Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 18
Found at i:891823 original size:21 final size:21
Alignment explanation
Indices: 891794--891886 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
891784 ATAGTCAGTA
891794 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
891815 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
891835 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
891856 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
891876 TCGCATTGCGA
1 TCGCATTGCGA
891887 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:891824 original size:41 final size:41
Alignment explanation
Indices: 891733--891867 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
891723 AAAGTCAGTA
* * * ** *
891733 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
891773 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
891815 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
891856 TCGCGTTGCGAT
1 TCGCGTTGCGAT
891868 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:891868 original size:41 final size:41
Alignment explanation
Indices: 891794--891886 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
891784 ATAGTCAGTA
891794 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
891835 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
891876 TCGCATTGCGA
1 TCGCATTGCGA
891887 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:895711 original size:21 final size:22
Alignment explanation
Indices: 895674--895714 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
895664 TTAAAAATTA
895674 TAAAGGTAGTACTGATACTCAT
1 TAAAGGTAGTACTGATACTCAT
895696 TAAAGG-AGTA-TCGATACTC
1 TAAAGGTAGTACT-GATACTC
895715 CCTGTCATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 11 0.61
22 6 0.33
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (22 bp):
TAAAGGTAGTACTGATACTCAT
Found at i:896292 original size:57 final size:57
Alignment explanation
Indices: 896204--896318 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
896194 TTATACTCCT
896204 TACTCCCTAAACTCAAAAAACCAATTCACCCATTCTTAGCAATTATTCGGTTGATCA
1 TACTCCCTAAACTCAAAAAACCAATTCACCCATTCTTAGCAATTATTCGGTTGATCA
896261 TACTCCCTAAACTCAAAAAACCAATTCACCCATTCTTAGCAATTATTCGGTTGATCA
1 TACTCCCTAAACTCAAAAAACCAATTCACCCATTCTTAGCAATTATTCGGTTGATCA
896318 T
1 T
896319 TGGGCTTCAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (57 bp):
TACTCCCTAAACTCAAAAAACCAATTCACCCATTCTTAGCAATTATTCGGTTGATCA
Found at i:901743 original size:26 final size:26
Alignment explanation
Indices: 901699--901753 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
901689 CTCTCTCATC
*
901699 TTTTAGAATTTATAATTTAATTCTTA
1 TTTTAGAATGTATAATTTAATTCTTA
* *
901725 TTTTAGAATGTA-AACTTTAGTTTTTA
1 TTTTAGAATGTATAA-TTTAATTCTTA
901751 TTT
1 TTT
901754 AATATAATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (26 bp):
TTTTAGAATGTATAATTTAATTCTTA
Found at i:905868 original size:24 final size:24
Alignment explanation
Indices: 905807--905868 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
905797 TATTAGGTTA
*
905807 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
905831 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
905855 AACATAACCGAACG
1 AACATAACTGAACG
905869 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:905928 original size:43 final size:40
Alignment explanation
Indices: 905879--905979 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 40
905869 TTCACGAACG
* *
905879 TAAATGAACGAACGAGACCTATGTTCATGTTCGTTCATTTAA
1 TAAATGAACG-ACAAAACCT-TGTTCATGTTCGTTCATTTAA
*
905921 TTAAATGAAC-ACAAAATCTTGTTCATGTTCGTTCATTTAA
1 -TAAATGAACGACAAAACCTTGTTCATGTTCGTTCATTTAA
*
905961 TAAATAAACGCACATAAAC
1 TAAATGAACG-ACA-AAAC
905980 GAACTTCCCG
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 8 0.16
40 21 0.42
41 9 0.18
42 3 0.06
43 9 0.18
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
TAAATGAACGACAAAACCTTGTTCATGTTCGTTCATTTAA
Found at i:906407 original size:29 final size:28
Alignment explanation
Indices: 906373--906438 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
906363 TACATCATTC
*
906373 TTTATTAAAA-TTTATATTTTCTCATTTTA
1 TTTATTAAAATTTTA-ATTTT-TCAATTTA
** *
906402 TTTATTGTACTTTTAATTTTTCAATTTA
1 TTTATTAAAATTTTAATTTTTCAATTTA
906430 TTTATTAAA
1 TTTATTAAA
906439 TTAACGAACC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 14 0.47
29 12 0.40
30 4 0.13
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTATTAAAATTTTAATTTTTCAATTTA
Found at i:913797 original size:3 final size:3
Alignment explanation
Indices: 913791--913840 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
913781 TGAAAAAAAC
* *
913791 TAA TAA TAAA TAA TTA TAA TTAA TAG TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA T-AA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
913837 -AA TA
1 TAA TA
913841 TCGGGACGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 4 0.10
3 29 0.74
4 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:914153 original size:134 final size:133
Alignment explanation
Indices: 913984--914845 Score: 982
Period size: 134 Copynumber: 6.5 Consensus size: 133
913974 TCCACTATTT
* * *
913984 CTTCAGGGTAGATT-AGATTGAGGCAGACTTGTTCCACTGTTACTCTA-GGAAAATCAAATCTTG
1 CTTCAGGGAAGATTGA-ATCGAGGCAGACTTGTTCCACTGTTACTC-AGGGAATATCAAATCTTG
* * ** * * *
914047 GAAGAGAGGGATATGTTTCGGTTCTTTTTTAGGGAAAATAAGATTCGGGGATGTTTAGTT-ATTA
64 AAAGAGAGGGATATGTTTCGCTTCTTCCTGAGGGAAAATCAGA-TCGGGGATGTTGA-TTCATT-
*
914111 CACTATT-
126 CACTGTTA
914118 CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
1 CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
*** * * * *
914183 AGAGAATAATATGTTCCGCTTC-T--T-AGGGAAAATTAGATCTGGGA--TTGATTCATTCTAGT
66 AGAGAGGGATATGTTTCGCTTCTTCCTGAGGGAAAATCAGATCGGGGATGTTGATTCATTC-ACT
914242 GTTA
130 GTTA
* ** *
914246 CTT-AGGGAATATTGAATATAGGAAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
1 CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
* * * * *
914310 AGAGAGGGATCTATTTCGCTTCTTCTTGAGGGAAAATCAGATCTTGGGATGTTGGTTCATTCCAC
66 AGAGAGGGATATGTTTCGCTTCTTCCTGAGGGAAAATCAGATC-GGGGATGTTGATTCATT-CAC
914375 TGTTA
129 TGTTA
* * * * * *
914380 CAT-AGGGAAGATTGAATCGAGACAAACTTATTCCATTGTTACTAAGGGAATATCAAATCTTGAA
1 CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
* * *
914444 AGAGAGGGATAT-TTTCCGCTTCTTTCTGAGGGAAAATCAGATTTGGGCATGTTGATTCATTCTA
66 AGAGAGGGATATGTTT-CGCTTCTTCCTGAGGGAAAATCAGA-TCGGGGATGTTGATTCATTC-A
914508 CTGTTA
128 CTGTTA
* * ** *
914514 -ATCAGAGAAGATTGAATCGAAACAGACTTGTTCCACTGTTACTCAAGGAATATCAAATCTTGAA
1 CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
* *
914578 AGAGAGGGATATGTTTCGTTTCTTCCTGAGGGAAAATCATATCAGGGGATGTTGATTCATTACAC
66 AGAGAGGGATATGTTTCGCTTCTTCCTGAGGGAAAATCAGATC-GGGGATGTTGATTCATT-CAC
914643 TGTTA
129 TGTTA
* * * *
914648 C-TAAGGGAAGATTGAATCGAGGTAGACTTATTCCACTGTTACTCAGGGAATATCAAATCTTAAA
1 CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
* * * * *
914712 AGAGAGGGATATATTCCGCTTCTTCCTGAGGGGAAATTAGATATGGGGATGTTGATTCATTCAAC
66 AGAGAGGGATATGTTTCGCTTCTTCCTGAGGGAAAATCAGAT-CGGGGATGTTGATTCATTC-AC
914777 TGTTA
129 TGTTA
* * *
914782 C-TCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTATTCAGGAAATATCAAATCTTGAA
1 CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
914846 GTATGTTGCT
Statistics
Matches: 629, Mismatches: 76, Indels: 46
0.84 0.10 0.06
Matches are distributed among these distances:
126 3 0.00
127 83 0.13
128 4 0.01
129 6 0.01
130 13 0.02
131 15 0.02
132 5 0.01
133 10 0.02
134 483 0.77
135 7 0.01
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (133 bp):
CTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAA
AGAGAGGGATATGTTTCGCTTCTTCCTGAGGGAAAATCAGATCGGGGATGTTGATTCATTCACTG
TTA
Found at i:914610 original size:268 final size:267
Alignment explanation
Indices: 914007--914845 Score: 1081
Period size: 268 Copynumber: 3.2 Consensus size: 267
913997 TAGATTGAGG
* * * *
914007 CAGACTTGTTCCACTGTTACTCTAGGAAAATCAAATCTTGGAAGAGAGGGATATGTTTCGGTTCT
1 CAGACTTGTTCCACTGTTACTCAAGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCT
* * * * * *
914072 TTTTTAGGGAAAATAAGAT-TCGGGGATGTTTAGTT-ATTACACTATT-CTTCAGGGAAGATTGA
66 TCTTGAGGGAAAATCAGATCT-GGGGATG-TTGGTTCATTACACTGTTAC-TAAGGGAAGATTGA
* *** *
914134 ATCGAGGCAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAATAATATGTTC
128 ATCGAGGCAGACTTATTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATATTC
* * * *
914199 CGCTTC--T-T-AGGGAAAATTAGATCTGGGA--TTGATTCATTCTAGTGTTACTTAGGGAATAT
193 CGCTTCTTTCTGAGGGAAAATTAGATATGGGATGTTGATTCATTCTACTGTTACTCAGGGAAGAT
**
914258 TGAATATAGGA
258 TGAATCGA-GA
* * *
914269 -AGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATCTATTTCGCTTCT
1 CAGACTTGTTCCACTGTTACTCAAGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCT
* *
914333 TCTTGAGGGAAAATCAGATCTTGGGATGTTGGTTCATTCCACTGTTAC-ATAGGGAAGATTGAAT
66 TCTTGAGGGAAAATCAGATCTGGGGATGTTGGTTCATTACACTGTTACTA-AGGGAAGATTGAAT
* * * * *
914397 CGAGACAAACTTATTCCATTGTTACTAAGGGAATATCAAATCTTGAAAGAGAGGGATATTTTCCG
130 CGAGGCAGACTTATTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATATTCCG
* * * *
914462 CTTCTTTCTGAGGGAAAATCAGATTTGGGCATGTTGATTCATTCTACTGTTAATCAGAGAAGATT
195 CTTCTTTCTGAGGGAAAATTAGATATGGG-ATGTTGATTCATTCTACTGTTACTCAGGGAAGATT
*
914527 GAATCGAAA
259 GAATCGAGA
*
914536 CAGACTTGTTCCACTGTTACTCAAGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGTTTCT
1 CAGACTTGTTCCACTGTTACTCAAGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCT
* * * *
914601 TCCTGAGGGAAAATCATATCAGGGGATGTTGATTCATTACACTGTTACTAAGGGAAGATTGAATC
66 TCTTGAGGGAAAATCAGATCTGGGGATGTTGGTTCATTACACTGTTACTAAGGGAAGATTGAATC
* *
914666 GAGGTAGACTTATTCCACTGTTACTCAGGGAATATCAAATCTTAAAAGAGAGGGATATATTCCGC
131 GAGGCAGACTTATTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATATTCCGC
* * *
914731 TTCTTCCTGAGGGGAAATTAGATATGGGGATGTTGATTCATTCAACTGTTACTCAGGGAAGATTG
196 TTCTTTCTGAGGGAAAATTAGATAT-GGGATGTTGATTCATTCTACTGTTACTCAGGGAAGATTG
*
914796 AATCGAGG
260 AATCGAGA
* *
914804 TAGACTTGTTCCACTGTTATTC-AGGAAATATCAAATCTTGAA
1 CAGACTTGTTCCACTGTTACTCAAGG-AATATCAAATCTTGAA
914846 GTATGTTGCT
Statistics
Matches: 500, Mismatches: 62, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
260 5 0.01
261 162 0.32
262 2 0.00
263 1 0.00
264 1 0.00
265 17 0.03
266 1 0.00
267 4 0.01
268 303 0.61
269 4 0.01
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (267 bp):
CAGACTTGTTCCACTGTTACTCAAGGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCT
TCTTGAGGGAAAATCAGATCTGGGGATGTTGGTTCATTACACTGTTACTAAGGGAAGATTGAATC
GAGGCAGACTTATTCCACTGTTACTCAGGGAATATCAAATCTTGAAAGAGAGGGATATATTCCGC
TTCTTTCTGAGGGAAAATTAGATATGGGATGTTGATTCATTCTACTGTTACTCAGGGAAGATTGA
ATCGAGA
Found at i:915411 original size:3 final size:3
Alignment explanation
Indices: 915403--915453 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
915393 TGAAAAGAAA
* *
915403 AAT AAT AAT AAT AAAT AAT TAT AATT AAT AGT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT -AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
915449 AAT AA
1 AAT AA
915454 AACTTTAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:916245 original size:24 final size:25
Alignment explanation
Indices: 916217--916274 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
916207 TTAATATTTT
916217 AATATATCAAATTA-AATTATAA-AA
1 AATATAT-AAATTATAATTATAATAA
*
916241 AATATA-AAAATATAATTATAATAA
1 AATATATAAATTATAATTATAATAA
*
916265 AAAATATAAA
1 AATATATAAA
916275 ATGAATCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 5 0.17
23 8 0.28
24 13 0.45
25 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AATATATAAATTATAATTATAATAA
Found at i:916320 original size:11 final size:11
Alignment explanation
Indices: 916307--916354 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
916297 TAGAAAAATT
*
916307 TAATTAATATT
1 TAATTAATATA
*
916318 TAATTAGTATA
1 TAATTAATATA
*
916329 TAATT-TTATA
1 TAATTAATATA
916339 TAATTAATATA
1 TAATTAATATA
916350 TAATT
1 TAATT
916355 TATAAAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (11 bp):
TAATTAATATA
Found at i:917243 original size:37 final size:37
Alignment explanation
Indices: 917167--917243 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
917157 TTTTTATATT
*
917167 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
917204 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
917241 TTT
1 TTT
917244 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:917918 original size:2 final size:2
Alignment explanation
Indices: 917913--917947 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
917903 ATTATTTTTA
*
917913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
917948 AAATTTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:919087 original size:98 final size:97
Alignment explanation
Indices: 918911--919109 Score: 301
Period size: 98 Copynumber: 2.0 Consensus size: 97
918901 CCGGAAAAAT
* * *
918911 TATAAAATTCAATTTTTACGGTTGGTTTAAAACTAGGGGTAGAGGGTTATCGGGGCTAAAGGGGC
1 TATAAAATTCAATTTTTACGGTTGGTTTAAAACCAAGGGCAGAGGGTTATCGGGGCTAAAGGGGC
918976 CCCGACCCCGCTCTAATTTGTAATTTTAAATTC
66 CCCGACCCCGCTCTAATTTGTAA-TTTAAATTC
* * *
919009 TATAAAATTCAATTTTTACTGTTGGTTTAAAACCAAGGGCGGAGGGTTATTGGGGCTAAAGGGG-
1 TATAAAATTCAATTTTTACGGTTGGTTTAAAACCAAGGGCAGAGGGTTATCGGGGCTAAAGGGGC
* *
919073 CCCGATCCCTGCTCTAATTTGTAATTTAAATTT
66 CCCGA-CCCCGCTCTAATTTGTAATTTAAATTC
919106 TATA
1 TATA
919110 CGGTATAAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
97 17 0.18
98 75 0.82
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (97 bp):
TATAAAATTCAATTTTTACGGTTGGTTTAAAACCAAGGGCAGAGGGTTATCGGGGCTAAAGGGGC
CCCGACCCCGCTCTAATTTGTAATTTAAATTC
Found at i:921137 original size:2 final size:2
Alignment explanation
Indices: 921130--921158 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
921120 TAAAGTCAAC
921130 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
921159 AGGAAAAAAA
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:922361 original size:3 final size:3
Alignment explanation
Indices: 922348--922399 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
922338 TCTGTAAAAA
*
922348 AAT AAT TAT AAT AAT ACAT AAT AAT AAT AAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
922393 AAT AAT A
1 AAT AAT A
922400 TGATGGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:922792 original size:113 final size:113
Alignment explanation
Indices: 922623--923228 Score: 582
Period size: 114 Copynumber: 5.3 Consensus size: 113
922613 ATTCCGCTGT
* * ** * *
922623 CTCTGAAGAGAATATCAAATC-TGGAGGTGAGAGTTCTGTTCCGCTT-CTTTCTGAAGGGAGTAT
1 CTCTGAAGGGAATATCAAATCTTGGAGGAGAGAGACCTGTTCCACTTAC-TTCTGAAGGGAATAT
* *
922686 CAGATCTAGGGGAATTGATCCATTGAATAGGGGCAGACTTGTTCCGCTTA
65 CAGATCT-GGGGAATTGATCCATTGAATAGGAGCAGACTTGTTCCACTTA
* * * *** * *
922736 CTCTGAAGGGAAAATCAATTC-TGGAGGTGAGAGTTTTGTTCCGCTT-CTTTCTGAAGGGAGTAT
1 CTCTGAAGGGAATATCAAATCTTGGAGGAGAGAGACCTGTTCCACTTAC-TTCTGAAGGGAATAT
* * * *
922799 CAGATCTAGGGGAGTTGATCCATTGAATAGGGGCAGACTTGTTCTGCTTGCTCTGCTTG
65 CAGATCT-GGGGAATTGATCCATTGAATAGGAGCAGAC----T-TG-TT-C-C-ACTTA
* * **
922858 CTCTGAAGGGAATATAAAATCTTTGAAAAGAGAGACCTGTTCCACTTAC-TCTGAAGGGAATATC
1 CTCTGAAGGGAATATCAAATCTTGGAGGAGAGAGACCTGTTCCACTTACTTCTGAAGGGAATATC
* * * * * *
922922 ATATATGAAGGAGTTTGATCTATTGAATTGGAGCAGACTTGTTCCACTTA
66 AGATCTG-GGGA-ATTGATCCATTGAATAGGAGCAGACTTGTTCCACTTA
* ** *
922972 CTCTGAAGGTAATATCAAATCTTGGAAAAGAGAGACATGTTCCACTTAC-TCTGAAGGGAATATC
1 CTCTGAAGGGAATATCAAATCTTGGAGGAGAGAGACCTGTTCCACTTACTTCTGAAGGGAATATC
* * *
923036 AGATCTTGGAGGAATTGATCCATCGAATCGGAGCAGACTTATTCCACTTA
66 AGATC-TGG-GGAATTGATCCATTGAATAGGAGCAGACTTGTTCCACTTA
*
923086 CTCTGAAGGGAATATCAAATC-TGG-GGAAAGAGAGACCTGTCCCACTTACTT-TGAAGGGAATA
1 CTCTGAAGGGAATATCAAATCTTGGAGG--AGAGAGACCTGTTCCACTTACTTCTGAAGGGAATA
* * * *
923148 TCAGATCTGAAGGAGTTTGATCCATTGAATTGGAGCAGACTTGTTGCACTTA
64 TCAGATCTG-GGGA-ATTGATCCATTGAATAGGAGCAGACTTGTTCCACTTA
923200 CTCTGAAGGGAATATCAAATCTTGGAGGA
1 CTCTGAAGGGAATATCAAATCTTGGAGGA
923229 ATTTGATCCA
Statistics
Matches: 421, Mismatches: 50, Indels: 43
0.82 0.10 0.08
Matches are distributed among these distances:
113 104 0.25
114 209 0.50
115 10 0.02
116 3 0.01
117 3 0.01
118 4 0.01
119 3 0.01
120 1 0.00
121 2 0.00
122 43 0.10
123 38 0.09
124 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (113 bp):
CTCTGAAGGGAATATCAAATCTTGGAGGAGAGAGACCTGTTCCACTTACTTCTGAAGGGAATATC
AGATCTGGGGAATTGATCCATTGAATAGGAGCAGACTTGTTCCACTTA
Found at i:924386 original size:11 final size:12
Alignment explanation
Indices: 924372--924435 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 12
924362 TTTTTATATA
924372 CTTTTTTCT-TT
1 CTTTTTTCTCTT
924383 CTTTTTTCTCTT
1 CTTTTTTCTCTT
* *
924395 CTCCTTAT-TCTT
1 CT-TTTTTCTCTT
*
924407 CTTTTTT-TCCT
1 CTTTTTTCTCTT
924418 -TTTTTTC-CTT
1 CTTTTTTCTCTT
924428 -TTTTTTCT
1 CTTTTTTCT
924436 TCAAGCAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
10 15 0.35
11 15 0.35
12 10 0.23
13 3 0.07
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (12 bp):
CTTTTTTCTCTT
Found at i:924422 original size:8 final size:9
Alignment explanation
Indices: 924407--924432 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
924397 CCTTATTCTT
924407 CTTTTTTTC
1 CTTTTTTTC
924416 CTTTTTTTC
1 CTTTTTTTC
924425 CTTTTTTT
1 CTTTTTTT
924433 TCTTCAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
CTTTTTTTC
Found at i:928860 original size:64 final size:64
Alignment explanation
Indices: 928779--928899 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
928769 ATTAATTTAA
*
928779 AAATAAAATATCAAATAGGATTTATGCATCAATGCATAAG-G-AGTGCATCGATGCATCCCCATT
1 AAATAAAACATCAAATAGGATTTATGCATCAATGCAT-AGTGTAGTGCATCGATGCATCCCCATT
* * * *
928842 AAATACAAACATCGAATAGGATTTATGCATCGATTCATGGTGTAGTGCATCGATGCAT
1 AAATA-AAACATCAAATAGGATTTATGCATCAATGCATAGTGTAGTGCATCGATGCAT
928900 ACCTATATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 6 0.12
64 29 0.58
65 15 0.30
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (64 bp):
AAATAAAACATCAAATAGGATTTATGCATCAATGCATAGTGTAGTGCATCGATGCATCCCCATT
Found at i:929539 original size:103 final size:103
Alignment explanation
Indices: 929360--929574 Score: 412
Period size: 103 Copynumber: 2.1 Consensus size: 103
929350 GTAGAGGGTC
*
929360 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGCGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGCGAGACACATAC
929425 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
929463 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGCGAGACACATAC
929528 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
929566 TATGTGGTC
1 TATGTGGTC
929575 TTATGGACAT
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGCGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:929620 original size:23 final size:22
Alignment explanation
Indices: 929593--929655 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
929583 ATTATTATAT
929593 GGCACTATGGTGCAATTCTACAC
1 GGCACT-TGGTGCAATTCTACAC
* * **
929616 GGCACTCCGATGCAATTCTACGT
1 GGCACT-TGGTGCAATTCTACAC
929639 GGCACTTAGGTGCAATT
1 GGCACTT-GGTGCAATT
929656 ATATGAGATG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (22 bp):
GGCACTTGGTGCAATTCTACAC
Found at i:935774 original size:65 final size:63
Alignment explanation
Indices: 935691--935849 Score: 160
Period size: 65 Copynumber: 2.5 Consensus size: 63
935681 TTTAAGGTGA
* * * * *
935691 ATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAAGAAAACATCGAATAGTATTTATG
1 ATCGATGCATAAGGAGTGCATCGATGCATCCAA-TT-AAAAA-AAAACATCGAATAGGATTTATG
935755 C
63 C
* * * *
935756 ATCGATGCATAAGGAGTGCATCGGTGCATCCCCATTAAATACAAACATCGAATAGGATTTATGC
1 ATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTATGC
*
935820 ATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 ATCGATGCATAAG-G-AGTGCATCGATGCAT
935850 ACCTCCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
63 1 0.01
64 32 0.41
65 43 0.54
66 2 0.03
67 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
ATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTATGC
Found at i:935821 original size:64 final size:67
Alignment explanation
Indices: 935734--935861 Score: 192
Period size: 64 Copynumber: 2.0 Consensus size: 67
935724 TTAAAAAAGA
* *
935734 AAACATCGAATAGTATTTATGCATCGATGCATAAG-G-AGTGCATCGGTGCAT-CC-CCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGCAT-AGTGTAGTGCATCGATGCATACCTCCATTAAA
935795 TAC
65 TAC
*
935798 AAACATCGAATAGGATTTATGCATCGATGCATGGTGTAGTGCATCGATGCATACCTCCATTAAA
1 AAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAA
935862 AGATGAAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
63 1 0.02
64 32 0.56
65 14 0.25
66 2 0.04
67 8 0.14
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (67 bp):
AAACATCGAATAGGATTTATGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAAT
AC
Found at i:936477 original size:103 final size:99
Alignment explanation
Indices: 936298--936519 Score: 374
Period size: 103 Copynumber: 2.2 Consensus size: 99
936288 GTAGAGGGTC
936298 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGATGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGATGAGACACATAC
936363 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATG--TATGA-TCTTAAGGAAT-A
* *
936401 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGATGAGACACATAC
936466 TTGATCCTTGGCATATGTATGATCTTAAGGAATA
66 TTGATCCTTGGCATATGTATGATCTTAAGGAATA
936500 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
936520 TATTATATGG
Statistics
Matches: 115, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
99 19 0.17
100 11 0.10
101 5 0.04
103 80 0.70
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (99 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGATGAGACACATAC
TTGATCCTTGGCATATGTATGATCTTAAGGAATA
Found at i:936577 original size:23 final size:23
Alignment explanation
Indices: 936526--936590 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
936516 ACATTATTAT
*
936526 ATGGCACTAC-GGTGCAATTCTAT
1 ATGGCACT-CTGGTGCAATTCTAC
*
936549 ACGGCACTCTGGTGCAATTCTAC
1 ATGGCACTCTGGTGCAATTCTAC
*
936572 GTGGCACT-TAGGTGCAATT
1 ATGGCACTCT-GGTGCAATT
936591 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.06
23 34 0.94
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (23 bp):
ATGGCACTCTGGTGCAATTCTAC
Found at i:949869 original size:18 final size:18
Alignment explanation
Indices: 949846--949880 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
949836 AGGGATTTTC
*
949846 AGTGGTCCTTCGAGACAT
1 AGTGGTCATTCGAGACAT
*
949864 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGAGACA
949881 AATATTCAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGAGACAT
Found at i:953557 original size:2 final size:2
Alignment explanation
Indices: 953552--953577 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
953542 TTTAGATTAC
953552 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
953578 TATTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:953690 original size:33 final size:32
Alignment explanation
Indices: 953652--953728 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 32
953642 TATATATATA
953652 TATATATTATTTT-TACTTTTT-TATTATTTTATT
1 TATATATT-TTTTCTACTTTTTCT-TTATTTT-TT
*
953685 TATATATTTTTATCTTCTTTTTCTTTATTTTTT
1 TATATATTTTT-TCTACTTTTTCTTTATTTTTT
953718 TA-ATATTTTTT
1 TATATATTTTTT
953729 ATTTATTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
31 1 0.03
32 11 0.28
33 13 0.32
34 14 0.35
35 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (32 bp):
TATATATTTTTTCTACTTTTTCTTTATTTTTT
Found at i:953727 original size:22 final size:23
Alignment explanation
Indices: 953702--953765 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
953692 TTTTATCTTC
953702 TTTTTCTTTATTTT-TTTAATAT
1 TTTTTCTTTATTTTATTTAATAT
* * *
953724 TTTTTATTTATTTTACTTACTAT
1 TTTTTCTTTATTTTATTTAATAT
* *
953747 TTTTTCTTTGTTTTCTTTA
1 TTTTTCTTTATTTTATTTA
953766 TCTTATCTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTTCTTTATTTTATTTAATAT
Found at i:953795 original size:26 final size:27
Alignment explanation
Indices: 953766--953829 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
953756 GTTTTCTTTA
*
953766 TCTTATCTTTTATTTAATTTGTTT-TT
1 TCTTATCTTTTATTTAATTTATTTATT
*
953792 TCTTCAT-TTTAATTTAATTTATTTATT
1 TCTT-ATCTTTTATTTAATTTATTTATT
*
953819 TCTTACCTTTT
1 TCTTATCTTTT
953830 TATCTAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTATCTTTTATTTAATTTATTTATT
Found at i:956930 original size:14 final size:13
Alignment explanation
Indices: 956875--956942 Score: 61
Period size: 14 Copynumber: 5.2 Consensus size: 13
956865 AACAAAAAGG
956875 AAAAAAGAG-AAA
1 AAAAAAGAGAAAA
*
956887 AAAGAAG-GAAAA
1 AAAAAAGAGAAAA
**
956899 AGCAAAGAGAAAA
1 AAAAAAGAGAAAA
956912 TAAAAAAGAGAAACA
1 -AAAAAAGAGAAA-A
956927 AAAATAA-AGAAAA
1 AAAA-AAGAGAAAA
956940 AAA
1 AAA
956943 TGAAGAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
11 1 0.02
12 13 0.29
13 9 0.20
14 19 0.42
15 3 0.07
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:956934 original size:19 final size:19
Alignment explanation
Indices: 956864--956930 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
956854 TATTCAATCA
956864 AAACAAAAAGGAAAAAAGAG
1 AAACAAAAA-GAAAAAAGAG
* *
956884 AAA-AAAGAAGGAAAAAG-C
1 AAACAAA-AAGAAAAAAGAG
* *
956902 AAAGAGAAAATAAAAAAGAG
1 AAACA-AAAAGAAAAAAGAG
956922 AAACAAAAA
1 AAACAAAAA
956931 TAAAGAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
18 3 0.08
19 23 0.62
20 11 0.30
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (19 bp):
AAACAAAAAGAAAAAAGAG
Found at i:958692 original size:37 final size:35
Alignment explanation
Indices: 958646--958731 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 35
958636 CAAGGGGTCG
*
958646 TCTCGCTTGAGACTAATTTACCCA-AAACAAAGTTTTA
1 TCTCTCTTGAGACTAATTT--CCATAAACAAA-TTTTA
* *
958683 TCTCTCTTGAGA-TAGTTTCCATTGAAACAAATTTTG
1 TCTCTCTTGAGACTAATTTCCA-T-AAACAAATTTTA
958719 TCTCTCTTGAGAC
1 TCTCTCTTGAGAC
958732 AGTTTCCCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
34 3 0.07
36 21 0.50
37 18 0.43
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (35 bp):
TCTCTCTTGAGACTAATTTCCATAAACAAATTTTA
Found at i:958730 original size:36 final size:37
Alignment explanation
Indices: 958670--958749 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 37
958660 AATTTACCCA
*
958670 AAACAAAGTTTTATCTCTCTTGAGATAGTTTCCATTG
1 AAACAAAGTTTTATCTCTCTTGAGACAGTTTCCATTG
* *
958707 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAAGTTTTATCTCTCTTGAGACAGTTTCCATTG
958743 AAACAAA
1 AAACAAA
958750 ATATTTGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 33 0.82
37 7 0.17
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (37 bp):
AAACAAAGTTTTATCTCTCTTGAGACAGTTTCCATTG
Found at i:958863 original size:36 final size:36
Alignment explanation
Indices: 958764--958922 Score: 194
Period size: 37 Copynumber: 4.4 Consensus size: 36
958754 TTGAATCTAT
* *
958764 TTTC-CTTGAAACAAATTTTGACTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * ** *
958799 TTTCTTTTGTAACTAGGTTTTGTCTCTCTTGATACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* *
958836 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
958872 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
*
958909 TTTTTCTTGAAACA
1 TTTCTCTTGAAACA
958923 CCAATCTTTG
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
35 4 0.04
36 39 0.38
37 59 0.58
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:958892 original size:73 final size:73
Alignment explanation
Indices: 958764--958922 Score: 212
Period size: 73 Copynumber: 2.2 Consensus size: 73
958754 TTGAATCTAT
* ** * * *
958764 TTTC-CTTGAAACAAATTTTGACTCCCTTGAGACAGTTTCTTTTGTAACTAGGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGACTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
*
958828 TGATACAG
66 TGAGACAG
* * *
958836 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTTGACTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
958901 TGAGACAG
66 TGAGACAG
*
958909 TTTTTCTTGAAACA
1 TTTCTCTTGAAACA
958923 CCAATCTTTG
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
72 4 0.05
73 70 0.95
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.42
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTTGACTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
TGAGACAG
Found at i:959683 original size:37 final size:37
Alignment explanation
Indices: 959627--959735 Score: 157
Period size: 37 Copynumber: 3.0 Consensus size: 37
959617 AAACAAACGT
* *
959627 TAGAGTTTTAGTA-TATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
959663 TAGCGTTTTACTAGGATTCAAACTCCTAAAAATAAGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
959700 TAGAGTTTTATTATGATTCAAACTCCTAAAAATAGG
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGG
959736 TTCCACAAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
36 11 0.17
37 53 0.83
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:960376 original size:41 final size:43
Alignment explanation
Indices: 960301--960403 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 43
960291 TTAGATTACA
*
960301 TATATATATATGTTA-TTTTTTATTATTTGTTTTA-TCAAT-T
1 TATATATATATATTATTTTTTTATTATTTGTTTTATTCAATAT
* *
960341 TATATATATAT-TTACTTTTTTTATGT-TTT-TATTTATTTATTAT
1 TATATATATATATTA-TTTTTTTAT-TATTTGT-TTTATTCAATAT
960384 TATATATATATATTATTTTT
1 TATATATATATATTATTTTT
960404 ACTTTTTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
39 3 0.06
40 12 0.22
41 15 0.28
42 4 0.07
43 17 0.31
44 3 0.06
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (43 bp):
TATATATATATATTATTTTTTTATTATTTGTTTTATTCAATAT
Found at i:960377 original size:4 final size:4
Alignment explanation
Indices: 960338--960474 Score: 57
Period size: 4 Copynumber: 33.0 Consensus size: 4
960328 TGTTTTATCA
* * *
960338 ATTT ATAT ATAT ATTT ACTTT TTTT ATGTT -TTT ATTT ATTT A-TT ATTAT
1 ATTT ATTT ATTT ATTT A-TTT ATTT AT-TT ATTT ATTT ATTT ATTT ATT-T
* * * * *
960387 ATAT ATAT ATTAT TTTT ACTTT TTTT A-TT ATTTT ATTT ATAT ATTT -TTT
1 ATTT ATTT ATT-T ATTT A-TTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT
* * * *
960436 CTTCT TTTT CTTT ATTT TTTAT ATTT ATTTT ATTT ATTT
1 ATT-T ATTT ATTT ATTT ATT-T ATTT A-TTT ATTT ATTT
960475 TACTTACTAT
Statistics
Matches: 103, Mismatches: 17, Indels: 26
0.71 0.12 0.18
Matches are distributed among these distances:
3 11 0.11
4 65 0.63
5 27 0.26
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:960417 original size:34 final size:34
Alignment explanation
Indices: 960366--960491 Score: 109
Period size: 34 Copynumber: 3.8 Consensus size: 34
960356 TTTTTTTATG
* *
960366 TTTTTA-TTTATTTATTATTATATATATATATTA
1 TTTTTACTTTTTTTATTATTTTATATATATATTA
*
960399 TTTTTACTTTTTTTATTATTTTATTTATATATT-
1 TTTTTACTTTTTTTATTATTTTATATATATATTA
* * * *
960432 TTTTCTTCTTTTTCT-TTATTTTTTATATTTATT-
1 TTTT-TACTTTTTTTATTATTTTATATATATATTA
* *
960465 TTATTTA-TTTTACTTACTATTTTATAT
1 TT-TTTACTTTT-TTTATTATTTTATAT
960492 TTGCTTTCTT
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
32 4 0.05
33 29 0.39
34 42 0.56
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (34 bp):
TTTTTACTTTTTTTATTATTTTATATATATATTA
Found at i:960426 original size:9 final size:9
Alignment explanation
Indices: 960349--960476 Score: 65
Period size: 9 Copynumber: 14.2 Consensus size: 9
960339 TTTATATATA
960349 TATTTACTTT
1 TATTTA-TTT
*
960359 T-TTTATGT
1 TATTTATTT
960367 T-TTTA-TT
1 TATTTATTT
960374 TATTTATTAT
1 TATTTATT-T
* *
960384 TATATA-TA
1 TATTTATTT
960392 TATATTATTTT
1 TAT-TTA-TTT
960403 TACTTT-TTT
1 TA-TTTATTT
960412 TA-TTATTT
1 TATTTATTT
*
960420 TATTTA-TA
1 TATTTATTT
*
960428 TATTTTTTCT
1 TATTTATT-T
* *
960438 TCTTTTTCTT
1 TATTTAT-TT
960448 TATTT-TTT
1 TATTTATTT
960456 ATATTTATTT
1 -TATTTATTT
960466 TATTTATTT
1 TATTTATTT
960475 TA
1 TA
960477 CTTACTATTT
Statistics
Matches: 93, Mismatches: 11, Indels: 29
0.70 0.08 0.22
Matches are distributed among these distances:
7 4 0.04
8 27 0.29
9 34 0.37
10 21 0.23
11 6 0.06
12 1 0.01
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (9 bp):
TATTTATTT
Found at i:960914 original size:2 final size:2
Alignment explanation
Indices: 960907--960943 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
960897 CGGTTACAAC
960907 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 A
960944 AAAGGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:961609 original size:5 final size:6
Alignment explanation
Indices: 961594--961628 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
961584 GAATCTAACC
961594 TTTTTA TTTTTA TTTTTA TTTTTA CTTGTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA -TT-TTTA TTT
961629 CTTTACATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.70
7 4 0.15
8 4 0.15
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:962140 original size:3 final size:3
Alignment explanation
Indices: 962127--962169 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
962117 ATGTAAAAAA
*
962127 AAT AAT TAT AAT AAAT AAT AAT AAT -AT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
962170 TGACGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:963163 original size:26 final size:28
Alignment explanation
Indices: 963111--963172 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 28
963101 CATTAACATT
*
963111 ATTTTAA-TTTTTTGAGTATTTTATT-A
1 ATTTTAATTTTTTTGAGTATTGTATTAA
*
963137 A-TTTAATTTTTTTTAGTATTAGT-TTAA
1 ATTTTAATTTTTTTGAGTATT-GTATTAA
963164 ATTTTAATT
1 ATTTTAATT
963173 CGTAGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 5 0.17
26 15 0.50
27 3 0.10
28 7 0.23
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (28 bp):
ATTTTAATTTTTTTGAGTATTGTATTAA
Found at i:965350 original size:18 final size:19
Alignment explanation
Indices: 965321--965356 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
965311 ATAATTGTAA
965321 TATTTGTATTTAATGTTTT
1 TATTTGTATTTAATGTTTT
965340 TATTT-TATTTAATGTTT
1 TATTTGTATTTAATGTTT
965357 ACGTTGTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (19 bp):
TATTTGTATTTAATGTTTT
Found at i:970447 original size:21 final size:21
Alignment explanation
Indices: 970421--970533 Score: 115
Period size: 21 Copynumber: 5.4 Consensus size: 21
970411 TCGTACCAAG
970421 GACGAGAAGAGCATTCATAAA
1 GACGAGAAGAGCATTCATAAA
* *
970442 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GAGCATTCATAAA
* *
970463 GACGAG-AGTGCTATTCATCAA
1 GACGAGAAGAGC-ATTCATAAA
* *
970484 GACGAGAAGACCCTTCATAAA
1 GACGAGAAGAGCATTCATAAA
* *
970505 GACGAGAAGA-CCTTCGTAAA
1 GACGAGAAGAGCATTCATAAA
970525 GACGAGAAG
1 GACGAGAAG
970534 TCCACATCGC
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
19 1 0.01
20 20 0.25
21 55 0.69
22 4 0.05
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.17
Consensus pattern (21 bp):
GACGAGAAGAGCATTCATAAA
Found at i:973148 original size:17 final size:17
Alignment explanation
Indices: 973128--973167 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
973118 AGAGAAGTGT
973128 AGAAAGAGAA-AAAGAAA
1 AGAAA-AGAAGAAAGAAA
973145 AGAAAAGAAGAAAGAAA
1 AGAAAAGAAGAAAGAAA
973162 AGAAAA
1 AGAAAA
973168 AATTGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AGAAAAGAAGAAAGAAA
Found at i:973158 original size:12 final size:12
Alignment explanation
Indices: 973128--973165 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
973118 AGAGAAGTGT
973128 AGAAAGAGAAA-A
1 AGAAAGA-AAAGA
973140 AGAAAAGAAAAGA
1 AG-AAAGAAAAGA
973153 AGAAAGAAAAGA
1 AGAAAGAAAAGA
973165 A
1 A
973166 AAAATTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAGA
Found at i:974719 original size:127 final size:127
Alignment explanation
Indices: 974449--974759 Score: 421
Period size: 127 Copynumber: 2.4 Consensus size: 127
974439 AAGTTGCGAT
* * * * * **
974449 ATGTTGTGGCACGGCTGAACCCACATTAGGTTGAGATGACAAGATTCAGAAGAAGAAGAAGGCAT
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAG-AGAAGGCAT
* * *
974514 GAAGAATAAGCCTTACAATCTGAGGTGATGGGACATTTTGAAGGCTCGTACCAGTATAAGGTA
65 GAAGAATAAGCCTTACAATCTGAGGTAATGGGACATTTTGAAGGCCCGTACCAGTATAAGATA
974577 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAG-G-AGGCATG
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGAGAAGGCATG
* * *
974640 AAGAATGAGCCTTACAATTTGAGGTAATAGGGGCATTTTGAAAGGCCCGTACCAGTATAAGATA
66 AAGAATAAGCCTTACAATCTGAGGTAAT-GGGACATTTTG-AAGGCCCGTACCAGTATAAGATA
* * *
974704 ATGTTGGGGCGCGACTGAACCCACATCATGATGAGA-AAATAAGATTCAGACCAAGA
1 ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAA-AAGATTCAGACCAAGA
974760 AGTTATTGAG
Statistics
Matches: 163, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
125 32 0.20
126 13 0.08
127 70 0.43
128 48 0.29
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (127 bp):
ATGTTGGGGCACGACTGAACCCACATCATGTTGAGATGAAAAGATTCAGACCAAGAGAAGGCATG
AAGAATAAGCCTTACAATCTGAGGTAATGGGACATTTTGAAGGCCCGTACCAGTATAAGATA
Found at i:975646 original size:36 final size:36
Alignment explanation
Indices: 975490--975679 Score: 238
Period size: 36 Copynumber: 5.2 Consensus size: 36
975480 AAGTCAATCC
975490 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
975526 GAAGCCTTCACCGGAGAATAGTGAAGCAATCAATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* *
975562 GAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCA
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * *
975598 TAAGTCTTCACCAGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
* * * * *
975634 TAAGTCTTCACC-AAAAAGTAGTGAAGCATATCCATTT
1 TAAGCCTTCACCGGAGAA-TAGTGAAGCA-AACCATCT
975671 TAAGCCTTC
1 TAAGCCTTC
975680 TCAGAAGAGT
Statistics
Matches: 135, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
35 2 0.01
36 119 0.88
37 14 0.10
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (36 bp):
TAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCT
Found at i:976126 original size:51 final size:51
Alignment explanation
Indices: 976061--976619 Score: 614
Period size: 51 Copynumber: 10.8 Consensus size: 51
976051 AAGATTATTT
* *
976061 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTTTGAAGATGTCC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * * *
976112 GAGTTCCATACTCCCTAGAGAAGGAATGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * * *
976163 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCAAACCCGTTTAAAGATGTCC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * *
976214 GAGTTCCATACTCCCTAGAGAAGGAAGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * * * *
976265 GAGTTCTATAATCCTTAAAGAAAGAAGGAGCGAACCCGTTTAAAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * *
976316 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAATAGATGTCT
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTCC
* * * *
976369 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * * *
976420 GAGTTCTATAATCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
* * * * * *
976471 GAGTTCTATACTCCTTAAAGAAGGAAGGAGCGAACTCGTTTGAAGAGATGTTC
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTCC
* ** *
976524 GAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCT
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAG---ATGTCC
* * * * *
976578 GAGTTCCATGCTCCCTAGAGAAATAGGGAGTGAACCCATTTG
1 GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTG
976620 TTGAAGATTG
Statistics
Matches: 429, Mismatches: 72, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
51 297 0.69
52 4 0.01
53 88 0.21
54 40 0.09
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (51 bp):
GAGTTCCATACTCCCTAGAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
Found at i:976423 original size:155 final size:154
Alignment explanation
Indices: 976060--976583 Score: 764
Period size: 155 Copynumber: 3.4 Consensus size: 154
976050 GAAGATTATT
* * * * * *
976060 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTTTGAAGATGTCCGAGTTCCATACTC
1 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATC
* * * * * * *
976125 CCTAGAGAAGGAATGAGCGAACCCGTGTGAAGATATGCGAGTTCTATACTCCTTAAAGAAAGAAG
66 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAG
*
976190 GAGCAAACCCGTTT-AAAGATGTC
131 GAGCGAACCCGTTTGAAAGATGTC
* * *
976213 CGAGTTCCATACTCCCTAGAGAAGGAAGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATC
1 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATC
* *
976278 CTTAAAGAAAGAAGGAGCGAACCCGTTTAAAGATGTTCGAGTTCCATACTCCTTAAAGAAAGAAG
66 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAG
976343 GAGCGAACCCGTTTGAATAGATGTC
131 GAGCGAACCCGTTTGAA-AGATGTC
976368 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATC
1 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATC
*
976433 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAGGAAG
66 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAG
*
976498 GAGCGAACTCGTTTGAAGAGATGT-
131 GAGCGAACCCGTTTGAA-AGATGTC
* * *
976522 TCGAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTGAGTTC
1 T-GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAG-ATATG-C-GAGTTC
976584 CATGCTCCCT
Statistics
Matches: 335, Mismatches: 30, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
153 125 0.37
154 3 0.01
155 195 0.58
156 5 0.01
157 1 0.00
158 6 0.02
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (154 bp):
TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGATATGCGAGTTCTATAATC
CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAG
GAGCGAACCCGTTTGAAAGATGTC
Found at i:976659 original size:53 final size:52
Alignment explanation
Indices: 976617--977100 Score: 587
Period size: 53 Copynumber: 9.0 Consensus size: 52
976607 GTGAACCCAT
* *
976617 TTGTTGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
1 TTGTTGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGG-GGAGACACGA
* * *
976670 TCGTTGAAGATTGTGGGTCTTATACTCTCTGAAGATATAGGGGGGAGACACGA
1 TTGTTGAAGATTGTGAGTCTTATACTCTCTGAAGAAATA-GGGGGAGACACGA
* * *
976723 TAGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAAAAATAGGGGGCAAACACGA
1 TTGTTGAAGATTG-T-GAGTCTTATACTCTCTGAAGAAATAGGGGG-AGACACGA
* *
976778 TTGATGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
1 TTGTTGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGG-AGACACGA
* *
976831 TTGATGAAGATTGTGAGTCTTATACTCTCTGAA-AGAATAGGGAGCAGACACGA
1 TTGTTGAAGATTGTGAGTCTTATACTCTCTGAAGA-AATAGGG-GGAGACACGA
* * *
976884 TTGTTGAAGATTATTCGAGTCTCATACTCTCTGAA-AGAATAGGGAGTAGACACGA
1 TTGTTGAAGATT-GT-GAGTCTTATACTCTCTGAAGA-AATAGGG-GGAGACACGA
* *
976939 TTGTTGAAGATTGTTCGAGTCTTATACTATCTGAAGAAATAGGGGGCAGACGCGA
1 TTGTTGAAGATTG-T-GAGTCTTATACTCTCTGAAGAAATAGGGGG-AGACACGA
* * *
976994 TTGATGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGA
1 TTGTTGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGG-AGACACGA
* *
977047 TTGATGAAGATTGT-AGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGA
1 TTGTTGAAGATTGTGA-GTCTTATACTCTCTGAAGAAATAGGGGG-AGACACGA
977100 T
1 T
977101 CGTGGAAGCA
Statistics
Matches: 389, Mismatches: 30, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
52 1 0.00
53 239 0.61
54 14 0.04
55 134 0.34
56 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (52 bp):
TTGTTGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGAGACACGA
Found at i:976800 original size:161 final size:160
Alignment explanation
Indices: 976621--977100 Score: 703
Period size: 161 Copynumber: 3.0 Consensus size: 160
976611 ACCCATTTGT
* * * * *
976621 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTTGAAGATTGTGG
1 TGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
* *
976686 GTCTTATACTCTCTGAAGATATAGGGGGGAGACACGATAGTTGAAGATTGTTCGAGTCTTATACT
66 GTCTTATACTCTCTGAAGA-ATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACT
*
976751 CTCTGAAAAAATAGGGGGCAAACACGATTGA
130 CTCTGAAAAAATAGGGGGCAGACACGATTGA
*
976782 TGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGA
1 TGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
* * *
976847 GTCTTATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTTGAAGATTATTCGAGTCTCATACT
66 GTCTTATACTCTCTG-AAGAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACT
* * * *
976912 CTCTGAAAGAATAGGGAGTAGACACGATTGT
130 CTCTGAAAAAATAGGGGGCAGACACGATTGA
*
976943 TGAAGATTGTTCGAGTCTTATACTATCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGT
1 TGAAGATTG-T-GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGT
* * *
977008 GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-TAG-GTCTTATA
64 GGGTCTTATACTCTCTGAAG-AATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATA
* *
977071 CTCTCTGAAGATATAGGGGGCAGACACGAT
128 CTCTCTGAAAAAATAGGGGGCAGACACGAT
977101 CGTGGAAGCA
Statistics
Matches: 286, Mismatches: 29, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
161 181 0.63
162 10 0.03
163 95 0.33
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (160 bp):
TGAAGATTGTGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
GTCTTATACTCTCTGAAGAATAGGGGGCAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTC
TCTGAAAAAATAGGGGGCAGACACGATTGA
Found at i:976998 original size:216 final size:213
Alignment explanation
Indices: 976621--977108 Score: 764
Period size: 216 Copynumber: 2.3 Consensus size: 213
976611 ACCCATTTGT
* *
976621 TGAAGATTGTGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTTGAAGATTGTGG
1 TGAAGATTGTGAGTCTTATACTCTCTGAAG-AATAGGGAGCAGACACGATCGTTGAAGATTGTGA
* *
976686 GTCTTATACTCTCTGAAGATATAGGGGGGAGACACGATAGTTGAAGATTGTTCGAGTCTTATACT
65 GTCTCATACTCTCTGAAGATATAGGGAGGAGACACGATAGTTGAAGATTGTTCGAGTCTTATACT
*
976751 CTCTGAAAAAATAGGGGGCAAACACGATTGATGAAGATTGTGAGTCTTATACTCTCTGAAGAAAT
130 ATCTGAAAAAATAGGGGGCAAACACGATTGATGAAGATTGTGAGTCTTATACTCTCTGAAGAAAT
976816 AGGGGGCAGACGCGATTGA
195 AGGGGGCAGACGCGATTGA
* *
976835 TGAAGATTGTGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTTGAAGATTATTC
1 TGAAGATTGTGAGTCTTATACTCTCTG-AAGAATAGGGAGCAGACACGATCGTTGAAGATT-GT-
* *
976900 GAGTCTCATACTCTCTGAAAGA-ATAGGGAGTAGACACGATTGTTGAAGATTGTTCGAGTCTTAT
63 GAGTCTCATACTCTCTG-AAGATATAGGGAGGAGACACGATAGTTGAAGATTGTTCGAGTCTTAT
* * * *
976964 ACTATCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGGTCTTATACTCTCTGAAGA
127 ACTATCTGAAAAAATAGGGGGCAAACACGATTGATGAAGATTGTGAGTCTTATACTCTCTGAAGA
977029 AATAGGGGGCAGACGCGATTGA
192 AATAGGGGGCAGACGCGATTGA
* *
977051 TGAAGATTGT-AGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATCGTGGAAG
1 TGAAGATTGTGA-GTCTTATACTCTCTGAAGA-ATAGGGAGCAGACACGATCGTTGAAG
977109 CAAGAGGGAG
Statistics
Matches: 252, Mismatches: 16, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
214 55 0.22
215 9 0.04
216 184 0.73
217 4 0.02
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (213 bp):
TGAAGATTGTGAGTCTTATACTCTCTGAAGAATAGGGAGCAGACACGATCGTTGAAGATTGTGAG
TCTCATACTCTCTGAAGATATAGGGAGGAGACACGATAGTTGAAGATTGTTCGAGTCTTATACTA
TCTGAAAAAATAGGGGGCAAACACGATTGATGAAGATTGTGAGTCTTATACTCTCTGAAGAAATA
GGGGGCAGACGCGATTGA
Found at i:981215 original size:159 final size:158
Alignment explanation
Indices: 980834--981237 Score: 467
Period size: 158 Copynumber: 2.6 Consensus size: 158
980824 TTCCTTTTTA
* * * * * *
980834 AAAGAAAGACTCGTTTTAGGGGAAGCGTTTTTCCTTTTCTTAGAGAATCTCTACCATGTCAC-AT
1 AAAGAAAGACTCGTTTCAAGGGAAGCATTGTTCTTTTTCTCAGAGAATCTCTACCATGTCACAAT
* * * *** *
980898 TTTCTCATCCCATCAAACATAATGGACTGGACCTTTTGGATTAAATCATAACTTCAACATACGAA
66 ATT-TCATCTCATCAAACATAATGGACTAGACCTTGCAGATTAAATCATAACTTCAACATAAGAA
* * *
980963 CTGAGTCTTGCAAATAAAATCTGACAAAG
130 CTGAGCCTTACAAATAAAATATGACAAAG
* *
980992 AAAGAAAGACTCGTTTCACGGGAAG-A--GCTTCTCCTTTTCGCAGAGAATCTCTACCATGTCAC
1 AAAGAAAGACTCGTTTCAAGGGAAGCATTG-TTCT--TTTTCTCAGAGAATCTCTACCATGTCAC
*
981054 AATATTTCATCTCATCGAACATAATGGACTA-AGCCTTGCAGATTAAATCATAACTTCAACATAA
63 AATATTTCATCTCATCAAACATAATGGACTAGA-CCTTGCAGATTAAATCATAACTTCAACATAA
* * *
981118 TAGACTGAGCCTTACAGATAGAATATGACAAAG
127 GA-ACTGAGCCTTACAAATAAAATATGACAAAG
* * *
981151 AAAGAAAGGCTCGTTCCAAGGGAAGCATTGTTCTTTTTCTCAGAGAATCTCTACCATGTAACAAT
1 AAAGAAAGACTCGTTTCAAGGGAAGCATTGTTCTTTTTCTCAGAGAATCTCTACCATGTCACAAT
* * *
981216 GTCTCATTTCATCAAACATAAT
66 ATTTCATCTCATCAAACATAAT
981238 TAAGAGGAAT
Statistics
Matches: 207, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
156 3 0.01
157 1 0.00
158 99 0.48
159 98 0.47
160 1 0.00
161 4 0.02
162 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (158 bp):
AAAGAAAGACTCGTTTCAAGGGAAGCATTGTTCTTTTTCTCAGAGAATCTCTACCATGTCACAAT
ATTTCATCTCATCAAACATAATGGACTAGACCTTGCAGATTAAATCATAACTTCAACATAAGAAC
TGAGCCTTACAAATAAAATATGACAAAG
Found at i:981344 original size:25 final size:25
Alignment explanation
Indices: 981316--981379 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 25
981306 ATCAAACATT
981316 ATATCTCTTAAACTCTCCAAT-TTTG
1 ATATCTCTTAAACTCT-CAATCTTTG
981341 ATATCT-TCT-AACTCTCAATCTTTG
1 ATATCTCT-TAAACTCTCAATCTTTG
* *
981365 AAAT-TCTAAAACTCT
1 ATATCTCTTAAACTCT
981380 TAAACTCTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
23 5 0.15
24 21 0.64
25 7 0.21
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.42
Consensus pattern (25 bp):
ATATCTCTTAAACTCTCAATCTTTG
Found at i:982117 original size:102 final size:102
Alignment explanation
Indices: 981919--982170 Score: 272
Period size: 102 Copynumber: 2.5 Consensus size: 102
981909 TTCCCTATGG
* * * ** * * * * * * *
981919 CAACATCCTTTCCAGTTCAAGGGGAAGATATTCATTTGTCAATTTCTTTGACCTGAATATGGAGA
1 CAACATCCCTTCAAGTTCAAGGGGAAGACACACATCTGCCAACTTGTTTTACCTCAGTATGGAGA
* *
981984 TGCCTTCGACACAACAATTTGTTCAATACCCATATGA
66 TGCCTTCGACACAACAATTAGTTCAATACCCATATCA
* * * * **
982021 CAATATGCCTTCAAGTTCCAGGGGGAGACATTCATCTGCCAACTTGTTTTACCTCAGTATGGAGA
1 CAACATCCCTTCAAGTTCAAGGGGAAGACACACATCTGCCAACTTGTTTTACCTCAGTATGGAGA
* * *
982086 TGCTTTTGACACAACAGTTAGTTCGAA-ACCCATATCA
66 TGCCTTCGACACAACAATTAGTTC-AATACCCATATCA
*
982123 CAACATCCCTTCAAGTTCAAGTGGAAGACACACATCTGCCAACTTGTT
1 CAACATCCCTTCAAGTTCAAGGGGAAGACACACATCTGCCAACTTGTT
982171 CAACCTAAAC
Statistics
Matches: 123, Mismatches: 26, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
102 121 0.98
103 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (102 bp):
CAACATCCCTTCAAGTTCAAGGGGAAGACACACATCTGCCAACTTGTTTTACCTCAGTATGGAGA
TGCCTTCGACACAACAATTAGTTCAATACCCATATCA
Found at i:984497 original size:20 final size:19
Alignment explanation
Indices: 984466--984523 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
984456 TGTAATTTTT
*
984466 AAAACTCTAAACCATTTAA
1 AAAACCCTAAACCATTTAA
**
984485 AAATACCCTAAACCAGCTAA
1 AAA-ACCCTAAACCATTTAA
* *
984505 AAACCCCTAAACAATTTAA
1 AAAACCCTAAACCATTTAA
984524 CCCTAAACAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAACCCTAAACCATTTAA
Found at i:985080 original size:22 final size:23
Alignment explanation
Indices: 985037--985082 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
985027 AAAGAATTTG
985037 AATGTTTTGATTAGAAAAATAAA
1 AATGTTTTGATTAGAAAAATAAA
985060 AATGTTTTGATTAG-AAAATAAA
1 AATGTTTTGATTAGAAAAATAAA
985082 A
1 A
985083 TAAAAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (23 bp):
AATGTTTTGATTAGAAAAATAAA
Found at i:985730 original size:3 final size:3
Alignment explanation
Indices: 985722--985799 Score: 149
Period size: 3 Copynumber: 26.3 Consensus size: 3
985712 GATTTTGCAC
985722 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
985770 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
985800 ATGAGTGCCC
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 72 0.97
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1000189 original size:19 final size:19
Alignment explanation
Indices: 1000165--1000206 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1000155 AGTGAGCTTC
*
1000165 GAAAATATTACACCTTTTT
1 GAAAATATTACACCTTATT
*
1000184 GAAAATATTATACCTTATT
1 GAAAATATTACACCTTATT
1000203 GAAA
1 GAAA
1000207 GGTTATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (19 bp):
GAAAATATTACACCTTATT
Found at i:1003550 original size:54 final size:54
Alignment explanation
Indices: 1003486--1003591 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 54
1003476 AATCATTGTT
* * *
1003486 TGACACGTAGCATTTTTTTAATTTCTTTCAATTTTAGTATAGTAGTAGATAAAA
1 TGACAAGTAGCATTTTTTTAATTTCTTTCAATTTTAGAATAATAGTAGATAAAA
* *
1003540 TGACAAGTAGCATTTTTTTTATTTCTTTCAATTTTAGAATAATAGTATATAA
1 TGACAAGTAGCATTTTTTTAATTTCTTTCAATTTTAGAATAATAGTAGATAA
1003592 GACTAGAGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.46
Consensus pattern (54 bp):
TGACAAGTAGCATTTTTTTAATTTCTTTCAATTTTAGAATAATAGTAGATAAAA
Found at i:1003707 original size:23 final size:22
Alignment explanation
Indices: 1003681--1003744 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
1003671 TTTTAATAAT
*
1003681 TTTGTCTTTATAACACATTTTTC
1 TTTGTCTTT-TAACACATTTTTA
**
1003704 TTTGT-TTTTATGACATTTTTA
1 TTTGTCTTTTAACACATTTTTA
*
1003725 TTTGTCTTTTGACACATTTT
1 TTTGTCTTTTAACACATTTT
1003745 CGGTTGTTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.44
22 14 0.41
23 5 0.15
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.61
Consensus pattern (22 bp):
TTTGTCTTTTAACACATTTTTA
Found at i:1005904 original size:15 final size:16
Alignment explanation
Indices: 1005875--1005904 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1005865 TAAGCTTTTG
1005875 AAGATTTATAAATTTA
1 AAGATTTATAAATTTA
1005891 AAGATTTA-AAATTT
1 AAGATTTATAAATTT
1005905 TAGTATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (16 bp):
AAGATTTATAAATTTA
Found at i:1005906 original size:16 final size:17
Alignment explanation
Indices: 1005870--1005906 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1005860 CTTTTTAAGC
*
1005870 TTTTGAAGATTTATAAA
1 TTTTAAAGATTTATAAA
1005887 -TTTAAAGATTTA-AAA
1 TTTTAAAGATTTATAAA
1005902 TTTTA
1 TTTTA
1005907 GTATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (17 bp):
TTTTAAAGATTTATAAA
Found at i:1006361 original size:15 final size:14
Alignment explanation
Indices: 1006340--1006380 Score: 61
Period size: 12 Copynumber: 3.1 Consensus size: 14
1006330 GTGTATGTTA
1006340 ATATATATATTATT
1 ATATATATATTATT
1006354 AT-TATATA-TATT
1 ATATATATATTATT
1006366 A-ATATATATTATT
1 ATATATATATTATT
1006379 AT
1 AT
1006381 TACAAATGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 11 0.46
13 11 0.46
14 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATATATATTATT
Found at i:1007771 original size:23 final size:22
Alignment explanation
Indices: 1007735--1007779 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1007725 TTATAATAGA
*
1007735 ATTATTAATATTTATGTTAAAT
1 ATTATTAATATTTATATTAAAT
*
1007757 ATTATTTAGTATTTATATTAAAT
1 ATTA-TTAATATTTATATTAAAT
1007780 TATTTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
ATTATTAATATTTATATTAAAT
Found at i:1013249 original size:42 final size:43
Alignment explanation
Indices: 1013169--1013249 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
1013159 ACAACTTGGA
* *
1013169 ATGTGAGGGTATGCTGAAGGCCCATTACAATCAGAAATAATCT
1 ATGTGAGGGTATCCTGAAGGCCCATTACAATCAAAAATAATCT
*
1013212 ATGTG-GGGTATCCTGAAGGCCCATTTCAGA-CAAAAATA
1 ATGTGAGGGTATCCTGAAGGCCCATTACA-ATCAAAAATA
1013250 GGATATGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 28 0.82
43 6 0.18
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (43 bp):
ATGTGAGGGTATCCTGAAGGCCCATTACAATCAAAAATAATCT
Found at i:1014610 original size:20 final size:20
Alignment explanation
Indices: 1014582--1014660 Score: 95
Period size: 20 Copynumber: 4.0 Consensus size: 20
1014572 AAAATCAAAA
*
1014582 CCTCAGGGTAATTTGTAAAG
1 CCTCCGGGTAATTTGTAAAG
1014602 CCTCCGGGTAATTTGTAAAG
1 CCTCCGGGTAATTTGTAAAG
* * *
1014622 CCTTCGAGTCATTTGTAAAG
1 CCTCCGGGTAATTTGTAAAG
** *
1014642 CCTTTGGGTCATTTGTAAA
1 CCTCCGGGTAATTTGTAAA
1014661 TCCATTGGGT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
CCTCCGGGTAATTTGTAAAG
Found at i:1014668 original size:20 final size:19
Alignment explanation
Indices: 1014587--1014673 Score: 93
Period size: 20 Copynumber: 4.4 Consensus size: 19
1014577 CAAAACCTCA
* *
1014587 GGGTAATTTGTAAAGCCTCC
1 GGGTCATTTGTAAAGCCT-T
*
1014607 GGGTAATTTGTAAAGCCTT
1 GGGTCATTTGTAAAGCCTT
*
1014626 CGAGTCATTTGTAAAGCCTTT
1 -GGGTCATTTGTAAAGCC-TT
*
1014647 GGGTCATTTGTAAATCCATT
1 GGGTCATTTGTAAAGCC-TT
1014667 GGGTCAT
1 GGGTCAT
1014674 CTGTCAGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
20 57 0.97
21 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (19 bp):
GGGTCATTTGTAAAGCCTT
Found at i:1014673 original size:40 final size:40
Alignment explanation
Indices: 1014587--1014673 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
1014577 CAAAACCTCA
*
1014587 GGGTAATTTGTAAAGCCTCCGGGTAATTTGTAAAGCCTTC
1 GGGTCATTTGTAAAGCCTCCGGGTAATTTGTAAAGCCTTC
* ** * *
1014627 GAGTCATTTGTAAAGCCTTTGGGTCATTTGTAAATCCATT-
1 GGGTCATTTGTAAAGCCTCCGGGTAATTTGTAAAGCC-TTC
1014667 GGGTCAT
1 GGGTCAT
1014674 CTGTCAGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 37 0.95
41 2 0.05
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (40 bp):
GGGTCATTTGTAAAGCCTCCGGGTAATTTGTAAAGCCTTC
Found at i:1015023 original size:88 final size:88
Alignment explanation
Indices: 1014874--1015043 Score: 250
Period size: 88 Copynumber: 1.9 Consensus size: 88
1014864 GTCTCCCCAG
** * * * *
1014874 AAGAGTAGTGGAACGGATTTTTCAGCAGAGTATGAGAACTTCACGGAAGAACAGTGGAGTAATCC
1 AAGAGTAGTGGAACAAATTTTTCAGAAAAGTATGAGAACTTCACAGAAGAACAGTGAAGTAATCC
*
1014939 AAGTTTTAATCTGAACTCCACAA
66 AAGTTTGAATCTGAACTCCACAA
**
1014962 AAGAGTAGTGGAACAAATTTTTCAGAAAAGTATGAGAACTTCACAGAAGATTAGTGAAGTAATCC
1 AAGAGTAGTGGAACAAATTTTTCAGAAAAGTATGAGAACTTCACAGAAGAACAGTGAAGTAATCC
*
1015027 AAGTTTGAGTCTGAACT
66 AAGTTTGAATCTGAACT
1015044 TCACGGATAG
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 72 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (88 bp):
AAGAGTAGTGGAACAAATTTTTCAGAAAAGTATGAGAACTTCACAGAAGAACAGTGAAGTAATCC
AAGTTTGAATCTGAACTCCACAA
Found at i:1015494 original size:10 final size:10
Alignment explanation
Indices: 1015471--1015519 Score: 70
Period size: 10 Copynumber: 5.3 Consensus size: 10
1015461 GAGTGTTATG
1015471 TTAATATATA
1 TTAATATATA
1015481 -T-ATAT-TA
1 TTAATATATA
1015488 TT-ATATATA
1 TTAATATATA
1015497 TTAATATATA
1 TTAATATATA
1015507 TTAATATATA
1 TTAATATATA
1015517 TTA
1 TTA
1015520 TTATTACAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 2 0.06
8 9 0.25
9 5 0.14
10 20 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTAATATATA
Found at i:1017087 original size:23 final size:22
Alignment explanation
Indices: 1017051--1017095 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1017041 TTATAAAAGG
*
1017051 ATTATTAATATTTATGTTAAAT
1 ATTATTAATATTTATATTAAAT
*
1017073 ATTATTTAGTATTTATATTAAAT
1 ATTA-TTAATATTTATATTAAAT
1017096 TATTTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
ATTATTAATATTTATATTAAAT
Found at i:1018243 original size:14 final size:14
Alignment explanation
Indices: 1018220--1018249 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1018210 ATACGTACAT
1018220 ATTATACAAACTTA
1 ATTATACAAACTTA
*
1018234 ATTATTCAAACTTA
1 ATTATACAAACTTA
1018248 AT
1 AT
1018250 ATCTTTAGAC
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:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTATACAAACTTA
Found at i:1018863 original size:2 final size:2
Alignment explanation
Indices: 1018856--1018882 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1018846 AAAGGGACAA
1018856 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
1018883 ATGTTTGTCT
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:1019394 original size:21 final size:21
Alignment explanation
Indices: 1019353--1019407 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1019343 AGGGATAAAT
*
1019353 TTTATAAT-TAAAAATTATTA
1 TTTAAAATATAAAAATTATTA
1019373 TTTAAACCATATAAAAA-T-TTA
1 TTTAAA--ATATAAAAATTATTA
1019394 TTTAAAATATAAAA
1 TTTAAAATATAAAA
1019408 TCATAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 8 0.26
20 5 0.16
21 9 0.29
22 3 0.10
23 6 0.19
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAAAATATAAAAATTATTA
Found at i:1019808 original size:21 final size:19
Alignment explanation
Indices: 1019783--1019821 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1019773 TTTTAAACAA
1019783 TTTTATACTTTAAATAATATT
1 TTTTAT-CTTTAAA-AATATT
*
1019804 TTTTATTTTTAAAAATAT
1 TTTTATCTTTAAAAATAT
1019822 AAAAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATCTTTAAAAATATT
Found at i:1033809 original size:20 final size:21
Alignment explanation
Indices: 1033785--1033865 Score: 85
Period size: 21 Copynumber: 3.8 Consensus size: 21
1033775 TTGGTGCAGA
1033785 GGGAATCGATTCCCCCTTAA-
1 GGGAATCGATTCCCCCTTAAG
*
1033805 GGGAATCAATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCC-TT-AAG
* *
1033828 GGGAACCGATTCCCCC-CACAG
1 GGGAATCGATTCCCCCTTA-AG
*
1033849 GGGAATCGATACCCCCT
1 GGGAATCGATTCCCCCT
1033866 GAGGTTATGG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
20 16 0.32
21 18 0.36
22 2 0.04
23 14 0.28
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.20
Consensus pattern (21 bp):
GGGAATCGATTCCCCCTTAAG
Found at i:1037704 original size:15 final size:15
Alignment explanation
Indices: 1037684--1037715 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1037674 GCATGGATGT
1037684 TATCATTGTAGAAGA
1 TATCATTGTAGAAGA
1037699 TATCATTGTAGAAGA
1 TATCATTGTAGAAGA
1037714 TA
1 TA
1037716 AACTACAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (15 bp):
TATCATTGTAGAAGA
Found at i:1042907 original size:15 final size:15
Alignment explanation
Indices: 1042868--1042907 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
1042858 GCCTCCCCCT
*
1042868 TCCTGCTCCCATTCC
1 TCCTTCTCCCATTCC
1042883 TCC-TCT--CATTCC
1 TCCTTCTCCCATTCC
1042895 TCCTTCTCCCATT
1 TCCTTCTCCCATT
1042908 ATTGTCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
12 9 0.43
13 3 0.14
14 2 0.10
15 7 0.33
ACGTcount: A:0.07, C:0.50, G:0.03, T:0.40
Consensus pattern (15 bp):
TCCTTCTCCCATTCC
Found at i:1043979 original size:14 final size:13
Alignment explanation
Indices: 1043953--1043998 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
1043943 GTGGAGAGAT
1043953 TATTTTGCTATAA
1 TATTTTGCTATAA
**
1043966 TATTTTTTTGATAA
1 TATTTTGCT-ATAA
1043980 TATTTTGCTATAA
1 TATTTTGCTATAA
1043993 TATTTT
1 TATTTT
1043999 AGAACTGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (13 bp):
TATTTTGCTATAA
Found at i:1047688 original size:47 final size:47
Alignment explanation
Indices: 1047618--1047714 Score: 158
Period size: 47 Copynumber: 2.1 Consensus size: 47
1047608 GTCAAGTTGC
*
1047618 AATAATTCCGCTAAATTTGTAACGACAAAATACTAAAATGAAACAAA
1 AATAATTCCACTAAATTTGTAACGACAAAATACTAAAATGAAACAAA
* * *
1047665 AATAATTCCACTAAATTTTTAACGACAATATATTAAAATGAAACAAA
1 AATAATTCCACTAAATTTGTAACGACAAAATACTAAAATGAAACAAA
1047712 AAT
1 AAT
1047715 CAAACATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.54, C:0.13, G:0.06, T:0.27
Consensus pattern (47 bp):
AATAATTCCACTAAATTTGTAACGACAAAATACTAAAATGAAACAAA
Found at i:1047971 original size:17 final size:16
Alignment explanation
Indices: 1047949--1047982 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1047939 ATTTTTTCAA
1047949 AATAAAAAATATAATTT
1 AATAAAAAAT-TAATTT
*
1047966 AATAAAATATTAATTT
1 AATAAAAAATTAATTT
1047982 A
1 A
1047983 TTCAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAAAAATTAATTT
Found at i:1048618 original size:39 final size:39
Alignment explanation
Indices: 1048564--1048642 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
1048554 ATTAGAGTCG
* * * * *
1048564 CCGCTACAGAGCCATATTTTAATGGCATTTTTCGACAAA
1 CCGCTACAGAACCATACTATAATGGCATTTGTAGACAAA
*
1048603 CCGCTACAGAACCATACTATAGTGGCATTTGTAGACAAA
1 CCGCTACAGAACCATACTATAATGGCATTTGTAGACAAA
1048642 C
1 C
1048643 GCCGTTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (39 bp):
CCGCTACAGAACCATACTATAATGGCATTTGTAGACAAA
Found at i:1049034 original size:34 final size:34
Alignment explanation
Indices: 1048996--1049088 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 34
1048986 TTCTTTTTGA
* * *
1048996 GGGCGTTTCTATGTTTTTGATATGCGAAAACTTT
1 GGGCGTTTCTCTGTTTTTCATAAGCGAAAACTTT
*
1049030 GGGCGTTTCTCTGTTTTTCATAAGCGAAAATTTT
1 GGGCGTTTCTCTGTTTTTCATAAGCGAAAACTTT
* *
1049064 GGACATTTCTCTGTTTTTCATAAGC
1 GGGCGTTTCTCTGTTTTTCATAAGC
1049089 AACCACTAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (34 bp):
GGGCGTTTCTCTGTTTTTCATAAGCGAAAACTTT
Found at i:1051023 original size:12 final size:13
Alignment explanation
Indices: 1050989--1051023 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1050979 CCGAAGCAAG
1050989 AGAAGT-AGAGAT
1 AGAAGTGAGAGAT
1051001 AGAAGTGAGAGA-
1 AGAAGTGAGAGAT
1051013 AGAAGTGAGAG
1 AGAAGTGAGAG
1051024 CAGCGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.40, T:0.11
Consensus pattern (13 bp):
AGAAGTGAGAGAT
Found at i:1051031 original size:21 final size:22
Alignment explanation
Indices: 1050981--1051055 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 22
1050971 AATAAAAGCC
* * *
1050981 GAAGCA-AGAGAAGTAGAGATA
1 GAAGCAGAGAGAAGAAGGGAGA
* *
1051002 GAAG-TGAGAGAAGAAGTGAGA
1 GAAGCAGAGAGAAGAAGGGAGA
* *
1051023 GCAGC-GAGAGAAGCAGGGAGA
1 GAAGCAGAGAGAAGAAGGGAGA
1051044 GAAGCAGAGAGA
1 GAAGCAGAGAGA
1051056 GAAACATCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
21 37 0.86
22 6 0.14
ACGTcount: A:0.47, C:0.07, G:0.41, T:0.05
Consensus pattern (22 bp):
GAAGCAGAGAGAAGAAGGGAGA
Found at i:1051037 original size:12 final size:12
Alignment explanation
Indices: 1051022--1051058 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1051012 AAGAAGTGAG
*
1051022 AGCAGCGAGAGA
1 AGCAGAGAGAGA
*
1051034 AGCAGGGAGAGA
1 AGCAGAGAGAGA
1051046 AGCAGAGAGAGA
1 AGCAGAGAGAGA
1051058 A
1 A
1051059 ACATCATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.46, C:0.11, G:0.43, T:0.00
Consensus pattern (12 bp):
AGCAGAGAGAGA
Found at i:1052944 original size:33 final size:33
Alignment explanation
Indices: 1052906--1052974 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1052896 GTTGATGAAT
*
1052906 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
1052939 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
1052972 GAA
1 GAA
1052975 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:1057427 original size:33 final size:33
Alignment explanation
Indices: 1057389--1057457 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1057379 GTTGATGAAT
*
1057389 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
1057422 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
1057455 GAA
1 GAA
1057458 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:1066345 original size:27 final size:27
Alignment explanation
Indices: 1066307--1066359 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1066297 AGTTGCAAGA
1066307 AAAAAATATAAAATTAAGAG-ATTAAAT
1 AAAAAATATAAAATTAA-AGTATTAAAT
*
1066334 AAAAAATATAAATTTAAAGTATTAAA
1 AAAAAATATAAAATTAAAGTATTAAA
1066360 ATAGCGAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (27 bp):
AAAAAATATAAAATTAAAGTATTAAAT
Found at i:1066801 original size:21 final size:21
Alignment explanation
Indices: 1066777--1066820 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1066767 GATAATTTGA
*
1066777 TCGGCCATCGAATTAATTCGG
1 TCGGCCACCGAATTAATTCGG
*
1066798 TCGGTCACCGAATTAATTCGG
1 TCGGCCACCGAATTAATTCGG
1066819 TC
1 TC
1066821 AGGGAACGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (21 bp):
TCGGCCACCGAATTAATTCGG
Found at i:1067187 original size:35 final size:35
Alignment explanation
Indices: 1067141--1067216 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
1067131 AAAACAGTCC
*
1067141 TCAATTTCATTCTAAACCCCAATTTCC-AAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAAG-AAT
*
1067176 TCAATTTCATTCTAAACCCTAAATTCCAAAAGAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAAGAAT
1067211 TCAATT
1 TCAATT
1067217 AAATTCAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 34 0.89
36 4 0.11
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAAGAAT
Found at i:1067756 original size:130 final size:130
Alignment explanation
Indices: 1067613--1067860 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
1067603 TATTTATATA
* **
1067613 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
*
1067678 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
* *
1067743 ATCAATTTTGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATTTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
1067808 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
1067861 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1067891 original size:130 final size:129
Alignment explanation
Indices: 1067627--1067891 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
1067617 ATTTGGTCCT
* ** *
1067627 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
*** * * **** *
1067692 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTTGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
1067757 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATTTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
1067822 TGATATGTGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1067886 -A
128 CA
1067887 AAATT
1 AAATT
1067892 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1068221 original size:28 final size:27
Alignment explanation
Indices: 1068190--1068252 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1068180 AGTTGATACA
*
1068190 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1068218 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1068246 ATATTTT
1 ATATTTT
1068253 TTGATATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1068354 original size:16 final size:18
Alignment explanation
Indices: 1068333--1068366 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1068323 ATTTCTTATT
1068333 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1068349 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1068367 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1071119 original size:114 final size:113
Alignment explanation
Indices: 1070699--1071147 Score: 582
Period size: 111 Copynumber: 3.9 Consensus size: 113
1070689 GATCCGTTGG
* * * *
1070699 GCACGATATCCTTCTTTGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCCTTG
* * * *
1070764 AATTAGATATCCTTCATCATGAAGATGAAATCCAAGGGT-TACATTACCGCTTGTAT
66 AATTAGATATCCTTCGTCATGAAGTTGAAATCCAA---TCTA-A--A--G-ATGAAT
* * * *
1070820 GCACGATATCCTTCGTTGTGAAGTTAAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTA
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCCTTG
* *
1070885 AATTAGATATCCTTCGTCGTGAAGTTGAAATCCAAGCTAAAGATGAAT
66 AATTAGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAAT
* *
1070933 GGCACGATATCC-T--TCGTGAAGTTGAAATTGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTT
1 -GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCCTT
*
1070995 GAATTAGATATCTTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAAT
65 GAATTAGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAAT
*
1071044 GTCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACTCCTTCGTTGTGAAGTTGAGCCTT
1 G-CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCCTT
* **
1071109 GAATTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCT
65 GAATTAGATATCCTTCGTCATGAAGTTGAAATCCAATCT
1071148 CGAGTAAATG
Statistics
Matches: 296, Mismatches: 26, Indels: 19
0.87 0.08 0.06
Matches are distributed among these distances:
110 1 0.00
111 99 0.33
112 1 0.00
113 5 0.02
114 93 0.31
116 1 0.00
118 1 0.00
119 2 0.01
121 93 0.31
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (113 bp):
GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCCTTG
AATTAGATATCCTTCGTCATGAAGTTGAAATCCAATCTAAAGATGAAT
Found at i:1071134 original size:225 final size:229
Alignment explanation
Indices: 1070698--1071144 Score: 636
Period size: 225 Copynumber: 1.9 Consensus size: 229
1070688 CGATCCGTTG
* *
1070698 GGCACGATATCCTTCTTTGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTT
1 GGCACGATATCCTTC--TGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTT
* *
1070763 GAATTAGATATCCTTCATCATGAAGATGAAATCCAAGGGTTACATTACCGCTTGTATGCACGATA
64 GAATTAGATATCCTTCATCATGAAGATGAAATCCAA--GTTACA-TA-CGCATGAATGCACGATA
* * *
1070828 TCCTTCGTTGTGAAGTTAAAATCGTGGATGGCTCCTTCGTTGTGAAGTTGAGCTTTAAATTAGAT
125 TCCTTCGTCGTGAAGTTAAAATCGTGGATGACTCCTTCGTTGTGAAGTTGAGCCTTAAATTAGAT
1070893 ATCCTTCGTCGTGAAGTTGAAATCCAAGCTAAAGATGAAT
190 ATCCTTCGTCGTGAAGTTGAAATCCAAGCTAAAGATGAAT
* *
1070933 GGCACGATATCCTTC-GTGAAGTTGAAATTGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGA
1 GGCACGATATCCTTCTGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
* * *
1070997 ATTAGATATCTTTCGTCATGAAGTTGAAATCCAA-TCTA-A-A-G-ATGAATGTCACGATATCCT
66 ATTAGATATCCTTCATCATGAAGATGAAATCCAAGT-TACATACGCATGAATG-CACGATATCCT
* * *
1071057 TCGTCGTGAAGTTGAAATCGTGGATGACTCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCC
129 TCGTCGTGAAGTTAAAATCGTGGATGACTCCTTCGTTGTGAAGTTGAGCCTTAAATTAGATATCC
*
1071122 TTCGTTGTGAAGTTGAAATCCAA
194 TTCGTCGTGAAGTTGAAATCCAA
1071145 TCTCGAGTAA
Statistics
Matches: 194, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
224 5 0.03
225 93 0.48
227 1 0.01
229 2 0.01
230 2 0.01
232 76 0.39
235 15 0.08
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (229 bp):
GGCACGATATCCTTCTGTGAAGTTGAAATCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGA
ATTAGATATCCTTCATCATGAAGATGAAATCCAAGTTACATACGCATGAATGCACGATATCCTTC
GTCGTGAAGTTAAAATCGTGGATGACTCCTTCGTTGTGAAGTTGAGCCTTAAATTAGATATCCTT
CGTCGTGAAGTTGAAATCCAAGCTAAAGATGAAT
Found at i:1071311 original size:65 final size:65
Alignment explanation
Indices: 1071168--1071363 Score: 340
Period size: 65 Copynumber: 3.0 Consensus size: 65
1071158 ATGTCGCCTC
* *
1071168 GAGTCCAATATCCTTCATTGTGAAGTTAAAATTGACTCTGAATGAAAC-TGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTTGGAAAGTTGTTTGTT
* *
1071232 GAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTGTGAATGAAACTTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTTGGAAAGTTGTTTGTT
*
1071297 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTTGGAAAGTTGTTTGTT
1071362 GA
1 GA
1071364 CAGACGCTCA
Statistics
Matches: 124, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 44 0.35
65 80 0.65
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (65 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTTGGAAAGTTGTTTGTT
Found at i:1071738 original size:32 final size:32
Alignment explanation
Indices: 1071633--1071753 Score: 129
Period size: 32 Copynumber: 3.8 Consensus size: 32
1071623 TTCGCATCAG
* *
1071633 GATGTTGAATCC-CTAAAGAAT-CCCCAATATTC
1 GATGTTGAA-CCTCTAAA-AATGCCCCAACATTT
* * **
1071665 GATGTTGAATCTCCAAAAATATCCCAACATTT
1 GATGTTGAACCTCTAAAAATGCCCCAACATTT
*
1071697 GATGTTGAACCTTTAAAAATGCCCCAACATTT
1 GATGTTGAACCTCTAAAAATGCCCCAACATTT
* *
1071729 GATGTTGAACCTTTAAAGATGCCCC
1 GATGTTGAACCTCTAAAAATGCCCC
1071754 TATTGTTCCT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
31 4 0.05
32 72 0.95
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (32 bp):
GATGTTGAACCTCTAAAAATGCCCCAACATTT
Found at i:1073030 original size:2 final size:2
Alignment explanation
Indices: 1073023--1073057 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1073013 ACAACAAGGG
* *
1073023 AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1073058 GATAAATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1074917 original size:21 final size:21
Alignment explanation
Indices: 1074890--1074941 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1074880 TGACTATAAA
*
1074890 ATTGCGATTTCCCAAATTTGC
1 ATTGCGATTTCCCAAATTCGC
* * *
1074911 GTTGCGATTTTCCTAATTCGC
1 ATTGCGATTTCCCAAATTCGC
1074932 ATTGCGATTT
1 ATTGCGATTT
1074942 ACATAGCGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.42
Consensus pattern (21 bp):
ATTGCGATTTCCCAAATTCGC
Found at i:1075496 original size:20 final size:20
Alignment explanation
Indices: 1075471--1075521 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1075461 TTCTAAACAT
*
1075471 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
1075491 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
1075511 ACTATCGCAAC
1 AAAATCGCAAC
1075522 GAGAGAATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1075599 original size:33 final size:33
Alignment explanation
Indices: 1075554--1075720 Score: 226
Period size: 33 Copynumber: 4.8 Consensus size: 33
1075544 AAAAATCGCA
1075554 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1075587 TTACGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1075620 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
1075653 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
*
1075693 TTGCGATTTTCATTCTCTCGTTGCGATT
1 TTGCGATTTTCATT-TCGCGTTGCGATT
1075721 TTCATTTCAA
Statistics
Matches: 119, Mismatches: 7, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
33 77 0.65
34 12 0.10
40 29 0.24
41 1 0.01
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1075623 original size:14 final size:14
Alignment explanation
Indices: 1075571--1075659 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
1075561 TTTCATTTCG
1075571 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1075585 CGTTACGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1075604 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1075618 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1075637 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1075651 CGTTGCGAT
1 CGTTGCGAT
1075660 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 28 0.47
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1075685 original size:20 final size:18
Alignment explanation
Indices: 1075554--1075726 Score: 118
Period size: 20 Copynumber: 9.8 Consensus size: 18
1075544 AAAAATCGCA
*
1075554 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCA-TTCTCG
1075573 TTGCGA--TTC--TCTCG
1 TTGCGATTTTCATTCTCG
* *
1075587 TTACGATTTTCATTTCGCG
1 TTGCGATTTTCA-TTCTCG
1075606 TTGCGA--TTC--TCTCG
1 TTGCGATTTTCATTCTCG
*
1075620 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCA-TTCTCG
1075639 TTGCGA--TTC--TCTCG
1 TTGCGATTTTCATTCTCG
** *
1075653 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCA-TT-CTCG
1075673 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCA-T-TCTCG
1075693 TTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCA-T-TCTCG
1075713 TTGCGATTTTCATT
1 TTGCGATTTTCATT
1075727 TCAACCAAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 35
0.73 0.07 0.20
Matches are distributed among these distances:
14 29 0.23
16 8 0.06
17 9 0.07
18 1 0.01
19 27 0.22
20 50 0.40
21 1 0.01
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTCATTCTCG
Found at i:1077625 original size:94 final size:93
Alignment explanation
Indices: 1077415--1077788 Score: 587
Period size: 94 Copynumber: 4.1 Consensus size: 93
1077405 TAGATTGCTT
* *
1077415 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
1077476 ATTTGTCTTT-TGTTGTGTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1077503 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1077568 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
1077597 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1077662 ATTTGTCTTTGTTTTGTCCTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* ** * *
1077691 AGTAAATTTGTTCATTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1077756 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
1077784 AGTAA
1 AGTAA
1077789 TGCAATCCAT
Statistics
Matches: 267, Mismatches: 13, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
88 35 0.13
90 3 0.01
91 2 0.01
92 29 0.11
93 19 0.07
94 179 0.67
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1077906 original size:20 final size:20
Alignment explanation
Indices: 1077881--1077942 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
1077871 TTTTGGTTGA
1077881 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
1077901 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
1077920 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1077940 AAT
1 AAT
1077943 CGTAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1077969 original size:20 final size:20
Alignment explanation
Indices: 1077940--1077995 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1077930 GCAACGAGAG
*
1077940 AATCGTAACGCGAAACCAAA
1 AATCGCAACGCGAAACCAAA
*
1077960 AATCGCAACGCAAAACCAAA
1 AATCGCAACGCGAAACCAAA
1077980 AATCGCAACGCGAAAC
1 AATCGCAACGCGAAAC
1077996 TATAATCGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.29, G:0.14, T:0.07
Consensus pattern (20 bp):
AATCGCAACGCGAAACCAAA
Found at i:1078028 original size:19 final size:19
Alignment explanation
Indices: 1078001--1078146 Score: 149
Period size: 19 Copynumber: 7.8 Consensus size: 19
1077991 GAAACTATAA
1078001 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1078020 CCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1078034 TCTCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1078053 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
1078072 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1078091 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
**
1078111 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
1078132 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
1078147 AAGTTCCATA
Statistics
Matches: 102, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
14 7 0.07
16 3 0.03
17 3 0.03
19 57 0.56
20 18 0.18
21 14 0.14
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1078113 original size:39 final size:38
Alignment explanation
Indices: 1078001--1078146 Score: 151
Period size: 39 Copynumber: 3.9 Consensus size: 38
1077991 GAAACTATAA
*
1078001 TCGCGTTGCGATTTTCATTC-CGCATTGCGA--TTC--
1 TCGCGTTGCGATTTTCATTCTCGCGTTGCGATTTTCTT
* *
1078034 TCTCGTTGTGATTTTCATT-TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATTCTCGCGTTGCGATTTTC-TT
*
1078072 TCGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTCTCGCGTTGCGATTTTC-TT
** * *
1078111 TCGCGTTGCGATAGTCATTTTTCACGTTGCGATTTT
1 TCGCGTTGCGATTTTCA-TTCTCGCGTTGCGATTTT
1078147 AAGTTCCATA
Statistics
Matches: 94, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
33 26 0.28
35 3 0.03
38 17 0.18
39 32 0.34
40 16 0.17
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTCTCGCGTTGCGATTTTCTT
Done.