Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold75
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: 1998514
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
File 8 of 12
Found at i:1132209 original size:32 final size:32
Alignment explanation
Indices: 1132168--1132238 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
1132158 AGCTTCGTAG
1132168 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1132200 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1132232 CGATACA
1 CGATACA
1132239 AATCGTTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1143676 original size:2 final size:2
Alignment explanation
Indices: 1143664--1143730 Score: 50
Period size: 2 Copynumber: 34.0 Consensus size: 2
1143654 GTACTAATAC
* *
1143664 TA TA TA AA TA TA TA TA TA TA TA TA TCA GTA TA TA -A TA TA -A AA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A -TA TA TA TA TA TA TA TA
* * *
1143706 TT TA TA AA TA TA TA T- TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1143731 GGTACATACA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
1 3 0.06
2 45 0.88
3 2 0.04
4 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1144891 original size:26 final size:25
Alignment explanation
Indices: 1144858--1144907 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
1144848 GCAAATTAGA
* *
1144858 TTAAATTATTATAAAATTTATTATT
1 TTAAATTAATATAAAATTAATTATT
*
1144883 TTAATATTAATGTAAAATTAATTAT
1 TTAA-ATTAATATAAAATTAATTAT
1144908 GAAGATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTAAATTAATATAAAATTAATTATT
Found at i:1150225 original size:20 final size:20
Alignment explanation
Indices: 1150184--1150225 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1150174 AAATTGAAAA
*
1150184 AAATAAAAATTATATATTTC
1 AAATAAAAATTATATATATC
*
1150204 AAATAAAATTTCATATA-ATC
1 AAATAAAAATT-ATATATATC
1150224 AA
1 AA
1150226 TTTAATTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATAAAAATTATATATATC
Found at i:1150245 original size:18 final size:19
Alignment explanation
Indices: 1150210--1150251 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1150200 TTTCAAATAA
*
1150210 AATTTCATATAATCAATTT
1 AATTTCATATAATCAATTC
1150229 AATTTCA-ATAA-CAAATTC
1 AATTTCATATAATC-AATTC
1150247 AATTT
1 AATTT
1150252 TAAATCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 13 0.62
19 7 0.33
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTTCATATAATCAATTC
Found at i:1150452 original size:113 final size:112
Alignment explanation
Indices: 1150334--1150537 Score: 288
Period size: 113 Copynumber: 1.8 Consensus size: 112
1150324 AAAAAGATAC
* *
1150334 AAAACTCAA-AAAATAAA-TAGAAGTTTTAAAAAATGATTTAATATGAATTTAATAAAAATATTT
1 AAAACT-AATAAAATAAATTA-AAATTTTAAAAAATGATTTAATATGAATTAAATAAAAATATTT
1150397 -AATAAATTTTAAAAATTATAAACTTCATATTTTGAAAATAAAAAAAATTA
64 GAAT-AATTTTAAAAATTATAAAC-TCATATTTTGAAAATAAAAAAAATTA
* * *
1150447 AAAACTAATAAAATAAATTAAAATTTTAAAAATTGATTTAATATGAATTAAATTATAATATTTGA
1 AAAACTAATAAAATAAATTAAAATTTTAAAAAATGATTTAATATGAATTAAATAAAAATATTTGA
* *
1150512 ATAATTTTGAAAATTCTAAACTCATA
66 ATAATTTTAAAAATTATAAACTCATA
1150538 AAAATCTTAT
Statistics
Matches: 81, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
112 7 0.09
113 69 0.85
114 5 0.06
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (112 bp):
AAAACTAATAAAATAAATTAAAATTTTAAAAAATGATTTAATATGAATTAAATAAAAATATTTGA
ATAATTTTAAAAATTATAAACTCATATTTTGAAAATAAAAAAAATTA
Found at i:1150554 original size:113 final size:113
Alignment explanation
Indices: 1150317--1150554 Score: 243
Period size: 113 Copynumber: 2.1 Consensus size: 113
1150307 GAAAAAATTG
* *
1150317 TTATATGAAAAAGATACAAAACTCAAAAAATAAATAGAAGTTTTAAAAAATGATTTAATATGAAT
1 TTAT-TGAAAAAAATACAAAACTCAAAAAATAAATAGAAATTTTAAAAAATGATTTAATATGAAT
* *** *
1150382 TTAATAAAAATATTTAATAAATTTTAAAAATTATAAACTTCATATTTTG
65 TAAATAAAAATATTTAATAAATTTTAAAAATTATAAACTTCATAAAATC
** * * *
1150431 AAAATAAAAAAAATTA-AAAACT-AATAAAATAAATTA-AAATTTTAAAAATTGATTTAATATGA
1 TTATTGAAAAAAA-TACAAAACTCAA-AAAATAAA-TAGAAATTTTAAAAAATGATTTAATATGA
* * * *
1150493 ATTAAATTATAATATTTGAAT-AATTTTGAAAATTCTAAAC-TCATAAAAATC
63 ATTAAATAAAAATATTT-AATAAATTTTAAAAATTATAAACTTCAT-AAAATC
1150544 TTATTGAAAAA
1 TTATTGAAAAA
1150555 TTTACAGAGT
Statistics
Matches: 99, Mismatches: 20, Indels: 11
0.76 0.15 0.08
Matches are distributed among these distances:
112 6 0.06
113 85 0.86
114 8 0.08
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.35
Consensus pattern (113 bp):
TTATTGAAAAAAATACAAAACTCAAAAAATAAATAGAAATTTTAAAAAATGATTTAATATGAATT
AAATAAAAATATTTAATAAATTTTAAAAATTATAAACTTCATAAAATC
Found at i:1153289 original size:20 final size:20
Alignment explanation
Indices: 1153264--1153302 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1153254 TGGAACTCAA
1153264 GCATCTTGCTGTGAATAAAG
1 GCATCTTGCTGTGAATAAAG
1153284 GCATCTTGCTGTGAATAAA
1 GCATCTTGCTGTGAATAAA
1153303 AGAAACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (20 bp):
GCATCTTGCTGTGAATAAAG
Found at i:1153847 original size:2 final size:2
Alignment explanation
Indices: 1153840--1153872 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1153830 TTAAATTTGA
1153840 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 A
1153873 ACATGCTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1154852 original size:3 final size:3
Alignment explanation
Indices: 1154846--1154877 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1154836 AATAATAATA
1154846 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1154878 TTGAAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:1156021 original size:8 final size:8
Alignment explanation
Indices: 1156008--1156041 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1155998 CTATCATCTC
1156008 TTTTTCTT
1 TTTTTCTT
1156016 TTTTTCTT
1 TTTTTCTT
*
1156024 TTTTTTTT
1 TTTTTCTT
*
1156032 TTTTTGTT
1 TTTTTCTT
1156040 TT
1 TT
1156042 GCTTTGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1156579 original size:154 final size:154
Alignment explanation
Indices: 1156392--1156784 Score: 455
Period size: 153 Copynumber: 2.6 Consensus size: 154
1156382 TGATATATAC
* * * * *
1156392 AAAAAATTC-AAAACTCATGAAACAAATTAAATTTTTCAAAATTGATTTAATGTAAATTAAACAA
1 AAAAAATTCTAAAACTCATAAAATAAATTAAATTTTTCAAAACTAATTTAATATAAATTAAACAA
* * *
1156456 TAATATTTGATGAATTTTAAAAATTTTTAA-T-TGAGAAAAATCCAACCGAAAAAATTTACGGAA
66 TAATATTTGATGAATTTTAAAAATTTATAAGTAT-AAAAAAATACAACCG-AAAAATTTAC-GAA
*
1156519 -TAAAAAACTCATTATTTT-A-AAAATG
128 GTAAAAAACTCAGTATTTTGATAAAA-G
* * * *
1156544 AAAAAAATTCTAAAGCTCATAAAATAAATTGAATTTTTTAAAACTAATTTAATATGAATTAAACA
1 -AAAAAATTCTAAAACTCATAAAATAAATTAAATTTTTCAAAACTAATTTAATATAAATTAAACA
* * **
1156609 TTAATATTTGAAGAATTTTAAAAA-TTATAAGTATAAAAAAATATTACCGAAAAATTTACGAAGT
65 ATAATATTTGATGAATTTTAAAAATTTATAAGTATAAAAAAATACAACCGAAAAATTTACGAAGT
* * *
1156673 AGAAAACTCCGTATTTTGATAACAG
130 AAAAAACTCAGTATTTTGATAAAAG
* *
1156698 AAAAAATTTTAAAACTCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATAAATT-AA-AA
1 AAAAAATTCTAAAACTCATAAAATAAATTAAATTTTTCAAAACTAATTTAATATAAATTAAACAA
*
1156761 TAATATTTGAAT-AATTTTAGAAAT
66 TAATATTTG-ATGAATTTTAAAAAT
1156785 CATATATTCA
Statistics
Matches: 203, Mismatches: 29, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
151 20 0.10
152 6 0.03
153 92 0.45
154 81 0.40
155 4 0.02
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (154 bp):
AAAAAATTCTAAAACTCATAAAATAAATTAAATTTTTCAAAACTAATTTAATATAAATTAAACAA
TAATATTTGATGAATTTTAAAAATTTATAAGTATAAAAAAATACAACCGAAAAATTTACGAAGTA
AAAAACTCAGTATTTTGATAAAAG
Found at i:1156739 original size:28 final size:28
Alignment explanation
Indices: 1156700--1156761 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
1156690 GATAACAGAA
*
1156700 AAAATTTTAAAACTCA-TAAAATAAATT
1 AAAATTTTAAAACTAATTAAAATAAATT
*
1156727 AAAATTTTCAAAACTAATTTAATATAAATT
1 AAAATTTT-AAAACTAA-TTAAAATAAATT
1156757 AAAAT
1 AAAAT
1156762 AATATTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 8 0.27
28 7 0.23
30 15 0.50
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAATTTTAAAACTAATTAAAATAAATT
Found at i:1156854 original size:151 final size:153
Alignment explanation
Indices: 1156392--1156855 Score: 426
Period size: 153 Copynumber: 3.0 Consensus size: 153
1156382 TGATATATAC
* * * * * * *
1156392 AAAAAATTC-AAAACTCATGAAACAAATTAAATTTTTCAAAATTGATTTAATGTAAATTAAACAA
1 AAAAAATTCTAAAACTCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATAAATTAAACAT
* ** * *** * **
1156456 TAATATTTGATGAATTTTAAAAATTTTTAA-T-TGAGAAAAATCCAACCGAAAAAATTTACGGAA
66 TAATATTTGAAGAATTTTAAAAA-TCATAAGTAT-AAAAAAATATTACAG-AAAAATTTA-AAAA
* ** * **
1156519 -TAAAAAACTCATTATTTTAAAAATGA
127 GTAGAAAACTCCGTATTTTGAAAACAA
* * * * *
1156545 AAAAAATTCTAAAGCTCATAAAATAAATTGAATTTTTTAAAACTAATTTAATATGAATTAAACAT
1 AAAAAATTCTAAAACTCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATAAATTAAACAT
* * **
1156610 TAATATTTGAAGAATTTTAAAAATTATAAGTATAAAAAAATATTACCGAAAAATTTACGAAGTAG
66 TAATATTTGAAGAATTTTAAAAATCATAAGTATAAAAAAATATTACAGAAAAATTTAAAAAGTAG
* *
1156675 AAAACTCCGTATTTTGATAACAG
131 AAAACTCCGTATTTTGAAAACAA
*
1156698 AAAAAATTTTAAAACTCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATAAATTAAA-A-
1 AAAAAATTCTAAAACTCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATAAATTAAACAT
* * * *
1156761 TAATATTTGAATAATTTTAGAAATCAT-A-TATTCAGAAAAA-ATTACTAGAGAAATTTAAAAAG
66 TAATATTTGAAGAATTTTAAAAATCATAAGTA-T-AAAAAAATATTAC-AGAAAAATTTAAAAAG
*
1156823 TCA-AAAACTTCGTATTTTGAAAACAA
128 T-AGAAAACTCCGTATTTTGAAAACAA
1156849 AAAAAAT
1 AAAAAAT
1156856 ATGAAAGAAA
Statistics
Matches: 261, Mismatches: 42, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
149 2 0.01
150 7 0.03
151 70 0.27
152 5 0.02
153 97 0.37
154 79 0.30
155 1 0.00
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.33
Consensus pattern (153 bp):
AAAAAATTCTAAAACTCATAAAATAAATTAAAATTTTCAAAACTAATTTAATATAAATTAAACAT
TAATATTTGAAGAATTTTAAAAATCATAAGTATAAAAAAATATTACAGAAAAATTTAAAAAGTAG
AAAACTCCGTATTTTGAAAACAA
Found at i:1164963 original size:17 final size:17
Alignment explanation
Indices: 1164943--1164978 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1164933 AAGGAAGATG
* *
1164943 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
1164960 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
1164977 AA
1 AA
1164979 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:1171463 original size:36 final size:34
Alignment explanation
Indices: 1171391--1171463 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 34
1171381 AGTTCCCTTC
* *
1171391 AAAATGAAAAAAAAAGTCAAAAGCAAAAGCACAA
1 AAAATGAAAAAAAAAGTCAAAAGCAAAAGAAAAA
*
1171425 AAAATGAAAAGAAAAAGTGCAAAAGCAAAATAAAAA
1 AAAATGAAAA-AAAAAGT-CAAAAGCAAAAGAAAAA
1171461 AAA
1 AAA
1171464 GGGAACAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 10 0.29
35 7 0.21
36 17 0.50
ACGTcount: A:0.73, C:0.08, G:0.12, T:0.07
Consensus pattern (34 bp):
AAAATGAAAAAAAAAGTCAAAAGCAAAAGAAAAA
Found at i:1171752 original size:14 final size:14
Alignment explanation
Indices: 1171733--1171760 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1171723 ATCCTAAAAA
1171733 AAAAAAAAAAAACC
1 AAAAAAAAAAAACC
1171747 AAAAAAAAAAAACC
1 AAAAAAAAAAAACC
1171761 TTTTCACCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAACC
Found at i:1172853 original size:27 final size:27
Alignment explanation
Indices: 1172810--1173371 Score: 935
Period size: 27 Copynumber: 20.6 Consensus size: 27
1172800 GTGGCATTTT
1172810 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1172838 CTTTTAAGTCCACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1172865 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* **
1172892 CTTTCAAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1172919 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1172946 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
1172974 TTTTTAAGTCCACAACTCTGTGGCCCC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1173001 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1173028 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1173055 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1173082 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1173110 CTTTTAAGTCCACAACTCCGTGGCCCC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1173137 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1173164 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1173192 CTTTTAAGTCCACAGCTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1173219 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1173247 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1173274 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1173301 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
1173329 CTTTTAAGTTCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1173356 CTTTTTAAGTCCACAA
1 C-TTTTAAGTCCACAA
1173372 GGCGGTGGCA
Statistics
Matches: 501, Mismatches: 27, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
27 357 0.71
28 144 0.29
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.28
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1173011 original size:109 final size:109
Alignment explanation
Indices: 1172810--1173371 Score: 941
Period size: 109 Copynumber: 5.1 Consensus size: 109
1172800 GTGGCATTTT
*
1172810 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCA-CCCTTTTAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGT
* **
1172874 CCACAACTCCGTGGCACCCTTTCAAGTCCACAACTCCGTGGCATT
65 CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* *
1172919 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
* *
1172984 CACAACTCTGTGGCCCCCTTTTAAGTCCACAACTCCGTGGCACC
66 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1173028 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCAT-CCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
*
1173092 CACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCCCC
66 CACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
1173137 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
* *
1173202 CACAGCTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCC
66 CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
1173247 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
* *
1173311 CACAACTCCGTGGCATCCCTTTTAAGTTCACAACTTCGTGGCACC
66 CACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
1173356 CTTTTTAAGTCCACAA
1 C-TTTTAAGTCCACAA
1173372 GGCGGTGGCA
Statistics
Matches: 427, Mismatches: 20, Indels: 11
0.93 0.04 0.02
Matches are distributed among these distances:
108 68 0.16
109 242 0.57
110 117 0.27
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.28
Consensus pattern (109 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
CACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1173024 original size:82 final size:81
Alignment explanation
Indices: 1172810--1173371 Score: 935
Period size: 82 Copynumber: 6.9 Consensus size: 81
1172800 GTGGCATTTT
*
1172810 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGTC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1172875 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* ** *
1172892 CTTTCAAGTCCACAACTCCGTGGCATTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1172957 ACAACTCCGTGGCATCC
66 ACAACTCCGTGGCA-CC
* * *
1172974 TTTTTAAGTCCACAACTCTGTGGCCCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1173039 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
*
1173055 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
1173120 CACAACTCCGTGGCCCC
65 CACAACTCCGTGGCACC
1173137 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
* *
1173202 CACAGCTCCGTGGCATC
65 CACAACTCCGTGGCACC
1173219 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
1173284 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
1173301 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTTCACAACTTCGTGGCACCCTTTTTAAGT
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCC-TTTTAAGT
1173366 CCACAA
64 CCACAA
1173372 GGCGGTGGCA
Statistics
Matches: 451, Mismatches: 25, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
81 120 0.27
82 290 0.64
83 41 0.09
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.28
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:1173400 original size:30 final size:28
Alignment explanation
Indices: 1172874--1174124 Score: 605
Period size: 32 Copynumber: 42.6 Consensus size: 28
1172864 CCTTTTAAGT
* * * *
1172874 CCACAACTCCGTGGCACCCTTTC-AAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * * * *
1172901 CCACAACTCCGTGGCATTCTTT-TAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * * * *
1172928 CCACAACTCTGTGGCACCCTTT-TAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * ** *
1172955 CCACAACTCCGTGGCATCCTTTTTAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * ** * *
1172983 CCACAACTCTGTGGCCCCCTTT-TAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * * * *
1173010 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * * * *
1173037 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * * *
1173064 CCACAACTCCGTGGCATCCTTT-TAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * * *
1173091 CCACAACTCCGTGGCATCCCTTT-TAAGT
1 CCACAAGTCGGTGGCAT-CCTTTCAAAGC
* * ** * *
1173119 CCACAACTCCGTGGCCCCCTTT-TAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * * * *
1173146 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * * *
1173173 CCACAACTCCGTGGCATCCCTTT-TAAGT
1 CCACAAGTCGGTGGCAT-CCTTTCAAAGC
* * *
1173201 CCAC-AGCTCCGTGGCATCCTTT-TAAGT
1 CCACAAG-TCGGTGGCATCCTTTCAAAGC
* * * *
1173228 CCACAACTCCGTGGCATCCCTTT-TAAGT
1 CCACAAGTCGGTGGCAT-CCTTTCAAAGC
* * * * *
1173256 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * * * *
1173283 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* * * *
1173310 CCACAACTCCGTGGCATCCCTTT-TAAGT
1 CCACAAGTCGGTGGCAT-CCTTTCAAAGC
* * * ** *
1173338 TCACAACTTC-GTGGCACCCTTTTTAAGT
1 CCACAA-GTCGGTGGCATCCTTTCAAAGC
* *
1173366 CCACAAGGCGGTGGCATTCCCTTCTAAAGC
1 CCACAAGTCGGTGGCA-TCCTTTC-AAAGC
**
1173396 CCACAAGTTAGTGGCA-CCTTTTTCAAAGCC
1 CCACAAGTCGGTGGCATCC--TTTCAAAG-C
*
1173426 CACACAAGTCGGTGGCAACCCATTTCAAAGC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAGC
* *
1173457 CCACAAGTCAGTGGCATCTTTTCAAAGTC
1 CCACAAGTCGGTGGCATCCTTTCAAAG-C
*
1173486 CACACAAGTTGGTGGCATCCTTTCAAAGC
1 C-CACAAGTCGGTGGCATCCTTTCAAAGC
*
1173515 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
1173543 CCACAAGTCGGTGGCAATCCATTTCAAAGC
1 CCACAAGTCGGTGGC-ATCC-TTTCAAAGC
** *
1173573 CCACAAGTTAGTGGCATCTTTTCAAAGC
1 CCACAAGTCGGTGGCATCCTTTCAAAGC
* *
1173601 CCACAAGTCGGTGGCAACCCATTCCAAAGCC
1 CCACAAGTCGGTGGC-ATCC-TTTCAAAG-C
* *
1173632 CACACAAGTCGATGGCAACCCATTTCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
*
1173664 CACACAAGTCGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
* *
1173696 CACACAAGTCGGTGGCAACCCATTCCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
*
1173728 CACACAAGTCGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
*
1173760 CACACAAGTCGGTGGCACCCATTTCAAAGC
1 C-CACAAGTCGGTGGCATCC-TTTCAAAGC
* *
1173790 CCACAAGTCGGTGGCAACCCATTCCAAAGCC
1 CCACAAGTCGGTGGC-ATCC-TTTCAAAG-C
*
1173821 CACACAAGTCGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
*
1173853 CACACAAGTCGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
*
1173885 CACACAAGTCGGTGGCGACCCTTTTCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
*
1173917 CACACAAGTCGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
*
1173949 CACACAAGTCGGTGGCACCCATTTCAAAGCC
1 C-CACAAGTCGGTGGCATCC-TTTCAAAG-C
*
1173980 CACACAAGTCGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
*
1174012 CACACAAGTCGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
*
1174044 CACACAAGTCGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
* *
1174076 CACACAAGTCGGTGGCGACCCATTCCAAAGCC
1 C-CACAAGTCGGTGGC-ATCC-TTTCAAAG-C
1174108 CACACAAGTCGGTGGCA
1 C-CACAAGTCGGTGGCA
1174125 ACCCATTTAA
Statistics
Matches: 1124, Mismatches: 69, Indels: 58
0.90 0.06 0.05
Matches are distributed among these distances:
27 304 0.27
28 208 0.19
29 39 0.03
30 100 0.09
31 63 0.06
32 408 0.36
33 2 0.00
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.22
Consensus pattern (28 bp):
CCACAAGTCGGTGGCATCCTTTCAAAGC
Found at i:1173457 original size:32 final size:32
Alignment explanation
Indices: 1173416--1174168 Score: 1109
Period size: 32 Copynumber: 24.2 Consensus size: 32
1173406 GTGGCACCTT
1173416 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1173448 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
1173476 TTTCAAAGTCCACACAAGTTGGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1173506 TTTCAAAG-CC-CACAAGTCAGTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1173534 TTTCAAAG-CC-CACAAGTCGGTGGCAATCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
** * *
1173564 TTTCAAAG-CC-CACAAGTTAGTGGC-A-TCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1173592 TTTCAAAG-CC-CACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1173622 TTCCAAAGCCCACACAAGTCGATGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1173654 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1173686 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1173718 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1173750 TTTCAAAGCCCACACAAGTCGGTGGC-ACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1173781 TTTCAAAG-CC-CACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1173811 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1173843 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
1173875 TTTCAAAGCCCACACAAGTCGGTGGCGACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1173907 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1173939 TTTCAAAGCCCACACAAGTCGGTGGC-ACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1173970 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1174002 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1174034 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1174066 TTTCAAAGCCCACACAAGTCGGTGGCGACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
1174098 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ** ** *
1174130 TTTAAAAGCCCATGCAAGTTAGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1174162 TTTCAAA
1 TTTCAAA
1174169 TCACCATTTT
Statistics
Matches: 668, Mismatches: 40, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
28 71 0.11
29 25 0.04
30 78 0.12
31 51 0.08
32 443 0.66
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:1174252 original size:45 final size:47
Alignment explanation
Indices: 1174201--1174319 Score: 127
Period size: 49 Copynumber: 2.5 Consensus size: 47
1174191 GTCCGATATT
*
1174201 GCTGGCCTTGAATCAGCATATTGG-CACCTTT-CTAAGCCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCCACCTTTCCTAAGCCCAATGTC
* * * *
1174246 GCTGGCCTTGAGTCAGCACATTGGTCCACTTTTCCCTTAGCCCGATGTC
1 GCTGGCCTTGAATCAGCACATTGG-CCACCTTT-CCTAAGCCCAATGTC
* *
1174295 GCTGACCTTGAAAT-GGCACATTGGC
1 GCTGGCCTTG-AATCAGCACATTGGC
1174320 ATTCCTCTCA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
45 22 0.36
47 6 0.10
48 1 0.02
49 30 0.49
50 2 0.03
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (47 bp):
GCTGGCCTTGAATCAGCACATTGGCCACCTTTCCTAAGCCCAATGTC
Found at i:1175434 original size:17 final size:17
Alignment explanation
Indices: 1175414--1175449 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1175404 AAGGAAGATG
* *
1175414 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
1175431 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
1175448 AA
1 AA
1175450 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:1175833 original size:2 final size:2
Alignment explanation
Indices: 1175820--1175850 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1175810 TTATTTTATT
*
1175820 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1175851 TTTGAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1187213 original size:43 final size:42
Alignment explanation
Indices: 1187131--1187213 Score: 96
Period size: 43 Copynumber: 2.0 Consensus size: 42
1187121 TTTTATTTAA
* * * *
1187131 TAATTGATTTTTTAATTAAAAAAATTAATAGTTTTTAATTGG
1 TAATTAATTTTTAAATTAAAAAAATAAATAGTTTATAATTGG
*
1187173 TAATTAATTTTTGAAATTAAAATACATAAATA-TTTATAATT
1 TAATTAATTTTT-AAATTAAAA-AAATAAATAGTTTATAATT
1187214 ATATTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
42 11 0.32
43 16 0.47
44 7 0.21
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (42 bp):
TAATTAATTTTTAAATTAAAAAAATAAATAGTTTATAATTGG
Found at i:1187283 original size:14 final size:14
Alignment explanation
Indices: 1187261--1187290 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1187251 ATCAATATTT
*
1187261 TTATTATAACTTAA
1 TTATAATAACTTAA
1187275 TTATAATAACTTAA
1 TTATAATAACTTAA
1187289 TT
1 TT
1187291 CGGTTTTTAT
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:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
TTATAATAACTTAA
Found at i:1187507 original size:6 final size:6
Alignment explanation
Indices: 1187496--1187540 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
1187486 TTAAAAAGGA
* * *
1187496 TTTAAT TTTAAT TTTATT TTTATT TTTATT TTTACT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
1187541 TAATTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:1195331 original size:26 final size:26
Alignment explanation
Indices: 1195281--1195331 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1195271 TAGTTAATCT
**
1195281 GTCGTTTTGCATCAATTTTTTAAGTG
1 GTCGTTTTGCATCAATTTTAAAAGTG
*
1195307 GTCGTTTTGCATTAATTTTAAAAGT
1 GTCGTTTTGCATCAATTTTAAAAGT
1195332 ACAAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.49
Consensus pattern (26 bp):
GTCGTTTTGCATCAATTTTAAAAGTG
Found at i:1198196 original size:12 final size:12
Alignment explanation
Indices: 1198179--1198203 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1198169 TATGCAAAAT
1198179 TTAAACTTATTC
1 TTAAACTTATTC
1198191 TTAAACTTATTC
1 TTAAACTTATTC
1198203 T
1 T
1198204 AATGGCCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAACTTATTC
Found at i:1202548 original size:18 final size:19
Alignment explanation
Indices: 1202519--1202561 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
1202509 AAAAATGAGG
1202519 AAGAAAATGAAAAAAAAAA
1 AAGAAAATGAAAAAAAAAA
*
1202538 AAGAAAA-GAAAAGAAAAA
1 AAGAAAATGAAAAAAAAAA
1202556 AAGAAA
1 AAGAAA
1202562 CAGAGATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAGAAAATGAAAAAAAAAA
Found at i:1206572 original size:18 final size:18
Alignment explanation
Indices: 1206545--1206579 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1206535 ACTTTTTAGA
1206545 CTCTCCCTCTCTCCCCCT
1 CTCTCCCTCTCTCCCCCT
*
1206563 CTCTCTCTCTCTCCCCC
1 CTCTCCCTCTCTCCCCC
1206580 CCCCCCCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (18 bp):
CTCTCCCTCTCTCCCCCT
Found at i:1206597 original size:3 final size:3
Alignment explanation
Indices: 1206591--1206635 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1206581 CCCCCCCCCC
*
1206591 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CAT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1206636 TCCCAGGACG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1207828 original size:2 final size:2
Alignment explanation
Indices: 1207823--1207851 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1207813 ATAGAGAAAT
1207823 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1207852 CAATCATGCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1208795 original size:37 final size:37
Alignment explanation
Indices: 1208753--1208848 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 37
1208743 TAATATATAA
*
1208753 TATTAATTTAAT-TAATTAATTTTATCTT-ATTCATTTT
1 TATTAATTTAATATAATTAATTTTATCTTAATT--TATT
1208790 TATTAATTATATATAATATATTAATTTTATCTTAATTTATT
1 TATTAATT-TA-AT-ATA-ATTAATTTTATCTTAATTTATT
1208831 TATTAAATTTAATATAAT
1 TATT-AATTTAATATAAT
1208849 ATATTAATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
37 8 0.16
38 4 0.08
39 5 0.10
40 2 0.04
41 11 0.22
42 18 0.35
43 3 0.06
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (37 bp):
TATTAATTTAATATAATTAATTTTATCTTAATTTATT
Found at i:1208813 original size:18 final size:17
Alignment explanation
Indices: 1208790--1208916 Score: 67
Period size: 18 Copynumber: 6.5 Consensus size: 17
1208780 TATTCATTTT
1208790 TATTAATTATATATAATA
1 TATTAATT-TATATAATA
*
1208808 TATTAATTTTATCTTAATTTA
1 TATTAA-TTTAT-ATAA--TA
1208829 TTTATTAAATTTAATATAATA
1 --TATT-AATTT-ATATAATA
1208850 TATTAATTT-TATTAATTA
1 TATTAATTTATA-TAA-TA
* *
1208868 TATTTTAATTTTTAATAAAA
1 TA--TTAATTTAT-ATAATA
1208888 TTATTAAATTTAATATAATA
1 -TATT-AATTT-ATATAATA
1208908 TATTAATTT
1 TATTAATTT
1208917 TATTAATTAT
Statistics
Matches: 87, Mismatches: 5, Indels: 34
0.69 0.04 0.27
Matches are distributed among these distances:
16 2 0.02
17 3 0.03
18 23 0.26
19 15 0.17
20 18 0.21
21 11 0.13
22 1 0.01
23 10 0.11
24 4 0.05
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAATTTATATAATA
Found at i:1208820 original size:42 final size:42
Alignment explanation
Indices: 1208767--1208861 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
1208757 AATTTAATTA
*
1208767 ATTAATTTTATCTT-ATTCATTT-TTATTAA-TTATATATAATAT
1 ATTAATTTTATCTTAATTTATTTATTA--AATTTA-ATATAATAT
1208809 ATTAATTTTATCTTAATTTATTTATTAAATTTAATATAATAT
1 ATTAATTTTATCTTAATTTATTTATTAAATTTAATATAATAT
1208851 ATTAATTTTAT
1 ATTAATTTTAT
1208862 TAATTATATT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
42 36 0.73
43 10 0.20
44 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (42 bp):
ATTAATTTTATCTTAATTTATTTATTAAATTTAATATAATAT
Found at i:1208896 original size:58 final size:59
Alignment explanation
Indices: 1208830--1208948 Score: 222
Period size: 58 Copynumber: 2.0 Consensus size: 59
1208820 CTTAATTTAT
1208830 TTATTAAATTTAATATAATATATTAATTTTATTAATTATATTTTAA-TTTTTAATAAAA
1 TTATTAAATTTAATATAATATATTAATTTTATTAATTATATTTTAATTTTTTAATAAAA
*
1208888 TTATTAAATTTAATATAATATATTAATTTTATTAATTATTTTTTAATTTTTTAATAAAA
1 TTATTAAATTTAATATAATATATTAATTTTATTAATTATATTTTAATTTTTTAATAAAA
1208947 TT
1 TT
1208949 TAAACGATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 45 0.76
59 14 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (59 bp):
TTATTAAATTTAATATAATATATTAATTTTATTAATTATATTTTAATTTTTTAATAAAA
Found at i:1208923 original size:40 final size:40
Alignment explanation
Indices: 1208838--1208917 Score: 101
Period size: 38 Copynumber: 2.0 Consensus size: 40
1208828 ATTTATTAAA
* * * * *
1208838 TTTAATATAATATATTAATTTTATTAATTATATTTTAATT
1 TTTAATAAAATATATTAAATTTAATAATAATATATTAATT
1208878 TTTAATAAAAT-TATTAAATTTAAT-ATAATATATTAATT
1 TTTAATAAAATATATTAAATTTAATAATAATATATTAATT
1208916 TT
1 TT
1208918 ATTAATTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 14 0.40
39 11 0.31
40 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (40 bp):
TTTAATAAAATATATTAAATTTAATAATAATATATTAATT
Found at i:1208927 original size:97 final size:95
Alignment explanation
Indices: 1208726--1208933 Score: 246
Period size: 97 Copynumber: 2.1 Consensus size: 95
1208716 TCATATATTA
* * **
1208726 TAATAATTTATTAAATTTAATATATAATATTAATTTAATTAATTAATTTTATCTTATTCATTTTT
1 TAATTATTTATTAAATTTAATATATAATATTAATTTAATTAATTAATTTTATCTTATTAATAATT
1208791 ATTAATTATATATAATATATTAATTTTATCT
66 ATTAATTATATATAATATATTAATTTTA-CT
*
1208822 TAATTTATTTATTAAATTTAATATA-ATATATTAATTTTATTAATTATATTTTAAT-TT-TTAAT
1 TAA-TTATTTATTAAATTTAATATATA-ATATTAATTTAATTAATTA-ATTTT-ATCTTATTAAT
1208884 AAAATTATTAAATT-TAATATAATATATTAATTTTA-T
62 --AATTATT-AATTAT-ATATAATATATTAATTTTACT
*
1208920 TAATTATTTTTTAA
1 TAATTATTTATTAA
1208934 TTTTTTAATA
Statistics
Matches: 98, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
96 4 0.04
97 52 0.53
98 11 0.11
99 8 0.08
100 23 0.23
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (95 bp):
TAATTATTTATTAAATTTAATATATAATATTAATTTAATTAATTAATTTTATCTTATTAATAATT
ATTAATTATATATAATATATTAATTTTACT
Found at i:1209049 original size:20 final size:23
Alignment explanation
Indices: 1209018--1209068 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
1209008 TTTAAAATAT
* *
1209018 ATATAAATTTT-TATAAATTAAA
1 ATATTAATTTTATATATATTAAA
1209040 A-ATTAATTTTATATATATTAAA
1 ATATTAATTTTATATATATTAAA
1209062 ATATTAA
1 ATATTAA
1209069 CAGGTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.32
22 12 0.48
23 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTAATTTTATATATATTAAA
Found at i:1210000 original size:46 final size:46
Alignment explanation
Indices: 1209929--1210018 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
1209919 GTAATTAACT
1209929 ATTTTATCTTCAATTAAATTAAATTAATAAACAAATAAATAAAAGA
1 ATTTTATCTTCAATTAAATTAAATTAATAAACAAATAAATAAAAGA
* * * *
1209975 ATTTTATCTTTAATTAAATTTAATTAATTAAGAAATAAATAAAA
1 ATTTTATCTTCAATTAAATTAAATTAATAAACAAATAAATAAAA
1210019 AAGATAAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (46 bp):
ATTTTATCTTCAATTAAATTAAATTAATAAACAAATAAATAAAAGA
Found at i:1213439 original size:21 final size:21
Alignment explanation
Indices: 1213410--1213452 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1213400 AGTTAGGATA
*
1213410 GTTTGCAAATTTCTTGATTTG
1 GTTTGCAAATTTCTTAATTTG
*
1213431 GTTTTCAAATTTCTTAATTTG
1 GTTTGCAAATTTCTTAATTTG
1213452 G
1 G
1213453 ATCAAGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.16, T:0.53
Consensus pattern (21 bp):
GTTTGCAAATTTCTTAATTTG
Found at i:1213688 original size:37 final size:37
Alignment explanation
Indices: 1213647--1213730 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
1213637 GATAAGTTAT
**
1213647 CTAAAAGTTAGATATTATCTTAA-CTAAGACAAACAAC
1 CTAAAAGTTAGATAACATC-TAATCTAAGACAAACAAC
* * **
1213684 CTAAAAGTTAGGTAACATCTAATTTAAGACAAACTTC
1 CTAAAAGTTAGATAACATCTAATCTAAGACAAACAAC
1213721 CTAAAAGTTA
1 CTAAAAGTTA
1213731 AGAATTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
36 3 0.08
37 37 0.93
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (37 bp):
CTAAAAGTTAGATAACATCTAATCTAAGACAAACAAC
Found at i:1215272 original size:51 final size:51
Alignment explanation
Indices: 1215209--1215387 Score: 236
Period size: 51 Copynumber: 3.5 Consensus size: 51
1215199 AAATAACGGG
* *
1215209 GTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* * * *
1215260 GTTGGAGTATCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* * * *
1215311 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAACTGGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAAT-AAAATCGGA
*
1215363 -TTGGAGTATCCCCGA-GATGAAAAAT
1 GTTGGAGTATCCCCGATTATGAAAAAT
1215388 CTAGAAATTT
Statistics
Matches: 111, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
50 8 0.07
51 98 0.88
52 5 0.05
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.28
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:1215274 original size:79 final size:81
Alignment explanation
Indices: 1214964--1215274 Score: 339
Period size: 79 Copynumber: 3.9 Consensus size: 81
1214954 TGGAGTTGAC
* * * * *
1214964 AACGGGGCTGGAGTATCCCCTGATTAT-AGAAAATCGACGTTTT-GAGAATAAAATCGGGGTTAG
1 AACGGGGTTAGAGTATCCCC-GATTATGAGAAAATTGATGTTTTGGA-AATAAAATCGGGGTTGG
* *
1215027 AGTATCTCCTTCGAAAAT
64 AGTATCCCCGTCGAAAAT
* * * *
1215045 AACGGGGTTAGAGTATCCCCGATTGTG-GAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAG
1 AACGGGGTTAGAGTATCCCCGATTATGAGAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAG
1215109 TATCCCC-TCGAAAAT
66 TATCCCCGTCGAAAAT
* ** * * *** *
1215124 AACGGGATTAGAGTATCCCAAATTATGA-AAAATTGATGCTTTAGAAATAACGGCGGGGTTGAAG
1 AACGGGGTTAGAGTATCCCCGATTATGAGAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAG
1215188 TATCCCCGT-GAAAAT
66 TATCCCCGTCGAAAAT
* * * *
1215203 AACGGGGTTGGAGTATCCCCGATTGTGAG-AAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAG
1 AACGGGGTTAGAGTATCCCCGATTATGAGAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAG
1215267 TATCCCCG
66 TATCCCCG
1215275 ATTATGAAAA
Statistics
Matches: 190, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
79 130 0.68
80 41 0.22
81 19 0.10
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (81 bp):
AACGGGGTTAGAGTATCCCCGATTATGAGAAAATTGATGTTTTGGAAATAAAATCGGGGTTGGAG
TATCCCCGTCGAAAAT
Found at i:1215328 original size:102 final size:101
Alignment explanation
Indices: 1215205--1215387 Score: 278
Period size: 102 Copynumber: 1.8 Consensus size: 101
1215195 GTGAAAATAA
** * *
1215205 CGGGGTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAAT-AAAATCGGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAAATCGGA-TTGGAGTA
*
1215269 TCCCCGATTATGAAAAATGGGTGTTTTAGAAATAAAAC
65 TCCCCGA-GATGAAAAATGGGTGTTTTAGAAATAAAAC
* *
1215307 CGGGGTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAACTGGGATTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAAATCGGATTGGAGTAT
1215372 CCCCGAGATGAAAAAT
66 CCCCGAGATGAAAAAT
1215388 CTAGAAATTT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 9 0.12
102 57 0.78
103 7 0.10
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.28
Consensus pattern (101 bp):
CGGGGTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGAAAATCGGATTGGAGTAT
CCCCGAGATGAAAAATGGGTGTTTTAGAAATAAAAC
Found at i:1217734 original size:33 final size:33
Alignment explanation
Indices: 1217692--1217761 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
1217682 TACATTGTAA
1217692 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
*
1217725 AATGTATCGATACAATGAGCAATGTATTGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
1217758 AATG
1 AATG
1217762 CAAAATGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.29
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:1217736 original size:53 final size:53
Alignment explanation
Indices: 1217674--1217778 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
1217664 AATGCCTGAG
* *
1217674 TGTATCGATACATTGTA-AAATGTATCGATACAATG-AGCAATGTATCGATACAA
1 TGTATCGATACAATG-AGAAATGTATCGATACAATGCA-AAATGTATCGATACAA
* *
1217727 TGTATCGATACAATGAGCAATGTATTGATACAATGCAAAATGTATCGATACA
1 TGTATCGATACAATGAGAAATGTATCGATACAATGCAAAATGTATCGATACA
1217779 TCTAGGTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
52 1 0.02
53 44 0.96
54 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (53 bp):
TGTATCGATACAATGAGAAATGTATCGATACAATGCAAAATGTATCGATACAA
Found at i:1217747 original size:20 final size:19
Alignment explanation
Indices: 1217674--1217778 Score: 96
Period size: 20 Copynumber: 5.6 Consensus size: 19
1217664 AATGCCTGAG
* *
1217674 TGTATCGATACATTGTAAAA
1 TGTATCGATACAATG-ACAA
1217694 TGTATCGATACAATGAGCAA
1 TGTATCGATACAATGA-CAA
1217714 TGTATCG-----AT-ACAA
1 TGTATCGATACAATGACAA
1217727 TGTATCGATACAATGAGCAA
1 TGTATCGATACAATGA-CAA
* *
1217747 TGTATTGATACAATGCAAAA
1 TGTATCGATACAATG-ACAA
1217767 TGTATCGATACA
1 TGTATCGATACA
1217779 TCTAGGTAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
13 10 0.14
14 1 0.01
15 2 0.03
18 2 0.03
19 2 0.03
20 53 0.75
21 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAATGACAA
Found at i:1217760 original size:13 final size:13
Alignment explanation
Indices: 1217711--1217741 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1217701 ATACAATGAG
1217711 CAATGTATCGATA
1 CAATGTATCGATA
1217724 CAATGTATCGATA
1 CAATGTATCGATA
1217737 CAATG
1 CAATG
1217742 AGCAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1217814 original size:13 final size:13
Alignment explanation
Indices: 1217796--1217820 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1217786 AAACCCAGAA
1217796 TGTATCGATACAG
1 TGTATCGATACAG
1217809 TGTATCGATACA
1 TGTATCGATACA
1217821 ATATACAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1217832 original size:20 final size:20
Alignment explanation
Indices: 1217803--1217841 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1217793 GAATGTATCG
*
1217803 ATACAGTGTATCGATACAAT
1 ATACAATGTATCGATACAAT
1217823 ATACAATGTATCGATACAA
1 ATACAATGTATCGATACAA
1217842 ATTGTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATACAATGTATCGATACAAT
Found at i:1220570 original size:20 final size:19
Alignment explanation
Indices: 1220547--1220587 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1220537 TTTATTTTAA
1220547 TTTTTACATATTTAATATTT
1 TTTTTACATATTTAAT-TTT
**
1220567 TTTTTATTTATTTAATTTT
1 TTTTTACATATTTAATTTT
1220586 TT
1 TT
1220588 ACAGGCTAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTACATATTTAATTTT
Found at i:1220938 original size:29 final size:27
Alignment explanation
Indices: 1220906--1220973 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
1220896 ATTTTTAATG
1220906 AATTTTTTATTAGAATTA-CTACATGATTA
1 AATTTTTTATTAGAATTATC-ACATG--TA
* * *
1220935 AATTCTTGATTAGATTTATCACATGTA
1 AATTTTTTATTAGAATTATCACATGTA
*
1220962 AACTTTTTATTA
1 AATTTTTTATTA
1220974 ACCTCTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
27 11 0.34
29 20 0.62
30 1 0.03
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (27 bp):
AATTTTTTATTAGAATTATCACATGTA
Found at i:1222213 original size:51 final size:51
Alignment explanation
Indices: 1222155--1222347 Score: 221
Period size: 51 Copynumber: 3.8 Consensus size: 51
1222145 GAGTTGATTG
* *
1222155 TGAATATTGTTGTGTTGATTATGAGATCATGTAAATTCATGTTTTCATTTA
1 TGAATATTGTTGTGTTGATTATGAGATCATATAAATTCATGATTTCATTTA
* * * *
1222206 TGTATATTGATGTGTTGATTATGAGATCATGTAAATTCAT-ATTTCTATTTG
1 TGAATATTGTTGTGTTGATTATGAGATCATATAAATTCATGATTTC-ATTTA
* * * *
1222257 TGAATATTTTTTTGTTGATTATGAGATCAAATAAATTCATGCATTT-ATATA
1 TGAATATTGTTGTGTTGATTATGAGATCATATAAATTCATG-ATTTCATTTA
* * *
1222308 TGAATTTTAG-AGTGTTGATTGTGAGATCATATAAATTCAT
1 TGAATATT-GTTGTGTTGATTATGAGATCATATAAATTCAT
1222348 TCCATGAAAT
Statistics
Matches: 120, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
50 4 0.03
51 112 0.93
53 4 0.03
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.47
Consensus pattern (51 bp):
TGAATATTGTTGTGTTGATTATGAGATCATATAAATTCATGATTTCATTTA
Found at i:1222264 original size:102 final size:102
Alignment explanation
Indices: 1222152--1222347 Score: 270
Period size: 102 Copynumber: 1.9 Consensus size: 102
1222142 TATGAGTTGA
** * * *
1222152 TTGTGAATATTGTTGTGTTGATTATGAGATCATGTAAATTCATG-TTTTCATTTATGTATATT-G
1 TTGTGAATATTGTTGTGTTGATTATGAGATCAAATAAATTCATGCATTT-ATATATGAATATTAG
*
1222215 ATGTGTTGATTATGAGATCATGTAAATTCATATTTCTAT
65 A-GTGTTGATTATGAGATCATATAAATTCATATTTCTAT
* * *
1222254 TTGTGAATATTTTTTTGTTGATTATGAGATCAAATAAATTCATGCATTTATATATGAATTTTAGA
1 TTGTGAATATTGTTGTGTTGATTATGAGATCAAATAAATTCATGCATTTATATATGAATATTAGA
*
1222319 GTGTTGATTGTGAGATCATATAAATTCAT
66 GTGTTGATTATGAGATCATATAAATTCAT
1222348 TCCATGAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
102 77 0.94
103 5 0.06
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (102 bp):
TTGTGAATATTGTTGTGTTGATTATGAGATCAAATAAATTCATGCATTTATATATGAATATTAGA
GTGTTGATTATGAGATCATATAAATTCATATTTCTAT
Found at i:1225079 original size:154 final size:149
Alignment explanation
Indices: 1224903--1225311 Score: 401
Period size: 153 Copynumber: 2.7 Consensus size: 149
1224893 GCATATCTTC
** * * *
1224903 GGCATAAAAGTATCT-AGTGACTATCTAAGACTCGATTCTAGAGAAATCACCAAAATGCCCTTAA
1 GGCATAAAAAAATCTCAGTGACTATATCAGACTCGATTCTAGA-AAATCACCAAAAT-CCCTTAG
* * * *
1224967 GGTATACCTTTGAAGTGAAAGCATCTTGGTAACCTTAAAGGACATGAAAAATTCGTAAAAAAATA
64 GGTATA-CTTTGAA-TAAAAGCATCTTGATAACCATAAAGGACATGAAAAATT-ATAAAAAAATA
*
1225032 AACCTATCCTAAATGAACACCTTT
126 AACCTATCCTAAATGAACACCATT
* * * *
1225056 GGCATAAAAAAATCTCAGTGACTATATCAGACTCGGTTCTAGAAAAACTACCAAAATACCTTTGG
1 GGCATAAAAAAATCTCAGTGACTATATCAGACTCGATTCTAGAAAATC-ACCAAAATCCCTTAGG
** ** * * * * *
1225121 AGTATACTTTCGACATAAAAATATCTCAATAACCCTAAAAGACATGAAAGATTATAAAAATATGA
65 -GTATACTTT-GA-ATAAAAGCATCTTGATAACCATAAAGGACATGAAAAATTATAAAAAAATAA
* * *
1225186 ACCTATCCTAAATGCATATCATT
127 ACCTATCCTAAATGAACACCATT
* * * * *
1225209 GGCATAAAAACATCTCGGTGACTATATCAGACTTC-ATTATA-AAAATTATCAAAATACCCTTAG
1 GGCATAAAAAAATCTCAGTGACTATATCAGAC-TCGATTCTAGAAAATCACCAAAAT-CCCTTAG
1225272 GGTATTACTTTGAAATAAAAGCATCTTGATAACCATAAAG
64 GGTA-TACTTTG-AATAAAAGCATCTTGATAACCATAAAG
1225312 ACTAAAAAAT
Statistics
Matches: 207, Mismatches: 40, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
151 31 0.15
152 17 0.08
153 88 0.43
154 70 0.34
155 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (149 bp):
GGCATAAAAAAATCTCAGTGACTATATCAGACTCGATTCTAGAAAATCACCAAAATCCCTTAGGG
TATACTTTGAATAAAAGCATCTTGATAACCATAAAGGACATGAAAAATTATAAAAAAATAAACCT
ATCCTAAATGAACACCATT
Found at i:1227236 original size:28 final size:28
Alignment explanation
Indices: 1227205--1227260 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1227195 AATTTTTTAG
* *
1227205 AATTTTACATGAT-TAAACTTTTAATTAA
1 AATTTTACAT-ATGTAAAATTTCAATTAA
*
1227233 AATTTTTCATATGTAAAATTTCAATTAA
1 AATTTTACATATGTAAAATTTCAATTAA
1227261 CTTCTTTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 2 0.08
28 22 0.92
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (28 bp):
AATTTTACATATGTAAAATTTCAATTAA
Found at i:1228963 original size:29 final size:28
Alignment explanation
Indices: 1228900--1229043 Score: 103
Period size: 28 Copynumber: 5.0 Consensus size: 28
1228890 TAGGAAATAG
*
1228900 TCAAAGTGTAATTTCAAAAAGGTTAAGGG-
1 TCAAAGTGTAATTT-AAAAA-GTTTAGGGA
* * *
1228929 TTAAAATGCAATTTGAAAAAGTTTAGGGA
1 TCAAAGTGTAATTT-AAAAAGTTTAGGGA
*** * * * *
1228958 TCAAAACATGATTTTAAAAGTTTTGTGA
1 TCAAAGTGTAATTTAAAAAGTTTAGGGA
*
1228986 TCAAAGTGTAATTTTGAAAAAGTTTAAAGG-
1 TCAAAGTGTAA-TTT-AAAAAGTTT-AGGGA
*
1229016 TCAAAGTGTAATTTTAAAAGTTTAGGGA
1 TCAAAGTGTAATTTAAAAAGTTTAGGGA
1229044 CTTAGTAGCA
Statistics
Matches: 87, Mismatches: 23, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
27 3 0.03
28 33 0.38
29 31 0.36
30 19 0.22
31 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (28 bp):
TCAAAGTGTAATTTAAAAAGTTTAGGGA
Found at i:1229009 original size:30 final size:28
Alignment explanation
Indices: 1228968--1229039 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 28
1228958 TCAAAACATG
***
1228968 ATTTTAAAAGTTTTGTGATCAAAGTGTA
1 ATTTTAAAAGTTTAAAGATCAAAGTGTA
*
1228996 ATTTTGAAAAAGTTTAAAGGTCAAAGTGTA
1 ATTTT--AAAAGTTTAAAGATCAAAGTGTA
1229026 ATTTTAAAAGTTTA
1 ATTTTAAAAGTTTA
1229040 GGGACTTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 14 0.37
30 24 0.63
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (28 bp):
ATTTTAAAAGTTTAAAGATCAAAGTGTA
Found at i:1232824 original size:20 final size:21
Alignment explanation
Indices: 1232795--1232846 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1232785 ACAGGCTCTA
* *
1232795 GTATCAATACATTCACTTA-T
1 GTATCAATACATTAAATTATT
*
1232815 GTATCTATACATTAAATTATT
1 GTATCAATACATTAAATTATT
*
1232836 GTATCGATACA
1 GTATCAATACA
1232847 AATTATTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (21 bp):
GTATCAATACATTAAATTATT
Found at i:1233436 original size:2 final size:2
Alignment explanation
Indices: 1233429--1233469 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1233419 AAGATCAAGG
1233429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1233470 AGGGGTGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1233789 original size:51 final size:51
Alignment explanation
Indices: 1233725--1233863 Score: 224
Period size: 51 Copynumber: 2.7 Consensus size: 51
1233715 TTTGGAATAA
* * *
1233725 AAATGTATCGATACATTTTTCATTATACCGATACATTTTGGGTTTTGATCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTTTGGGTTTTGACCC
*
1233776 AAATGTATCGATACATTTTTTATTGTATCGATACATTTTGGGTTTTGACCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTTTGGGTTTTGACCC
* *
1233827 AAATATATCGATACATTCTTCATTGTATCGATACATT
1 AAATGTATCGATACATTTTTCATTGTATCGATACATT
1233864 CTTTAATGTA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (51 bp):
AAATGTATCGATACATTTTTCATTGTATCGATACATTTTGGGTTTTGACCC
Found at i:1233857 original size:20 final size:20
Alignment explanation
Indices: 1233832--1233876 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1233822 GACCCAAATA
*
1233832 TATCGATACATTCTTCATTG
1 TATCGATACATTCTTCAATG
*
1233852 TATCGATACATTCTTTAATG
1 TATCGATACATTCTTCAATG
1233872 TATCG
1 TATCG
1233877 GTATATGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:1236203 original size:97 final size:97
Alignment explanation
Indices: 1236008--1236213 Score: 227
Period size: 97 Copynumber: 2.1 Consensus size: 97
1235998 TTATTCATCA
* * * * *
1236008 GGGATACTGCAACCCAGTTTTTGAACTTGTCAAGATTTAAATCTTATTTTTGCTTAAATTGTCAT
1 GGGATACTCCAACCCAGTTTTTAAACTTCTCAAGATTTAAATCTTATTTTTGCCTAAATTATCAT
* * * * * ** **
1236073 CATTAATGATACTCTAACCATGTTTTTGTAAG
66 CATCAAGGACACTCCAACCACGTTCCTCCAAG
*
1236105 GGGATACTCCAACCTC-GTTTTTAAATTTCTCAAGATTTAAATCTTATTTTTGCCTAAATTATCA
1 GGGATACTCCAACC-CAGTTTTTAAACTTCTCAAGATTTAAATCTTATTTTTGCCTAAATTATCA
* *
1236169 TCGTCGAGGACACTCCAACC-CGATTCCTCCAAG
65 TCATCAAGGACACTCCAACCACG-TTCCTCCAAG
1236202 GGGATACTCCAA
1 GGGATACTCCAA
1236214 GCCCGCTCTT
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
96 1 0.01
97 88 0.98
98 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (97 bp):
GGGATACTCCAACCCAGTTTTTAAACTTCTCAAGATTTAAATCTTATTTTTGCCTAAATTATCAT
CATCAAGGACACTCCAACCACGTTCCTCCAAG
Found at i:1238249 original size:2 final size:2
Alignment explanation
Indices: 1238242--1238275 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1238232 TTTACATTTC
* *
1238242 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1238276 CTTTGATCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1240090 original size:21 final size:20
Alignment explanation
Indices: 1240050--1240104 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1240040 AAAATTATAA
*
1240050 AAAAATCCCT-AAA-ATGTT
1 AAAAATGCCTAAAACATGTT
1240068 AAAAATGCCTAAAACATGTTT
1 AAAAATGCCTAAAACATG-TT
* *
1240089 AAACATGCATAAAACA
1 AAAAATGCCTAAAACA
1240105 CATCTTAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.29
19 3 0.10
20 3 0.10
21 16 0.52
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (20 bp):
AAAAATGCCTAAAACATGTT
Found at i:1247463 original size:13 final size:13
Alignment explanation
Indices: 1247445--1247469 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1247435 CATAAAGTGT
1247445 TGTATCGATACAA
1 TGTATCGATACAA
1247458 TGTATCGATACA
1 TGTATCGATACA
1247470 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1247480 original size:32 final size:33
Alignment explanation
Indices: 1247425--1247488 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
1247415 TTCAACGATT
1247425 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1247458 TGTATCGATACAT-AAGTGTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACA
1247489 TAAGTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1247482 original size:19 final size:19
Alignment explanation
Indices: 1247424--1247507 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
1247414 TTTCAACGAT
1247424 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
1247444 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
1247458 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1247476 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
1247495 TTGTATCGATACA
1 TTGTATCGATACA
1247508 ATATAAGCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 2 0.04
19 30 0.53
20 12 0.21
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1247617 original size:52 final size:52
Alignment explanation
Indices: 1247581--1247754 Score: 312
Period size: 52 Copynumber: 3.3 Consensus size: 52
1247571 CACTGATCTT
1247581 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1247633 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* * *
1247685 TGTATCGATACATGCAGGCAAATTTGCCTAGATGTATCGAAACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1247737 TGTATCGATACATGCAGG
1 TGTATCGATACATGCAGG
1247755 TAACTTTTCA
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1254184 original size:26 final size:25
Alignment explanation
Indices: 1254147--1254196 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
1254137 GACAAAAATC
1254147 AAATATTATATATTTAATATATTATT
1 AAATATTATATATTTAAT-TATTATT
1254173 AAATA-TAGTATATTTAATTATTAT
1 AAATATTA-TATATTTAATTATTAT
1254197 ATTATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
AAATATTATATATTTAATTATTATT
Found at i:1254245 original size:18 final size:19
Alignment explanation
Indices: 1254196--1254248 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
1254186 TTAATTATTA
1254196 TATTATATTATTTATAAAATT
1 TATT-TATTA-TTATAAAATT
*
1254217 T-TTTATATATT-TAAATTT
1 TATTTAT-TATTATAAAATT
1254235 TATTTATTATTATA
1 TATTTATTATTATA
1254249 TATTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 11 0.39
19 12 0.43
20 4 0.14
21 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTATTATTATAAAATT
Found at i:1254417 original size:13 final size:12
Alignment explanation
Indices: 1254398--1254458 Score: 65
Period size: 12 Copynumber: 5.2 Consensus size: 12
1254388 TATATTTTTT
1254398 TATAAAATATTA
1 TATAAAATATTA
1254410 TCATAAAATATTA
1 T-ATAAAATATTA
*
1254423 TATAATATATTA
1 TATAAAATATTA
* *
1254435 TAT--TATACTA
1 TATAAAATATTA
1254445 TAT-AAATATTA
1 TATAAAATATTA
1254456 TAT
1 TAT
1254459 TATTAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
10 9 0.21
11 8 0.19
12 14 0.33
13 12 0.28
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (12 bp):
TATAAAATATTA
Found at i:1254455 original size:21 final size:22
Alignment explanation
Indices: 1254421--1254461 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1254411 CATAAAATAT
1254421 TATATAATATATTATATTATAC
1 TATATAATATATTATATTATAC
1254443 TATATAA-ATATTATATTAT
1 TATATAATATATTATATTAT
1254462 TAAATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATAATATATTATATTATAC
Found at i:1254465 original size:15 final size:15
Alignment explanation
Indices: 1254415--1254495 Score: 60
Period size: 15 Copynumber: 5.3 Consensus size: 15
1254405 TATTATCATA
*
1254415 AAATATTATATAATAT
1 AAATATTATATTAT-T
* *
1254431 ATTATATTATACTATAT
1 A-AATATTATATTAT-T
1254448 AAATATTATATTATT
1 AAATATTATATTATT
1254463 AAATATT-TAATTATT
1 AAATATTAT-ATTATT
*
1254478 ACATTATTAT-TT-TT
1 A-AATATTATATTATT
1254492 AAAT
1 AAAT
1254496 GTTAAATATA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
13 2 0.04
14 4 0.07
15 17 0.31
16 17 0.31
17 14 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATATTATATTATT
Found at i:1258040 original size:3 final size:3
Alignment explanation
Indices: 1258028--1258072 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
1258018 TTTGTATTTC
1258028 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1258073 ATATTAATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1259559 original size:15 final size:15
Alignment explanation
Indices: 1259541--1259580 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1259531 ATATTTATTT
1259541 ATTTAATATTTAAAA
1 ATTTAATATTTAAAA
1259556 ATTTAGATA-TTAAAA
1 ATTTA-ATATTTAAAA
1259571 ATTT-ATATTT
1 ATTTAATATTT
1259581 TATATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.13
14 2 0.09
15 15 0.65
16 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTAATATTTAAAA
Found at i:1260747 original size:15 final size:18
Alignment explanation
Indices: 1260721--1260764 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 18
1260711 GGTTAAACTA
*
1260721 TTGAAGAGTTATTT-T-T
1 TTGAATAGTTATTTCTAT
1260737 TT-AATAGTTATTTCTAT
1 TTGAATAGTTATTTCTAT
1260754 TTGAATAGTTA
1 TTGAATAGTTA
1260765 CATTTGTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 10 0.42
16 3 0.12
17 3 0.12
18 8 0.33
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.55
Consensus pattern (18 bp):
TTGAATAGTTATTTCTAT
Found at i:1262596 original size:18 final size:17
Alignment explanation
Indices: 1262555--1262597 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1262545 AGACACTGTT
*
1262555 AGAAAGATTGCTTGAAA
1 AGAAAGATGGCTTGAAA
*
1262572 TGTAAAGCATGGCTTGAAA
1 AG-AAAG-ATGGCTTGAAA
1262591 AGAAAGA
1 AGAAAGA
1262598 CAAACCAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
17 2 0.10
18 8 0.38
19 11 0.52
ACGTcount: A:0.47, C:0.07, G:0.26, T:0.21
Consensus pattern (17 bp):
AGAAAGATGGCTTGAAA
Found at i:1267254 original size:21 final size:21
Alignment explanation
Indices: 1267202--1267257 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1267192 TAATTATGTA
*
1267202 ACAATAA-ATAGAT-AAATAT
1 ACAATAACATAAATAAAATAT
1267221 -CAATATACA-AAATAAAATAT
1 ACAATA-ACATAAATAAAATAT
1267241 ACAATAACATAAATAAA
1 ACAATAACATAAATAAA
1267258 TTAGTACATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 5 0.16
19 4 0.13
20 10 0.32
21 12 0.39
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (21 bp):
ACAATAACATAAATAAAATAT
Found at i:1267258 original size:20 final size:20
Alignment explanation
Indices: 1267202--1267258 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
1267192 TAATTATGTA
*
1267202 ACAATAA-ATAGATAAATAT
1 ACAATAACATAAATAAATAT
1267221 -CAATATACA-AAATAAAATAT
1 ACAATA-ACATAAAT-AAATAT
1267241 ACAATAACATAAATAAAT
1 ACAATAACATAAATAAAT
1267259 TAGTACATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
18 5 0.16
19 4 0.12
20 14 0.44
21 9 0.28
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.25
Consensus pattern (20 bp):
ACAATAACATAAATAAATAT
Found at i:1267549 original size:20 final size:21
Alignment explanation
Indices: 1267514--1267553 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1267504 TAATCTCAAC
*
1267514 ACTATAGTACCTAATCTTATA
1 ACTATAGTAACTAATCTTATA
1267535 ACTATA-TAACTAATCTTAT
1 ACTATAGTAACTAATCTTAT
1267554 CATCATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (21 bp):
ACTATAGTAACTAATCTTATA
Found at i:1274624 original size:40 final size:40
Alignment explanation
Indices: 1274580--1274669 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 40
1274570 TATGCCTTCG
1274580 GTAAGAATAGTGATAGTTTTTATTCTAAACCGTACCACCA
1 GTAAGAATAGTGATAGTTTTTATTCTAAACCGTACCACCA
* * * *
1274620 GTAAGAATA---ATAGTTTTTATTTTGAACTGTACCACTA
1 GTAAGAATAGTGATAGTTTTTATTCTAAACCGTACCACCA
*
1274657 GTTAAGAAAAGTG
1 G-TAAGAATAGTG
1274670 GTTTTTGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
37 25 0.61
38 7 0.17
40 9 0.22
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (40 bp):
GTAAGAATAGTGATAGTTTTTATTCTAAACCGTACCACCA
Found at i:1274674 original size:38 final size:37
Alignment explanation
Indices: 1274592--1274685 Score: 109
Period size: 37 Copynumber: 2.5 Consensus size: 37
1274582 AAGAATAGTG
* *
1274592 ATAGTTTTTATTCTAAACCGTACCACCAGTAAGAATA
1 ATAGTTTTTATTTTGAACCGTACCACCAGTAAGAATA
* *
1274629 ATAGTTTTTATTTTGAACTGTACCACTAGTTAAGAA-A
1 ATAGTTTTTATTTTGAACCGTACCACCAG-TAAGAATA
* *
1274666 AGTGGTTTTTGTTTTGAACC
1 A-TAGTTTTTATTTTGAACC
1274686 ATGTCACCGG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
37 27 0.56
38 21 0.44
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (37 bp):
ATAGTTTTTATTTTGAACCGTACCACCAGTAAGAATA
Found at i:1279446 original size:23 final size:23
Alignment explanation
Indices: 1279419--1279471 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1279409 TTTTTAATAT
1279419 AAAATATTTAGTAATATTTTTTG
1 AAAATATTTAGTAATATTTTTTG
*
1279442 AAAATATTTAGTAATGTTTTTTG
1 AAAATATTTAGTAATATTTTTTG
*
1279465 AATATAT
1 AAAATAT
1279472 AAATACCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (23 bp):
AAAATATTTAGTAATATTTTTTG
Found at i:1283188 original size:2 final size:2
Alignment explanation
Indices: 1283176--1283215 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1283166 GTTTTGAACA
* *
1283176 AT AT GT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1283216 TTATTGCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1284161 original size:28 final size:28
Alignment explanation
Indices: 1284124--1284179 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1284114 AACAACAATA
1284124 AAAAAATATATTTATAATAATATTTAAT
1 AAAAAATATATTTATAATAATATTTAAT
*
1284152 AAAAAATATATTTTTAATAATATTTAAT
1 AAAAAATATATTTATAATAATATTTAAT
1284180 TTTTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAAAATATATTTATAATAATATTTAAT
Found at i:1285103 original size:18 final size:18
Alignment explanation
Indices: 1285076--1285134 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
1285066 CATTGAAAAA
1285076 ATAACTAAAATAAACGTAAT
1 ATAA-TAAAATAAACG-AAT
*
1285096 ATAA-AAAATAATAAGAAT
1 ATAATAAAATAA-ACGAAT
*
1285114 ATAATATAAATAAACAAAT
1 ATAATA-AAATAAACGAAT
1285133 AT
1 AT
1285135 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 14 0.42
19 9 0.27
20 10 0.30
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.25
Consensus pattern (18 bp):
ATAATAAAATAAACGAAT
Found at i:1285127 original size:27 final size:27
Alignment explanation
Indices: 1285071--1285133 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
1285061 CTGAACATTG
*
1285071 AAAAAATAACTAAAATAAACGTAATAT
1 AAAAAATAACTAAAATAAACATAATAT
*
1285098 AAAAAATAA-TAAGAATATAATATAA-AT
1 AAAAAATAACTAA-AATA-AACATAATAT
1285125 AAACAAATA
1 AAA-AAATA
1285134 TTTTAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 3 0.10
27 18 0.58
28 10 0.32
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (27 bp):
AAAAAATAACTAAAATAAACATAATAT
Found at i:1285190 original size:24 final size:24
Alignment explanation
Indices: 1285162--1285212 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1285152 ATGAATTATT
*
1285162 AATATGTCAAAATTTTTATAAATA
1 AATATGTCAAAATTTATATAAATA
*
1285186 AATATGTTAAAATTTATATAAATA
1 AATATGTCAAAATTTATATAAATA
1285210 AAT
1 AAT
1285213 TATTAATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
AATATGTCAAAATTTATATAAATA
Found at i:1285233 original size:55 final size:55
Alignment explanation
Indices: 1285123--1285249 Score: 159
Period size: 55 Copynumber: 2.3 Consensus size: 55
1285113 TATAATATAA
* * * *
1285123 ATAAACAAATATTTTAAAATTTACGTAAAATGAATTATTAATATGTCAAAATTTTT
1 ATAAATAAATATCTTAAAATTTAC-TAAAATAAATTATTAATATATCAAAATTTTT
* *
1285179 ATAAATAAATATGTTAAAATTTA-TATAAATAAATTATTAATGTATCAAAATTTTT
1 ATAAATAAATATCTTAAAATTTACTA-AAATAAATTATTAATATATCAAAATTTTT
*
1285234 ATATAT-AATATCTTAA
1 ATAAATAAATATCTTAA
1285250 TTATGATTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
54 11 0.17
55 31 0.49
56 21 0.33
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (55 bp):
ATAAATAAATATCTTAAAATTTACTAAAATAAATTATTAATATATCAAAATTTTT
Found at i:1285542 original size:421 final size:421
Alignment explanation
Indices: 1284758--1285606 Score: 1545
Period size: 421 Copynumber: 2.0 Consensus size: 421
1284748 GGTTTTGACA
1284758 ATAAATAAATATGTTAAAATTTATATAAATAAATTATTAATCTATCAAAATTTTTATATATAATA
1 ATAAATAAATATGTTAAAATTTATATAAATAAATTATTAATCTATCAAAATTTTTATATATAATA
1284823 TCTTAATTATGATTATTACATAAAAACACGAACATGACATGTGACACAAAAGTGAGAATTCTTTG
66 TCTTAATTATGATTATTACATAAAAACACGAACATGACATGTGACACAAAAGTGAGAATTCTTTG
* * *
1284888 AATAGTTTTAGTTAGATCAGAAATTTTTAAATATAATATAATTATATAATATGAAATCAACAGGA
131 AATAGTTTTAGTTAGATAAAAAAATTTTAAATATAATATAATTATATAATATGAAATCAACAGGA
*
1284953 TAAAAATAATTAAAATACAATTAGAAAAATAATATAAGCATAATGTGAATAGGCATCAAAATTTA
196 TAAAAATAATTAAAATACAACTAGAAAAATAATATAAGCATAATGTGAATAGGCATCAAAATTTA
*
1285018 TAAAATTATAAAATAGCTTTACGATTATGAGATGAAAGGTTAACTGAACATTGAAAAAATAACTA
261 TAAAAATATAAAATAGCTTTACGATTATGAGATGAAAGGTTAACTGAACATTGAAAAAATAACTA
* * *
1285083 AAATAAACGTAATATAAAAAATAATAAGAATATAATATAAATAAACAAATATTTTAAAATTTACG
326 AAATAAACGTAATACAAAAAATAATAAGAACATAATATAAATAAACAAACATTTTAAAATTTACG
* *
1285148 TAAAATGAATTATTAATATGTCAAAATTTTT
391 TAAAATGAATTATTAATATATCAAAATTTAT
*
1285179 ATAAATAAATATGTTAAAATTTATATAAATAAATTATTAATGTATCAAAATTTTTATATATAATA
1 ATAAATAAATATGTTAAAATTTATATAAATAAATTATTAATCTATCAAAATTTTTATATATAATA
*
1285244 TCTTAATTATGATTATTACATAAAAACACGAACATGACATGTGATACAAAAGTGAGAATTCTTTG
66 TCTTAATTATGATTATTACATAAAAACACGAACATGACATGTGACACAAAAGTGAGAATTCTTTG
* *
1285309 AATAGTTTTAGTTAGATAAAAAAATTTTAAATATAATATAATTATATGATATGAAATCAACGGGA
131 AATAGTTTTAGTTAGATAAAAAAATTTTAAATATAATATAATTATATAATATGAAATCAACAGGA
*
1285374 TAAAAATAATTAAAATACAACTAGAAAAATAATGTAAGCATAATGTGAATAGGCATCAAAATTTA
196 TAAAAATAATTAAAATACAACTAGAAAAATAATATAAGCATAATGTGAATAGGCATCAAAATTTA
* *
1285439 TAAAAATATAAAATAGCTTTACGATTATGGGTTGAAAGGTTAACTGAACATTGAAAAAATAACTA
261 TAAAAATATAAAATAGCTTTACGATTATGAGATGAAAGGTTAACTGAACATTGAAAAAATAACTA
1285504 AAATAAACGTAATACAAAAAATAATAAGAACATAATATAAATAAACAAACATTTTAAAATTTACG
326 AAATAAACGTAATACAAAAAATAATAAGAACATAATATAAATAAACAAACATTTTAAAATTTACG
1285569 TAAAATGAATTATTAATATATCAAAATTTAT
391 TAAAATGAATTATTAATATATCAAAATTTAT
1285600 ATAAATA
1 ATAAATA
1285607 CAAAATACTT
Statistics
Matches: 411, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
421 411 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.33
Consensus pattern (421 bp):
ATAAATAAATATGTTAAAATTTATATAAATAAATTATTAATCTATCAAAATTTTTATATATAATA
TCTTAATTATGATTATTACATAAAAACACGAACATGACATGTGACACAAAAGTGAGAATTCTTTG
AATAGTTTTAGTTAGATAAAAAAATTTTAAATATAATATAATTATATAATATGAAATCAACAGGA
TAAAAATAATTAAAATACAACTAGAAAAATAATATAAGCATAATGTGAATAGGCATCAAAATTTA
TAAAAATATAAAATAGCTTTACGATTATGAGATGAAAGGTTAACTGAACATTGAAAAAATAACTA
AAATAAACGTAATACAAAAAATAATAAGAACATAATATAAATAAACAAACATTTTAAAATTTACG
TAAAATGAATTATTAATATATCAAAATTTAT
Found at i:1285829 original size:15 final size:15
Alignment explanation
Indices: 1285787--1285833 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1285777 CTTATGAATT
1285787 AAATATGAAAAAAAT-
1 AAATAT-AAAAAAATA
* *
1285802 AACTAAAACAAAAATA
1 AAATATAA-AAAAATA
1285818 AAATATAAAAAAATA
1 AAATATAAAAAAATA
1285833 A
1 A
1285834 TACTAACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 2 0.08
15 18 0.69
16 6 0.23
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (15 bp):
AAATATAAAAAAATA
Found at i:1286935 original size:20 final size:21
Alignment explanation
Indices: 1286912--1286955 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1286902 ATTTTAGTTA
1286912 AATTTAATTAAT-TTTAAAAT
1 AATTTAATTAATATTTAAAAT
* *
1286932 AATTTTATTAATATTTTAAAT
1 AATTTAATTAATATTTAAAAT
1286953 AAT
1 AAT
1286956 AATTTGAGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTAATTAATATTTAAAAT
Found at i:1286952 original size:21 final size:21
Alignment explanation
Indices: 1286895--1286955 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1286885 TATAAAAATA
**
1286895 AATTAATATTTTAGTTAAATTT
1 AATTAATATTTTAAAT-AATTT
*
1286917 AATTAAT-TTTAAAATAATTT
1 AATTAATATTTTAAATAATTT
*
1286937 TATTAATATTTTAAATAAT
1 AATTAATATTTTAAATAAT
1286956 AATTTGAGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 11 0.33
21 15 0.45
22 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AATTAATATTTTAAATAATTT
Found at i:1287834 original size:27 final size:25
Alignment explanation
Indices: 1287795--1287860 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
1287785 ATTTTTAAAT
*
1287795 AAAAGAAATAAATAAATAAACTCTATTA
1 AAAAGTAA-AAATAAA-AAA-TCTATTA
* * *
1287823 AAAAGTAAAAATTAAAAATGTATTT
1 AAAAGTAAAAATAAAAAATCTATTA
*
1287848 TAAAGTAAAAATA
1 AAAAGTAAAAATA
1287861 TTGAAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 16 0.50
26 3 0.09
27 6 0.19
28 7 0.22
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (25 bp):
AAAAGTAAAAATAAAAAATCTATTA
Found at i:1287857 original size:59 final size:56
Alignment explanation
Indices: 1287787--1287932 Score: 136
Period size: 58 Copynumber: 2.5 Consensus size: 56
1287777 AATTCAACAT
* *
1287787 TTTTAAA-TAAAAGAAAT-AAATAAATAAACTCTATTAAAAAGTAAAAATTAAAAATGTA
1 TTTTAAAGTAAAA-AAATAAAATAAATAAA--ATATTAAAAAGTAAAAATTAAAAAT-AA
* * * *
1287845 TTTTAAAGTAAAAATATTGAAAA-AATTAAAATATTAAAAAGTATACATTAAAAATAA
1 TTTTAAAGTAAAAA-AAT-AAAATAAATAAAATATTAAAAAGTAAAAATTAAAAATAA
1287902 TGTTTAAAGGTAAAAAAAATAAAATAAATAA
1 T-TTTAAA-GT-AAAAAAATAAAATAAATAA
1287933 GGGGTAAAGT
Statistics
Matches: 72, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
57 2 0.03
58 40 0.56
59 16 0.22
60 11 0.15
61 3 0.04
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (56 bp):
TTTTAAAGTAAAAAAATAAAATAAATAAAATATTAAAAAGTAAAAATTAAAAATAA
Found at i:1290109 original size:56 final size:56
Alignment explanation
Indices: 1290021--1290129 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 56
1290011 CTAAGGGCGA
* * * *
1290021 GGTCAGTAGAAATAGTGAAAAAGCTTACGATGGAAGCATCACGAGATTAGGTGCGG
1 GGTCAGCAAAAATAGTGAAAAAGCTCACGATGGAAGCATAACGAGATTAGGTGCGG
* * *
1290077 GGTCAGCAAAAATGGTGAAAAAGCTCATGATGGAAGCATAACGAGATTGGGTG
1 GGTCAGCAAAAATAGTGAAAAAGCTCACGATGGAAGCATAACGAGATTAGGTG
1290130 AGAGAAAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.37, C:0.12, G:0.32, T:0.19
Consensus pattern (56 bp):
GGTCAGCAAAAATAGTGAAAAAGCTCACGATGGAAGCATAACGAGATTAGGTGCGG
Found at i:1290657 original size:16 final size:16
Alignment explanation
Indices: 1290638--1290686 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1290628 AAGTAAGAGC
1290638 TATTCTAAATAACAAT
1 TATTCTAAATAACAAT
* *
1290654 TATTCTGAATAAAAAT
1 TATTCTAAATAACAAT
*
1290670 TA-TCTTCAATAACAAT
1 TATTC-TAAATAACAAT
1290686 T
1 T
1290687 GTTTTGAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 2 0.07
16 26 0.93
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (16 bp):
TATTCTAAATAACAAT
Found at i:1290979 original size:109 final size:109
Alignment explanation
Indices: 1290778--1290994 Score: 330
Period size: 109 Copynumber: 2.0 Consensus size: 109
1290768 TTGAACAAAC
* * * *
1290778 TGTTTCCAATAGATGAGCATTTAACTATCTTTGCTATTTTGAAAGTGCAATTGACTATTAAATAA
1 TGTTTCCAATAAAAGAGCATTCAACTATCTTTGCTATTTTGAAAGTGCAATTGACTATTAAACAA
1290843 TTTTATATTTTTTAAGAATAGATAATATAA-AGAGTAACCAAAAG
66 TTTTATATTTTTTAAGAATAGATAATATAATA-AGTAACCAAAAG
* * *
1290887 TGTTTCCAGTAAAAGAGCATTCAACTATTTTTGCTATTTTGGAAGTGCAATTGACTATTAAACAA
1 TGTTTCCAATAAAAGAGCATTCAACTATCTTTGCTATTTTGAAAGTGCAATTGACTATTAAACAA
*
1290952 TTTTAT-TTTTTTAAGAATAGATAAATATAATAAGTAACTAAAA
66 TTTTATATTTTTTAAGAATAGAT-AATATAATAAGTAACCAAAA
1290995 TTAAGTATTT
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
108 16 0.16
109 81 0.83
110 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (109 bp):
TGTTTCCAATAAAAGAGCATTCAACTATCTTTGCTATTTTGAAAGTGCAATTGACTATTAAACAA
TTTTATATTTTTTAAGAATAGATAATATAATAAGTAACCAAAAG
Found at i:1298178 original size:18 final size:17
Alignment explanation
Indices: 1298155--1298197 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
1298145 TATATATCTA
1298155 TATATAATATTAATTTGT
1 TATATAATATTAATTT-T
*
1298173 TATATAAAATTAATTTT
1 TATATAATATTAATTTT
*
1298190 TAAATAAT
1 TATATAAT
1298198 TTAGTATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TATATAATATTAATTTT
Found at i:1299365 original size:21 final size:21
Alignment explanation
Indices: 1299339--1299383 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1299329 TGAAAAAGTC
*
1299339 ACATTTTTTAAATGTATCGAT
1 ACATTTCTTAAATGTATCGAT
*
1299360 ACATTTCTTGAATGTATCGAT
1 ACATTTCTTAAATGTATCGAT
1299381 ACA
1 ACA
1299384 AGGTCCCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (21 bp):
ACATTTCTTAAATGTATCGAT
Found at i:1300245 original size:32 final size:31
Alignment explanation
Indices: 1300175--1300245 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
1300165 CCACTCCAAA
*
1300175 CCATTTCCCCTCATACTACAACTCAAATAGC
1 CCATTTTCCCTCATACTACAACTCAAATAGC
*
1300206 CTATTTTCCCTCATACTACAACTCAAATAGC
1 CCATTTTCCCTCATACTACAACTCAAATAGC
1300237 CCACTTTTC
1 CCA-TTTTC
1300246 AGCTTGTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 31 0.86
32 5 0.14
ACGTcount: A:0.30, C:0.37, G:0.03, T:0.31
Consensus pattern (31 bp):
CCATTTTCCCTCATACTACAACTCAAATAGC
Found at i:1305339 original size:21 final size:19
Alignment explanation
Indices: 1305309--1305368 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 19
1305299 TTAAAAAGTG
1305309 ATTTATTAATTTAAATCAT
1 ATTTATTAATTTAAATCAT
**
1305328 ATTTAAATTAATAAAAATCAT
1 ATTT--ATTAATTTAAATCAT
1305349 ATTTATTAATTTAAAT-AT
1 ATTTATTAATTTAAATCAT
1305367 AT
1 AT
1305369 AATATTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.11
19 14 0.40
21 17 0.49
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTATTAATTTAAATCAT
Found at i:1305374 original size:19 final size:20
Alignment explanation
Indices: 1305312--1305375 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
1305302 AAAAGTGATT
1305312 TATTAATTTAAATCATATTTAA
1 TATTAATTTAAATCATA--TAA
** *
1305334 -ATTAATAAAAATCATAT-T
1 TATTAATTTAAATCATATAA
1305352 TATTAATTTAAAT-ATATAA
1 TATTAATTTAAATCATATAA
1305371 TATTA
1 TATTA
1305376 TTAAATAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.12
19 16 0.47
21 14 0.41
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTAATTTAAATCATATAA
Found at i:1305889 original size:15 final size:16
Alignment explanation
Indices: 1305861--1305893 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1305851 ATTTATTTAA
1305861 ATTTTTTATCATAATT
1 ATTTTTTATCATAATT
*
1305877 ATTTTTT-TTATAATT
1 ATTTTTTATCATAATT
1305892 AT
1 AT
1305894 ATTTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTTTTATCATAATT
Found at i:1309955 original size:16 final size:16
Alignment explanation
Indices: 1309846--1309967 Score: 60
Period size: 16 Copynumber: 7.8 Consensus size: 16
1309836 TAATTATATT
*
1309846 TATTTTATTTTATATT-
1 TATTATATTTTA-ATTA
*
1309862 TATATACATTTTAA-TA
1 TAT-TATATTTTAATTA
**
1309878 TATTATTAAATTATATTA
1 TATTA-TATTTTA-ATTA
*
1309896 TATTA-ATTTTAA-GA
1 TATTATATTTTAATTA
* *
1309910 TATT-TA-TATACTTA
1 TATTATATTTTAATTA
*
1309924 TATTA-AATTTATATTA
1 TATTATATTTTA-ATTA
1309940 TATTATATTTTAATTA
1 TATTATATTTTAATTA
* *
1309956 TTTTTTATTTTA
1 TATTATATTTTA
1309968 TATTCGTATC
Statistics
Matches: 79, Mismatches: 16, Indels: 22
0.68 0.14 0.19
Matches are distributed among these distances:
13 3 0.04
14 12 0.15
15 7 0.09
16 37 0.47
17 13 0.16
18 7 0.09
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.61
Consensus pattern (16 bp):
TATTATATTTTAATTA
Found at i:1310442 original size:16 final size:18
Alignment explanation
Indices: 1310421--1310455 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1310411 AATTTTAATT
1310421 TATGTT-TA-TTATTTTA
1 TATGTTATATTTATTTTA
1310437 TATGTTATATTTATTTTA
1 TATGTTATATTTATTTTA
1310455 T
1 T
1310456 TAGCTTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TATGTTATATTTATTTTA
Found at i:1310449 original size:21 final size:19
Alignment explanation
Indices: 1310412--1310451 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
1310402 TTATATATAA
*
1310412 ATTTTAATTTATGTTTATT
1 ATTTTAATTTATATTTATT
1310431 ATTTTATATGTTATATTTATT
1 ATTTTA-AT-TTATATTTATT
1310452 TTATTAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
ATTTTAATTTATATTTATT
Found at i:1310874 original size:6 final size:6
Alignment explanation
Indices: 1310863--1310928 Score: 75
Period size: 6 Copynumber: 11.5 Consensus size: 6
1310853 AAATAATAAC
* *
1310863 TATTTA TATTTA TATTTA TA-TT- TATTT- TATTTA TATCTA TATCTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
* *
1310908 TATCTA TATTTA TATCTA TAT
1 TATTTA TATTTA TATTTA TAT
1310929 CTCTATTATC
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
4 2 0.04
5 9 0.16
6 44 0.80
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (6 bp):
TATTTA
Found at i:1310880 original size:12 final size:12
Alignment explanation
Indices: 1310867--1310942 Score: 86
Period size: 12 Copynumber: 6.3 Consensus size: 12
1310857 AATAACTATT
*
1310867 TATATTTATATT
1 TATATTTATATC
1310879 TATATTTAT-T-
1 TATATTTATATC
1310889 T-TATTTATATC
1 TATATTTATATC
*
1310900 TATATCTATATC
1 TATATTTATATC
1310912 TATATTTATATC
1 TATATTTATATC
1310924 TATATCTCTATTATC
1 TATAT-T-TA-TATC
1310939 TATA
1 TATA
1310943 CACTATATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
9 7 0.12
10 2 0.04
11 2 0.04
12 34 0.61
13 1 0.02
14 2 0.04
15 8 0.14
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATTTATATC
Found at i:1310895 original size:15 final size:16
Alignment explanation
Indices: 1310869--1310920 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
1310859 TAACTATTTA
1310869 TATTTATATTTATATT
1 TATTTATATTTATATT
1310885 TATTT-TATTTATATCT
1 TATTTATATTTATAT-T
* *
1310901 ATATCTATATCTATATT
1 -TATTTATATTTATATT
1310918 TAT
1 TAT
1310921 ATCTATATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 9 0.29
16 9 0.29
17 5 0.16
18 8 0.26
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTATATTTATATT
Found at i:1311107 original size:20 final size:19
Alignment explanation
Indices: 1311080--1311118 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1311070 AAATTATTTT
1311080 TATTTAAAT-TTAATTATAA
1 TATTTAAATATTAA-TATAA
1311099 TATTATAAATATTAATATAA
1 TATT-TAAATATTAATATAA
1311119 ACTAAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTTAAATATTAATATAA
Found at i:1312752 original size:20 final size:21
Alignment explanation
Indices: 1312706--1312776 Score: 76
Period size: 20 Copynumber: 3.4 Consensus size: 21
1312696 TCTACTTCAA
1312706 TAATTAATTAAAATATAAATTT
1 TAATTAA-TAAAATATAAATTT
1312728 T--TTAATAAAATAT-AATTT
1 TAATTAATAAAATATAAATTT
**
1312746 TAATTAATTTAATATAAATTTT
1 TAATTAATAAAATATAAA-TTT
1312768 TAATCTAAT
1 TAAT-TAAT
1312777 TTATAAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 6 0.14
19 8 0.19
20 14 0.33
21 2 0.05
22 8 0.19
23 4 0.10
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATTAATAAAATATAAATTT
Found at i:1312789 original size:23 final size:22
Alignment explanation
Indices: 1312706--1312779 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
1312696 TCTACTTCAA
*
1312706 TAATTAATTAAAATATAAATTTTT
1 TAATTAATT-TAATATAAA-TTTT
1312730 TAA-TAA---AATAT-AA-TTT
1 TAATTAATTTAATATAAATTTT
1312746 TAATTAATTTAATATAAATTTT
1 TAATTAATTTAATATAAATTTT
1312768 TAATCTAATTTA
1 TAAT-TAATTTA
1312780 TAAATTATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
16 6 0.14
17 3 0.07
18 2 0.05
19 5 0.12
20 5 0.12
21 2 0.05
22 7 0.16
23 10 0.23
24 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTAATTTAATATAAATTTT
Found at i:1313101 original size:33 final size:33
Alignment explanation
Indices: 1313064--1313126 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1313054 GACCCAATCT
** *
1313064 CTTTTTCTCATCGTTCTCTTCTAATCCCTATCC
1 CTTTTTCTCATAATTCTCTACTAATCCCTATCC
*
1313097 CTTTTTCTTATAATTCTCTACTAATCCCTA
1 CTTTTTCTCATAATTCTCTACTAATCCCTA
1313127 ATTTCTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.17, C:0.32, G:0.02, T:0.49
Consensus pattern (33 bp):
CTTTTTCTCATAATTCTCTACTAATCCCTATCC
Found at i:1315380 original size:13 final size:13
Alignment explanation
Indices: 1315362--1315395 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1315352 AATGAATTGA
1315362 AGAGGGATACAAG
1 AGAGGGATACAAG
**
1315375 AGAGGGATACTTG
1 AGAGGGATACAAG
1315388 AGAGGGAT
1 AGAGGGAT
1315396 GCTTCAGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.06, G:0.41, T:0.15
Consensus pattern (13 bp):
AGAGGGATACAAG
Found at i:1315537 original size:27 final size:27
Alignment explanation
Indices: 1315486--1315559 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
1315476 AAATAACATG
*
1315486 CCACCATTTTTGACAAA-ATAAAAAGAAA
1 CCACCATTTTTAACAAACAT--AAAGAAA
* *
1315514 CCACTATTTTTAACAAACATAAAGTAA
1 CCACCATTTTTAACAAACATAAAGAAA
1315541 CCACCATTTTTAACAAACA
1 CCACCATTTTTAACAAACA
1315560 AAGGGTGGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
27 24 0.59
28 15 0.37
29 2 0.05
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.26
Consensus pattern (27 bp):
CCACCATTTTTAACAAACATAAAGAAA
Done.