Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_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: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 18
Found at i:2129183 original size:113 final size:113
Alignment explanation
Indices: 2128926--2129263 Score: 554
Period size: 113 Copynumber: 3.0 Consensus size: 113
2128916 AAGTGCCATG
2128926 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
2128991 TGGTTTGGTATGAACCCCAAAAACCAATCATTGGATTTTAAAGATGAATT
66 TGGTTTGGTATGAACCCC-AAAACCAATCATTGGA-TTAAAAGATGAATT
2129041 TGCTCATAGTAG-AATAAGAAGACTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
2129104 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTAAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTAAAAGATGAATT
* *
2129152 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * *
2129217 TGATTCGGTAGGAACCCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGG-ATTAAAAGATGAA
2129264 CTGCATGATC
Statistics
Matches: 211, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
111 25 0.12
112 27 0.13
113 122 0.58
114 25 0.12
115 12 0.06
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (113 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTAAAAGATGAATT
Found at i:2131381 original size:54 final size:54
Alignment explanation
Indices: 2131299--2131410 Score: 188
Period size: 54 Copynumber: 2.1 Consensus size: 54
2131289 CAATGATTGA
* * *
2131299 GAACATCTGAGCAGAAACTACAGGAAAGGATGAATGTGTCGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
*
2131353 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
2131407 GAAC
1 GAAC
2131411 CTGCTATTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
Found at i:2131794 original size:22 final size:22
Alignment explanation
Indices: 2131768--2131846 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
2131758 ACATCTACAT
*
2131768 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
2131790 TCTTCAAAGATGATAGATTCCC
1 TCTTCAAAGATGATAGATTCTC
* * *
2131812 TTTTTAAAGATGACAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
2131834 TTTTCAAAGATGA
1 TCTTCAAAGATGA
2131847 AAGCTTTATC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:2132452 original size:113 final size:113
Alignment explanation
Indices: 2132284--2132941 Score: 806
Period size: 113 Copynumber: 5.6 Consensus size: 113
2132274 TTACCAGTTC
**
2132284 AAGTTCATAATGAGAAGAACTCATCTGAAGAATAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
2132349 CAA-CTTTTCGCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGA
66 CAACCTTTT-GCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGA
*
2132397 AAGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
2132462 TAA-CTTTTCGCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGA
66 CAACCTTTT-GCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGA
2132510 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
2132575 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTGCCAG-GTA
66 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAG-A
* * *
2132623 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * ** * *
2132688 AAACCTTTTGCTCG-ACTCTATCCCAGAAGGAAATAAATCAGCATCAACATTTCCAGAGA
66 CAACCTTTTGCTTGAATTC-AT--C-------ATTCGAT--GGATCAACTTTTCCAGAGA
*
2132747 AAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *** * *
2132811 CAACCTTTTGCTCG-ACTCTATCGCAGAAGGAGATAGATCAGCATCAATTTTTCAGAGA
66 CAACCTTTTGCTTGAATTC-AT--C---ATTCGATGGATCA--A-C--TTTTCCAGAGA
*
2132869 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
2132934 CAACCTTT
66 CAACCTTT
2132942 GTTTGATTCT
Statistics
Matches: 491, Mismatches: 33, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
112 4 0.01
113 286 0.58
114 5 0.01
115 1 0.00
117 4 0.01
119 7 0.01
120 1 0.00
122 43 0.09
123 95 0.19
124 44 0.09
125 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGA
Found at i:2132648 original size:226 final size:229
Alignment explanation
Indices: 2132284--2133029 Score: 837
Period size: 226 Copynumber: 3.2 Consensus size: 229
2132274 TTACCAGTTC
**
2132284 AAGTTCATAATGAGAAGAACTCATCTGAAGAATAAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
2132349 CAA-CTTTTCGCTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAA
66 CAACCTTTT-GCTTGAATTCATCATTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAA
* * *
2132413 GAACTCATCTGAATAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA-CTTTTCGCTTGA
130 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTT-GCTCGA
* * ** * *
2132477 AT-TCAT-C-ATTCGAT-GGATCAACTTTTCCAGAGA
194 CTCT-ATCCAAATAAATAGCATCAACATTTCCAGAGA
2132510 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
2132575 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAA
66 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAA
* *
2132639 GAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTTAAACCTTTTGCTCGAC
130 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGCTCGAC
2132704 TCTATCCCAGAAGGAAATAAATCAGCATCAACATTTCCAGAGA
195 TCTAT-CC------AAATAAAT-AGCATCAACATTTCCAGAGA
*
2132747 AAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *** * *
2132811 CAACCTTTTGCTCG-ACTCTATCGCAGAAGGAGATAGATCAGCATCAATTTTTCAGAGAAAGTTC
66 CAACCTTTTGCTTGAATTC-AT--C---ATTCGATGGATCA--A-C-A-TTTCCAGAGAAAGTTC
* *
2132875 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC-
120 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCT
* * * * * *
2132939 TTTGTTTGATTCTATCACAGAATGAGATAGATCAGTATCAACATTTCCATAAA
185 TTTGCTCGACTCTATC-CA-AAT---A-A-AT-AGCATCAACATTTCCAGAGA
* *
2132992 AAGTTCATAATAAGAAGAACTTATCTGAAGAAGGAAGA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
2133030 GAATTTGTTC
Statistics
Matches: 447, Mismatches: 38, Indels: 50
0.84 0.07 0.09
Matches are distributed among these distances:
225 1 0.00
226 172 0.38
227 11 0.02
228 1 0.00
235 7 0.02
236 48 0.11
237 47 0.11
238 1 0.00
239 1 0.00
240 3 0.01
241 9 0.02
243 2 0.00
244 3 0.01
245 62 0.14
246 78 0.17
247 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (229 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACCTTTTGCTCGACT
CTATCCAAATAAATAGCATCAACATTTCCAGAGA
Found at i:2132966 original size:122 final size:124
Alignment explanation
Indices: 2132606--2133029 Score: 622
Period size: 123 Copynumber: 3.4 Consensus size: 124
2132596 CATTCGATGG
* * *
2132606 ATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCA
1 ATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * * * *
2132670 TAATAAGAAGAACTTGTTAAACCTTTTGCTCGACTCTATCCCAGAAGGAAATAAATCAGC
65 TAATGAGAAGAGCTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
2132730 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
2132794 AATGAGAAGAGCTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* *
2132853 ATCAA-TTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * *
2132917 AATGAGAAGAGCTTGTTCAACC-TTTGTTTGATTCTATCACAGAATGAGATAGATCAGT
66 AATGAGAAGAGCTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* * * *
2132975 ATCAACATTTCCATAAAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGGAAGA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
2133030 GAATTTGTTC
Statistics
Matches: 274, Mismatches: 23, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
122 74 0.27
123 156 0.57
124 43 0.16
125 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (124 bp):
ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:2134716 original size:20 final size:19
Alignment explanation
Indices: 2134686--2134734 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
2134676 CAAATATGAT
*
2134686 ATTTTTAAATTATATATTA
1 ATTTTTTAATTATATATTA
* *
2134705 ATTGTTTTAATTATTTATTT
1 ATT-TTTTAATTATATATTA
2134725 ATTTTTTAAT
1 ATTTTTTAAT
2134735 ATCAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTTTTAATTATATATTA
Found at i:2139291 original size:21 final size:21
Alignment explanation
Indices: 2139255--2139329 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
2139245 GCGAATACAT
** *
2139255 ATTCGCATTGTAATTTTCTTA
1 ATTCGCATTGCGATTTTCATA
* * *
2139276 ATTTGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTTCATA
*
2139296 ATTCGCGTTGCGATTTTCATA
1 ATTCGCATTGCGATTTTCATA
*
2139317 ATTCGCAATGCGA
1 ATTCGCATTGCGA
2139330 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (21 bp):
ATTCGCATTGCGATTTTCATA
Found at i:2139344 original size:20 final size:20
Alignment explanation
Indices: 2139319--2139412 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
2139309 TTTTCATAAT
2139319 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** * *
2139339 TCGCAACACGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
2139359 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
2139380 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2139400 TCGCAATGCGAAT
1 TCGCAATGCGAAT
2139413 CTGACTATCG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 44 0.71
21 18 0.29
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2139351 original size:41 final size:41
Alignment explanation
Indices: 2139319--2139412 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
2139309 TTTTCATAAT
*
2139319 TCGCAATGCGAA-TACGTAAATCGCAACACGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACACGATTAAGTAAA
* ** * *
2139359 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACACGATTAAGTAAA
2139400 TCGCAATGCGAAT
1 TCGCAATGCGAAT
2139413 CTGACTATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACACGATTAAGTAAA
Found at i:2140002 original size:14 final size:14
Alignment explanation
Indices: 2139983--2140038 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
2139973 GGAAATGACT
2139983 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
2139997 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
2140016 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
2140030 ATCGCAACG
1 ATCGCAACG
2140039 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:2140020 original size:33 final size:33
Alignment explanation
Indices: 2139962--2140054 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
2139952 CGAGAATGAA
**
2139962 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
2139996 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
2140029 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
2140055 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
33 44 0.80
34 11 0.20
ACGTcount: A:0.43, C:0.25, G:0.23, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:2140101 original size:33 final size:34
Alignment explanation
Indices: 2140050--2140153 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 34
2140040 GAAACCAAAA
* **
2140050 TCGCATTGCGATTTTCATTTCGCGTTGCGATTC-
1 TCGCGTTGCGATAGTCATTTCGCGTTGCGATTCT
* *
2140083 TCTCGTTGCGATAGTCATTTCGCATTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATTTCGCGTTGCGAT--TC--T
2140121 TCGCGTTGCGATAGTCATTTCCGCGTTGCGATT
1 TCGCGTTGCGATAGTCATTT-CGCGTTGCGATT
2140154 TTCATTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
33 26 0.45
35 2 0.03
37 1 0.02
38 19 0.33
39 10 0.17
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.39
Consensus pattern (34 bp):
TCGCGTTGCGATAGTCATTTCGCGTTGCGATTCT
Found at i:2140179 original size:20 final size:19
Alignment explanation
Indices: 2140050--2140172 Score: 121
Period size: 19 Copynumber: 6.6 Consensus size: 19
2140040 GAAACCAAAA
* **
2140050 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATAGTCATT
2140069 TCGCGTTGCGAT--TC---
1 TCGCGTTGCGATAGTCATT
*
2140083 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATT
*
2140102 TCGCATTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATT
2140121 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATAGTCATT
**
2140140 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATAGTCATT
*
2140160 ATCTCGTTGCGAT
1 -TCGCGTTGCGAT
2140173 TTTCATTTCA
Statistics
Matches: 89, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
14 11 0.12
16 2 0.02
17 2 0.02
19 47 0.53
20 26 0.29
21 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATAGTCATT
Found at i:2142073 original size:94 final size:93
Alignment explanation
Indices: 2141871--2142246 Score: 589
Period size: 94 Copynumber: 4.1 Consensus size: 93
2141861 TAGATTGCTT
* *
2141871 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
2141932 ATTTGTCTTTTGTTTTGTCTTTAGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* *
2141961 AGTAAATTTATTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGCAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2142026 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
2142055 AGTAATTTTGTTCGGTTGCTGCCAATTCTGTTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2142120 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
2142149 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2142214 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
2142242 AGTAA
1 AGTAA
2142247 TGCAATCCAT
Statistics
Matches: 266, Mismatches: 15, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
90 34 0.13
92 3 0.01
93 27 0.10
94 202 0.76
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:2142109 original size:17 final size:17
Alignment explanation
Indices: 2142079--2142111 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2142069 GTTGCTGCCA
2142079 ATTCTGTTAAACTGTGT
1 ATTCTGTTAAACTGTGT
2142096 ATTCT-TTAACACTGTG
1 ATTCTGTTAA-ACTGTG
2142112 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.45
Consensus pattern (17 bp):
ATTCTGTTAAACTGTGT
Found at i:2142393 original size:19 final size:19
Alignment explanation
Indices: 2142333--2142422 Score: 73
Period size: 19 Copynumber: 4.9 Consensus size: 19
2142323 TGTCTTTTGG
*
2142333 TTTCGCGTTGCGATTTTTA
1 TTTCGCGTTGCGATTTTCA
*
2142352 TTTTGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
2142368 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
**
2142385 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
2142404 TTTTTCACGTTGCGATTTT
1 --TTTCGCGTTGCGATTTT
2142423 AAGTTCCAGA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
14 9 0.17
16 3 0.06
17 2 0.04
19 26 0.48
21 14 0.26
ACGTcount: A:0.11, C:0.19, G:0.21, T:0.49
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:2142899 original size:21 final size:21
Alignment explanation
Indices: 2142875--2142941 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2142865 TCATTCCTCG
2142875 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
2142896 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
2142917 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
2142938 AGAG
1 AGAG
2142942 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:2142899 original size:41 final size:42
Alignment explanation
Indices: 2142824--2142941 Score: 107
Period size: 41 Copynumber: 2.8 Consensus size: 42
2142814 AACTCGCCTG
* * * * * *
2142824 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC-CTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
2142865 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
2142907 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
2142942 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 36 0.56
42 26 0.41
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:2144307 original size:14 final size:14
Alignment explanation
Indices: 2144288--2144323 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2144278 ATTGTTTAAT
2144288 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2144302 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2144316 TGATTTGT
1 TGATTTGT
2144324 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2144524 original size:19 final size:19
Alignment explanation
Indices: 2144430--2144519 Score: 137
Period size: 19 Copynumber: 4.7 Consensus size: 19
2144420 AAAAATGACT
*
2144430 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2144449 ATCGCAACGTGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2144468 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2144487 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
*
2144506 ATTGCAACGCGAAA
1 ATCGCAACGCGAAA
2144520 CTAAATTCGC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
19 65 0.98
20 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2144547 original size:19 final size:19
Alignment explanation
Indices: 2144525--2144675 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
2144515 CGAAACTAAA
2144525 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2144544 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
2144559 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
2144577 TTCGTATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2144592 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
2144610 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
2144625 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * **
2144643 TTCGCATTACGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
2144662 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
2144676 AACATTAAGA
Statistics
Matches: 94, Mismatches: 22, Indels: 31
0.64 0.15 0.21
Matches are distributed among these distances:
14 25 0.27
16 9 0.10
17 9 0.10
19 42 0.45
20 9 0.10
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:2144602 original size:14 final size:14
Alignment explanation
Indices: 2144550--2144637 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
2144540 TCATTTCGCT
*
2144550 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
2144564 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
2144581 TATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
2144597 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
2144614 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
2144630 TTGCGATT
1 TTGCGATT
2144638 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 13 0.22
19 12 0.20
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2144648 original size:33 final size:33
Alignment explanation
Indices: 2144529--2144655 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
2144519 ACTAAATTCG
* *
2144529 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
2144562 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
2144595 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
2144628 CGTTGCGATTTTCATTTCGCATTACGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2144656 AGTCATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:2146997 original size:12 final size:12
Alignment explanation
Indices: 2146980--2147004 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2146970 TCTTCGGGGA
2146980 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2146992 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2147004 C
1 C
2147005 AGAATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2148026 original size:20 final size:20
Alignment explanation
Indices: 2147962--2148076 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
2147952 GATTATGTAT
* *
2147962 TATCTCGTTACGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
2147982 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2148002 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
2148022 TATCGCATTGCGATTTTGAAT
1 TATCGCGTTGCGATAGT-CAG
*
2148043 TATCGCGTTGCGATAGTGAG
1 TATCGCGTTGCGATAGTCAG
*
2148063 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
2148077 TTTCCAAATT
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 62 0.81
21 15 0.19
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:2148048 original size:21 final size:20
Alignment explanation
Indices: 2148020--2148079 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 20
2148010 TGCGAAAGTC
2148020 AGTATCGCATTGCGATTTTG
1 AGTATCGCATTGCGATTTTG
* * **
2148040 AATTATCGCGTTGCGATAGTG
1 -AGTATCGCATTGCGATTTTG
2148061 AGTATCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
2148080 CCAAATTCGC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (20 bp):
AGTATCGCATTGCGATTTTG
Found at i:2148091 original size:21 final size:20
Alignment explanation
Indices: 2148065--2148116 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2148055 ATAGTGAGTA
*
2148065 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
* **
2148086 TCGCATTGTGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
2148106 TCGCATTGCGA
1 TCGCATTGCGA
2148117 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:2148158 original size:21 final size:22
Alignment explanation
Indices: 2148106--2148158 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2148096 ATTTACTTAT
2148106 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
2148127 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2148148 TCGCATTGCGA
1 TCGCATTGCGA
2148159 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2151345 original size:24 final size:25
Alignment explanation
Indices: 2151318--2151369 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
2151308 ATAATTTGAT
* *
2151318 AAATTTATAATTTTTTTATTTTA-A
1 AAATATATAATTTTTTTATGTTACA
*
2151342 AAATATATGATTTTTTTATGTTACA
1 AAATATATAATTTTTTTATGTTACA
2151367 AAA
1 AAA
2151370 ATACATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (25 bp):
AAATATATAATTTTTTTATGTTACA
Found at i:2153070 original size:2 final size:2
Alignment explanation
Indices: 2153065--2153094 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2153055 ACACACACAC
2153065 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
2153095 GGAATGAGGA
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:2155636 original size:103 final size:103
Alignment explanation
Indices: 2155500--2155702 Score: 307
Period size: 103 Copynumber: 2.0 Consensus size: 103
2155490 CTGTTTTGCC
* ** * *
2155500 AAATTCAAACTTAGTAAGCTATTTTTTTGACATTTTATCTTTCAATTTAATATGAATTTTCACTT
1 AAATTCAAACTCAGTAAGCTATTTTTTTGACATTTTATCTCCCAATTCAATATGAATTTTCACGT
*
2155565 TTAAATTTCGTTTCTAATGTAATTGGGTTTTCCATTTT
66 TTAAATTTCGTTTCTAATGTAATTAGGTTTTCCATTTT
* *
2155603 AAATTCAAACTCAGTAAGCTATTTTTTTTACATTTTATCTCCCGATTCAATATGAATTTTCACGT
1 AAATTCAAACTCAGTAAGCTATTTTTTTGACATTTTATCTCCCAATTCAATATGAATTTTCACGT
* * *
2155668 TTAAGTTTTGTTTCTAATGTAATTAGTTTTTCCAT
66 TTAAATTTCGTTTCTAATGTAATTAGGTTTTCCAT
2155703 GTATCCGAGA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 89 1.00
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (103 bp):
AAATTCAAACTCAGTAAGCTATTTTTTTGACATTTTATCTCCCAATTCAATATGAATTTTCACGT
TTAAATTTCGTTTCTAATGTAATTAGGTTTTCCATTTT
Found at i:2157359 original size:21 final size:21
Alignment explanation
Indices: 2157334--2157373 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2157324 ACTATATAAC
*
2157334 ATATATTATATTTTCAAAACT
1 ATATAATATATTTTCAAAACT
*
2157355 ATATAATATTTTTTCAAAA
1 ATATAATATATTTTCAAAA
2157374 ATCGTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATAATATATTTTCAAAACT
Found at i:2157431 original size:23 final size:24
Alignment explanation
Indices: 2157384--2157434 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
2157374 ATCGTTTTAA
*
2157384 AAAACTATATATATATATATATTC
1 AAAACTATATATATATACATATTC
* *
2157408 AAAACTATA-ATATATACGTTTTC
1 AAAACTATATATATATACATATTC
2157431 AAAA
1 AAAA
2157435 ATCGCTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (24 bp):
AAAACTATATATATATACATATTC
Found at i:2157436 original size:61 final size:60
Alignment explanation
Indices: 2157334--2157461 Score: 172
Period size: 61 Copynumber: 2.1 Consensus size: 60
2157324 ACTATATAAC
* **
2157334 ATATAT-TATATTTTCAAAACTATATAATATTTTTTCAAAAATCG-TTTTAAAAAACTAT
1 ATATATATATATATTCAAAACTATATAATACGTTTTCAAAAATCGCTTTTAAAAAACTAT
**
2157392 ATATATATATATATTCAAAACTATAATATATACGTTTTCAAAAATCGCTTTTTTAAAACTAT
1 ATATATATATATATTCAAAACTAT-ATA-ATACGTTTTCAAAAATCGCTTTTAAAAAACTAT
2157454 ATAT-TATA
1 ATATATATA
2157462 CGTTTTCAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
58 6 0.10
59 16 0.26
60 3 0.05
61 20 0.33
62 16 0.26
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (60 bp):
ATATATATATATATTCAAAACTATATAATACGTTTTCAAAAATCGCTTTTAAAAAACTAT
Found at i:2157462 original size:38 final size:37
Alignment explanation
Indices: 2157408--2157639 Score: 233
Period size: 37 Copynumber: 6.2 Consensus size: 37
2157398 ATATATATTC
*
2157408 AAAACTATA-ATATATACGTTTTCAAAAATCGCTTTTTT
1 AAAACTATATAT-TATACGTTTTCAAAAATCG-TTTTTA
*
2157446 AAAACTATATATTATACGTTTTCAAAAAT-GTGTTTTC
1 AAAACTATATATTATACGTTTTCAAAAATCGT-TTTTA
*
2157483 AAAACTATATATTATACGTTTTCAAAAAT-GTGTTTTC
1 AAAACTATATATTATACGTTTTCAAAAATCGT-TTTTA
* * * * *
2157520 AAAACCATAT-TATATATGTTTTCCAAAATCGATTTAA
1 AAAACTATATAT-TATACGTTTTCAAAAATCGTTTTTA
* *
2157557 AAAACTATATATTATA-TTCTTTCAAAAACCGTTTTCTA
1 AAAACTATATATTATACGT-TTTCAAAAATCGTTTT-TA
* * * *
2157595 AAAACTGTATATTATATGTTTTCAAAAAT-ATTTTCA
1 AAAACTATATATTATACGTTTTCAAAAATCGTTTTTA
2157631 AAAACTATA
1 AAAACTATA
2157640 CTATATTATT
Statistics
Matches: 167, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
36 12 0.07
37 99 0.59
38 53 0.32
39 3 0.02
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (37 bp):
AAAACTATATATTATACGTTTTCAAAAATCGTTTTTA
Found at i:2162994 original size:29 final size:29
Alignment explanation
Indices: 2162962--2163019 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2162952 TTGTTTAATC
*
2162962 GGTTTCTAATTTGTATCTTGTATTTATTT
1 GGTTTCTAATTTGTATATTGTATTTATTT
2162991 GGTTTCTAATTTGTATATTGTATTTATTT
1 GGTTTCTAATTTGTATATTGTATTTATTT
2163020 CAGTCTATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.62
Consensus pattern (29 bp):
GGTTTCTAATTTGTATATTGTATTTATTT
Found at i:2165781 original size:24 final size:25
Alignment explanation
Indices: 2165754--2165808 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
2165744 TCTATTAGTT
*
2165754 AAATATTAATTATT-AAAGTATTTA
1 AAATATTAATTATTAAAAATATTTA
*
2165778 AAATA-TATTTATTAAAAATATTTA
1 AAATATTAATTATTAAAAATATTTA
2165802 ATAATAT
1 A-AATAT
2165809 AGTACACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 7 0.27
24 15 0.58
25 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
AAATATTAATTATTAAAAATATTTA
Found at i:2165871 original size:28 final size:27
Alignment explanation
Indices: 2165818--2165882 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
2165808 TAGTACACTA
* *
2165818 TTATTATTTAAATAAATAATTATAATAT
1 TTATTATTTTAATAAATAATTATAAT-C
2165846 TTATTATTTTAAT-AA-AATATATTAATC
1 TTATTATTTTAATAAATAAT-TA-TAATC
2165873 TTATTATTTT
1 TTATTATTTT
2165883 GTTTATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 3 0.09
27 14 0.42
28 16 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (27 bp):
TTATTATTTTAATAAATAATTATAATC
Found at i:2168870 original size:37 final size:37
Alignment explanation
Indices: 2168820--2168894 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2168810 TTGGGTAAAT
2168820 TACACCCATGATGAACACCTTAACTATTGAGATTTTA
1 TACACCCATGATGAACACCTTAACTATTGAGATTTTA
2168857 TACACCCATGATGAACACCTTAACTATTGAGATTTTA
1 TACACCCATGATGAACACCTTAACTATTGAGATTTTA
2168894 T
1 T
2168895 TATGAGCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (37 bp):
TACACCCATGATGAACACCTTAACTATTGAGATTTTA
Found at i:2184742 original size:2 final size:2
Alignment explanation
Indices: 2184735--2184799 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
2184725 CCCAACACAT
2184735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2184777 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2184800 TTTTTTTTCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2196879 original size:4 final size:4
Alignment explanation
Indices: 2196870--2196960 Score: 128
Period size: 4 Copynumber: 22.8 Consensus size: 4
2196860 TGATGATATA
* * * *
2196870 ATAG ATAG ATAT AAAG ATAT AAAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
* *
2196918 ATAG ATAC ATAG ATAC ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
2196961 AAATGATTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 75 1.00
ACGTcount: A:0.53, C:0.02, G:0.20, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:2197242 original size:23 final size:21
Alignment explanation
Indices: 2197194--2197244 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
2197184 TTTGGTATAA
2197194 TTATATATTTGACCTTTTTAC
1 TTATATATTTGACCTTTTTAC
*
2197215 TTATATATTTGATCTTTTTAC
1 TTATATATTTGACCTTTTTAC
2197236 TTATATATT
1 TTATATATT
2197245 CTATCAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.04, T:0.61
Consensus pattern (21 bp):
TTATATATTTGACCTTTTTAC
Found at i:2197447 original size:16 final size:17
Alignment explanation
Indices: 2197416--2197448 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2197406 AGGTGCTGTC
2197416 ACGTTGTTGCCAACTGG
1 ACGTTGTTGCCAACTGG
*
2197433 ACGTTG-TGTCAACTGG
1 ACGTTGTTGCCAACTGG
2197449 GGTAGTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.30
Consensus pattern (17 bp):
ACGTTGTTGCCAACTGG
Found at i:2198250 original size:21 final size:21
Alignment explanation
Indices: 2198224--2198270 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2198214 AAATACGGTA
2198224 GGAATTGAGAGTACTTGAATG
1 GGAATTGAGAGTACTTGAATG
2198245 GGAATTGAGAGTACTTGAATG
1 GGAATTGAGAGTACTTGAATG
*
2198266 CGAAT
1 GGAAT
2198271 CACCCAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.32, T:0.28
Consensus pattern (21 bp):
GGAATTGAGAGTACTTGAATG
Found at i:2199467 original size:85 final size:83
Alignment explanation
Indices: 2199336--2199870 Score: 662
Period size: 84 Copynumber: 6.4 Consensus size: 83
2199326 GATATGCCCC
* * ** *
2199336 TGAGCTGAATGAAATC-ACACTCGAAGGTCTTTAATGACAGATAACCCTTCTCGCCTTGAGCTAT
1 TGAGCTGAGTGTAATCGA-ACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTAT
*
2199400 GCTGTAAATTTGATGTGTCTT
65 GCTGTAAA--TGATGTGCCTT
* * *
2199421 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTATAGCTTTGAGTTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATG
* * * *
2199486 CTATAATTGATATACCTT
66 CTGTAAATGATGTGCCTT
* * **
2199504 TGAGCTGAGTGTAGA-CGAACTCGAAGGTCTTTTGTCGGCAGATAACCCTTCTTTCCTTGAGCTA
1 TGAGCTGAGTGTA-ATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGCCTTGAGCTA
* *
2199568 TACTGCAAATGATGTGCCTT
64 TGCTGTAAATGATGTGCCTT
* * *
2199588 TGAGCTGAGTGAAATCGAACTCGAAGGTGTTT-TTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATG
* *
2199652 CTATAAATGATGTGCATT
66 CTGTAAATGATGTGCCTT
*
2199670 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATG
* *
2199735 CTGTAAATGATATGCCCT
66 CTGTAAATGATGTGCCTT
* * * * * *
2199753 CGAAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGTTGACAGATAGCCCTTCTTGACTTAAGCTA
1 TG-AGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTAGCCTTGAGCTA
* *
2199818 TGCTGCAAATGAAGTGCCTT
64 TGCTGTAAATGATGTGCCTT
*
2199838 TGAGCTTAGTGTAATCGAACTCGAAGGTCTTTG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG
2199871 GCATATACTC
Statistics
Matches: 387, Mismatches: 56, Indels: 16
0.84 0.12 0.03
Matches are distributed among these distances:
82 71 0.18
83 87 0.22
84 125 0.32
85 103 0.27
86 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (83 bp):
TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGCTATG
CTGTAAATGATGTGCCTT
Found at i:2201814 original size:2 final size:2
Alignment explanation
Indices: 2201807--2201870 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
2201797 ACAACAAGGG
*
2201807 AT AT AT AT AG 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
*
2201849 AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2201871 GGATAAATGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2206418 original size:29 final size:29
Alignment explanation
Indices: 2206351--2206420 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 29
2206341 CCATAGACTT
*** *
2206351 TTAACTTAAAAAAATATTTTATTCTTGTC
1 TTAACTTAAAAAAATATTTTATAAATATC
*
2206380 TTAATTTTAAAAAAATATTTT-TAAAATATC
1 TTAA-CTTAAAAAAATATTTTAT-AAATATC
2206410 TTAACTTAAAA
1 TTAACTTAAAA
2206421 TATATCTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 11 0.33
30 22 0.67
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (29 bp):
TTAACTTAAAAAAATATTTTATAAATATC
Found at i:2207183 original size:26 final size:26
Alignment explanation
Indices: 2207143--2207200 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
2207133 TGAATATTTT
*
2207143 AAAAATAAATATAAAAACATTAAAATA
1 AAAAATAAATATAAAAA-ATAAAAATA
*
2207170 AAAAAT-AATTTAAAAAATAAAAATA
1 AAAAATAAATATAAAAAATAAAAATA
2207195 ATAAAA
1 A-AAAA
2207201 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.32
26 13 0.46
27 6 0.21
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (26 bp):
AAAAATAAATATAAAAAATAAAAATA
Found at i:2207200 original size:27 final size:27
Alignment explanation
Indices: 2207142--2207203 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
2207132 TTGAATATTT
*
2207142 TAAAAATAAATATAAAAACATTAAAATA
1 TAAAAAT-AATATAAAAACATAAAAATA
*
2207170 -AAAAATAATTTAAAAA-ATAAAAATAA
1 TAAAAATAATATAAAAACATAAAAAT-A
2207196 TAAAAATA
1 TAAAAATA
2207204 TGAAAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 7 0.23
26 10 0.33
27 13 0.43
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (27 bp):
TAAAAATAATATAAAAACATAAAAATA
Found at i:2207209 original size:18 final size:17
Alignment explanation
Indices: 2207164--2207215 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
2207154 TAAAAACATT
2207164 AAAATAAAAAATAATTTAA
1 AAAAT-AAAAATAA-TTAA
2207183 AAAATAAAAATAA-TAA
1 AAAATAAAAATAATTAA
* *
2207199 AAATATGAAAATTATTA
1 AAA-ATAAAAATAATTA
2207216 TTATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 8 0.28
18 10 0.34
19 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATAAAAATAATTAA
Found at i:2207634 original size:24 final size:23
Alignment explanation
Indices: 2207603--2207649 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2207593 ATTCAAGTTT
*
2207603 GAGTTCGAGATTGAATCGAGCTC
1 GAGTTCGAGATTCAATCGAGCTC
*
2207626 GAGTCTCGAGCTTCAATCGAGCTC
1 GAGT-TCGAGATTCAATCGAGCTC
2207650 CTGAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (23 bp):
GAGTTCGAGATTCAATCGAGCTC
Found at i:2208880 original size:187 final size:186
Alignment explanation
Indices: 2208560--2208939 Score: 634
Period size: 187 Copynumber: 2.0 Consensus size: 186
2208550 ATAAAATATT
* *
2208560 AAATATTAAATGTATTATATATAACATATGTGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
*
2208625 TTTAAGATCAAATAACTTTTAAACCTAAATCAATATTAAAAAATTAAAAAATTTATATAAATTTT
66 TTTAAGATCAAATAACTTTTAAACCTAAATCAATATTAAAAAATTAAAAAATTTATATAAAATTT
*
2208690 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTCTGAATTAAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTCTGAATT-AAA
* * *
2208747 AAATATTAAATATATTATATATAACATTTGAGTTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
* **
2208812 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCAAATAACTTTTAAACCTAAATCAATATTAAAAAATTAAAAAATTTATATAAAATTT
* * *
2208877 TTATTTTATAATTATATATTATTTAAATTAATTATAAATTGTTTTTTTGAATTATA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTCTGAATTAAA
2208933 AAATATT
1 AAATATT
2208940 TATTTTTTAT
Statistics
Matches: 180, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
186 9 0.05
187 171 0.95
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (186 bp):
AAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCAAATAACTTTTAAACCTAAATCAATATTAAAAAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTCTGAATTAAA
Found at i:2211088 original size:12 final size:12
Alignment explanation
Indices: 2211073--2211115 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
2211063 GTTATTTAAA
2211073 CGGGTATTGGGC
1 CGGGTATTGGGC
*
2211085 CGGGTATTGGGT
1 CGGGTATTGGGC
* *
2211097 CGGGAATCGGGC
1 CGGGTATTGGGC
2211109 CGGGTAT
1 CGGGTAT
2211116 ATATATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.12, C:0.16, G:0.49, T:0.23
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:2211120 original size:2 final size:2
Alignment explanation
Indices: 2211113--2211206 Score: 74
Period size: 2 Copynumber: 50.0 Consensus size: 2
2211103 TCGGGCCGGG
* * * *
2211113 TA TA TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2211153 TA TT TA AA T- TA AA TT TA T- TA -A TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2211191 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
2211207 AATAAATAAT
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
1 6 0.08
2 65 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2211179 original size:24 final size:24
Alignment explanation
Indices: 2211116--2211214 Score: 96
Period size: 24 Copynumber: 4.1 Consensus size: 24
2211106 GGCCGGGTAT
2211116 ATATATATATATATATTTAAATTAA
1 ATATATATATAT-TATTTAAATTAA
*
2211141 ATATATATATTTTATTTAAATTAA
1 ATATATATATATTATTTAAATTAA
* * * *
2211165 ATTTAT-TAATATTATATATA-TAT
1 ATATATAT-ATATTATTTAAATTAA
*
2211188 ATATATATATATATATATAAA-TAA
1 ATATATATATAT-TATTTAAATTAA
2211212 ATA
1 ATA
2211215 ATTATTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
23 12 0.19
24 39 0.63
25 11 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATATATATATTATTTAAATTAA
Found at i:2211261 original size:13 final size:12
Alignment explanation
Indices: 2211230--2211266 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
2211220 TTTTAATATT
2211230 TATCGGGGCGGG
1 TATCGGGGCGGG
2211242 TATCGGGGCGGG
1 TATCGGGGCGGG
2211254 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
2211267 GATTACCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.11, C:0.16, G:0.57, T:0.16
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:2212416 original size:22 final size:22
Alignment explanation
Indices: 2212389--2212470 Score: 98
Period size: 22 Copynumber: 3.7 Consensus size: 22
2212379 ATAACTAAAA
2212389 AATATAATGTTATAATAATAAG
1 AATATAATGTTATAATAATAAG
* *
2212411 AATATAAACGTTTTATACTAA-AA-
1 AATAT-AA--TGTTATAATAATAAG
2212434 AATATAATGTTATAATAATAAG
1 AATATAATGTTATAATAATAAG
2212456 AATATAATGTT-TAAT
1 AATATAATGTTATAAT
2212471 GGTAATTGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 9 0.18
21 6 0.12
22 18 0.35
23 7 0.14
24 2 0.04
25 9 0.18
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (22 bp):
AATATAATGTTATAATAATAAG
Found at i:2212810 original size:15 final size:15
Alignment explanation
Indices: 2212787--2212822 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2212777 TTATTTAACT
2212787 TAAAAATATAAAATA
1 TAAAAATATAAAATA
* *
2212802 TAAATATATTAAATA
1 TAAAAATATAAAATA
2212817 TAAAAA
1 TAAAAA
2212823 ACTAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATATAAAATA
Found at i:2213225 original size:78 final size:77
Alignment explanation
Indices: 2213131--2213314 Score: 223
Period size: 77 Copynumber: 2.4 Consensus size: 77
2213121 AAACAAACAT
*
2213131 GTTTTTAATTT-TTTTTA-TATT-TT-CTTAAAAATGAAAATTAAAATAACATATATTTTCTAAA
1 GTTTTT-ATTTGTTTTTACT-TTGTTACTTAAAAA-G-AAAGTAAAATAA-ATATATTTTCTAAA
2213192 ACCAAATCAACCTTAAA
61 ACCAAATCAACCTTAAA
*** * * *
2213209 GTTTTTATTTGTTTTTACTTTGTTACTTATGTAGAAGGTAAACTCAATATATTTTCTAAAACCAA
1 GTTTTTATTTGTTTTTACTTTGTTACTTAAAAAGAAAGTAAAATAAATATATTTTCTAAAACCAA
2213274 ATCAACCTTAAA
66 ATCAACCTTAAA
*
2213286 GTTTCTATTTGTTTTTACTTTGTTACTTA
1 GTTTTTATTTGTTTTTACTTTGTTACTTA
2213315 TGTAGAAGGT
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
77 63 0.67
78 22 0.23
79 4 0.04
80 5 0.05
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (77 bp):
GTTTTTATTTGTTTTTACTTTGTTACTTAAAAAGAAAGTAAAATAAATATATTTTCTAAAACCAA
ATCAACCTTAAA
Found at i:2213267 original size:77 final size:77
Alignment explanation
Indices: 2213178--2213332 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
2213168 TTAAAATAAC
*
2213178 ATATATTTTCTAAAACCAAATCAACCTTAAAGTTTTTATTTGTTTTTACTTTGTTACTTATGTAG
1 ATATATTTTCTAAAACCAAATCAACCTTAAAGTTTCTATTTGTTTTTACTTTGTTACTTATGTAG
2213243 AAGGTAAACTCA
66 AAGGTAAACTCA
2213255 ATATATTTTCTAAAACCAAATCAACCTTAAAGTTTCTATTTGTTTTTACTTTGTTACTTATGTAG
1 ATATATTTTCTAAAACCAAATCAACCTTAAAGTTTCTATTTGTTTTTACTTTGTTACTTATGTAG
2213320 AAGGTAAACTCA
66 AAGGTAAACTCA
2213332 A
1 A
2213333 AGAATGATAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (77 bp):
ATATATTTTCTAAAACCAAATCAACCTTAAAGTTTCTATTTGTTTTTACTTTGTTACTTATGTAG
AAGGTAAACTCA
Found at i:2214278 original size:33 final size:33
Alignment explanation
Indices: 2214227--2214315 Score: 103
Period size: 32 Copynumber: 2.7 Consensus size: 33
2214217 TATTAATATA
*
2214227 TAATTAAAATAAAAAAATAAATTT-AAATGTTAGAG
1 TAATT-AAATTAAAAAATAAATTTGAAA-GTTA-AG
* *
2214262 TGATTAAATT-AGAAAT-AATTTGAAAGTTAAG
1 TAATTAAATTAAAAAATAAATTTGAAAGTTAAG
2214293 TAATTAAATTAAAAAATAAATTT
1 TAATTAAATTAAAAAATAAATTT
2214316 CAATTACCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
31 11 0.24
32 14 0.30
33 13 0.28
34 4 0.09
35 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (33 bp):
TAATTAAATTAAAAAATAAATTTGAAAGTTAAG
Found at i:2215049 original size:21 final size:22
Alignment explanation
Indices: 2215007--2215069 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
2214997 ATATTTGTCA
*
2215007 TTGTGGCACGTTTTTGTCTGCTC
1 TTGTGGCACGTTTTT-TATGCTC
*
2215030 TTGTGACAC-TTTTTTATGCTC
1 TTGTGGCACGTTTTTTATGCTC
*
2215051 TTGTGGCACGTTCTTTATG
1 TTGTGGCACGTTTTTTATG
2215070 GTTTTTGGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.40
22 13 0.37
23 8 0.23
ACGTcount: A:0.10, C:0.19, G:0.22, T:0.49
Consensus pattern (22 bp):
TTGTGGCACGTTTTTTATGCTC
Found at i:2228640 original size:19 final size:20
Alignment explanation
Indices: 2228588--2228641 Score: 92
Period size: 19 Copynumber: 2.7 Consensus size: 20
2228578 CTCAGAGGGA
2228588 ACCGATTCCCCCCAAGGGGGT
1 ACCGATTCCCCCC-AGGGGGT
2228609 ACCGATTCCCCCCA-GGGGT
1 ACCGATTCCCCCCAGGGGGT
2228628 ACCGATTCCCCCCA
1 ACCGATTCCCCCCA
2228642 CTGTTCAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 19 0.58
20 1 0.03
21 13 0.39
ACGTcount: A:0.19, C:0.44, G:0.22, T:0.15
Consensus pattern (20 bp):
ACCGATTCCCCCCAGGGGGT
Found at i:2247649 original size:26 final size:26
Alignment explanation
Indices: 2247620--2247670 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
2247610 AAAAGGTCTG
2247620 TTTAGTTATCATCCCAAATGTAAGCT
1 TTTAGTTATCATCCCAAATGTAAGCT
2247646 TTTAGTTATCATCCCAAATGTAAGC
1 TTTAGTTATCATCCCAAATGTAAGC
2247671 GCATTGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (26 bp):
TTTAGTTATCATCCCAAATGTAAGCT
Found at i:2270614 original size:21 final size:21
Alignment explanation
Indices: 2270571--2270614 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2270561 GAAAATATTA
* *
2270571 AAAAATATTAATACCTTAGAT
1 AAAAATAATAATACCTTAAAT
**
2270592 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATACCTTAAAT
2270613 AA
1 AA
2270615 TTTTCTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAAATAATAATACCTTAAAT
Found at i:2275121 original size:2 final size:2
Alignment explanation
Indices: 2275114--2275161 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2275104 ATATGTAAAC
2275114 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
2275156 AT AT AT
1 AT AT AT
2275162 CACTTCTACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2279249 original size:23 final size:23
Alignment explanation
Indices: 2279215--2279283 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
2279205 CAATCTTATA
2279215 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
2279238 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
2279261 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
2279284 AGTTGTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:2282481 original size:22 final size:22
Alignment explanation
Indices: 2282450--2282506 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
2282440 TGAAATTGTT
*
2282450 CCGAATGACCACTGTATATGTC
1 CCGAAAGACCACTGTATATGTC
2282472 CCGAAAGACCACTGTATATGTC
1 CCGAAAGACCACTGTATATGTC
* *
2282494 TCGAAGGACCACT
1 CCGAAAGACCACT
2282507 ATCCATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (22 bp):
CCGAAAGACCACTGTATATGTC
Found at i:2282540 original size:30 final size:29
Alignment explanation
Indices: 2282504--2282564 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
2282494 TCGAAGGACC
*
2282504 ACTATCCATATGTTCCAAAGAACATAGGTA
1 ACTATCCATATGTCCCAAAGAACATA-GTA
*
2282534 ACTATCCATATGTCCCAAAGGACATAGTA
1 ACTATCCATATGTCCCAAAGAACATAGTA
2282563 AC
1 AC
2282565 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.25
Consensus pattern (29 bp):
ACTATCCATATGTCCCAAAGAACATAGTA
Found at i:2282991 original size:2 final size:2
Alignment explanation
Indices: 2282984--2283019 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2282974 TACTTTGAAA
2282984 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
2283020 CACTTATTAT
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):
AT
Found at i:2283792 original size:22 final size:22
Alignment explanation
Indices: 2283767--2283830 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
2283757 GGTATGTGAA
2283767 ATATGTTCTGAATGACCACTGT
1 ATATGTTCTGAATGACCACTGT
* * *
2283789 ATATGTCCCGAAAGACCACTGT
1 ATATGTTCTGAATGACCACTGT
2283811 ATATG-TCTCGAATGACCACT
1 ATATGTTCT-GAATGACCACT
2283831 ATCCATATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (22 bp):
ATATGTTCTGAATGACCACTGT
Found at i:2283864 original size:30 final size:30
Alignment explanation
Indices: 2283828--2283889 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
2283818 TCGAATGACC
*
2283828 ACTATCCATATGTTCCAAAGAACATAGGTA
1 ACTATCCATATGTCCCAAAGAACATAGGTA
*
2283858 ACTATCCATATGTCCCAAAGGACATAGGTA
1 ACTATCCATATGTCCCAAAGAACATAGGTA
2283888 AC
1 AC
2283890 CCTCGACTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.24
Consensus pattern (30 bp):
ACTATCCATATGTCCCAAAGAACATAGGTA
Found at i:2284335 original size:2 final size:2
Alignment explanation
Indices: 2284328--2284357 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2284318 ATACTTTGAA
2284328 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
2284358 CACTTATATT
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:2286261 original size:16 final size:16
Alignment explanation
Indices: 2286240--2286270 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2286230 TAACAAGTCA
2286240 ACACATATACTCATAT
1 ACACATATACTCATAT
2286256 ACACATATACTCATA
1 ACACATATACTCATA
2286271 ACAAACACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (16 bp):
ACACATATACTCATAT
Found at i:2289710 original size:18 final size:18
Alignment explanation
Indices: 2289684--2289723 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2289674 AAGCTTGTCA
* *
2289684 ATCTCTTCATCTTTATCC
1 ATCTATTCATCTTCATCC
2289702 ATCTATTCATCTTCATCC
1 ATCTATTCATCTTCATCC
2289720 ATCT
1 ATCT
2289724 CTCTACTAGA
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:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (18 bp):
ATCTATTCATCTTCATCC
Found at i:2296111 original size:36 final size:36
Alignment explanation
Indices: 2296067--2296136 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
2296057 TTATAATGAC
2296067 CCTTGGTGTCAGTATTAGACCTAAGATCGTGATTGA
1 CCTTGGTGTCAGTATTAGACCTAAGATCGTGATTGA
2296103 CCTTGGTGTCAGTATTAGACCTAAGATCGTGATT
1 CCTTGGTGTCAGTATTAGACCTAAGATCGTGATT
2296137 ACTACTCCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (36 bp):
CCTTGGTGTCAGTATTAGACCTAAGATCGTGATTGA
Found at i:2297347 original size:2 final size:2
Alignment explanation
Indices: 2297342--2297374 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2297332 ATGTATGAAT
*
2297342 TA TA TA TA TA TA TA CA TA -A 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
2297375 ACATTAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2297365 original size:15 final size:15
Alignment explanation
Indices: 2297345--2297375 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2297335 TATGAATTAT
2297345 ATATATATATACATA
1 ATATATATATACATA
*
2297360 ATATATATATATATA
1 ATATATATATACATA
2297375 A
1 A
2297376 CATTAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATATATACATA
Found at i:2298458 original size:24 final size:24
Alignment explanation
Indices: 2298416--2298461 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2298406 GTAAAAGAAC
*
2298416 TTATAAACAAGTCGATAAACGATT
1 TTATAAACAAGCCGATAAACGATT
2298440 TTATAAACAAGCC-AGTAAACGA
1 TTATAAACAAGCCGA-TAAACGA
2298462 GCTTGTTCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (24 bp):
TTATAAACAAGCCGATAAACGATT
Found at i:2301240 original size:55 final size:56
Alignment explanation
Indices: 2301180--2301291 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
2301170 AAACGATCAA
2301180 TAGGAAAAACATTCCAGTGC-TACCAGAGGCATGTATTCGGAGTGTTACATGTCGC
1 TAGGAAAAACATTCCAGTGCTTACCAGAGGCATGTATTCGGAGTGTTACATGTCGC
2301235 TAGGAAAAACATTCCAGTGCTTACCAGAGGCATGTATTCGGAGTGTTACATGTCGC
1 TAGGAAAAACATTCCAGTGCTTACCAGAGGCATGTATTCGGAGTGTTACATGTCGC
2301291 T
1 T
2301292 GCTCTGACTC
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 20 0.36
56 36 0.64
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (56 bp):
TAGGAAAAACATTCCAGTGCTTACCAGAGGCATGTATTCGGAGTGTTACATGTCGC
Found at i:2309082 original size:23 final size:24
Alignment explanation
Indices: 2309056--2309114 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
2309046 ACTAAATATT
* *
2309056 AAATATAATTTTTTAAAA-AACTA
1 AAATATAATTTATTAAAATAAATA
* *
2309079 AAATTTAA-GTATTAAAATAAATA
1 AAATATAATTTATTAAAATAAATA
2309102 AAATAATAATTTA
1 AAAT-ATAATTTA
2309115 ATACTAAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
22 7 0.26
23 15 0.56
24 3 0.11
25 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATAATTTATTAAAATAAATA
Found at i:2310906 original size:157 final size:154
Alignment explanation
Indices: 2310609--2310921 Score: 567
Period size: 157 Copynumber: 2.0 Consensus size: 154
2310599 AATAAAATAA
2310609 ATAAGTTTGACGTTTTACACAATATCACCTAACATAATTAATTACTTTATCACCATTTTAAAAAT
1 ATAAGTTTGACGTTTTACACAATATCACCTAACATAATTAATTACTTTATCACCATTTTAAAAAT
2310674 ATTTACAAAATTAACACTCGATTTTTTACACGTTTACAAGACGCGGTGCATGAGCCGCCCCACGT
66 ATTTACAAAATTAACACTCGATTTTTTACACGTTTACAAGACGCGGTGCATGAGCCGCCCCACGT
2310739 GACATCACATCAACGTAAGACGCG
131 GACATCACATCAACGTAAGACGCG
2310763 ATAAG-TTGACGTTTTACACAATATCACCTAAC-TAAATTAATTACATATTTATCACCATTTTAA
1 ATAAGTTTGACGTTTTACACAATATCACCTAACAT-AATTAATTAC---TTTATCACCATTTTAA
2310826 AAATATTTACAAAATTAACACTCGATTTTTTACACGTTTTACAAGACGCGGTGCATGAGCCGCCC
62 AAATATTTACAAAATTAACACTCGATTTTTTACACG-TTTACAAGACGCGGTGCATGAGCCGCCC
2310891 CACGTGACATCACATCAACGTAAGACGCG
126 CACGTGACATCACATCAACGTAAGACGCG
2310920 AT
1 AT
2310922 GCATTGATCA
Statistics
Matches: 154, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
152 1 0.01
153 37 0.24
154 5 0.03
156 52 0.34
157 59 0.38
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.30
Consensus pattern (154 bp):
ATAAGTTTGACGTTTTACACAATATCACCTAACATAATTAATTACTTTATCACCATTTTAAAAAT
ATTTACAAAATTAACACTCGATTTTTTACACGTTTACAAGACGCGGTGCATGAGCCGCCCCACGT
GACATCACATCAACGTAAGACGCG
Found at i:2314589 original size:3 final size:3
Alignment explanation
Indices: 2314583--2314615 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
2314573 AATTATTACC
2314583 AAT AAT AAT AAT AAT AAT AA- ATAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
2314616 TAATTCTGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.04
3 26 0.93
4 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2328321 original size:21 final size:22
Alignment explanation
Indices: 2328300--2328356 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
2328290 GTGCAGAGGA
2328300 AATCGA-TCCCCCCTTG-AGGG
1 AATCGATTCCCCCCTTGAAGGG
* * *
2328320 AACCAATTCCCCCATTGAAGGGG
1 AATCGATTCCCCCCTTGAA-GGG
2328343 AATCGATTCCCCCC
1 AATCGATTCCCCCC
2328357 ACAGGGGAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 4 0.14
21 9 0.32
22 1 0.04
23 14 0.50
ACGTcount: A:0.25, C:0.37, G:0.19, T:0.19
Consensus pattern (22 bp):
AATCGATTCCCCCCTTGAAGGG
Found at i:2334083 original size:5 final size:5
Alignment explanation
Indices: 2334073--2334099 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2334063 ATTATTGTTC
2334073 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
2334100 GCATGATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2336808 original size:45 final size:45
Alignment explanation
Indices: 2336737--2336869 Score: 212
Period size: 45 Copynumber: 3.0 Consensus size: 45
2336727 TATAAACTAA
* * *
2336737 AATGAAGAAGGCATGGATGATAACATGGTCGCAATAATTCCTTTT
1 AATGCAGAAGGCATGGATGATGACATGGTCGAAATAATTCCTTTT
* *
2336782 AATGCATAAGGCATGGATGATGACATGGTCGGAATAATTCCTTTT
1 AATGCAGAAGGCATGGATGATGACATGGTCGAAATAATTCCTTTT
*
2336827 AGTGCAGAAGGCATGGATGATGACATGGTCGAAATAATTCCTT
1 AATGCAGAAGGCATGGATGATGACATGGTCGAAATAATTCCTT
2336870 GGGATAAAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 81 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.29
Consensus pattern (45 bp):
AATGCAGAAGGCATGGATGATGACATGGTCGAAATAATTCCTTTT
Found at i:2342557 original size:18 final size:18
Alignment explanation
Indices: 2342534--2342569 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2342524 ATCCGTTCGG
2342534 CTTGGGGGCTTTGTGACT
1 CTTGGGGGCTTTGTGACT
2342552 CTTGGGGGCTTTGTGACT
1 CTTGGGGGCTTTGTGACT
2342570 TTACGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.17, G:0.39, T:0.39
Consensus pattern (18 bp):
CTTGGGGGCTTTGTGACT
Found at i:2349984 original size:18 final size:21
Alignment explanation
Indices: 2349933--2349982 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2349923 AGTATAATTA
**
2349933 ATTTATAAT-ATAAAATGAAT
1 ATTTATAATAATTTAATGAAT
2349953 ATTTATAATAATTTAATG-AT
1 ATTTATAATAATTTAATGAAT
2349973 ATTTTATAAT
1 A-TTTATAAT
2349983 TTTAACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
ATTTATAATAATTTAATGAAT
Found at i:2355642 original size:21 final size:21
Alignment explanation
Indices: 2355617--2355657 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2355607 CCATAACAGG
*
2355617 GGGTATCAGTACCCCTTCATA
1 GGGTATCAGTACACCTTCATA
*
2355638 GGGTATCGGTACACCTTCAT
1 GGGTATCAGTACACCTTCAT
2355658 TAAATTCAAA
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:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
GGGTATCAGTACACCTTCATA
Found at i:2355766 original size:36 final size:36
Alignment explanation
Indices: 2355700--2355768 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
2355690 TTGCAGCCTG
*
2355700 AGTGTATGGATACACTGCAGGGTGTGTCGGTACACC
1 AGTGTATGGATACACTGCAGGGTGTATCGGTACACC
2355736 AGTGTATGGATACACT-CATAGGG-GTATCGGTAC
1 AGTGTATGGATACACTGC--AGGGTGTATCGGTAC
2355769 CCTTTTTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 1 0.03
36 25 0.83
37 4 0.13
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (36 bp):
AGTGTATGGATACACTGCAGGGTGTATCGGTACACC
Found at i:2356091 original size:23 final size:22
Alignment explanation
Indices: 2356065--2356112 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2356055 CCTAATAAAA
*
2356065 TGTTTAATGAAAAAGATACCAAT
1 TGTTTAA-CAAAAAGATACCAAT
* *
2356088 TG-TTAACAAAAGGATATCAAT
1 TGTTTAACAAAAAGATACCAAT
2356109 TGTT
1 TGTT
2356113 AAAAATATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
21 14 0.67
22 5 0.24
23 2 0.10
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (22 bp):
TGTTTAACAAAAAGATACCAAT
Found at i:2356098 original size:21 final size:19
Alignment explanation
Indices: 2356074--2356131 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 19
2356064 ATGTTTAATG
2356074 AAAAAGATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
*
2356093 ACAAAAGGATATCAATTGTT-
1 A-AAAA-GATACCAATTGTTA
*
2356113 AAAAATATACCAATTGTTA
1 AAAAAGATACCAATTGTTA
2356132 CCAATTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 11 0.33
19 5 0.15
20 5 0.15
21 12 0.36
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:2356126 original size:18 final size:18
Alignment explanation
Indices: 2356074--2356131 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
2356064 ATGTTTAATG
2356074 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
*
2356092 AACAAAAGGATATCAATTGTT
1 -A-AAAA-GATACCAATTGTT
*
2356113 AAAAATATACCAATTGTT
1 AAAAAGATACCAATTGTT
2356131 A
1 A
2356132 CCAATTGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 5 0.15
21 12 0.35
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:2357282 original size:18 final size:19
Alignment explanation
Indices: 2357248--2357294 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
2357238 TCTAAATCCT
2357248 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAA-TTCATTTTGG
*
2357268 TTTTCAAAA-TCATTTTTG
1 TTTTCAAAATTCATTTTGG
*
2357286 CTTTCAAAA
1 TTTTCAAAA
2357295 GAAAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.64
20 9 0.36
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (19 bp):
TTTTCAAAATTCATTTTGG
Found at i:2358270 original size:22 final size:23
Alignment explanation
Indices: 2358252--2358296 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2358242 GTCCCGAATG
2358252 ACCACATA-GGTTGCACCGAAGT
1 ACCACATAGGGTTGCACCGAAGT
*
2358274 ACCACATAGGGTTGCACCAAAGT
1 ACCACATAGGGTTGCACCGAAGT
2358297 GATACATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (23 bp):
ACCACATAGGGTTGCACCGAAGT
Found at i:2358488 original size:21 final size:21
Alignment explanation
Indices: 2358459--2358508 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2358449 AAAGAGTATA
* *
2358459 TTCACATTCAC-TGATTCGAAG
1 TTCATATTCACATG-TTCAAAG
2358480 TTCATATTCACATGTTCAAAG
1 TTCATATTCACATGTTCAAAG
2358501 TTCATATT
1 TTCATATT
2358509 TTCCTAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (21 bp):
TTCATATTCACATGTTCAAAG
Found at i:2358918 original size:54 final size:55
Alignment explanation
Indices: 2358855--2359107 Score: 406
Period size: 54 Copynumber: 4.6 Consensus size: 55
2358845 TCATAGTTGG
*
2358855 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAATACTCAATG-TTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAATACTCGATGTTTTGA
2358909 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAATACTCGATG-TTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAATACTCGATGTTTTGA
*
2358963 GGGTATCGATACACTCCTCAGTGTACCGATACATAAATGGAAT--TCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAAT--AATACTCGATGTTTTGA
* *
2359018 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAGTATTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAATACTCGATGTTTTGA
* *
2359073 GTGTATCGATACACTCCTCAGTGTACTGATACACA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACA
2359108 CTCATACAAT
Statistics
Matches: 188, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
53 2 0.01
54 96 0.51
55 87 0.46
56 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (55 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAATACTCGATGTTTTGA
Found at i:2359051 original size:109 final size:108
Alignment explanation
Indices: 2358855--2359107 Score: 402
Period size: 109 Copynumber: 2.3 Consensus size: 108
2358845 TCATAGTTGG
2358855 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAATACTCAATGTTTGAGGGTATCGATA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAATA-TCAATGTTTGAGGGTATCGATA
2358920 CACTCCTCAGTGTACCGATACACAAATAATACTCGATG-TTTGA
65 CACTCCTCAGTGTACCGATACACAAATAATACTCGATGTTTTGA
* *
2358963 GGGTATCGATACACTCCTCAGTGTACCGATACATAAATGGAAT-TCGATGTTTTGAGGGTATCGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAAT--AATATCAATG-TTTGAGGGTATCGA
* *
2359027 TACACTCCTCAGTGTACCGATACACAAATAGTATTCGATGTTTTGA
63 TACACTCCTCAGTGTACCGATACACAAATAATACTCGATGTTTTGA
* *
2359073 GTGTATCGATACACTCCTCAGTGTACTGATACACA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACA
2359108 CTCATACAAT
Statistics
Matches: 134, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
108 42 0.31
109 52 0.39
110 40 0.30
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29
Consensus pattern (108 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAATATCAATGTTTGAGGGTATCGATAC
ACTCCTCAGTGTACCGATACACAAATAATACTCGATGTTTTGA
Found at i:2360585 original size:22 final size:22
Alignment explanation
Indices: 2360560--2360605 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2360550 ATATTTTTCC
*
2360560 CACGATCCAGCAAAATCTATCA
1 CACGAACCAGCAAAATCTATCA
2360582 CACGAACCAGCAAAATCTATCA
1 CACGAACCAGCAAAATCTATCA
2360604 CA
1 CA
2360606 TACGCTCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.33, G:0.09, T:0.15
Consensus pattern (22 bp):
CACGAACCAGCAAAATCTATCA
Found at i:2365272 original size:22 final size:23
Alignment explanation
Indices: 2365250--2365294 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2365240 GTACCATATA
*
2365250 GGTTACATCGAAGTGCCACATAG
1 GGTTACACCGAAGTGCCACATAG
*
2365273 GGTTGCACCGAAGTGCCACATA
1 GGTTACACCGAAGTGCCACATA
2365295 TTTGTCCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (23 bp):
GGTTACACCGAAGTGCCACATAG
Found at i:2365480 original size:21 final size:21
Alignment explanation
Indices: 2365456--2365496 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2365446 ATATTCACAT
* *
2365456 TCACTTATTCGAAGTTCATAA
1 TCACATATTCAAAGTTCATAA
*
2365477 TCACATGTTCAAAGTTCATA
1 TCACATATTCAAAGTTCATA
2365497 TTTTCCTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (21 bp):
TCACATATTCAAAGTTCATAA
Found at i:2365974 original size:55 final size:55
Alignment explanation
Indices: 2365847--2366043 Score: 279
Period size: 55 Copynumber: 3.6 Consensus size: 55
2365837 ATAATTAGGG
* * * * *
2365847 GTATCGATACACTCCTCAGTATACCAATAAACAAATAGCACTCGATG-TTTGAGG
1 GTATCGATACACTCCTCAGTATACCGATACACAAATGGCATTCGATGTTTTGAGT
*
2365901 GTATCGATACACTCCTCAGTGTACCGATACACAAATGGCATTCGATGTTTTGAGT
1 GTATCGATACACTCCTCAGTATACCGATACACAAATGGCATTCGATGTTTTGAGT
* * * *
2365956 GTATCGATACACTCCTCAGTATACTGATACACAAATGGTATTCGTTGTTTTAAGT
1 GTATCGATACACTCCTCAGTATACCGATACACAAATGGCATTCGATGTTTTGAGT
* *
2366011 GTATCGATACACTCCTCAGTGTATCGATACACA
1 GTATCGATACACTCCTCAGTATACCGATACACA
2366044 CTCATACAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
54 42 0.33
55 86 0.67
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (55 bp):
GTATCGATACACTCCTCAGTATACCGATACACAAATGGCATTCGATGTTTTGAGT
Found at i:2367925 original size:15 final size:15
Alignment explanation
Indices: 2367906--2367939 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2367896 ATTTATTTTA
2367906 ATTTTTTAGTTAC-T
1 ATTTTTTAGTTACTT
*
2367920 ATTTTTTATTTACTT
1 ATTTTTTAGTTACTT
2367935 ATTTT
1 ATTTT
2367940 ATTTCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (15 bp):
ATTTTTTAGTTACTT
Found at i:2384059 original size:21 final size:21
Alignment explanation
Indices: 2384026--2384100 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
2384016 GTTTCCAGAT
* *
2384026 TCGCAACGCGAACTTTGACTA
1 TCGCAATGCGAACTTGGACTA
*
2384047 TCGTAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
2384068 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
2384089 TCCCAATGCGAA
1 TCGCAATGCGAA
2384101 TATGTAAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:2384141 original size:21 final size:21
Alignment explanation
Indices: 2384109--2384196 Score: 140
Period size: 21 Copynumber: 4.2 Consensus size: 21
2384099 AATATGTAAA
*
2384109 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
2384130 TTGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
2384151 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
2384172 TCGCATTGCAATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
2384193 TCGC
1 TCGC
2384197 GTTACGATTT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:2384289 original size:21 final size:19
Alignment explanation
Indices: 2384269--2384409 Score: 104
Period size: 21 Copynumber: 6.8 Consensus size: 19
2384259 CATATTCGCA
*
2384269 TTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCCAAATTCG
*
2384288 CATTGCGATTTATTCCAAATTCG
1 --TTGCGA--TAGTCCAAATTCG
2384311 TTGCGATAGT-CAAAGTTCGTG
1 TTGCGATAGTCCAAA-TTC--G
*
2384332 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAATTCG
* *
2384353 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
*
2384374 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAATTCG
2384395 TTGCGATAGTCCAAA
1 TTGCGATAGTCCAAA
2384410 ATCGCAACGA
Statistics
Matches: 97, Mismatches: 11, Indels: 26
0.72 0.08 0.19
Matches are distributed among these distances:
18 4 0.04
19 22 0.23
21 42 0.43
23 25 0.26
24 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (19 bp):
TTGCGATAGTCCAAATTCG
Found at i:2384327 original size:42 final size:42
Alignment explanation
Indices: 2384269--2384405 Score: 238
Period size: 42 Copynumber: 3.3 Consensus size: 42
2384259 CATATTCGCA
* *
2384269 TTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
2384311 TTGCGATAGTCAAAGTTCGTGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
2384353 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
2384395 TTGCGATAGTC
1 TTGCGATAGTC
2384406 CAAAATCGCA
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:2385162 original size:42 final size:42
Alignment explanation
Indices: 2385113--2385230 Score: 209
Period size: 42 Copynumber: 2.8 Consensus size: 42
2385103 TGCGATTTTT
*
2385113 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
2385155 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2385197 GACTATCGCAACGAATTTGGAATAAATCGCAACG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACG
2385231 AATTTGGAAT
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:0.22, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:2385226 original size:63 final size:63
Alignment explanation
Indices: 2385159--2385303 Score: 236
Period size: 63 Copynumber: 2.3 Consensus size: 63
2385149 AACTTCGACT
* * *
2385159 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAA
*
2385222 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAA
2385285 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
2385304 CTATCGCAAT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
63 66 0.88
65 9 0.12
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (63 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAA
Found at i:2385247 original size:42 final size:41
Alignment explanation
Indices: 2385116--2385303 Score: 177
Period size: 42 Copynumber: 4.4 Consensus size: 41
2385106 GATTTTTGAC
* * *
2385116 TATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGAC
1 TATCGCAACGAACTTGGAATAAATCGCAA-GCGAACTTGGAA
*
2385158 TATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAC
1 TATCGCAACGAACTTGGAATAAATCGCAA-GCGAACTTGGAA
* *
2385200 TATCGCAACGAATTTGGAATAAATCGCAA-CGAATTTGGAA
1 TATCGCAACGAACTTGGAATAAATCGCAAGCGAACTTGGAA
* * *
2385240 TAAATCGCAACGCGAACTTCGACT--ATCACAA-CGAACTTGGAA
1 T--ATCGCAA--CGAACTTGGAATAAATCGCAAGCGAACTTGGAA
2385282 TAAATCGCAACGCGAACTTGGA
1 T--ATCGCAA--CGAACTTGGA
2385304 CTATCGCAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
40 10 0.08
42 111 0.85
44 9 0.07
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (41 bp):
TATCGCAACGAACTTGGAATAAATCGCAAGCGAACTTGGAA
Found at i:2385299 original size:105 final size:105
Alignment explanation
Indices: 2385117--2385312 Score: 374
Period size: 105 Copynumber: 1.9 Consensus size: 105
2385107 ATTTTTGACT
* *
2385117 ATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTATCGCAACGAACTTGGAATAAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAAAT
2385182 CGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
66 CGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
2385222 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAAAT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAAAT
2385287 CGCAACGCGAACTTGGACTATCGCAA
66 CGCAACGCGAACTTGGACTATCGCAA
2385313 TGCGAATATG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 89 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (105 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCACAACGAACTTGGAATAAAT
CGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:2386615 original size:20 final size:21
Alignment explanation
Indices: 2386590--2386640 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2386580 TGAAAATATT
* *
2386590 TAATAAAATAAAATA-GATAA
1 TAATAAAATAAAAGAGGAAAA
2386610 TAAT-AAATAAAAGAGGAAAA
1 TAATAAAATAAAAGAGGAAAA
2386630 TAATAAAATAA
1 TAATAAAATAA
2386641 TAAATAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 12 0.44
21 6 0.22
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (21 bp):
TAATAAAATAAAAGAGGAAAA
Found at i:2386723 original size:17 final size:18
Alignment explanation
Indices: 2386687--2386728 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2386677 GTTGTTTTTA
*
2386687 AAATAAAATATAAGAATT
1 AAATAAAAGATAAGAATT
*
2386705 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
2386722 AAATAAA
1 AAATAAA
2386729 TAACTGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:2386737 original size:21 final size:23
Alignment explanation
Indices: 2386704--2386751 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 23
2386694 ATATAAGAAT
*
2386704 TAAATAAAAGAAATA-ATT-AAA
1 TAAATAAAAGAAAGAGATTAAAA
**
2386725 TAAATAACTGAAAGAGATTAAAA
1 TAAATAAAAGAAAGAGATTAAAA
2386748 TAAA
1 TAAA
2386752 GAGAAACTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 12 0.55
22 3 0.14
23 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (23 bp):
TAAATAAAAGAAAGAGATTAAAA
Found at i:2390457 original size:75 final size:75
Alignment explanation
Indices: 2390341--2390547 Score: 283
Period size: 75 Copynumber: 2.7 Consensus size: 75
2390331 TCTTAAATTC
* * * *
2390341 TAATTAAAACACTTAAAA-CTATTTAAACTAAAATATCTAAAACAAAAATAATAT-TTAAAATAA
1 TAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAAATAA
*
2390404 TATTCTAAATCT
65 TATCCTAAA-CT
**
2390416 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATCTAAAATATAAAAATAAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAAATAAT
2390481 ATCCTAAACT
66 ATCCTAAACT
* * *
2390491 TAATTAAAATACTAGAACATATTTAAACTAAAATACCTAAAACAAAGATAAATATAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAA-ATAT
2390548 TATTTAAAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
74 5 0.04
75 93 0.79
76 20 0.17
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (75 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAAATAAAATATAAAAATAAT
ATCCTAAACT
Found at i:2394366 original size:20 final size:21
Alignment explanation
Indices: 2394341--2394381 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2394331 GAATCAAAGA
2394341 TTAC-TTGCAGCATTGAAGGC
1 TTACTTTGCAGCATTGAAGGC
2394361 TTACTTTGCAGCATTGAAGGC
1 TTACTTTGCAGCATTGAAGGC
2394382 GGTTGGGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (21 bp):
TTACTTTGCAGCATTGAAGGC
Found at i:2396838 original size:6 final size:6
Alignment explanation
Indices: 2396827--2396859 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2396817 TGAGAGGCCT
2396827 TAACAG TAACAG TAACAG TAACAG TAACAG TAA
1 TAACAG TAACAG TAACAG TAACAG TAACAG TAA
2396860 TAGCAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.18
Consensus pattern (6 bp):
TAACAG
Found at i:2397142 original size:21 final size:19
Alignment explanation
Indices: 2397124--2397308 Score: 127
Period size: 21 Copynumber: 9.0 Consensus size: 19
2397114 CATATTCGTA
2397124 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
2397145 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
2397166 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* *
2397187 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* *
2397208 TTGCGATAGTCGAAGTACGTG
1 TTGCGATAGTCCAAGTTC--G
* *
2397229 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
* * *
2397250 TTGCGATTTATTCCAAATTCA
1 TTGCGA--TAGTCCAAGTTCG
2397271 TTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCG
*
2397290 TTGCGATAGTCGAAGTTCG
1 TTGCGATAGTCCAAGTTCG
2397309 CGTTGTAATT
Statistics
Matches: 141, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
19 36 0.26
21 89 0.63
23 16 0.11
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:2397191 original size:63 final size:61
Alignment explanation
Indices: 2397124--2397286 Score: 209
Period size: 63 Copynumber: 2.6 Consensus size: 61
2397114 CATATTCGTA
* *
2397124 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAATT--CGTTGCGATAGTCGAAGTACGCGTTGCGATTTATTCCAAATTCG
* *
2397187 TTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTACGTGTTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAATTCGTTGCGATAGTCGAAGTACGCGTTGCGATTTATTCCAAATTCG
* * *
2397250 TTGCGATTTATTCCAAATTCATTGCGATAGTCCAAGT
1 TTGCGA--TAGTCCAAATTCGTTGCGATAGTCGAAGT
2397287 TCGTTGCGAT
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
63 83 0.90
65 9 0.10
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (61 bp):
TTGCGATAGTCCAAATTCGTTGCGATAGTCGAAGTACGCGTTGCGATTTATTCCAAATTCG
Done.