0.20
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (24 bp):
TATATACAAAAATTAAATTGATAA
Found at i:2338711 original size:18 final size:20
Alignment explanation
Indices: 2338680--2338717 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
2338670 TATTTTTAAA
2338680 AATATATTTGATAATTTTTT
1 AATATATTTGATAATTTTTT
2338700 AATATA-TT-ATAATTTTTT
1 AATATATTTGATAATTTTTT
2338718 TAAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
AATATATTTGATAATTTTTT
Found at i:2338728 original size:20 final size:18
Alignment explanation
Indices: 2338690--2338729 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
2338680 AATATATTTG
*
2338690 ATAATTTTTTAATATATT
1 ATAATTTTTTAAAATATT
2338708 ATAATTTTTTTAAAATAATT
1 ATAA-TTTTTTAAAAT-ATT
2338728 AT
1 AT
2338730 TTTTAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 10 0.53
20 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAATTTTTTAAAATATT
Found at i:2343446 original size:23 final size:23
Alignment explanation
Indices: 2343420--2343476 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
2343410 TAAAATTTTT
2343420 AATTAATAATTT-AATATTAAAAA
1 AATTAATAATTTAAATA-TAAAAA
* *
2343443 AATTTA-AATGTTAAATATATAAA
1 AATTAATAAT-TTAAATATAAAAA
2343466 AA-TAATAATTT
1 AATTAATAATTT
2343477 TAATTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 7 0.25
23 17 0.61
24 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
AATTAATAATTTAAATATAAAAA
Found at i:2349185 original size:20 final size:20
Alignment explanation
Indices: 2349160--2349197 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2349150 AAGACACCCA
*
2349160 AGATTGAAAAATCAAACATC
1 AGATTGAAAAAGCAAACATC
2349180 AGATTGAAAAAGCAAACA
1 AGATTGAAAAAGCAAACA
2349198 ACCCCACAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (20 bp):
AGATTGAAAAAGCAAACATC
Found at i:2360564 original size:20 final size:20
Alignment explanation
Indices: 2360514--2360584 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
2360504 GTATTATATT
*
2360514 TTTTTATA-ATTATATTTAAA
1 TTTTTATATATT-TATATAAA
* * *
2360534 GTGTTACATATTTATATAAA
1 TTTTTATATATTTATATAAA
2360554 TTTTTATATATATTA-AT-AA
1 TTTTTATATAT-TTATATAAA
2360573 TTTTTATTATAT
1 TTTTTA-TATAT
2360585 AAATTTTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 8 0.20
20 27 0.66
21 6 0.15
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTTTATATATTTATATAAA
Found at i:2360630 original size:5 final size:5
Alignment explanation
Indices: 2360602--2360685 Score: 54
Period size: 5 Copynumber: 17.2 Consensus size: 5
2360592 AATACGTTTA
* *
2360602 TATAT TCATAT TATTT TAATAT TATAT TATAT T-T-T T-TAT TATAT T-TTT
1 TATAT T-ATAT TATAT T-ATAT TATAT TATAT TATAT TATAT TATAT TATAT
* *
2360650 TA-AT TATTT TATAT TAT-T ATATAAT TAAAT TATAT T
1 TATAT TATAT TATAT TATAT -TAT-AT TATAT TATAT T
2360686 TAAAATTATT
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
3 3 0.05
4 10 0.16
5 37 0.60
6 11 0.18
7 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (5 bp):
TATAT
Found at i:2360655 original size:13 final size:12
Alignment explanation
Indices: 2360626--2360671 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
2360616 TTTAATATTA
2360626 TATTATATTTTT
1 TATTATATTTTT
2360638 TATTATATTTTT
1 TATTATATTTTT
2360650 TAATTAT-TTTATAT
1 T-ATTATATTT-T-T
2360664 TATTATAT
1 TATTATAT
2360672 AATTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 16 0.53
13 11 0.37
14 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTATATTTTT
Found at i:2360674 original size:21 final size:21
Alignment explanation
Indices: 2360611--2360685 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
2360601 ATATATTCAT
2360611 ATTATTTTA-A-TATTATATTA
1 ATTATTTTATATTATTATA-TA
* *
2360631 TATT-TTTTAT-TATATTTTTTA
1 -ATTATTTTATAT-TATTATATA
2360652 ATTATTTTATATTATTATATA
1 ATTATTTTATATTATTATATA
**
2360673 ATTAAATTATATT
1 ATTATTTTATATT
2360686 TAAAATTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 8 0.19
21 29 0.67
22 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATTTTATATTATTATATA
Found at i:2360680 original size:26 final size:28
Alignment explanation
Indices: 2360637--2360696 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
2360627 ATTATATTTT
** * *
2360637 TTATTATATTTTTTAATTAT-TTT-ATA
1 TTATTATATAATTAAATTATATTTAAAA
2360663 TTATTATATAATTAAATTATATTTAAAA
1 TTATTATATAATTAAATTATATTTAAAA
2360691 TTATTA
1 TTATTA
2360697 AGTCTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 17 0.61
27 3 0.11
28 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
TTATTATATAATTAAATTATATTTAAAA
Found at i:2361034 original size:97 final size:99
Alignment explanation
Indices: 2360875--2361080 Score: 231
Period size: 97 Copynumber: 2.1 Consensus size: 99
2360865 AAACACTAGG
* * * * * * *
2360875 TTAAAAAAATTTAAATTAAAAATTAAATTGATGTTTTATTGTTGAATTAATTGATTTAATTAATT
1 TTAAAAAATTTTAAATTAAAAATTAAATCGATGTTTTATTATTAAATCAATTAATTCAATTAATT
* *
2360940 GT-TTCTATGGTT-CAATTAAAATAA-TTTAAATA
66 GTATT-GATGATTACAATTAAAATAATTTTAAATA
* * *
2360972 TTAAAAAATTTTAGATTAAAAATTAAATCGAT-TATTTCTTATTAAATCAATTAATTCGATTAAT
1 TTAAAAAATTTTAAATTAAAAATTAAATCGATGT-TTTATTATTAAATCAATTAATTCAATTAAT
* *
2361036 TGTATTGATGATTACATTTGAAATAATTTTTAAATA
65 TGTATTGATGATTACAATTAAAATAA-TTTTAAATA
2361072 TTAAAAAAT
1 TTAAAAAAT
2361081 ATTTCAAGTG
Statistics
Matches: 90, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
96 1 0.01
97 60 0.67
98 12 0.13
100 17 0.19
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (99 bp):
TTAAAAAATTTTAAATTAAAAATTAAATCGATGTTTTATTATTAAATCAATTAATTCAATTAATT
GTATTGATGATTACAATTAAAATAATTTTAAATA
Found at i:2361525 original size:15 final size:16
Alignment explanation
Indices: 2361502--2361534 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2361492 TATCAATTAA
*
2361502 AATTTTAAAATAAAAT
1 AATTTAAAAATAAAAT
2361518 AATTTAAAAATAAAAT
1 AATTTAAAAATAAAAT
2361534 A
1 A
2361535 TGTGATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTTAAAAATAAAAT
Found at i:2362856 original size:18 final size:16
Alignment explanation
Indices: 2362823--2362854 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2362813 TTACATTTAA
2362823 ACTCTTTATATTTTTT
1 ACTCTTTATATTTTTT
2362839 ACTCTTTATATTTTTT
1 ACTCTTTATATTTTTT
2362855 TTTATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (16 bp):
ACTCTTTATATTTTTT
Found at i:2364237 original size:19 final size:20
Alignment explanation
Indices: 2364213--2364253 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
2364203 ATATGTCATG
*
2364213 ATATTTATTAAT-TAAAATA
1 ATATTTATAAATATAAAATA
*
2364232 ATATTTATAAATATTAAATA
1 ATATTTATAAATATAAAATA
2364252 AT
1 AT
2364254 TAAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATTTATAAATATAAAATA
Found at i:2364477 original size:23 final size:23
Alignment explanation
Indices: 2364441--2364486 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2364431 AATTACCATT
2364441 AATAAATATATTTA-AATATTATA
1 AATAAATATATTTATAAT-TTATA
* *
2364464 AATAAATTTTTTTATAATTTATA
1 AATAAATATATTTATAATTTATA
2364487 TTTAATACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATAAATATATTTATAATTTATA
Found at i:2365791 original size:15 final size:16
Alignment explanation
Indices: 2365765--2365797 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2365755 ATATTTATAT
2365765 AAATTTTGATATAATA
1 AAATTTTGATATAATA
*
2365781 AAATTTT-ATATTATA
1 AAATTTTGATATAATA
2365796 AA
1 AA
2365798 TATTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AAATTTTGATATAATA
Found at i:2366099 original size:14 final size:15
Alignment explanation
Indices: 2366077--2366105 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2366067 AACTCAAACT
2366077 ATTATAATCAATTAA
1 ATTATAATCAATTAA
2366092 ATTA-AATCAATTAA
1 ATTATAATCAATTAA
2366106 TTTTAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTATAATCAATTAA
Found at i:2368616 original size:26 final size:26
Alignment explanation
Indices: 2368533--2368617 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
2368523 TAAATTTAAA
* * *
2368533 ATTTAATTTAATTAAATTATATAATT
1 ATTTAATATAATTTAATAATATAATT
** * * * *
2368559 ATTTTTTAAAAAATTAATAATTTTAAAT
1 ATTTAAT-ATAATTTAATAA-TATAATT
2368587 -TTTAATATAATTTAATAATATAATT
1 ATTTAATATAATTTAATAATATAATT
2368612 ATTTAA
1 ATTTAA
2368618 AAATAATATT
Statistics
Matches: 41, Mismatches: 15, Indels: 6
0.66 0.24 0.10
Matches are distributed among these distances:
25 5 0.12
26 20 0.49
27 11 0.27
28 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTAATATAATTTAATAATATAATT
Found at i:2368627 original size:13 final size:15
Alignment explanation
Indices: 2368596--2368635 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
2368586 TTTTAATATA
2368596 ATTTAATAATATAATT
1 ATTTAATAA-ATAATT
2368612 ATTTAA-AAATAA-T
1 ATTTAATAAATAATT
2368625 ATTTAATAAAT
1 ATTTAATAAAT
2368636 TTCAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.30
14 8 0.35
15 2 0.09
16 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTAATAAATAATT
Found at i:2368923 original size:34 final size:33
Alignment explanation
Indices: 2368836--2368927 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 33
2368826 TATTAATAAA
* * *
2368836 ATAAT-TAAAATATTTTTATATTTTAAAATTTAT
1 ATAATATAAAATA-TTTTAAATATTAAAATTTAC
** *
2368869 ATAATATAAGTTA-TTAAAATATTAAAATTTAC
1 ATAATATAAAATATTTTAAATATTAAAATTTAC
2368901 ATAAATATAAAATATTTTAAATATTAA
1 AT-AATATAAAATATTTTAAATATTAA
2368928 TATAATATAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
32 17 0.36
33 14 0.30
34 16 0.34
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (33 bp):
ATAATATAAAATATTTTAAATATTAAAATTTAC
Found at i:2368972 original size:9 final size:9
Alignment explanation
Indices: 2368883--2368973 Score: 62
Period size: 9 Copynumber: 10.1 Consensus size: 9
2368873 TATAAGTTAT
2368883 TAAAATAT-
1 TAAAATATA
*
2368891 TAAAATTTA
1 TAAAATATA
* *
2368900 CATAA-ATA
1 TAAAATATA
*
2368908 TAAAATATT
1 TAAAATATA
*
2368917 TTAAATATTAA
1 TAAAATA-T-A
*
2368928 TATAATATAA
1 TAAAATAT-A
2368938 TAAAATATA
1 TAAAATATA
*
2368947 AAAAATA-A
1 TAAAATATA
2368955 TAAAATATA
1 TAAAATATA
*
2368964 TAAATTATA
1 TAAAATATA
2368973 T
1 T
2368974 TTAAAAATTA
Statistics
Matches: 63, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
8 19 0.30
9 28 0.44
10 11 0.17
11 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (9 bp):
TAAAATATA
Found at i:2369433 original size:21 final size:21
Alignment explanation
Indices: 2369383--2369440 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
2369373 ATATTAATAC
*
2369383 ATTATAAATATAAT-AATTTAAT
1 ATTA-AAATA-AATAAATTTAAA
* *
2369405 TTTTAAATAAATAAATTTAAA
1 ATTAAAATAAATAAATTTAAA
2369426 ATTAAAATTAAATAA
1 ATTAAAA-TAAATAA
2369441 TTATGATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 3 0.10
21 17 0.59
22 9 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAAAATAAATAAATTTAAA
Found at i:2370224 original size:21 final size:21
Alignment explanation
Indices: 2370195--2370239 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2370185 ATGTATTATT
* *
2370195 TATATATTTT-ATATTTATTAA
1 TATAAATTTTAATATATA-TAA
2370216 TATAAATTTTAATATATATAA
1 TATAAATTTTAATATATATAA
2370237 TAT
1 TAT
2370240 TATATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATAAATTTTAATATATATAA
Found at i:2370276 original size:31 final size:32
Alignment explanation
Indices: 2370194--2370278 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
2370184 TATGTATTAT
*
2370194 TTATATATTTTATATTTATTAATATAAATTTTA
1 TTATATA-TTTATATATATTAATATAAATTTTA
* *
2370227 ATATATATAATATTATATATTAA-A-AATATTTTA
1 TTATATAT-TTA-TATATATTAATATAA-ATTTTA
2370260 TTATATATTTATATATATT
1 TTATATATTTATATATATT
2370279 TTATATTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
31 8 0.18
32 5 0.11
33 22 0.50
34 9 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TTATATATTTATATATATTAATATAAATTTTA
Found at i:2370330 original size:17 final size:18
Alignment explanation
Indices: 2370268--2370322 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
2370258 TATTATATAT
*
2370268 TTATA-TATATTTTAT-A
1 TTATATTATATTTAATAA
*
2370284 TTAT-TTTTATTTTAATAA
1 TTATATTATA-TTTAATAA
2370302 TTATATTATATTTAA-AA
1 TTATATTATATTTAATAA
2370319 TTAT
1 TTAT
2370323 TTAATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 7 0.22
17 11 0.34
18 10 0.31
19 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTATATTTAATAA
Found at i:2370543 original size:28 final size:26
Alignment explanation
Indices: 2370511--2370562 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
2370501 TTGGAGTGGC
2370511 TGTATTAAAATTATATAATTTTTATTTA
1 TGTATT-AAATT-TATAATTTTTATTTA
* *
2370539 TGTATTATATTTATATTTTTTATT
1 TGTATTAAATTTATAATTTTTATT
2370563 ATTTATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 4 0.18
28 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (26 bp):
TGTATTAAATTTATAATTTTTATTTA
Found at i:2370576 original size:22 final size:22
Alignment explanation
Indices: 2370520--2370572 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
2370510 CTGTATTAAA
*
2370520 ATTATATAATTTTTATTTATGT
1 ATTATATAATATTTATTTATGT
*
2370542 ATTATATTTATATTT-TTTAT-T
1 ATTATA-TAATATTTATTTATGT
2370563 ATTTATATAA
1 A-TTATATAA
2370573 ATATAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 4 0.15
22 16 0.62
23 6 0.23
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTATATAATATTTATTTATGT
Found at i:2370618 original size:7 final size:7
Alignment explanation
Indices: 2370606--2370660 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
2370596 TAAATTATAA
2370606 AAATATT
1 AAATATT
*
2370613 ATATA-T
1 AAATATT
*
2370619 GAATATT
1 AAATATT
*
2370626 ATATATT
1 AAATATT
2370633 AAATATT
1 AAATATT
2370640 AAATATT
1 AAATATT
*
2370647 AATTATT
1 AAATATT
*
2370654 AATTATT
1 AAATATT
2370661 TAACTTATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
6 4 0.10
7 36 0.90
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (7 bp):
AAATATT
Found at i:2370623 original size:13 final size:13
Alignment explanation
Indices: 2370601--2370645 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
2370591 TTTTTTAAAT
*
2370601 TATAAAAATATTA
1 TATATAAATATTA
*
2370614 TATATGAATATTA
1 TATATAAATATTA
2370627 TATATTAAATATTA
1 TATA-TAAATATTA
*
2370641 AATAT
1 TATAT
2370646 TAATTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
TATATAAATATTA
Found at i:2370655 original size:14 final size:14
Alignment explanation
Indices: 2370609--2370689 Score: 67
Period size: 14 Copynumber: 5.7 Consensus size: 14
2370599 ATTATAAAAA
* *
2370609 TATTATATATGAA-
1 TATTAAATATTAAT
* *
2370622 TATTATATATTAAA
1 TATTAAATATTAAT
2370636 TATTAAATATTAAT
1 TATTAAATATTAAT
*
2370650 TATTAATTATTTAACT
1 TATTAAATA-TTAA-T
*
2370666 TATTATATCA-TAAT
1 TATTAAAT-ATTAAT
2370680 TATTAAATAT
1 TATTAAATAT
2370690 ATCATGTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
13 13 0.23
14 28 0.50
15 7 0.12
16 7 0.12
17 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (14 bp):
TATTAAATATTAAT
Found at i:2370712 original size:13 final size:14
Alignment explanation
Indices: 2370668--2370723 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
2370658 ATTTAACTTA
*
2370668 TTATATCATA-ATTA
1 TTATAT-ATATATTT
* *
2370682 TTAAATATATCATGT
1 TTATATATAT-ATTT
2370697 TTATAT-TATATTT
1 TTATATATATATTT
2370710 TTATATATATATTT
1 TTATATATATATTT
2370724 AAAATAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 12 0.35
14 15 0.44
15 7 0.21
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (14 bp):
TTATATATATATTT
Found at i:2372576 original size:22 final size:20
Alignment explanation
Indices: 2372548--2372595 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
2372538 TTAATTATAT
* *
2372548 ATATTTAATATTATCTCTATTA
1 ATATTTAATAATAT-T-TAATA
2372570 ATATTTAATAATATTTAATA
1 ATATTTAATAATATTTAATA
2372590 ATATTT
1 ATATTT
2372596 TTCTTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 1 0.04
22 13 0.54
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTTAATAATATTTAATA
Found at i:2372583 original size:10 final size:10
Alignment explanation
Indices: 2372548--2372595 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
2372538 TTAATTATAT
2372548 ATATTTAATA
1 ATATTTAATA
* *
2372558 TTATCTCTATTA
1 ATAT-T-TAATA
2372570 ATATTTAATA
1 ATATTTAATA
2372580 ATATTTAATA
1 ATATTTAATA
2372590 ATATTT
1 ATATTT
2372596 TTCTTATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 23 0.72
11 2 0.06
12 7 0.22
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (10 bp):
ATATTTAATA
Found at i:2373128 original size:26 final size:25
Alignment explanation
Indices: 2373074--2373129 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
2373064 GATGCATTTA
2373074 AAATTAAAATCAACAAAAATGAAAAT
1 AAATTAAAAT-AACAAAAATGAAAAT
*
2373100 AAATTAAAAT-ACAAACATTGAAAACT
1 AAATTAAAATAACAAA-AATGAAAA-T
2373126 AAAT
1 AAAT
2373130 GAACCTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 5 0.19
25 7 0.26
26 15 0.56
ACGTcount: A:0.66, C:0.09, G:0.04, T:0.21
Consensus pattern (25 bp):
AAATTAAAATAACAAAAATGAAAAT
Found at i:2377015 original size:21 final size:22
Alignment explanation
Indices: 2376989--2377037 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
2376979 TTTACTTATT
2376989 TTATTAAAAATTAAAA-TTTAA
1 TTATTAAAAATTAAAATTTTAA
2377010 TTATT-AAAATTAAAATTTTAA
1 TTATTAAAAATTAAAATTTTAA
2377031 TATATTA
1 T-TATTA
2377038 TTAATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.40
21 11 0.44
22 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATTAAAAATTAAAATTTTAA
Found at i:2377818 original size:13 final size:13
Alignment explanation
Indices: 2377802--2377841 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
2377792 TGATTAAAAA
2377802 TTATTTAATTATT
1 TTATTTAATTATT
2377815 TTATTTAAATT-TT
1 TTATTT-AATTATT
2377828 TTATTTAATATATT
1 TTATTTAAT-TATT
2377842 ATGTTTACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.12
13 15 0.62
14 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTAATTATT
Found at i:2378831 original size:22 final size:20
Alignment explanation
Indices: 2378800--2378859 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 20
2378790 TATATTATAT
2378800 AAATAAAATATAAAAATAATTA
1 AAATAAAATAT-AAAA-AATTA
*
2378822 AAATATAATATAAAAAATTA
1 AAATAAAATATAAAAAATTA
*
2378842 AAA-AAGATA-AAAAAATTA
1 AAATAAAATATAAAAAATTA
2378860 TGAATATGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.26
19 4 0.11
20 8 0.23
21 4 0.11
22 10 0.29
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AAATAAAATATAAAAAATTA
Found at i:2378842 original size:20 final size:22
Alignment explanation
Indices: 2378800--2378857 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 22
2378790 TATATTATAT
2378800 AAATAAAATATAAAAATAATTA
1 AAATAAAATATAAAAATAATTA
*
2378822 AAATATAATAT-AAAA-AATTA
1 AAATAAAATATAAAAATAATTA
* *
2378842 AAA-AAGATAAAAAAAT
1 AAATAAAATATAAAAAT
2378858 TATGAATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 4 0.13
20 12 0.40
21 4 0.13
22 10 0.33
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AAATAAAATATAAAAATAATTA
Found at i:2381971 original size:21 final size:21
Alignment explanation
Indices: 2381926--2381978 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2381916 AATATATGAT
* *
2381926 AAATATAAT-AATTTAAATTTT
1 AAATA-AATAAATTTAAAATTA
2381947 AAATAAATAAATTTAAAATTA
1 AAATAAATAAATTTAAAATTA
2381968 AAATTAAATAA
1 AAA-TAAATAA
2381979 TAATGATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 18 0.64
22 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAAATAAATTTAAAATTA
Found at i:2382701 original size:8 final size:8
Alignment explanation
Indices: 2382684--2382772 Score: 51
Period size: 8 Copynumber: 11.1 Consensus size: 8
2382674 ATTTACGTAC
2382684 TATTTATA
1 TATTTATA
*
2382692 TATTTTTA
1 TATTTATA
2382700 TATTTAT-
1 TATTTATA
*
2382707 TA-ATATA
1 TATTTATA
*
2382714 AATTT-TAA
1 TATTTAT-A
*
2382722 TATATATA
1 TATTTATA
*
2382730 AATATTATA
1 TAT-TTATA
2382739 TTATTTCATA
1 -TATTT-ATA
* *
2382749 -ATTAAAA
1 TATTTATA
2382756 TATTTATA
1 TATTTATA
2382764 TATTTATA
1 TATTTATA
2382772 T
1 T
2382773 TATATTTAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
6 3 0.05
7 6 0.10
8 38 0.64
9 7 0.12
10 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (8 bp):
TATTTATA
Found at i:2382718 original size:22 final size:22
Alignment explanation
Indices: 2382688--2382734 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2382678 ACGTACTATT
* * * *
2382688 TATATATTTTTATATTTATTAA
1 TATAAATTTTAATATATATAAA
2382710 TATAAATTTTAATATATATAAA
1 TATAAATTTTAATATATATAAA
2382732 TAT
1 TAT
2382735 TATATTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATAAATTTTAATATATATAAA
Found at i:2384123 original size:22 final size:22
Alignment explanation
Indices: 2384091--2384141 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2384081 TATTGAAAAG
*
2384091 TATAAAAATTTAAATCTAAATT
1 TATAAAAATTTAAAACTAAATT
* *
2384113 TATAAATATTTAAAAGTAAATT
1 TATAAAAATTTAAAACTAAATT
*
2384135 TAGAAAA
1 TATAAAA
2384142 TGATCACAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
TATAAAAATTTAAAACTAAATT
Found at i:2384230 original size:20 final size:21
Alignment explanation
Indices: 2384205--2384248 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
2384195 TAAACTCTAA
2384205 TTTAAAAAAAAATTT-AAAAT
1 TTTAAAAAAAAATTTAAAAAT
* *
2384225 TTT-AAATACAATTTAAAAAT
1 TTTAAAAAAAAATTTAAAAAT
2384245 TTTA
1 TTTA
2384249 CATTTAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTAAAAAAAAATTTAAAAAT
Found at i:2385995 original size:2 final size:2
Alignment explanation
Indices: 2385988--2386022 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2385978 ATAATAATAA
2385988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2386023 AAAAAGGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2389666 original size:2 final size:2
Alignment explanation
Indices: 2389659--2389685 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2389649 AGAGTTTCAA
2389659 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2389686 GATTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2389947 original size:27 final size:30
Alignment explanation
Indices: 2389917--2389977 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 30
2389907 AATTAAAAAA
2389917 TTATTATATGTAT-T-ATTTATAAATTT-T
1 TTATTATATGTATGTAATTTATAAATTTAT
* *
2389944 TTATTATATTTATGTAATTTATAATTTTAT
1 TTATTATATGTATGTAATTTATAAATTTAT
2389974 TTAT
1 TTAT
2389978 AAAATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 12 0.41
28 1 0.03
29 11 0.38
30 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (30 bp):
TTATTATATGTATGTAATTTATAAATTTAT
Found at i:2389974 original size:21 final size:22
Alignment explanation
Indices: 2389929--2389993 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 22
2389919 ATTATATGTA
* *
2389929 TTATTTAT-AAATTT-TTTATT
1 TTATTTATAAAATTTAATAATT
* **
2389949 ATATTTATGTAATTT-ATAATT
1 TTATTTATAAAATTTAATAATT
2389970 TTATTTATAAAATTTAATAATT
1 TTATTTATAAAATTTAATAATT
2389992 TT
1 TT
2389994 TCTCTTTATA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 7 0.19
21 21 0.58
22 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATTTATAAAATTTAATAATT
Found at i:2389990 original size:29 final size:29
Alignment explanation
Indices: 2389931--2389992 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
2389921 TATATGTATT
* * *
2389931 ATTTATAAATTTTTTATTATATTTATGTA
1 ATTTATAAATTTTTTATAAAATTTATATA
*
2389960 ATTTATAATTTTATTTATAAAATTTA-ATA
1 ATTTATAAATTT-TTTATAAAATTTATATA
2389989 ATTT
1 ATTT
2389993 TTCTCTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
ATTTATAAATTTTTTATAAAATTTATATA
Found at i:2390576 original size:15 final size:15
Alignment explanation
Indices: 2390553--2390584 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2390543 TATATGTTTT
*
2390553 TACCTTTATAATTTA
1 TACCCTTATAATTTA
2390568 TACCCTTATAATTTA
1 TACCCTTATAATTTA
2390583 TA
1 TA
2390585 TATCTAGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (15 bp):
TACCCTTATAATTTA
Found at i:2396282 original size:3 final size:3
Alignment explanation
Indices: 2396274--2396305 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2396264 ATTTGGGTGA
2396274 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2396306 AAAATGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:2407193 original size:5 final size:5
Alignment explanation
Indices: 2407171--2407287 Score: 59
Period size: 5 Copynumber: 24.0 Consensus size: 5
2407161 TCACGCCAAA
* * * *
2407171 ATATT ATATT -TA-T ATATT TTATT ATATT ATAATT ATATTT AAAAT ATTTT
1 ATATT ATATT ATATT ATATT ATATT ATATT AT-ATT ATA-TT ATATT ATATT
* * ** * *
2407221 ATATT -TATAT ATATT TTAAT ACGTT A-ATA AT-TT A-ATT ATATT ATATA
1 ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
2407268 ATA-T ATATT CATATT ATATT
1 ATATT ATATT -ATATT ATATT
2407288 TTAAATATTT
Statistics
Matches: 82, Mismatches: 19, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
3 1 0.01
4 17 0.21
5 47 0.57
6 17 0.21
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (5 bp):
ATATT
Done.