Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008449.1 Hibiscus syriacus cultivar Beakdansim tig00111254_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: 1344907
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1222905 original size:22 final size:21
Alignment explanation
Indices: 1222858--1222937 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 21
1222848 TGTAAAAATG
* * *
1222858 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
1222880 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
* * *
1222902 TAATAATATTAAAACAAAATAA
1 TAATAATAAT-AAATAATATAA
1222924 TAATAATAACTAAA
1 TAATAATAA-TAAA
1222938 ACAAATGGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 39 0.81
23 9 0.19
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:1222943 original size:22 final size:21
Alignment explanation
Indices: 1222880--1222943 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 21
1222870 ATTATTTATT
* *
1222880 TAATAATAATAATATAATATAA
1 TAATAATAATAAAACAA-ATAA
*
1222902 TAATAATATTAAAACAAAATAA
1 TAATAATAATAAAAC-AAATAA
1222924 TAATAATAACTAAAACAAAT
1 TAATAATAA-TAAAACAAAT
1222944 GGAATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 28 0.78
23 8 0.22
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
TAATAATAATAAAACAAATAA
Found at i:1223423 original size:113 final size:113
Alignment explanation
Indices: 1223299--1223541 Score: 346
Period size: 113 Copynumber: 2.2 Consensus size: 113
1223289 TCGAACAAGC
* *
1223299 TCTTCTTATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAAT-TTCTCTG
1 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAATCTAC-CTG
*
1223363 GAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAA-AGTTGAACAAAT
65 GAAAAGTTGATCAATCGAGTGATGAATTCAAACAAAATA-TTGAACAAAT
* * *
1223412 TCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATTAGTTCTTCTCATTATGAACTCTACCTGG
1 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAATCTACCTGG
* * * * *
1223477 CAATGTTGATCAATCGTGTGATGAATTCAAGCAAAATATTGAACAAGT
66 AAAAGTTGATCAATCGAGTGATGAATTCAAACAAAATATTGAACAAAT
*
1223525 TATTCTCATTATGAACT
1 TCTTCTCATTATGAACT
1223542 CTACCTGGCA
Statistics
Matches: 115, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
113 112 0.97
114 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.40
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAATCTACCTGG
AAAAGTTGATCAATCGAGTGATGAATTCAAACAAAATATTGAACAAAT
Found at i:1223539 original size:73 final size:73
Alignment explanation
Indices: 1223449--1223614 Score: 289
Period size: 73 Copynumber: 2.3 Consensus size: 73
1223439 TCTTCAGATT
1223449 AGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGA-TCAATCGTGTGATGAATTCAAGCAAAA
1 AGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATTC-ATCGTGTGATGAATTCAAGCAAAA
*
1223513 TATTGAACA
65 GATTGAACA
* *
1223522 AGTTATTCTCATTATGAACTCTACCTGGCAATGTTGATTCATCGTTTGATGAATTCAAGCAAAAG
1 AGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATTCATCGTGTGATGAATTCAAGCAAAAG
1223587 ATTGAACA
66 ATTGAACA
1223595 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
1223615 TCTTCTTCAT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
73 86 0.98
74 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATTCATCGTGTGATGAATTCAAGCAAAAG
ATTGAACA
Found at i:1223655 original size:186 final size:185
Alignment explanation
Indices: 1223336--1223727 Score: 572
Period size: 186 Copynumber: 2.1 Consensus size: 185
1223326 TCTTCAGATG
* *
1223336 AGTTCTTCTCATTATGAAATTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAA
1 AGTTCTTCTCATTATGAACTTACTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAA
* *
1223401 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATTAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGA
* * ** *
1223466 ACTCTACCTGGCAATGTTGATCAATCGTGTGATGAATTCAAGCAAAATATTGAACA
131 ACTCT-CCTGGAAATGCTGATCAATCGAATGATGAATTCAAGCAAAAGATTGAACA
* * * * ** *
1223522 AGTTATTCTCATTATGAACTCTAC-CTGGCAATGTTGATTCATCGTTTGATGAATTCAAGC-AAA
1 AGTTCTTCTCATTATGAACT-TACTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAA
*
1223585 AGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTAT
65 AG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTAT
* *
1223650 GAACTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGATTGAACA
129 GAACTCTCCTGGAAATGCTGATCAATCGAATGATGAATTCAAGCAAAAGATTGAACA
1223707 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
1223728 CTTCTTCCTT
Statistics
Matches: 184, Mismatches: 20, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
184 1 0.01
185 67 0.36
186 114 0.62
187 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (185 bp):
AGTTCTTCTCATTATGAACTTACTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAA
GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGA
ACTCTCCTGGAAATGCTGATCAATCGAATGATGAATTCAAGCAAAAGATTGAACA
Found at i:1223725 original size:112 final size:112
Alignment explanation
Indices: 1223522--1224117 Score: 980
Period size: 112 Copynumber: 5.3 Consensus size: 112
1223512 ATATTGAACA
* * * * **
1223522 AGTTATTCTCATTATGAACTCTACCTGGCAATGTTGATTCATCGTTTGATGAATTCAAGCAAAAG
1 AGTTCTTCTCATTATGAACTCT-TCTGGAAATGTTGATCCATCGAATGATGAATTCAAGCAAAAG
1223587 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATG
65 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATG
*
1223635 AGTTCTTCTCATTATGAACTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGA
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCATCGAATGATGAATTCAAGCAAAAGA
*
1223700 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATG
* *
1223747 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCATCGAATGATGAATTTAAGCAAAAAA
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCATCGAATGATGAATTCAAGC-AAAAG
*
1223812 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATG
65 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATG
*
1223860 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCATCGAATGATGAATTCAAGAAAAAG-
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCATCGAATGATGAATTCAAGCAAAAGA
*
1223924 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGGTG
66 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATG
* *
1223971 AGTTCTTCTCATTATGAACTCTACTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAA-A
1 AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCATCGAATGATGAATTCAAGCAAAAGA
* *
1224035 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGGTG
66 -TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATG
*
1224083 AGTTCTTCTCATTATGAACTCTACCTGGAAATGTT
1 AGTTCTTCTCATTATGAACTCT-TCTGGAAATGTT
1224118 TTAAGAAAAA
Statistics
Matches: 456, Mismatches: 23, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
111 105 0.23
112 212 0.46
113 139 0.30
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
AGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCATCGAATGATGAATTCAAGCAAAAGA
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATG
Found at i:1223831 original size:298 final size:299
Alignment explanation
Indices: 1223291--1223839 Score: 879
Period size: 298 Copynumber: 1.8 Consensus size: 299
1223281 GTAAAAGGTC
*
1223291 GAACAAGCTCTTCTTATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAAT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAAT
* * *
1223356 TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCAT
66 CTCTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCAT
* * *
1223421 TATGAATTTCTTCTTCATTCTTCAGATTAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGA
131 TATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGA
** *
1223486 TCAATCGTGTGATGAATTCAAGCAAAATATTGAACAAGTTATTCTCATTATGAACTCTACCTGGC
196 TCAATCGAATGATGAATTCAAGCAAAAAATTGAACAAGTTATTCTCATTATGAACTCTACCTGGC
1223551 AATGTTGATTCATCGTTTGATGAATTCAAGCAAAAGATT
261 AATGTTGATTCATCGTTTGATGAATTCAAGCAAAAGATT
* *
1223590 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAAT
* * *
1223655 CT-TCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGATTGAACAAGTTCTTCTCA
66 CTCTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAG-TTGAACAAATTCTTCTCA
* *
1223718 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCT-TCTGGAAATGTTG
130 TTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTG
* * *
1223782 ATCCATCGAATGATGAATTTAAGCAAAAAAATTGAACAAGTTCTTCTCATTATGAACT
195 ATCAATCGAATGATGAATTCAAGC-AAAAAATTGAACAAGTTATTCTCATTATGAACT
1223840 TCTTCTTCTT
Statistics
Matches: 228, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
297 36 0.16
298 129 0.57
299 63 0.28
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.37
Consensus pattern (299 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAAT
CTCTCTGGAAAAGCTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCAT
TATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATGTTGA
TCAATCGAATGATGAATTCAAGCAAAAAATTGAACAAGTTATTCTCATTATGAACTCTACCTGGC
AATGTTGATTCATCGTTTGATGAATTCAAGCAAAAGATT
Found at i:1224287 original size:77 final size:76
Alignment explanation
Indices: 1224129--1224310 Score: 262
Period size: 77 Copynumber: 2.4 Consensus size: 76
1224119 TAAGAAAAAA
* * *
1224129 AAACATTC-TGCATTGTAGGGC-TACAGCTGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCG
1 AAACA-TCATGCATTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCG
1224192 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* **
1224204 AAACATCATGCACTGTAGGACTTACAGATGACCTTAAGGCTTTGAAAACATCAAAAAAAGCT-CC
1 AAACATCATGCATTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC--AAAAAGCTCCC
1224268 GAAGGCTTTTTGG
64 GAAGGCTTTTTGG
1224281 AAACATCATGCATTGTAGGACTTACAGATG
1 AAACATCATGCATTGTAGGACTTACAGATG
1224311 TGAGAAATAG
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
74 2 0.02
75 16 0.17
76 26 0.27
77 44 0.46
78 8 0.08
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (76 bp):
AAACATCATGCATTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1225192 original size:22 final size:22
Alignment explanation
Indices: 1224982--1225190 Score: 330
Period size: 22 Copynumber: 9.5 Consensus size: 22
1224972 AATAAAGCTT
1224982 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1225004 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1225026 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1225048 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1225070 TCATCTTT-AAAGAGAGAATCTA
1 TCATCTTTGAAA-AGAGAATCTA
* *
1225092 TCATCTTTAAAAAAAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1225114 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1225136 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1225158 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1225180 TCATCTTTGAA
1 TCATCTTTGAA
1225191 GAATGTAGAT
Statistics
Matches: 171, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
21 3 0.02
22 165 0.96
23 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1225652 original size:54 final size:54
Alignment explanation
Indices: 1225562--1225711 Score: 136
Period size: 54 Copynumber: 2.9 Consensus size: 54
1225552 TGACTGGTTC
* * * *
1225562 GTAAAACATTTGTCAATACATTCATCATCTCATGTGGTTTATGCTCAGATGCTA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
* * * * *
1225616 GTAAAACATTTGACAACATATTCATCCTTTCTTGTGGCTTCTGCACAGATGC--
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
* * *
1225668 -T-----ATTTGACAACACATTCATTATTTCATGTGACTTATGCACAGAT
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGAT
1225712 TTCTGGTCAA
Statistics
Matches: 81, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
46 37 0.46
51 1 0.01
54 43 0.53
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTATGCACAGATGCTA
Found at i:1225707 original size:46 final size:46
Alignment explanation
Indices: 1225623--1225711 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
1225613 CTAGTAAAAC
* * * * *
1225623 ATTTGACAACATATTCATCCTTTCTTGTGGCTTCTGCACAGATGCT
1 ATTTGACAACACATTCATCATTTCATGTGACTTATGCACAGATGCT
*
1225669 ATTTGACAACACATTCATTATTTCATGTGACTTATGCACAGAT
1 ATTTGACAACACATTCATCATTTCATGTGACTTATGCACAGAT
1225712 TTCTGGTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (46 bp):
ATTTGACAACACATTCATCATTTCATGTGACTTATGCACAGATGCT
Found at i:1227975 original size:114 final size:114
Alignment explanation
Indices: 1227775--1227994 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
1227765 GATCATGCAG
* * * * *
1227775 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCATATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1227840 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * *
1227889 TTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1227954 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
1227995 CGAGAACGTG
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1232208 original size:7 final size:7
Alignment explanation
Indices: 1232174--1232215 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1232164 ATAAGAGTAT
1232174 AAATGCA
1 AAATGCA
* *
1232181 CAATGAA
1 AAATGCA
1232188 AAATGCA
1 AAATGCA
1232195 AAGATGCA
1 AA-ATGCA
1232203 AAATGC-
1 AAATGCA
1232209 AAATGCA
1 AAATGCA
1232216 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:1233671 original size:13 final size:13
Alignment explanation
Indices: 1233655--1233711 Score: 62
Period size: 13 Copynumber: 4.4 Consensus size: 13
1233645 ATACTTGAAT
1233655 AAAATAAATAAAA
1 AAAATAAATAAAA
1233668 AAAAT-AATAAAA
1 AAAATAAATAAAA
* *
1233680 ATAATATATAAAA
1 AAAATAAATAAAA
* *
1233693 ATAATAAGTAATAA
1 AAAATAAATAA-AA
1233707 AAAAT
1 AAAAT
1233712 TTGAAAGAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
12 11 0.30
13 20 0.54
14 6 0.16
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (13 bp):
AAAATAAATAAAA
Found at i:1233683 original size:22 final size:22
Alignment explanation
Indices: 1233655--1233699 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1233645 ATACTTGAAT
1233655 AAAATAA-ATAAAAAAAATAATA
1 AAAATAATAT-AAAAAAATAATA
*
1233677 AAAATAATATATAAAAATAATA
1 AAAATAATATAAAAAAATAATA
1233699 A
1 A
1233700 GTAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAATAATATAAAAAAATAATA
Found at i:1234489 original size:17 final size:17
Alignment explanation
Indices: 1234469--1234502 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1234459 TATGTGTGAC
1234469 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
1234486 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
1234503 CAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:1234524 original size:16 final size:16
Alignment explanation
Indices: 1234505--1234540 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1234495 AGTAATAACA
1234505 AAATAATA-TTATAAAT
1 AAATAATATTTA-AAAT
1234521 AAATAATATTTAAAAT
1 AAATAATATTTAAAAT
1234537 AAAT
1 AAAT
1234541 TTAAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATATTTAAAAT
Found at i:1235813 original size:3 final size:3
Alignment explanation
Indices: 1235807--1235859 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
1235797 ATTATTTATT
* * *
1235807 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAT TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1235851 TAA TAA TAA
1 TAA TAA TAA
1235860 CTAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1235829 original size:19 final size:19
Alignment explanation
Indices: 1235807--1235859 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
1235797 ATTATTTATT
* *
1235807 TAATAATAATAATATAATA
1 TAATAATAATAATAAAACA
* *
1235826 TAATAATATTATTAAAACA
1 TAATAATAATAATAAAACA
*
1235845 AAATAATAATAATAA
1 TAATAATAATAATAA
1235860 CTAAAACAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TAATAATAATAATAAAACA
Found at i:1235830 original size:13 final size:14
Alignment explanation
Indices: 1235807--1235859 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1235797 ATTATTTATT
1235807 TAATAATAATAATA
1 TAATAATAATAATA
1235821 TAAT-ATAATAATA
1 TAATAATAATAATA
* * *
1235834 TTATTAA-AACAAAA
1 -TAATAATAATAATA
1235848 TAATAATAATAA
1 TAATAATAATAA
1235860 CTAAAACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 14 0.45
14 16 0.52
15 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:1235832 original size:22 final size:21
Alignment explanation
Indices: 1235785--1235864 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 21
1235775 TGTAAAAATG
* * *
1235785 TAATAATAATAAATTATTTATT
1 TAATAATAATAAATAATATA-A
1235807 TAATAATAATAATATAATATAA
1 TAATAATAATAA-ATAATATAA
* * * *
1235829 TAATATTATTAAAACAAAATAA
1 TAATAATAAT-AAATAATATAA
1235851 TAATAATAACTAAA
1 TAATAATAA-TAAA
1235865 ACAAATGAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 37 0.80
23 9 0.20
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATAATAATAAATAATATAA
Found at i:1235870 original size:22 final size:21
Alignment explanation
Indices: 1235807--1235870 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
1235797 ATTATTTATT
* *
1235807 TAATAATAATAATATAATATAA
1 TAATAATAATAAAACAA-ATAA
* *
1235829 TAATATTATTAAAACAAAATAA
1 TAATAATAATAAAAC-AAATAA
1235851 TAATAATAACTAAAACAAAT
1 TAATAATAA-TAAAACAAAT
1235871 GAAATAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
TAATAATAATAAAACAAATAA
Found at i:1238639 original size:104 final size:104
Alignment explanation
Indices: 1238503--1238710 Score: 371
Period size: 104 Copynumber: 2.0 Consensus size: 104
1238493 TGTTAATTTC
*
1238503 AGGTCTAGTATCATGATTATTGTGTACAGATTAACATAGTATATAAATGTAATTGTTAATCAATA
1 AGGTCTAGTATCATGATTATTGTGTACAGATTAACATAGTATATAAATGCAATTGTTAATCAATA
1238568 AATTTGGTCCTAACAGGTATCTCAAGTCTGTTAAGATCT
66 AATTTGGTCCTAACAGGTATCTCAAGTCTGTTAAGATCT
* * * *
1238607 AGGTCTATTATCATGATTATTTTTTACAGATTAACATAGTATATAAATGCAATTGTTCATCAATA
1 AGGTCTAGTATCATGATTATTGTGTACAGATTAACATAGTATATAAATGCAATTGTTAATCAATA
1238672 AATTTGGTCCTAACAGGTATCTCAAGTCTGTTAAGATCT
66 AATTTGGTCCTAACAGGTATCTCAAGTCTGTTAAGATCT
1238711 TTTCAAGTGT
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (104 bp):
AGGTCTAGTATCATGATTATTGTGTACAGATTAACATAGTATATAAATGCAATTGTTAATCAATA
AATTTGGTCCTAACAGGTATCTCAAGTCTGTTAAGATCT
Found at i:1240981 original size:24 final size:23
Alignment explanation
Indices: 1240933--1241030 Score: 76
Period size: 23 Copynumber: 4.3 Consensus size: 23
1240923 CACCGCTGCT
1240933 CACATA-ATTT-TCACCGAAGTG-C
1 CACATAGATTTATC-CCGAAG-GAC
*
1240955 CACATAGAATTTAACCCGAAGGAC
1 CACATAG-ATTTATCCCGAAGGAC
* * * * *
1240979 CACACATATTTTTCTCAAAGGAC
1 CACATAGATTTATCCCGAAGGAC
* *
1241002 CACATAGATTTGTCTCGAAGGAC
1 CACATAGATTTATCCCGAAGGAC
1241025 CACATA
1 CACATA
1241031 AAACCTTCGA
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
22 6 0.10
23 38 0.62
24 16 0.26
25 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (23 bp):
CACATAGATTTATCCCGAAGGAC
Found at i:1241029 original size:23 final size:23
Alignment explanation
Indices: 1240971--1241030 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1240961 GAATTTAACC
* * *
1240971 CGAAGGACCACACATATTTTTCT
1 CGAAGGACCACATAGATTTGTCT
*
1240994 CAAAGGACCACATAGATTTGTCT
1 CGAAGGACCACATAGATTTGTCT
1241017 CGAAGGACCACATA
1 CGAAGGACCACATA
1241031 AAACCTTCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (23 bp):
CGAAGGACCACATAGATTTGTCT
Found at i:1241250 original size:16 final size:16
Alignment explanation
Indices: 1241210--1241270 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
1241200 ATATATCATA
* * *
1241210 TTCACGTAGATCATTT
1 TTCACGTATAACACTT
1241226 TTCACGTATAACACTT
1 TTCACGTATAACACTT
* *
1241242 TTCACGTATGACA-TA
1 TTCACGTATAACACTT
*
1241257 TTCACTTATAACAC
1 TTCACGTATAACAC
1241271 GTATACTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
15 12 0.32
16 25 0.68
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (16 bp):
TTCACGTATAACACTT
Found at i:1242483 original size:18 final size:17
Alignment explanation
Indices: 1242451--1242497 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
1242441 TATTAATGGA
1242451 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
1242468 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
1242486 G-AATAAAAATAA
1 GTAA-AAAAATAA
1242498 TGTGTACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:1242710 original size:37 final size:34
Alignment explanation
Indices: 1242645--1242724 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 34
1242635 ATATATATAT
*
1242645 ATATAAATAAAAACAAAAATAGAATATTAAGAAA
1 ATATATATAAAAACAAAAATAGAATATTAAGAAA
*
1242679 ATATATATAAAAACGTATAAAATATAATATTAAGAAA
1 ATATATATAAAAAC--A-AAAATAGAATATTAAGAAA
*
1242716 AAATATATA
1 ATATATATA
1242725 CATAGTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
34 13 0.32
36 1 0.03
37 26 0.65
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (34 bp):
ATATATATAAAAACAAAAATAGAATATTAAGAAA
Found at i:1242817 original size:22 final size:22
Alignment explanation
Indices: 1242777--1242852 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
1242767 ATATATAATG
* * *
1242777 ATATAAGATATATATAAAAATA
1 ATATAAAATAAATAAAAAAATA
* *
1242799 ATATAATATAAATAAAAAAAGGA
1 ATATAAAATAAATAAAAAAA-TA
*
1242822 ATATAGTAAATAAATAAAAATATA
1 ATATA--AAATAAATAAAAAAATA
1242846 AT-TAAAA
1 ATATAAAA
1242853 ATATATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.07
22 17 0.39
23 8 0.18
24 3 0.07
25 13 0.30
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (22 bp):
ATATAAAATAAATAAAAAAATA
Found at i:1244350 original size:111 final size:110
Alignment explanation
Indices: 1244169--1244427 Score: 316
Period size: 111 Copynumber: 2.4 Consensus size: 110
1244159 AGTATTGTTT
* *
1244169 GAGTCCAATAT-CCTC-CGTCGTGAAGTTGAAATTGGCTCTG---G-AACTGGGAAA-TTGTTTG
1 GAGTCCAATATCCCTCAC-T-GTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTTGTTTG
* *
1244227 TTGACAGCCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTC
63 TTGACAACCAGCCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTC
* *
1244275 GAGTTCAATATCCTTCACTGTGAAGTTGAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTT
1 GAGTCCAATATCCCTCACTGTGAAGTTG-AAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTT
* * ** *
1244340 GACAATCAGCCGCTCATTCGTTGTGAAGTTGAGCTTGTGTTGTCTT
65 GACAACCAGCCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTC
* *
1244386 GAGTCCAATATCCCTCGCTGTGAAGTTGAAATTGGCTCTGAA
1 GAGTCCAATATCCCTCACTGTGAAGTTGAAATTGACTCTGAA
1244428 ACTGGGAAAC
Statistics
Matches: 130, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
106 19 0.15
107 15 0.12
108 1 0.01
110 18 0.14
111 77 0.59
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (110 bp):
GAGTCCAATATCCCTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTG
ACAACCAGCCGCCCATTCACTGTGAAGTTGAGCTTGTGTTGTCTC
Found at i:1245248 original size:67 final size:65
Alignment explanation
Indices: 1245147--1245450 Score: 227
Period size: 65 Copynumber: 4.5 Consensus size: 65
1245137 ATGAAAATGA
* **
1245147 TCTCAAGGGAAACAAAATTTTGTTTTAAGAGAAATAAATTTGAAGATTTTGTGTTTCAAGAGAAA
1 TCTCAAGGGAGACAAAA-TTTGTTTTAAGAGAAATAAATTCAAAGA-TTT-TGTTTCAAGAGAAA
1245212 CTG
63 CTG
* * *
1245215 TCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAACTG
1 TCTCAAGGGAGACAAAATTTGTTTTAAGAGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTG
* * * ** * * *
1245280 TCTCAAGAGAGACGAAATTTGTTTAAAGAGAAAT-TGTCTCAAGAGAGACAAAACTTAGTTCCAA
1 TCTCAAGGGAGACAAAATTTGTTTTAAGAGAAATAAAT-TC-A-A-AG-----ATTTTGTTTCAA
*
1245344 AAGAAACTG
57 GAGAAACTG
** * * * * *
1245353 TCTCAAGGGAGATGAAATTTGTTTCAA-ATAAA-ACATATTCAAATAATTTGTTTCAAGGGAAAC
1 TCTCAAGGGAGACAAAATTTGTTTTAAGAGAAATA-A-ATTCAAAGATTTTGTTTCAAGAGAAAC
*
1245416 TA
64 TG
* * *
1245418 TCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TCTCAAGGGAGACAAAATTTGTTTTAAGAGAAA
1245451 CTGTCTCAAG
Statistics
Matches: 187, Mismatches: 36, Indels: 28
0.75 0.14 0.11
Matches are distributed among these distances:
64 1 0.01
65 86 0.46
66 7 0.04
67 25 0.13
68 18 0.10
70 1 0.01
71 1 0.01
72 5 0.03
73 42 0.22
74 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (65 bp):
TCTCAAGGGAGACAAAATTTGTTTTAAGAGAAATAAATTCAAAGATTTTGTTTCAAGAGAAACTG
Found at i:1245298 original size:65 final size:67
Alignment explanation
Indices: 1245147--1245313 Score: 230
Period size: 65 Copynumber: 2.5 Consensus size: 67
1245137 ATGAAAATGA
* **
1245147 TCTCAAGGGAAACAAAATTTTGTTTTAAGAGAAATAAATTTGAAGATTTTGTGTTTCAAGAGAAA
1 TCTCAAGGGAGACAAAA-TTTGTTTTAAGAGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAA
1245212 CTG
65 CTG
* * *
1245215 TCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGGGAAAC
1 TCTCAAGGGAGACAAAATTTGTTTTAAGAGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAAC
1245278 TG
66 TG
* * *
1245280 TCTCAAGAGAGACGAAATTTGTTTAAAGAGAAAT
1 TCTCAAGGGAGACAAAATTTGTTTTAAGAGAAAT
1245314 TGTCTCAAGA
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 45 0.51
66 3 0.03
67 24 0.27
68 16 0.18
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (67 bp):
TCTCAAGGGAGACAAAATTTGTTTTAAGAGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAAC
TG
Found at i:1245318 original size:36 final size:36
Alignment explanation
Indices: 1245261--1245486 Score: 216
Period size: 36 Copynumber: 6.4 Consensus size: 36
1245251 ATTCAAAGAT
1245261 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * * *
1245297 TTTGTTTAAAGAGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
* * ** * *
1245333 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*** * *
1245370 TTTGTTTCAAATAAAACATAT-TC---A-A-A--TAA
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACGAAA
* *
1245399 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1245435 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
*
1245471 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
1245487 TATTTTCAAT
Statistics
Matches: 154, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
28 3 0.02
29 18 0.12
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
36 98 0.64
37 30 0.19
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
Found at i:1245358 original size:37 final size:36
Alignment explanation
Indices: 1245273--1245364 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 36
1245263 TGTTTCAAGG
* * *
1245273 GAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCAAAGA
*
1245309 GAAATTGTCTCAAGAGAGACAAAACTTAGTTCCAAA-A
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTT-CAAAGA
*
1245346 GAAACTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
1245365 TGAAATTTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 22 0.46
37 23 0.48
38 3 0.06
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCAAAGA
Found at i:1245371 original size:138 final size:138
Alignment explanation
Indices: 1245207--1245466 Score: 376
Period size: 138 Copynumber: 1.9 Consensus size: 138
1245197 GTGTTTCAAG
* ** * * *
1245207 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* * *
1245272 GGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGAGAAATTGTCTCAAGAGAGACAAAACTTA
66 GGAAACTATCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
1245337 GTTCCAAA
131 GTTCCAAA
** * * *
1245345 AGAAACTGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* *
1245410 GGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
66 GGAAACTATCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGAGAGAC
1245467 GAAATTTATT
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 106 1.00
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTATCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:1245415 original size:29 final size:29
Alignment explanation
Indices: 1245368--1245423 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1245358 AGGGAGATGA
*
1245368 AATTTGTTTCAAATAAAACATAT-TCAAAT
1 AATTTGTTTCAAAGAAAAC-TATCTCAAAT
* *
1245397 AATTTGTTTCAAGGGAAACTATCTCAA
1 AATTTGTTTCAAAGAAAACTATCTCAA
1245424 GAGAGACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.13
29 20 0.87
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (29 bp):
AATTTGTTTCAAAGAAAACTATCTCAAAT
Found at i:1245479 original size:101 final size:102
Alignment explanation
Indices: 1245295--1245535 Score: 279
Period size: 101 Copynumber: 2.4 Consensus size: 102
1245285 AGAGAGACGA
* *
1245295 AATTTGTTTAAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
1 AATTTGTTTAAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
* * *
1245360 GGAGATGAAATTTGTTTCAAATAAAACATATTCAAAT
66 AGAGACGAAATTTATTTCAAATAAAACATATTCAAAT
* * * * **
1245397 AATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAG
1 AATTTGTTTAAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
*** * *
1245461 AGAGACGAAATTTATTTCAAGGGAAATATTTTC-AAT
66 AGAGACGAAATTTATTTCAAATAAAACATATTCAAAT
** * *
1245497 GTTTATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAA
1 AATT-TGTTTAAAGAGAAACTATCTCAAGAGAGACAAAA
1245536 GTCTGTTTTA
Statistics
Matches: 116, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
100 5 0.04
101 77 0.66
102 34 0.29
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (102 bp):
AATTTGTTTAAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
AGAGACGAAATTTATTTCAAATAAAACATATTCAAAT
Found at i:1247139 original size:15 final size:13
Alignment explanation
Indices: 1247097--1247147 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
1247087 TTTTCTTCAA
*
1247097 TTTC-CTTTGTTT
1 TTTCTCTTTTTTT
*
1247109 TTTCTCTTTTTAT
1 TTTCTCTTTTTTT
1247122 TTTCTCTTTGCTTTT
1 TTTCTCTTT--TTTT
1247137 TTTCTCTTTTT
1 TTTCTCTTTTT
1247148 GTTCTGATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 4 0.12
13 17 0.52
15 12 0.36
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTCTCTTTTTTT
Found at i:1250225 original size:11 final size:11
Alignment explanation
Indices: 1250211--1250236 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1250201 CAAAACACGT
1250211 AAAAAATAATA
1 AAAAAATAATA
1250222 AAAAAATAATA
1 AAAAAATAATA
1250233 AAAA
1 AAAA
1250237 TAAACAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATAATA
Found at i:1250350 original size:19 final size:17
Alignment explanation
Indices: 1250302--1250352 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
1250292 AATGGAGTAA
1250302 AAAAATAAATAAAAAAAT
1 AAAAA-AAATAAAAAAAT
**
1250320 AAAAAAGGTAAAAGAAATT
1 AAAAAAAATAAAA-AAA-T
1250339 AAAAAAAATAAAAA
1 AAAAAAAATAAAAA
1250353 TAATGTGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 6 0.22
18 9 0.33
19 12 0.44
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (17 bp):
AAAAAAAATAAAAAAAT
Found at i:1250403 original size:34 final size:34
Alignment explanation
Indices: 1250365--1250462 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 34
1250355 ATGTGTACAT
*
1250365 ATAAAGTAGTAT-TTACTAA-AACAAAAAATAAAAA
1 ATAAAGTA-TATAATACTAAGAA-AAAAAATAAAAA
*
1250399 ATAAA-TATATAATACTAAGTAAAACAAATAAAAA
1 ATAAAGTATATAATACTAAG-AAAAAAAATAAAAA
* *
1250433 ATAAAGATATACATGATATTAAGAAAAAAA
1 ATAAAG-TAT--ATAATACTAAGAAAAAAA
1250463 TAATAGAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
32 3 0.06
33 8 0.15
34 21 0.40
35 2 0.04
36 3 0.06
37 6 0.12
38 9 0.17
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.23
Consensus pattern (34 bp):
ATAAAGTATATAATACTAAGAAAAAAAATAAAAA
Found at i:1250482 original size:15 final size:13
Alignment explanation
Indices: 1250454--1250478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1250444 CATGATATTA
1250454 AGAAAAAAATAAT
1 AGAAAAAAATAAT
1250467 AGAAAAAAATAA
1 AGAAAAAAATAA
1250479 AATAAAGTAA
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:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AGAAAAAAATAAT
Found at i:1250482 original size:18 final size:18
Alignment explanation
Indices: 1250459--1250515 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 18
1250449 TATTAAGAAA
1250459 AAAATAATAGAAAAAAAT
1 AAAATAATAGAAAAAAAT
*
1250477 AAAATAA-AG-TAAAAAT
1 AAAATAATAGAAAAAAAT
* * *
1250493 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAAAAAAT
1250512 AAAA
1 AAAA
1250516 ATAAAAATAG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 11 0.37
17 3 0.10
18 8 0.27
19 8 0.27
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAATAATAGAAAAAAAT
Found at i:1250497 original size:31 final size:31
Alignment explanation
Indices: 1250456--1250529 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
1250446 TGATATTAAG
* *
1250456 AAAAAAATAATAGAAAAAAATAAA-ATAAAGT
1 AAAAATATAATAGAAAAAAATAAATA-AAAAT
* * *
1250487 AAAAATATAATATATATAAATAAATAAAAAT
1 AAAAATATAATAGAAAAAAATAAATAAAAAT
*
1250518 AAAAATAGAATA
1 AAAAATATAATA
1250530 TTAAGAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 35 0.97
32 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (31 bp):
AAAAATATAATAGAAAAAAATAAATAAAAAT
Found at i:1250542 original size:30 final size:31
Alignment explanation
Indices: 1250477--1250552 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
1250467 AGAAAAAAAT
* *
1250477 AAAAT-AAAGTAAAAATATAATATATATAAA
1 AAAATAAAAATAAAAATAGAATATATATAAA
*
1250507 TAAATAAAAATAAAAATAGAATAT-TA-AGAA
1 AAAATAAAAATAAAAATAGAATATATATA-AA
* *
1250537 AAAATATATATAAAAA
1 AAAATAAAAATAAAAA
1250553 CGTATAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 21 0.55
31 16 0.42
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (31 bp):
AAAATAAAAATAAAAATAGAATATATATAAA
Found at i:1250586 original size:17 final size:17
Alignment explanation
Indices: 1250527--1250586 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
1250517 TAAAAATAGA
1250527 ATATTAAGAAAAAATAT
1 ATATTAAGAAAAAATAT
* *
1250544 ATATAAAAACGTATAAAATAT
1 ATAT--TAA-G-AAAAAATAT
1250565 AATATTAAGAAAAAATAT
1 -ATATTAAGAAAAAATAT
1250583 ATAT
1 ATAT
1250587 GCATAGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 8 0.24
18 8 0.24
19 3 0.09
20 3 0.09
21 8 0.24
22 4 0.12
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (17 bp):
ATATTAAGAAAAAATAT
Found at i:1250668 original size:23 final size:25
Alignment explanation
Indices: 1250617--1250664 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1250607 TTAATACATC
*
1250617 TATATATATATATAATAATATAAGA
1 TATATATATATAAAATAATATAAGA
1250642 TATATATAGTA-AAAATAATATAA
1 TATATATA-TATAAAATAATATAA
1250665 TATAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TATATATATATAAAATAATATAAGA
Found at i:1250671 original size:14 final size:14
Alignment explanation
Indices: 1250631--1250673 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1250621 TATATATATA
1250631 ATAATATAAGATATAT
1 ATAATATAA-ATA-AT
* *
1250647 ATAGTAAAAATAAT
1 ATAATATAAATAAT
1250661 ATAATATAAATAA
1 ATAATATAAATAA
1250674 AAAAAGGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 13 0.57
15 3 0.13
16 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (14 bp):
ATAATATAAATAAT
Found at i:1250678 original size:23 final size:24
Alignment explanation
Indices: 1250652--1250701 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
1250642 TATATATAGT
* *
1250652 AAAAATAATATA-ATATAAATAAA
1 AAAAAGAATATAGAAATAAATAAA
*
1250675 AAAAGGAATATAGTAAATAAATAAA
1 AAAAAGAATATAG-AAATAAATAAA
1250700 AA
1 AA
1250702 TTATAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 10 0.45
25 12 0.55
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (24 bp):
AAAAAGAATATAGAAATAAATAAA
Found at i:1256178 original size:15 final size:15
Alignment explanation
Indices: 1256160--1256189 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1256150 CATAGAACAC
1256160 ATTTACATATATCAT
1 ATTTACATATATCAT
*
1256175 ATTTACGTATATCAT
1 ATTTACATATATCAT
1256190 TTTTCACGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (15 bp):
ATTTACATATATCAT
Found at i:1256200 original size:16 final size:16
Alignment explanation
Indices: 1256167--1256216 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
1256157 CACATTTACA
*
1256167 TATATCATATTT-ACG
1 TATATCATTTTTCACG
1256182 TATATCATTTTTCACG
1 TATATCATTTTTCACG
* *
1256198 TATAACACTTTTCACG
1 TATATCATTTTTCACG
1256214 TAT
1 TAT
1256217 GACATATTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.46
Consensus pattern (16 bp):
TATATCATTTTTCACG
Found at i:1256967 original size:20 final size:20
Alignment explanation
Indices: 1256944--1256985 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
1256934 CTTTGTATCA
1256944 ATAC-CTTCACATCAGTATTG
1 ATACACTTCA-ATCAGTATTG
*
1256964 ATACTACTTCAATCTGTATTG
1 ATAC-ACTTCAATCAGTATTG
1256985 A
1 A
1256986 CAATGTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (20 bp):
ATACACTTCAATCAGTATTG
Found at i:1257124 original size:23 final size:23
Alignment explanation
Indices: 1257098--1257169 Score: 126
Period size: 23 Copynumber: 3.1 Consensus size: 23
1257088 TCCGAAAATT
*
1257098 TACCCAACTTCACTTAAATATCC
1 TACCCAACTTCACTTAAATCTCC
1257121 TACCCAACTTCACTTAAATCTCC
1 TACCCAACTTCACTTAAATCTCC
*
1257144 TACCCAACATCACTTAAATCTCC
1 TACCCAACTTCACTTAAATCTCC
1257167 TAC
1 TAC
1257170 TTAAACTCTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.33, C:0.38, G:0.00, T:0.29
Consensus pattern (23 bp):
TACCCAACTTCACTTAAATCTCC
Found at i:1260465 original size:182 final size:181
Alignment explanation
Indices: 1260141--1260500 Score: 546
Period size: 182 Copynumber: 2.0 Consensus size: 181
1260131 TAATCGATTA
* **
1260141 AAATTTACACGGTTTTATTATTTTTGTGCATAACAAAAATGGTAAAAATTATCGAAAACATCATT
1 AAATTTACACGGTCTTATTATTTTTGTGCATAACAAAAACAGTAAAAATTATCGAAAACATCATT
* * *
1260206 ATTTTTACCGGTTTTGTTATTATTTTTGCATTTTACCGGGTTTCTTAACAAAACCGGTAAAAGAG
66 ATTTCTACCGGTTTTATTATTATTTTGGCATTTTACCGGGTTTCTTAACAAAACCGGTAAAAGAG
* * *
1260271 TTTCCGGTTTTGTTATTGTTGTTCATAACAAAA-CTGGTAAAAATTACCTTT
131 CTACCGGTTTTGTTATTGTTGTGCATAACAAAACCT-GTAAAAATTACCTTT
* * *
1260322 AAATTTACATCGGTCTTGTTATTTTTGTGCATAACAAAACCAGTAAAAATTA-CTGAAAACATTA
1 AAATTTACA-CGGTCTTATTATTTTTGTGCATAACAAAAACAGTAAAAATTATC-GAAAACATCA
*
1260386 TTATTTCTATCGGTTTTATTATTATTTTGGCATTTTACCGGGTTTCTTAACAAAACCGGTAAAAG
64 TTATTTCTACCGGTTTTATTATTATTTTGGCATTTTACCGGGTTTCTTAACAAAACCGGTAAAAG
1260451 CA-CTACCGGTTTTGTTATTGTTGTGCATAACAAAACCTGTAAAAATTACC
129 -AGCTACCGGTTTTGTTATTGTTGTGCATAACAAAACCTGTAAAAATTACC
1260501 GAAAACATTA
Statistics
Matches: 162, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
181 10 0.06
182 149 0.92
183 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (181 bp):
AAATTTACACGGTCTTATTATTTTTGTGCATAACAAAAACAGTAAAAATTATCGAAAACATCATT
ATTTCTACCGGTTTTATTATTATTTTGGCATTTTACCGGGTTTCTTAACAAAACCGGTAAAAGAG
CTACCGGTTTTGTTATTGTTGTGCATAACAAAACCTGTAAAAATTACCTTT
Found at i:1260493 original size:125 final size:125
Alignment explanation
Indices: 1260332--1260594 Score: 418
Period size: 125 Copynumber: 2.1 Consensus size: 125
1260322 AAATTTACAT
* * * *
1260332 CGGTCTTGTTATTTTTGTGCATAACAAAACCAGTAAAAATTACTGAAAACATTATTATTTCTATC
1 CGGTTTTGTTATTGTTGTGCATAACAAAACCAGTAAAAATTACCGAAAACATTATTATTTCTACC
* * *
1260397 GGTTTTATTATTATTTTGGCATTTTACCGGGTTTCTTAACAAAACCGGTAAAAGCACTAC
66 GGTTTTATTATTATTTTGGCATTTTACCAGGTTTCTTAACAAAACCAGTAAAAGCACAAC
*
1260457 CGGTTTTGTTATTGTTGTGCATAACAAAACCTGTAAAAATTACCGAAAACATTATTATTTCTACC
1 CGGTTTTGTTATTGTTGTGCATAACAAAACCAGTAAAAATTACCGAAAACATTATTATTTCTACC
* * *
1260522 GGTTTTGTTATTATTTTGGCATTTTACTAGGTTTCTTAACAAAACCAGTAAAAGCGCAAC
66 GGTTTTATTATTATTTTGGCATTTTACCAGGTTTCTTAACAAAACCAGTAAAAGCACAAC
*
1260582 CGATTTTGTTATT
1 CGGTTTTGTTATT
1260595 TTTTTACCGG
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
125 126 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (125 bp):
CGGTTTTGTTATTGTTGTGCATAACAAAACCAGTAAAAATTACCGAAAACATTATTATTTCTACC
GGTTTTATTATTATTTTGGCATTTTACCAGGTTTCTTAACAAAACCAGTAAAAGCACAAC
Found at i:1261155 original size:200 final size:198
Alignment explanation
Indices: 1260786--1261255 Score: 599
Period size: 200 Copynumber: 2.4 Consensus size: 198
1260776 GTAACATTAC
* * *
1260786 AAATTTACCTATTACATTATAATTATCGGTTTCGAAGTTTTTAGGATTAATACAATTT--TAAAT
1 AAATTTACCTATTACATTATAATTATCGGTTTCGAAGTTTTTGGGATTGATAC-TTTTAATAAAT
* *
1260849 GTATCGACACTTTATGCGTGCACCTCTTGGGCATTCATTCTGGAAAAAGGTATCGATACAAACTT
65 GTATCGACACTTTATGCGTGCACCTCTTGGACATTCATTCTGGAAAAAGGTATCGACACAAACTT
* * ** * *
1260914 AAAACGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTCTAACGGGTATA
130 AAAACGTGTCGATACATTATGTAGACCTATTCTATCATAAAACCAATATATTTATAACGGGTACA
1260979 TTGT
195 TTGT
* * * *
1260983 AAATTTACCTATTACATTGTAATTATCGGGTTCGATGTTTTTGGGATCGATACTTTTAATAAATG
1 AAATTTACCTATTACATTATAATTATCGGTTTCGAAGTTTTTGGGATTGATACTTTTAATAAATG
* * * * ***
1261048 TATCGGCACTTTATGCGTGCACCTCGTTTGACATTCATTCTGGACAAAATGTATTGACAC-TTTT
66 TATCGACACTTTATGCGTGCACCTC-TTGGACATTCATTCTGGA-AAAAGGTATCGACACAAACT
** * * * *
1261112 TAAATTTGTTTCGATACATTATGTTGACCTATTCTATCATAAAACCAATATATTTATACCGGTTA
129 TAAA-ACGTGTCGATACATTATGTAGACCTATTCTATCATAAAACCAATATATTTATAACGGGTA
1261177 CATTGT
193 CATTGT
*
1261183 AAATTTACCTATTACATTATAATTATCGGTTTCGAAGTTTTTGAG-TTGATACTTTTAGA-AAAT
1 AAATTTACCTATTACATTATAATTATCGGTTTCGAAGTTTTTGGGATTGATACTTTTA-ATAAAT
1261246 GTATCGACAC
65 GTATCGACAC
1261256 ATATGTTTAC
Statistics
Matches: 233, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
196 3 0.01
197 47 0.20
198 30 0.13
199 45 0.19
200 108 0.46
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (198 bp):
AAATTTACCTATTACATTATAATTATCGGTTTCGAAGTTTTTGGGATTGATACTTTTAATAAATG
TATCGACACTTTATGCGTGCACCTCTTGGACATTCATTCTGGAAAAAGGTATCGACACAAACTTA
AAACGTGTCGATACATTATGTAGACCTATTCTATCATAAAACCAATATATTTATAACGGGTACAT
TGT
Found at i:1261664 original size:81 final size:79
Alignment explanation
Indices: 1261550--1261755 Score: 207
Period size: 80 Copynumber: 2.6 Consensus size: 79
1261540 TTTTAACATT
* * *
1261550 TCCGGTAAAATGCC-CAACAATAACAAAACCGGTAAAAAAATAACAAAACCAGTAGCGCTTTTAC
1 TCCGGTAAAATGCCAAAAAAATAACAAAACCGGTAAAAAAATAACAAAACCAGTA--ACTTTTAC
*
1261614 CGGTTTTGTTAAGAAA
64 CGATTTTGTTAAGAAA
* * * * ****** *
1261630 TCCGGTAAAATACCAAAATAATAACAAAACCGGTAGAAATAATGATGTTTTCAGTAATTTTTACC
1 TCCGGTAAAATGCCAAAAAAATAACAAAACCGGTA-AAAAAATAACAAAACCAGTAACTTTTACC
1261695 GATTTTGTTAAGAAA
65 GATTTTGTTAAGAAA
* *
1261710 CCCGATAAAATGCCAAAAAAAATAACAAAACCGGTAAAAATAATAA
1 TCCGGTAAAATGCC-AAAAAAATAACAAAACCGGTAAAAA-AATAA
1261756 TGTTTTCGGT
Statistics
Matches: 102, Mismatches: 20, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
80 48 0.47
81 42 0.41
82 12 0.12
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (79 bp):
TCCGGTAAAATGCCAAAAAAATAACAAAACCGGTAAAAAAATAACAAAACCAGTAACTTTTACCG
ATTTTGTTAAGAAA
Found at i:1261692 original size:80 final size:81
Alignment explanation
Indices: 1261608--1261781 Score: 269
Period size: 81 Copynumber: 2.2 Consensus size: 81
1261598 CCAGTAGCGC
* * * *
1261608 TTTTACCGGTTTTGTTAAGAAATCCGGTAAAATACC-AAAATAATAACAAAACCGGTAGAAATAA
1 TTTTACCGGTTTTGTTAAGAAACCCGATAAAATACCAAAAAAAATAACAAAACCGGTAAAAATAA
*
1261672 TGATGTTTTCAGTAAT
66 TAATGTTTTCAGTAAT
* *
1261688 TTTTACCGATTTTGTTAAGAAACCCGATAAAATGCCAAAAAAAATAACAAAACCGGTAAAAATAA
1 TTTTACCGGTTTTGTTAAGAAACCCGATAAAATACCAAAAAAAATAACAAAACCGGTAAAAATAA
*
1261753 TAATGTTTTCGGTAAT
66 TAATGTTTTCAGTAAT
1261769 TTTTACCGGTTTT
1 TTTTACCGGTTTT
1261782 ATTATATACA
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 32 0.38
81 52 0.62
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (81 bp):
TTTTACCGGTTTTGTTAAGAAACCCGATAAAATACCAAAAAAAATAACAAAACCGGTAAAAATAA
TAATGTTTTCAGTAAT
Found at i:1264012 original size:9 final size:9
Alignment explanation
Indices: 1264000--1264027 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1263990 TACATTTCGA
1264000 ACATTCCAC
1 ACATTCCAC
1264009 ACATTCCAC
1 ACATTCCAC
1264018 ACATTCCAC
1 ACATTCCAC
1264027 A
1 A
1264028 ACAACATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (9 bp):
ACATTCCAC
Found at i:1268191 original size:3 final size:3
Alignment explanation
Indices: 1268183--1268230 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1268173 TATATGACTA
1268183 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1268231 TAAATATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1269614 original size:3 final size:3
Alignment explanation
Indices: 1269606--1269685 Score: 85
Period size: 3 Copynumber: 27.0 Consensus size: 3
1269596 GTTTGGCCTG
* * *
1269606 TAA TAA TAA TAA TAT TAA TTAA TAA TAA TAA -AA TAA TAA TAG TGA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1269651 TAAA TAA -AA TAA TAA CAA TAA TAA T-A TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1269686 AAACAAATGG
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
2 6 0.09
3 53 0.83
4 5 0.08
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1270291 original size:122 final size:120
Alignment explanation
Indices: 1270083--1270486 Score: 514
Period size: 122 Copynumber: 3.3 Consensus size: 120
1270073 TTCTTCTCTT
* * * * *
1270083 TCTTTAGATGAGTTATTCTCATTATGAACTCTTC-C-GGAAATGTTGTTGCTGATCTATCTCCTT
1 TCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGTT-ATGCTGATCTATCTCCTT
* * *
1270146 CTGTGATAGAGTCATACAAAGGTTGAGCAAGTTCTTCTAATTATGAACTACTTCTTCC
64 CTGTGATAGAGTCAT-CAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
*
1270204 TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTCATGCTGATCTATCTCTTTC
1 TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTT-ATGCTGATCTATCTCCTTC
1270269 TGTGATAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
65 TGTGATAGAGTCAT-CAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
* * * *** **
1270326 TTTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTGTATGCTAATCCATCGAGTGA
1 TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGT-TATGCTGATCTATCTCCTTC
* *
1270391 TG-AATTTGAG-CA--AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
65 TGTGA-TAGAGTCATCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
1270444 TTCTTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1 -TC-TTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1270487 TATTGATCCA
Statistics
Matches: 255, Mismatches: 22, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
118 41 0.16
119 1 0.00
120 42 0.16
121 31 0.12
122 139 0.55
123 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (120 bp):
TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTATGCTGATCTATCTCCTTCT
GTGATAGAGTCATCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC
Found at i:1270808 original size:22 final size:22
Alignment explanation
Indices: 1270783--1270843 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
1270773 AAATCCAATA
* * *
1270783 AATCTTTCTTCTTTGAAAAGAT
1 AATCTATCATCTTTGAAAAGAG
*
1270805 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAAAGAG
*
1270827 AATCTATCATATTTGAA
1 AATCTATCATCTTTGAA
1270844 GAATGTAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:1271319 original size:54 final size:54
Alignment explanation
Indices: 1271203--1271578 Score: 641
Period size: 54 Copynumber: 7.0 Consensus size: 54
1271193 ATAATTATTG
*
1271203 GTTCGTAAAACATTTGACAACACATTCATCC-TTCTTGTGGCTT-CTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGG-TTCCTGCACAGAT
* *
1271256 GTTCGTAAAACTTTTGACAACACATTCATCATTTCCTGTGGTTCCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
1271310 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
* * *
1271364 GTTCGTAAAACTTTTGACAACGCATTCATCCTTT-CTGTGGTTCCTGCATAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
1271417 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
*
1271471 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACATAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
* *
1271525 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
1271579 TTTCTTCTCT
Statistics
Matches: 305, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
53 81 0.27
54 224 0.73
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
Found at i:1271392 original size:161 final size:160
Alignment explanation
Indices: 1271203--1271578 Score: 628
Period size: 161 Copynumber: 2.3 Consensus size: 160
1271193 ATAATTATTG
*
1271203 GTTCGTAAAACATTTGACAACACATTCATCCTTCTTGTGGCTTCTGCACAGATGTTCGTAAAACT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTCTTGTGG-TTCTGCACAGATGTTCGTAAAACA
1271268 TTTGACAACACATTCATCATTTCCTGTGGTTCCTGCACAGATGTTCGTAAAACATTTGACAACAC
65 TTTGACAACACATTCATCATTTCCTGTGGTTCCTGCACAGATGTTCGTAAAACATTTGACAACAC
1271333 ATTCATCCTTTCCTGTGGTTCCTGCACAGAT
130 ATTCATCCTTTCCTGTGGTTCCTGCACAGAT
* * *
1271364 GTTCGTAAAACTTTTGACAACGCATTCATCCTT-TCTGTGGTTCCTGCATAGATGTTCGTAAAAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTCT-TGTGGTT-CTGCACAGATGTTCGTAAAAC
*
1271428 ATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGATGTTCGTAAAACATTTGACAACA
64 ATTTGACAACACATTCATCATTTCCTGTGGTTCCTGCACAGATGTTCGTAAAACATTTGACAACA
*
1271493 CATTCATCCTTTCCTGTGGTTCCTGCACATAT
129 CATTCATCCTTTCCTGTGGTTCCTGCACAGAT
* *
1271525 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCC-TTCTTGTGG-TTCTGCACAGAT
1271579 TTTCTTCTCT
Statistics
Matches: 199, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
160 3 0.02
161 179 0.90
162 15 0.08
163 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (160 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTCTTGTGGTTCTGCACAGATGTTCGTAAAACAT
TTGACAACACATTCATCATTTCCTGTGGTTCCTGCACAGATGTTCGTAAAACATTTGACAACACA
TTCATCCTTTCCTGTGGTTCCTGCACAGAT
Found at i:1271406 original size:107 final size:108
Alignment explanation
Indices: 1271203--1271578 Score: 650
Period size: 107 Copynumber: 3.5 Consensus size: 108
1271193 ATAATTATTG
*
1271203 GTTCGTAAAACATTTGACAACACATTCATCC-TTCTTGTGGCTT-CTGCACAGATGTTCGTAAAA
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGG-TTCCTGCACAGATGTTCGTAAAA
*
1271266 CTTTTGACAACACATTCATCATTTCCTGTGGTTCCTGCACAGAT
65 CTTTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
1271310 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGATGTTCGTAAAAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGATGTTCGTAAAAC
* *
1271375 TTTTGACAACGCATTCATCCTTT-CTGTGGTTCCTGCATAGAT
66 TTTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
1271417 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGATGTTCGTAAAAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGATGTTCGTAAAAC
* *
1271482 ATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACATAT
66 TTTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
* *
1271525 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
1271579 TTTCTTCTCT
Statistics
Matches: 256, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
107 137 0.54
108 119 0.46
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (108 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGATGTTCGTAAAAC
TTTTGACAACACATTCATCCTTTCCTGTGGTTCCTGCACAGAT
Found at i:1271805 original size:18 final size:18
Alignment explanation
Indices: 1271782--1271819 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1271772 TATATAAAAG
*
1271782 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTAGAA
*
1271800 AATAAATTGATTTTAGAA
1 AATAAATTGAATTTAGAA
1271818 AA
1 AA
1271820 GATAAACTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.34
Consensus pattern (18 bp):
AATAAATTGAATTTAGAA
Found at i:1284149 original size:19 final size:21
Alignment explanation
Indices: 1284127--1284181 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 21
1284117 AGAACCCCAG
1284127 GGGGGTATCGATTCCCCT-A-
1 GGGGGTATCGATTCCCCTCAT
* *
1284146 GGGGGAATCGGTT-CCCTCAT
1 GGGGGTATCGATTCCCCTCAT
*
1284166 GAGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
1284182 TCTGTACCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 4 0.14
19 12 0.43
20 10 0.36
21 2 0.07
ACGTcount: A:0.16, C:0.25, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTCAT
Found at i:1284182 original size:20 final size:20
Alignment explanation
Indices: 1284129--1284184 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1284119 AACCCCAGGG
*
1284129 GGGTATCGATTCCC-CTAGG
1 GGGTATCGATTCCCTCTAGA
* *
1284148 GGGAATCGGTTCCCTC-ATGA
1 GGGTATCGATTCCCTCTA-GA
1284168 GGGTATCGATTCCCTCT
1 GGGTATCGATTCCCTCT
1284185 GTACCAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.29
Consensus pattern (20 bp):
GGGTATCGATTCCCTCTAGA
Found at i:1290679 original size:9 final size:9
Alignment explanation
Indices: 1290665--1290703 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1290655 CTCCTTTTTA
*
1290665 TTTTCTACT
1 TTTTCTTCT
1290674 TTTTCTTCT
1 TTTTCTTCT
*
1290683 ATTTTTTTCT
1 -TTTTCTTCT
1290693 TTTTCTTCT
1 TTTTCTTCT
1290702 TT
1 TT
1290704 AAGCATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:1290687 original size:19 final size:19
Alignment explanation
Indices: 1290663--1290701 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1290653 CCCTCCTTTT
1290663 TATTTTCTACTTTTTCTTC
1 TATTTTCTACTTTTTCTTC
* *
1290682 TATTTTTTTCTTTTTCTTC
1 TATTTTCTACTTTTTCTTC
1290701 T
1 T
1290702 TTAAGCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTCTACTTTTTCTTC
Found at i:1303606 original size:3 final size:3
Alignment explanation
Indices: 1303598--1303704 Score: 123
Period size: 3 Copynumber: 36.0 Consensus size: 3
1303588 GTTTGGCCTG
* *
1303598 TAA TAA TAA TTAA TAA TAA TAT TAA TAT TAA TTAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
* *
1303645 T-A TAA TAA -AA TAA TAA TAA TGA TAAA TAA -AA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
1303688 TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
1303705 AAACAAATGA
Statistics
Matches: 89, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
2 8 0.09
3 73 0.82
4 8 0.09
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1303704 original size:41 final size:42
Alignment explanation
Indices: 1303599--1303704 Score: 128
Period size: 41 Copynumber: 2.5 Consensus size: 42
1303589 TTTGGCCTGT
* * *
1303599 AATAATAATTAATAATAATATTAATATTAATTAATAATAATAAT
1 AATAATAA-TAAT-ATAATAATAATATTAAATAATAATAATAAC
*
1303643 AAT-ATAATAAAATAATAATAATGA-TAAATAA-AATAATAAC
1 AATAATAATAATATAATAATAAT-ATTAAATAATAATAATAAC
1303683 AATAATAATAATATAATAATAA
1 AATAATAATAATATAATAATAA
1303705 AAACAAATGA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
40 11 0.20
41 33 0.60
42 4 0.07
43 4 0.07
44 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (42 bp):
AATAATAATAATATAATAATAATATTAAATAATAATAATAAC
Found at i:1304160 original size:21 final size:21
Alignment explanation
Indices: 1304136--1304178 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1304126 TTTAACTCTT
* *
1304136 CCTCATGTTAGCTCGAAACTA
1 CCTCATGCTAGATCGAAACTA
1304157 CCTCATGCTAGATCGAAACTA
1 CCTCATGCTAGATCGAAACTA
1304178 C
1 C
1304179 TAACATGAGA
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:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (21 bp):
CCTCATGCTAGATCGAAACTA
Found at i:1309657 original size:22 final size:23
Alignment explanation
Indices: 1309627--1309673 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1309617 AAAATATATT
1309627 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
1309650 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
1309672 TA
1 TA
1309674 AAATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:1309680 original size:30 final size:33
Alignment explanation
Indices: 1309621--1309700 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
1309611 ATATTTAAAA
* *
1309621 TATATTTATTAATATTTCTAATAATATAAT-AT
1 TATATTTATTAATATTTATAATAAAATAATAAT
1309653 TATATTT-TTAATA-TTATAATAAAATAATAAAT
1 TATATTTATTAATATTTATAATAAAATAAT-AAT
*
1309685 TATATTATAATAATAT
1 TATATT-TATTAATAT
1309701 AAGGTATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (33 bp):
TATATTTATTAATATTTATAATAAAATAATAAT
Found at i:1309688 original size:18 final size:18
Alignment explanation
Indices: 1309665--1309699 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1309655 TATTTTTAAT
1309665 ATTATAATAAAATAATAA
1 ATTATAATAAAATAATAA
* *
1309683 ATTATATTATAATAATA
1 ATTATAATAAAATAATA
1309700 TAAGGTATTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTATAATAAAATAATAA
Found at i:1309709 original size:23 final size:23
Alignment explanation
Indices: 1309663--1309713 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1309653 TATATTTTTA
*
1309663 ATATTATAATAAAATAATAAATT
1 ATATTATAATAAAATAAGAAATT
* **
1309686 ATATTATAATAATATAAGGTATT
1 ATATTATAATAAAATAAGAAATT
1309709 ATATT
1 ATATT
1309714 TTTATTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAAGAAATT
Found at i:1311658 original size:2 final size:2
Alignment explanation
Indices: 1311651--1311689 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1311641 GGAAGACTAA
1311651 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 A
1311690 GGTAGGTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1312182 original size:34 final size:34
Alignment explanation
Indices: 1312139--1312206 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1312129 GTTTAGATAC
1312139 TAAAAAAACGAAACTGATAGTTTAAGTATTAAAT
1 TAAAAAAACGAAACTGATAGTTTAAGTATTAAAT
1312173 TAAAAAAACGAAACTGATAGTTTAAGTATTAAAT
1 TAAAAAAACGAAACTGATAGTTTAAGTATTAAAT
1312207 GCGTAGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (34 bp):
TAAAAAAACGAAACTGATAGTTTAAGTATTAAAT
Found at i:1313435 original size:16 final size:16
Alignment explanation
Indices: 1313414--1313445 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1313404 CGATAAGCAG
1313414 CGATGAGCACCATTAA
1 CGATGAGCACCATTAA
1313430 CGATGAGCACCATTAA
1 CGATGAGCACCATTAA
1313446 TTTAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (16 bp):
CGATGAGCACCATTAA
Found at i:1315385 original size:22 final size:23
Alignment explanation
Indices: 1315325--1315394 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 23
1315315 AAAATATTAG
* *
1315325 ATATTAAAATATTTAA-AATATA
1 ATATTAATATTTTTAATAATATA
* *
1315347 TTATTAATATTTCTAATAATATA
1 ATATTAATATTTTTAATAATATA
*
1315370 ATATT-ATATTTTTAATATTATA
1 ATATTAATATTTTTAATAATATA
1315392 ATA
1 ATA
1315395 AAATAATCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 30 0.75
23 10 0.25
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTAATATTTTTAATAATATA
Found at i:1315433 original size:23 final size:23
Alignment explanation
Indices: 1315382--1315434 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1315372 ATTATATTTT
*
1315382 TAATATTATAATAAAATAATCAA
1 TAATATTATAATAAAATAAGCAA
* * **
1315405 TTATATTATAATAATATAAGGTA
1 TAATATTATAATAAAATAAGCAA
1315428 TAATATT
1 TAATATT
1315435 TTTATTTTTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
TAATATTATAATAAAATAAGCAA
Found at i:1317640 original size:24 final size:24
Alignment explanation
Indices: 1317613--1317664 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1317603 TAATGAGTTT
1317613 AAACAACATCTTCTAAACATCGTA
1 AAACAACATCTTCTAAACATCGTA
1317637 AAACAACATCTTCTAAACATCGTA
1 AAACAACATCTTCTAAACATCGTA
1317661 AAAC
1 AAAC
1317665 GTTTTCCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.48, C:0.25, G:0.04, T:0.23
Consensus pattern (24 bp):
AAACAACATCTTCTAAACATCGTA
Found at i:1329814 original size:16 final size:16
Alignment explanation
Indices: 1329795--1329831 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1329785 AAATATTTAA
1329795 ATATA-TGA-ATAAAT
1 ATATATTGATATAAAT
*
1329809 ATATATTTATATAAAT
1 ATATATTGATATAAAT
1329825 ATATATT
1 ATATATT
1329832 TTTATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 5 0.25
15 2 0.10
16 13 0.65
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
ATATATTGATATAAAT
Found at i:1329820 original size:22 final size:21
Alignment explanation
Indices: 1329761--1329821 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
1329751 AACTAATATT
* *
1329761 TAAAATATATTTATATTTTAA
1 TAAAATATATTTATATATGAA
*
1329782 CAAAA-ATATTTAAATATATGAA
1 TAAAATATATTT--ATATATGAA
1329804 TAAATATATATTTATATA
1 TAAA-ATATATTTATATA
1329822 AATATATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
20 6 0.19
21 4 0.12
22 15 0.47
23 1 0.03
24 6 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TAAAATATATTTATATATGAA
Found at i:1329830 original size:18 final size:18
Alignment explanation
Indices: 1329807--1329853 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1329797 ATATGAATAA
1329807 ATATATATTTATATAAAT
1 ATATATATTTATATAAAT
* *
1329825 ATATATTTTTATTTAAAT
1 ATATATATTTATATAAAT
*
1329843 GTATTATATTT
1 ATA-TATATTT
1329854 TTTATACATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATATATATTTATATAAAT
Found at i:1330505 original size:21 final size:21
Alignment explanation
Indices: 1330481--1330520 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1330471 CGTCACGGGT
*
1330481 GCTATTGCGGTCATCGTGGAC
1 GCTATTGCGGCCATCGTGGAC
*
1330502 GCTATTGCGGCCGTCGTGG
1 GCTATTGCGGCCATCGTGG
1330521 GTAACTCGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.38, T:0.28
Consensus pattern (21 bp):
GCTATTGCGGCCATCGTGGAC
Found at i:1333463 original size:27 final size:27
Alignment explanation
Indices: 1333425--1333479 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1333415 AAACCAGACT
1333425 ATAATTTGATGAAAGTGTTTGGCTGCA
1 ATAATTTGATGAAAGTGTTTGGCTGCA
1333452 ATAATTTGATGAAAGTGTTTGGCTGCA
1 ATAATTTGATGAAAGTGTTTGGCTGCA
1333479 A
1 A
1333480 GTGTTTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (27 bp):
ATAATTTGATGAAAGTGTTTGGCTGCA
Found at i:1334695 original size:26 final size:26
Alignment explanation
Indices: 1334659--1334711 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1334649 CTTATATGCT
1334659 CGTATATGTTGATGACATTGTTGTTG
1 CGTATATGTTGATGACATTGTTGTTG
1334685 CGTATATGTTGATGACATTGTTGTTG
1 CGTATATGTTGATGACATTGTTGTTG
1334711 C
1 C
1334712 TGGCAGCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.09, G:0.26, T:0.45
Consensus pattern (26 bp):
CGTATATGTTGATGACATTGTTGTTG
Done.