Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004117.1 Hibiscus syriacus cultivar Beakdansim tig00009009_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: 2456583
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 5 of 9
Found at i:1112124 original size:26 final size:26
Alignment explanation
Indices: 1112095--1112167 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 26
1112085 TCTTGAATTC
1112095 TATTTAATATCTGTAAAATTTATAGA
1 TATTTAATATCTGTAAAATTTATAGA
* * * *
1112121 TATTTCATTTTTTAGTTAAATTTATAGA
1 TATTT-AATATCT-GTAAAATTTATAGA
*
1112149 TATTTCATATCTGTAAAAT
1 TATTTAATATCTGTAAAAT
1112168 CGCATGCATT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
26 11 0.31
27 7 0.19
28 18 0.50
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (26 bp):
TATTTAATATCTGTAAAATTTATAGA
Found at i:1118690 original size:22 final size:21
Alignment explanation
Indices: 1118661--1118701 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1118651 GATACGAGTA
*
1118661 GATTTAAAATTTTTAAAATTG
1 GATTTAAAATTTTAAAAATTG
1118682 GATTCTAAAATTTTAAAAAT
1 GATT-TAAAATTTTAAAAAT
1118702 ATTATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (21 bp):
GATTTAAAATTTTAAAAATTG
Found at i:1120155 original size:328 final size:328
Alignment explanation
Indices: 1119701--1120445 Score: 858
Period size: 333 Copynumber: 2.2 Consensus size: 328
1119691 CGAGTTAAGG
* * *
1119701 AAAATCGGAGGAAAACGGAAAGTTGAAAACAATTGTTCCACTGTGATAAAGAACCTGCTTTTGTT
1 AAAATCGGAGGAAAACGGAAACTTG-AAACAATTGTTTCACTGTGCTAAAGAACCTGCTTTTG-T
* * * * *
1119766 CATCTGAGTTCAGCAAAAGGGTAGTATTTTATGTTCATTGGTTTTGAATGTTAAGAATGGAACAG
64 CATCTGAGTTCAG-TAAAGGGTAGCATTTCATGTTCATTGGTTTCGAATGTTAAAAATGGAACAG
* * * * * *
1119831 TTAGGTGTTGTTTGGTAAATGATAAGTGATTG-TCAA-T-C-TC-ATATAGGAGATTAGCCTTAA
128 GTAAGTGCTGTTTGGT--ATGATAAGTAATCGCTCAATTGCTTCTATATAGGAGAATA-CCTTAA
* *
1119891 ATTGGTTATTTTCAATAACACGTAGTACTTAATGAATTC-GAGCAATGCTATTTTTATTCATTAT
190 ATTGGTTATTTTCAATAACA--T-GTACTTAACGAATTCAG-GCAATGCTATTTTTATTCATCAT
* * *
1119955 TTGACGACATTACCTCATCATTTCTCACATTTGACTACA-ATTAATTCACTTCGTGTTTGGTTAC
251 TTGACCACATTACCTCAACATTTCTCACATTTGACTACAGA-TAATTCACTTCCTGTTTGGTTAC
*
1120019 CAATAAAAT-AACA
315 CAAGAAAATAAACA
* *
1120032 AAAATCGGAGGAAAATGGAAACTTGAAACAATTGTTTCACCGTGCTAAAGAACCTGCTTTTGTCA
1 AAAATCGGAGGAAAACGGAAACTTGAAACAATTGTTTCACTGTGCTAAAGAACCTGCTTTTGTCA
*
1120097 TCTGAGTTCAGTTAAGGGTAGCATTTCATGTTCATTGGTTTCGAATGTTAAAAATGGAACAGGTA
66 TCTGAGTTCAGTAAAGGGTAGCATTTCATGTTCATTGGTTTCGAATGTTAAAAATGGAACAGGTA
* * * * *
1120162 AGTGCTGTTTGGTGTGATAAGTAATCGCTCAATTCGTTTGCTTTCTTTTTTGGAGAATACCTTTA
131 AGTGCTGTTTGGTATGATAAGTAATCGCTCAA-----TTGC-TTCTATATAGGAGAATACCTTAA
** * * *
1120227 ATTGGTTATTTTCAATAACATGTACTTAACGCCTTCAGGCGATGCTATTTTTTTTCATCATTTGG
190 ATTGGTTATTTTCAATAACATGTACTTAACGAATTCAGGCAATGCTATTTTTATTCATCATTTGA
* * * *
1120292 CCACATTACCTTAACATTTCTCTCATTTGACTACAGATAGTTCACTTCCTGTTTGGTTACCGAGA
255 CCACATTACCTCAACATTTCTCACATTTGACTACAGATAATTCACTTCCTGTTTGGTTACCAAGA
* *
1120357 AAGTAAAGA
320 AAATAAACA
* * * * * *
1120366 AAAATTGGAGAAAAACGGAAACTTGAAACAATTTTTTCACTTTGCAAAAGAACTTGCTTTTGTCA
1 AAAATCGGAGGAAAACGGAAACTTGAAACAATTGTTTCACTGTGCTAAAGAACCTGCTTTTGTCA
* *
1120431 CCTGACTTCAGTAAA
66 TCTGAGTTCAGTAAA
1120446 TAGTAGTGAT
Statistics
Matches: 350, Mismatches: 50, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
326 11 0.03
327 4 0.01
328 58 0.17
329 14 0.04
330 34 0.10
331 23 0.07
333 94 0.27
334 76 0.22
336 27 0.08
337 9 0.03
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (328 bp):
AAAATCGGAGGAAAACGGAAACTTGAAACAATTGTTTCACTGTGCTAAAGAACCTGCTTTTGTCA
TCTGAGTTCAGTAAAGGGTAGCATTTCATGTTCATTGGTTTCGAATGTTAAAAATGGAACAGGTA
AGTGCTGTTTGGTATGATAAGTAATCGCTCAATTGCTTCTATATAGGAGAATACCTTAAATTGGT
TATTTTCAATAACATGTACTTAACGAATTCAGGCAATGCTATTTTTATTCATCATTTGACCACAT
TACCTCAACATTTCTCACATTTGACTACAGATAATTCACTTCCTGTTTGGTTACCAAGAAAATAA
ACA
Found at i:1121005 original size:23 final size:23
Alignment explanation
Indices: 1120975--1121026 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1120965 AAACCAACAA
*
1120975 ACCCAGGACCCCATCCGGATCC-G
1 ACCCAGGACCCCACCCGG-TCCAG
*
1120998 ACCCAGGACCCGACCCGGTCCAG
1 ACCCAGGACCCCACCCGGTCCAG
1121021 ACCCAG
1 ACCCAG
1121027 ATCCTGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.23, C:0.48, G:0.23, T:0.06
Consensus pattern (23 bp):
ACCCAGGACCCCACCCGGTCCAG
Found at i:1123012 original size:23 final size:23
Alignment explanation
Indices: 1122982--1123037 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
1122972 TAGAGGAGTG
1122982 AACTTATAATATTTTAAGGGATA
1 AACTTATAATATTTTAAGGGATA
1123005 AACTTATAATATTTTAAGGGATA
1 AACTTATAATATTTTAAGGGATA
1123028 AACTTATAAT
1 AACTTATAAT
1123038 TTTATACTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (23 bp):
AACTTATAATATTTTAAGGGATA
Found at i:1124544 original size:14 final size:14
Alignment explanation
Indices: 1124525--1124552 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1124515 ATTCATCCCT
1124525 TCAGTGGATTAGTG
1 TCAGTGGATTAGTG
1124539 TCAGTGGATTAGTG
1 TCAGTGGATTAGTG
1124553 CTATTGATGA
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:0.21, C:0.07, G:0.36, T:0.36
Consensus pattern (14 bp):
TCAGTGGATTAGTG
Found at i:1125115 original size:18 final size:18
Alignment explanation
Indices: 1125094--1125156 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
1125084 GTTTTGTTGT
*
1125094 TGGGTTGGGT-TCTGTATC
1 TGGGTTGGGTCT-TGTAAC
*
1125112 TGGGTTGTGTCTTGTAAC
1 TGGGTTGGGTCTTGTAAC
** * *
1125130 TGGGTTGAATCCTGTAAT
1 TGGGTTGGGTCTTGTAAC
1125148 TGGGTTGGG
1 TGGGTTGGG
1125157 CTTCAGGTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 35 0.97
19 1 0.03
ACGTcount: A:0.11, C:0.10, G:0.38, T:0.41
Consensus pattern (18 bp):
TGGGTTGGGTCTTGTAAC
Found at i:1126428 original size:2 final size:2
Alignment explanation
Indices: 1126421--1126446 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1126411 CGTTTCTGCA
1126421 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1126447 GGGGATAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1128983 original size:42 final size:42
Alignment explanation
Indices: 1128936--1129034 Score: 171
Period size: 42 Copynumber: 2.4 Consensus size: 42
1128926 GGAAGCGGTG
** *
1128936 AATGAGAAGATCTCCAAGCTGGATTCAACGCAGACAGAGGCC
1 AATGAGAAGATCTCCAAGCTGGAAGCAACGCAGACAAAGGCC
1128978 AATGAGAAGATCTCCAAGCTGGAAGCAACGCAGACAAAGGCC
1 AATGAGAAGATCTCCAAGCTGGAAGCAACGCAGACAAAGGCC
1129020 AATGAGAAGATCTCC
1 AATGAGAAGATCTCC
1129035 GAGGATGCTG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.13
Consensus pattern (42 bp):
AATGAGAAGATCTCCAAGCTGGAAGCAACGCAGACAAAGGCC
Found at i:1134429 original size:14 final size:14
Alignment explanation
Indices: 1134410--1134436 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1134400 TTCGTGATCT
1134410 ATATATATTTGTAA
1 ATATATATTTGTAA
1134424 ATATATATTTGTA
1 ATATATATTTGTA
1134437 GTGGAAGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
ATATATATTTGTAA
Found at i:1137350 original size:2 final size:2
Alignment explanation
Indices: 1137343--1137372 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1137333 AAAATTGTTA
*
1137343 AT AT AT AT AT AA 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
1137373 GAACAGAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1158419 original size:17 final size:17
Alignment explanation
Indices: 1158399--1158436 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1158389 TTTTCTTTTA
*
1158399 TTTTATATGAAATATTT
1 TTTTACATGAAATATTT
*
1158416 TTTTCCATGAAATATTT
1 TTTTACATGAAATATTT
1158433 TTTT
1 TTTT
1158437 CCAGTATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTTACATGAAATATTT
Found at i:1158437 original size:17 final size:17
Alignment explanation
Indices: 1158405--1158439 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1158395 TTTATTTTAT
1158405 ATGAAATATTTTTTTCC
1 ATGAAATATTTTTTTCC
1158422 ATGAAATATTTTTTTCC
1 ATGAAATATTTTTTTCC
1158439 A
1 A
1158440 GTATGAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (17 bp):
ATGAAATATTTTTTTCC
Found at i:1160795 original size:50 final size:50
Alignment explanation
Indices: 1160736--1160839 Score: 201
Period size: 50 Copynumber: 2.1 Consensus size: 50
1160726 GGAATAATTT
1160736 CTCATTATTAGTCATTGAAAAGCTATAAAGTGGAACTCTTAAATCTTTTA
1 CTCATTATTAGTCATTGAAAAGCTATAAAGTGGAACTCTTAAATCTTTTA
1160786 CTCATTATTAGTCATTGAAAAGCTATAAAGTGGAACTCTTAAATCTTTTA
1 CTCATTATTAGTCATTGAAAAGCTATAAAGTGGAACTCTTAAATCTTTTA
1160836 -TCAT
1 CTCAT
1160840 CAATGTAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 4 0.07
50 50 0.93
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (50 bp):
CTCATTATTAGTCATTGAAAAGCTATAAAGTGGAACTCTTAAATCTTTTA
Found at i:1161606 original size:2 final size:2
Alignment explanation
Indices: 1161599--1161635 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1161589 TCAACGTCGT
1161599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1161636 CAAACACCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1171620 original size:192 final size:192
Alignment explanation
Indices: 1171293--1171646 Score: 539
Period size: 192 Copynumber: 1.8 Consensus size: 192
1171283 AATGTTGTTT
*
1171293 AATTAGCTGACCCTATTCCCATAGTAATGGGGTAAGAGGGATGTAGGGTAGGAGGCTGCCCCCAA
1 AATTAGCTGACCCTATTCCCATAGTAATGGGGTAAGAGGGAGGTAGGGTAGGAGGCTGCCCCCAA
* * * * *
1171358 CACCAGGTTGAGAGCAACTTCCGTGGAAAACCTCCGGCAATCAGAATTATGAATTGCTCACCGTG
66 CACCAGGTTGAGAGCAACTTCCGTAGAAAACCTCCAGCAATCAAAATTATAAATTGCTCACCATG
1171423 GGACTCGATCCCACGACCACAAGGTTAAGAGCTCTACCAACTGAGTTAAGCGGGCAATTCAA
131 GGACTCGATCCCACGACCACAAGGTTAAGAGCTCTACCAACTGAGTTAAGCGGGCAATTCAA
* * *
1171485 AATTAGCTGACCCTATTCTCATATGTAATGGGGTAAG-GGGAGGTAGGGTAGTAGGCTGCCTCCA
1 AATTAGCTGACCCTATTCCCATA-GTAATGGGGTAAGAGGGAGGTAGGGTAGGAGGCTGCCCCCA
** * ** * * *
1171549 ACGTCAGGTTGAGTGCAGTTTCCTTAGAAGACCTCCAGCAGTCAAAATTATAAATTGCTCACCAT
65 ACACCAGGTTGAGAGCAACTTCCGTAGAAAACCTCCAGCAATCAAAATTATAAATTGCTCACCAT
1171614 GGGACTCGATCCCACGACCACAAGGTTAAGAGC
130 GGGACTCGATCCCACGACCACAAGGTTAAGAGC
1171647 CTTGAGCTCT
Statistics
Matches: 144, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
192 131 0.91
193 13 0.09
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.22
Consensus pattern (192 bp):
AATTAGCTGACCCTATTCCCATAGTAATGGGGTAAGAGGGAGGTAGGGTAGGAGGCTGCCCCCAA
CACCAGGTTGAGAGCAACTTCCGTAGAAAACCTCCAGCAATCAAAATTATAAATTGCTCACCATG
GGACTCGATCCCACGACCACAAGGTTAAGAGCTCTACCAACTGAGTTAAGCGGGCAATTCAA
Found at i:1174031 original size:20 final size:19
Alignment explanation
Indices: 1173978--1174036 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
1173968 CTCCCAGGAA
1173978 AACATGAACCAAGAGTTTC
1 AACATGAACCAAGAGTTTC
* *
1173997 AAAATAGAA-CAAGAGTTTT
1 AACAT-GAACCAAGAGTTTC
1174016 AACCATGAACCAAGAGTTTC
1 AA-CATGAACCAAGAGTTTC
1174036 A
1 A
1174037 GAACCATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (19 bp):
AACATGAACCAAGAGTTTC
Found at i:1177322 original size:23 final size:22
Alignment explanation
Indices: 1177278--1177320 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1177268 AAATCATTGG
1177278 GTTTTTTAATTATATTTTTTTA
1 GTTTTTTAATTATATTTTTTTA
1177300 GTTTTTTAATT-TAATTTTTTT
1 GTTTTTTAATTAT-ATTTTTTT
1177321 TAAATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (22 bp):
GTTTTTTAATTATATTTTTTTA
Found at i:1179610 original size:3 final size:3
Alignment explanation
Indices: 1179602--1179650 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
1179592 AAAATCATTC
* *
1179602 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TTT TAT TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
1179648 TAT
1 TAT
1179651 CACCAACCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1200736 original size:41 final size:41
Alignment explanation
Indices: 1200688--1200770 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
1200678 GCTGAACCGA
*
1200688 ATTCGAGCTTGATCGGCCTAACTTAGTCTCTGGTTTGGTTC
1 ATTCGAGCTTGATCGGCCTAACTTAGACTCTGGTTTGGTTC
1200729 ATTCGAGCTTGATCGGCCTAACTTAGACTCTGGTTTGGTTC
1 ATTCGAGCTTGATCGGCCTAACTTAGACTCTGGTTTGGTTC
1200770 A
1 A
1200771 AGTATGTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (41 bp):
ATTCGAGCTTGATCGGCCTAACTTAGACTCTGGTTTGGTTC
Found at i:1202221 original size:15 final size:15
Alignment explanation
Indices: 1202201--1202250 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
1202191 GCTTTGATCT
1202201 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
*
1202216 TCTTCAGAATTTTCA
1 TCTTCAGGATTTTCA
1202231 TCTTCAGGATTTTCA
1 TCTTCAGGATTTTCA
*
1202246 CCTTC
1 TCTTC
1202251 CTCGATCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.20, C:0.24, G:0.10, T:0.46
Consensus pattern (15 bp):
TCTTCAGGATTTTCA
Found at i:1205735 original size:420 final size:424
Alignment explanation
Indices: 1204941--1205839 Score: 1574
Period size: 420 Copynumber: 2.1 Consensus size: 424
1204931 TCATCAATAT
* * * ** ** * *
1204941 GCCATATTTTCTCAATGCCACCTATTGAGC-TCAAGCCCAACTGTTCCAAGGCAGGACGCGAAAC
1 GCCATGTTTTCTCAATGCCACCGATTGA-CTTCATGTACAACACTTCCAAAGCAGGACACGAAAC
*
1205005 CTGCAAATATATAAAACTCATGTTTCATATTCCATCAAGAATAATTCTTTCTTAATTAATAATTA
65 CTGCAAATATATAAAACTCAAGTTTCATATTCCATCAAGAATAATTCTTTCTTAATTAATAATTA
*
1205070 TCATTCAAAATATATATTGTGGTTTTTTTAGAAAGTCATAAATTCTTTTTGAAAATTATATAAAG
130 TCATTCAAAATATATA-----GTTTTTTTAGAAAGTCAAAAATTCTTTTTGAAAATTATATAAAG
1205135 ATAATAAAAGATATAATAAAAAACTCTTATAATAATAGTTTATAATTGTTTTAAAAATTGGTTTT
190 ATAATAAAAGATATAATAAAAAACTCTTATAATAATAGTTTATAATTGTTTTAAAAATTGGTTTT
1205200 TTTCCTTAAAATTTTCAACTGAATTGTGTAGATATAAATAAATATATACTCTTTTATCTAATTTA
255 TTTCCTTAAAATTTTCAACTGAATTGTGTAGATATAAATAAATATATACTCTTTTATCTAATTTA
1205265 AAGGAAAAAAAATGAAAAGACATCAAAATAAAAAAGAAAAATTGATGGATGCTGTAATTAACAGA
320 AAGGAAAAAAAATGAAAAGACATCAAAATAAAAAAGAAAAATTGATGGATGCTGTAATTAACAGA
1205330 TGAAAAAAAAAGATGAATATAAATACCTTTTTATCAAAAA
385 TGAAAAAAAAAGATGAATATAAATACCTTTTTATCAAAAA
1205370 GCCATGTTTTCTCAATGCCACCGATTGACTTCATGTACAACACTTCCAAAGCAGGACACGAAACC
1 GCCATGTTTTCTCAATGCCACCGATTGACTTCATGTACAACACTTCCAAAGCAGGACACGAAACC
* *
1205435 TGCAAATATATAAAACTCAAGTTTCATATTTCATCATGAATAATTCTTTCTTAATTAATAATTAT
66 TGCAAATATATAAAACTCAAGTTTCATATTCCATCAAGAATAATTCTTTCTTAATTAATAATTAT
* *
1205500 CATTC-AAA-A-ATA-TTTTTTTAGGATGTCAAAAATTCTTTTTGAAAATTATATAAAGATAATA
131 CATTCAAAATATATAGTTTTTTTAGAAAGTCAAAAATTCTTTTTGAAAATTATATAAAGATAATA
1205561 AAAGATATAATAAAAAACTCTTATAATAATAGTTTATAATTGTTTTAAAAATTGGTTTTTTTCCT
196 AAAGATATAATAAAAAACTCTTATAATAATAGTTTATAATTGTTTTAAAAATTGGTTTTTTTCCT
1205626 TAAAATTTTCAACTGAATTGTGTAGATATAAATAAATATATACTCTTTTATCTAATTTAAAGGAA
261 TAAAATTTTCAACTGAATTGTGTAGATATAAATAAATATATACTCTTTTATCTAATTTAAAGGAA
1205691 AAAAAATGAAAAGACATCAAAATAAAAAAGAAAAATTGATGGATGCTGTAATTAACAGATGAAAA
326 AAAAAATGAAAAGACATCAAAATAAAAAAGAAAAATTGATGGATGCTGTAATTAACAGATGAAAA
1205756 AAAAAGATGAATATAAATACCTTTTTATCAAAAA
391 AAAAAGATGAATATAAATACCTTTTTATCAAAAA
1205790 GCCATGTTTTCTCAATGCCACCGATTGACTTCATGTACAACACTTCCAAA
1 GCCATGTTTTCTCAATGCCACCGATTGACTTCATGTACAACACTTCCAAA
1205840 AGAAAATGTT
Statistics
Matches: 454, Mismatches: 15, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
420 325 0.72
426 3 0.01
427 1 0.00
428 4 0.01
429 121 0.27
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (424 bp):
GCCATGTTTTCTCAATGCCACCGATTGACTTCATGTACAACACTTCCAAAGCAGGACACGAAACC
TGCAAATATATAAAACTCAAGTTTCATATTCCATCAAGAATAATTCTTTCTTAATTAATAATTAT
CATTCAAAATATATAGTTTTTTTAGAAAGTCAAAAATTCTTTTTGAAAATTATATAAAGATAATA
AAAGATATAATAAAAAACTCTTATAATAATAGTTTATAATTGTTTTAAAAATTGGTTTTTTTCCT
TAAAATTTTCAACTGAATTGTGTAGATATAAATAAATATATACTCTTTTATCTAATTTAAAGGAA
AAAAAATGAAAAGACATCAAAATAAAAAAGAAAAATTGATGGATGCTGTAATTAACAGATGAAAA
AAAAAGATGAATATAAATACCTTTTTATCAAAAA
Found at i:1209208 original size:42 final size:42
Alignment explanation
Indices: 1209162--1209266 Score: 165
Period size: 42 Copynumber: 2.5 Consensus size: 42
1209152 CAGCATCCTC
* * **
1209162 GGAGATCTTCTCATTGGCCTTTGTCTGGGTTGCTTCCAGCTT
1 GGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAGCTT
1209204 GGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAGCTT
1 GGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAGCTT
*
1209246 GGAGATCTTATCATTGGCCTC
1 GGAGATCTTCTCATTGGCCTC
1209267 ATCCAACCAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.13, C:0.25, G:0.25, T:0.37
Consensus pattern (42 bp):
GGAGATCTTCTCATTGGCCTCTGTCTGCGTTGAATCCAGCTT
Found at i:1215140 original size:22 final size:22
Alignment explanation
Indices: 1215115--1215169 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1215105 TCAGGAGTTA
* *
1215115 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1215137 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1215159 CGGGAGTTATA
1 CAGGAGTTATA
1215170 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1219228 original size:26 final size:26
Alignment explanation
Indices: 1219177--1219228 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1219167 ATTTATTTTC
* * *
1219177 TTTTTCTATAAATTTTTTTAAGTTTA
1 TTTTTCTATAAATTTTATAAAATTTA
1219203 TTTTCTCTA-AAATTTTATAAAATTTA
1 TTTT-TCTATAAATTTTATAAAATTTA
1219229 AATTAAGCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTTCTATAAATTTTATAAAATTTA
Found at i:1220690 original size:15 final size:15
Alignment explanation
Indices: 1220670--1220699 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1220660 AGAGGTGGAA
1220670 GTAAAGGAAGAGAAG
1 GTAAAGGAAGAGAAG
*
1220685 GTAAAGGAGGAGAAG
1 GTAAAGGAAGAGAAG
1220700 AAGAAAGATG
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:0.50, C:0.00, G:0.43, T:0.07
Consensus pattern (15 bp):
GTAAAGGAAGAGAAG
Found at i:1222238 original size:232 final size:232
Alignment explanation
Indices: 1221832--1222291 Score: 893
Period size: 232 Copynumber: 2.0 Consensus size: 232
1221822 GTGCCAAGCT
1221832 GCTGGCTTATTTTCATTCCAAAGCTTCTGAGAGTAGGCTTCAGGTTGTGTATAAGAAGTACTCGA
1 GCTGGCTTATTTTCATTCCAAAGCTTCTGAGAGTAGGCTTCAGGTTGTGTATAAGAAGTACTCGA
*
1221897 GCTCTCTACGAGCAGGCGTCGCGTTGTTTCCGCCATCCAAGTATCTATTATGTGCTGAAAGCAGG
66 GCTCTCTACGAGCAGCCGTCGCGTTGTTTCCGCCATCCAAGTATCTATTATGTGCTGAAAGCAGG
1221962 CTACAGGTTGCTTAGATTTAGATTAGGATTTCTGGAAACTAATTCCTGCGTTTCTTCCAGTGAAA
131 CTACAGGTTGCTTAGATTTAGATTAGGATTTCTGGAAACTAATTCCTGCGTTTCTTCCAGTGAAA
*
1222027 CATTGATTTGTTGTCATTAAGTAGGTATTCATTGAAA
196 CATTGATTTGTTGCCATTAAGTAGGTATTCATTGAAA
1222064 GCTGGCTTATTTTCATTCCAAAGCTTCTGAGAGTAGGCTTCAGGTTGTGTATAAGAAGTACTCGA
1 GCTGGCTTATTTTCATTCCAAAGCTTCTGAGAGTAGGCTTCAGGTTGTGTATAAGAAGTACTCGA
*
1222129 GCTCTCTACGAGGAGCCGTCGCGTTGTTTCCGCCATCCAAGTATCTATTATGTGCTGAAAGCAGG
66 GCTCTCTACGAGCAGCCGTCGCGTTGTTTCCGCCATCCAAGTATCTATTATGTGCTGAAAGCAGG
1222194 CTACAGGTTGCTTAGATTTAGATTAGGATTTCTGGAAACTAATTCCTGCGTTTCTTCCAGTGAAA
131 CTACAGGTTGCTTAGATTTAGATTAGGATTTCTGGAAACTAATTCCTGCGTTTCTTCCAGTGAAA
1222259 CATTGATTTGTTGCCATTAAGTAGGTATTCATT
196 CATTGATTTGTTGCCATTAAGTAGGTATTCATT
1222292 TGAAGTGTTC
Statistics
Matches: 225, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
232 225 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (232 bp):
GCTGGCTTATTTTCATTCCAAAGCTTCTGAGAGTAGGCTTCAGGTTGTGTATAAGAAGTACTCGA
GCTCTCTACGAGCAGCCGTCGCGTTGTTTCCGCCATCCAAGTATCTATTATGTGCTGAAAGCAGG
CTACAGGTTGCTTAGATTTAGATTAGGATTTCTGGAAACTAATTCCTGCGTTTCTTCCAGTGAAA
CATTGATTTGTTGCCATTAAGTAGGTATTCATTGAAA
Found at i:1222516 original size:21 final size:20
Alignment explanation
Indices: 1222491--1222544 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1222481 TTAATTTTAT
1222491 AAATATAAAAAAATCAGAAA
1 AAATATAAAAAAATCAGAAA
*
1222511 AAA-ATACAAAAAATCCGAAA
1 AAATATA-AAAAAATCAGAAA
*
1222531 AATTATAAAAAAAT
1 AAATATAAAAAAAT
1222545 TAGTGTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 24 0.80
21 3 0.10
ACGTcount: A:0.72, C:0.07, G:0.04, T:0.17
Consensus pattern (20 bp):
AAATATAAAAAAATCAGAAA
Found at i:1239335 original size:20 final size:20
Alignment explanation
Indices: 1239283--1239329 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1239273 ATTATAAACG
1239283 AAAATATTAATTTTCAGTAA
1 AAAATATTAATTTTCAGTAA
1239303 AAAATATTAATTTTCAGTAA
1 AAAATATTAATTTTCAGTAA
1239323 AAAATAT
1 AAAATAT
1239330 ATATTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
AAAATATTAATTTTCAGTAA
Found at i:1239910 original size:57 final size:60
Alignment explanation
Indices: 1239822--1239946 Score: 184
Period size: 57 Copynumber: 2.1 Consensus size: 60
1239812 AAGTTTCGAA
*
1239822 TCATTTCAGGTTCAAGTCAGTTTCAAGTTCAAGTT-TTT-TTTAG-TGGATTAGTTCGGG
1 TCATTTCAGGTTCAAGTCAGCTTCAAGTTCAAGTTGTTTCTTTAGATGGATTAGTTCGGG
* * *
1239879 TCATTTCTGGTTCAAGTCAGCTTCAAGTTCAAGTTGTTTCTTTTGTATGGATTAGTTTGGG
1 TCATTTCAGGTTCAAGTCAGCTTCAAGTTCAAGTTGTTTCTTTAG-ATGGATTAGTTCGGG
1239940 TCATTTC
1 TCATTTC
1239947 GAGTACAAGT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
57 33 0.55
58 3 0.05
59 4 0.07
61 20 0.33
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.46
Consensus pattern (60 bp):
TCATTTCAGGTTCAAGTCAGCTTCAAGTTCAAGTTGTTTCTTTAGATGGATTAGTTCGGG
Found at i:1245008 original size:30 final size:30
Alignment explanation
Indices: 1244974--1245043 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
1244964 GCTTATTATA
1244974 CAAATTGGTATTGAACTTTGTAACACTTTT
1 CAAATTGGTATTGAACTTTGTAACACTTTT
* *
1245004 CAAATTAGTATTGAACTTTGTAACTCTTTT
1 CAAATTGGTATTGAACTTTGTAACACTTTT
1245034 CAAATTGGTA
1 CAAATTGGTA
1245044 CCCCAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAATTGGTATTGAACTTTGTAACACTTTT
Found at i:1249115 original size:22 final size:23
Alignment explanation
Indices: 1249081--1249123 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1249071 TTTCTTTATC
*
1249081 TATTTTTTGGGGGTTTTATTTTT
1 TATTTTTTGGGGGTTTAATTTTT
1249104 TATTTTTT-GGGGTTTAATTT
1 TATTTTTTGGGGGTTTAATTT
1249124 AATGATTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.12, C:0.00, G:0.21, T:0.67
Consensus pattern (23 bp):
TATTTTTTGGGGGTTTAATTTTT
Found at i:1253610 original size:65 final size:65
Alignment explanation
Indices: 1253529--1253667 Score: 233
Period size: 65 Copynumber: 2.1 Consensus size: 65
1253519 TTTCTAAAAA
* * *
1253529 TAGTTACTTATTTTTCCGTTTTCATAAATTGCCAATTATGTCATTTATCAACCTTAACTAGAAAC
1 TAGTAACTTATTTTTCCGTTTACATAAATTGCCAATTATGTCATTTATCAACCTTAACAAGAAAC
*
1253594 TAGTAACTTATTTTTCCGTTTACATAAATTGCCAATTATGTCATTTATTAACCTTAACAAGAAAC
1 TAGTAACTTATTTTTCCGTTTACATAAATTGCCAATTATGTCATTTATCAACCTTAACAAGAAAC
1253659 TAGTTAACT
1 TAG-TAACT
1253668 GTCCACTCTT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
65 64 0.93
66 5 0.07
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (65 bp):
TAGTAACTTATTTTTCCGTTTACATAAATTGCCAATTATGTCATTTATCAACCTTAACAAGAAAC
Found at i:1258779 original size:39 final size:39
Alignment explanation
Indices: 1258725--1258803 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
1258715 GTGTTGAGAG
*
1258725 GCATATTGGTAAAAATAGAATGAGCAAGTGCGGAGAAAT
1 GCATATTGGTAAAAATAGAATGAGCAAATGCGGAGAAAT
*
1258764 GCATATTGGTAAAAATTGAATGAGCAAATGCGGAGAAAT
1 GCATATTGGTAAAAATAGAATGAGCAAATGCGGAGAAAT
1258803 G
1 G
1258804 TTAGTGGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.43, C:0.08, G:0.28, T:0.22
Consensus pattern (39 bp):
GCATATTGGTAAAAATAGAATGAGCAAATGCGGAGAAAT
Found at i:1268201 original size:2 final size:2
Alignment explanation
Indices: 1268194--1268231 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1268184 GGTTTATTTA
1268194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1268232 CAATAAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1270803 original size:6 final size:6
Alignment explanation
Indices: 1270792--1270820 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1270782 ATATAGGGAT
1270792 GAAAGA GAAAGA GAAAGA GAAAGA GAAAG
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAG
1270821 GGGAAGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:1273801 original size:13 final size:13
Alignment explanation
Indices: 1273775--1273809 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1273765 CAATCCAGGC
1273775 GACATACG-GGGT
1 GACATACGAGGGT
1273787 GACATACGAGGGT
1 GACATACGAGGGT
1273800 GACATACGAG
1 GACATACGAG
1273810 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:1273990 original size:93 final size:91
Alignment explanation
Indices: 1273823--1274018 Score: 356
Period size: 93 Copynumber: 2.1 Consensus size: 91
1273813 TATACGAGTC
*
1273823 ATACGAGCCAATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGTAGGAATAGAGA
1 ATACGAGCC-ATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGA
1273888 GCCAATGGGGAGCATGCAACGAGCCAT
65 GCCAATGGGGAGCATGCAACGAGCCAT
1273915 ATACGAGCCATGGGGAGCATGCAACGAGCCATATACGAGCCAATGGGGAGCATGCAGGAATAGAG
1 ATACGAGCCATGGGGAGCATGCAACGAGCC--ATACGAGCCAATGGGGAGCATGCAGGAATAGAG
1273980 AGCCAATGGGGAGCATGCAACGAGCCAT
64 AGCCAATGGGGAGCATGCAACGAGCCAT
1274008 ATACGAGCCAT
1 ATACGAGCCAT
1274019 TCGAGCCAAT
Statistics
Matches: 101, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
91 21 0.21
92 9 0.09
93 71 0.70
ACGTcount: A:0.34, C:0.21, G:0.33, T:0.12
Consensus pattern (91 bp):
ATACGAGCCATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATGCAGGAATAGAGAG
CCAATGGGGAGCATGCAACGAGCCAT
Found at i:1274004 original size:61 final size:64
Alignment explanation
Indices: 1273823--1274017 Score: 248
Period size: 61 Copynumber: 3.2 Consensus size: 64
1273813 TATACGAGTC
* * *
1273823 ATACGAGCCAATGGGGAGCATGCAACGAGCCATACGAGCCAATGGGGAGCATG-TA-G-G-AAT
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATAAGAGCCAATGGGGAGCATGCAACGAGCCAT
*
1273883 AGA-GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCC-ATGGGGAGCATGCAACGAGCCA
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATA-A-GAGCCAATGGGGAGCATGCAACGAGCCA
1273946 T
64 T
*
1273947 ATACGAGCCAATGGGGAGCATGC-A-G-G-AATAGAGAGCCAATGGGGAGCATGCAACGAGCCAT
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATA-AGAGCCAATGGGGAGCATGCAACGAGCCAT
1274008 ATACGAGCCA
1 ATACGAGCCA
1274018 TTCGAGCCAA
Statistics
Matches: 120, Mismatches: 7, Indels: 15
0.85 0.05 0.11
Matches are distributed among these distances:
59 30 0.25
60 19 0.16
61 43 0.36
62 2 0.02
63 2 0.02
64 5 0.04
65 19 0.16
ACGTcount: A:0.34, C:0.22, G:0.33, T:0.12
Consensus pattern (64 bp):
ATACGAGCCAATGGGGAGCATGCAACGAGCCATAAGAGCCAATGGGGAGCATGCAACGAGCCAT
Found at i:1274099 original size:29 final size:29
Alignment explanation
Indices: 1274049--1274157 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
1274039 AAGAATAGAG
* *
1274049 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
1274078 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1274107 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1274136 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
1274158 CCATTCCCAT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:1274264 original size:18 final size:18
Alignment explanation
Indices: 1274241--1274275 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1274231 CCCAATGCAT
1274241 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
1274259 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
1274276 TTATTGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:1274405 original size:23 final size:23
Alignment explanation
Indices: 1274377--1274422 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1274367 AAAAGAAAGA
1274377 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
1274400 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
1274423 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:1274435 original size:4 final size:4
Alignment explanation
Indices: 1274426--1274491 Score: 55
Period size: 4 Copynumber: 16.5 Consensus size: 4
1274416 ATTGCAGCCG
** **
1274426 AGAA AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGGG AGAA AGGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA A-GAA
*
1274476 AGTA AG-A AG-A AGAA AG
1 AGAA AGAA AGAA AGAA AG
1274492 GGAGATAAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 6 0.12
4 36 0.72
5 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:1274437 original size:25 final size:23
Alignment explanation
Indices: 1274377--1274437 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
1274367 AAAAGAAAGA
**
1274377 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
1274400 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
1274423 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
1274438 AGAAAGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:1274457 original size:21 final size:21
Alignment explanation
Indices: 1274425--1274483 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
1274415 GATTGCAGCC
1274425 GAGAAA-GAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
1274445 GAGAAAGGAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
1274466 GAGAAAGGAAAGTAAGAA
1 GAGAAAGGAAAGAAAGAA
1274484 GAAGAAAGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 6 0.16
21 31 0.84
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAGAAAGGAAAGAAAGAAAGG
Found at i:1274663 original size:41 final size:41
Alignment explanation
Indices: 1274618--1274706 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 41
1274608 TATATGATTG
* *
1274618 TTAGTTTAAG-TT-ATAGTATACATAAATTAAAAATTATTTAA
1 TTAGTTTAAGTTTGATAGT-TACAT-AATTAAAAAATAATTAA
* * * *
1274659 TTAGTATATGTTTGATAGTTATATAGTTAAAAAATAATTAA
1 TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
1274700 TTAGTTT
1 TTAGTTT
1274707 GTATTGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 28 0.72
42 6 0.15
43 5 0.13
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (41 bp):
TTAGTTTAAGTTTGATAGTTACATAATTAAAAAATAATTAA
Found at i:1274730 original size:47 final size:47
Alignment explanation
Indices: 1274687--1274777 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
1274677 TTATATAGTT
1274687 AAAAAA-TAATTAATTAGTTTGTATT-GTT-AATAGTTAGTTATATA
1 AAAAAATTAATTAATTAGTTTGTATTAGTTAAATAGTTAGTTATATA
* *
1274731 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATTAATTAATTAGTTTGTATTAGTTAAATAGTT-AGTTATAT
1274778 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 6 0.15
45 17 0.41
46 3 0.07
47 7 0.17
48 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (47 bp):
AAAAAATTAATTAATTAGTTTGTATTAGTTAAATAGTTAGTTATATA
Found at i:1274749 original size:45 final size:44
Alignment explanation
Indices: 1274646--1274777 Score: 132
Period size: 45 Copynumber: 3.0 Consensus size: 44
1274636 TACATAAATT
*
1274646 AAAAATTATTTAATTAGTATATGTTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTGTTAATAGTTAGTTATA-TAA
*
1274688 AAAAA-TAATTAATTAGTTTGTATTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGT-TTGTTAATAGTTAGTTATATAA
1274732 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TT-GTT-AATAGTT-AGTTATAT
1274778 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 3 0.04
40 4 0.05
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 21 0.28
46 3 0.04
47 7 0.09
48 8 0.11
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (44 bp):
AAAAATTATTTAATTAGTTTGTTTGTTAATAGTTAGTTATATAA
Found at i:1274854 original size:32 final size:33
Alignment explanation
Indices: 1274818--1274894 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
1274808 TTAGTTAGTA
1274818 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-AT-AAAAGAAT
*
1274850 AGTTTATTAGTTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAGAAT
*
1274884 ATTTTATTAGT
1 AGTTTATTAGT
1274895 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 10 0.26
33 8 0.21
34 17 0.44
35 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAGAAT
Found at i:1277158 original size:17 final size:17
Alignment explanation
Indices: 1277136--1277168 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1277126 CAATGATTTT
*
1277136 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
1277153 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
1277169 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:1277297 original size:26 final size:26
Alignment explanation
Indices: 1277267--1277612 Score: 177
Period size: 26 Copynumber: 12.9 Consensus size: 26
1277257 TGTTATATAT
1277267 TAAATCATTATTATAAATCATTATTA
1 TAAATCATTATTATAAATCATTATTA
*
1277293 TAAAT-A--ATTACTAAAT-A--ATAA
1 TAAATCATTATTA-TAAATCATTATTA
*
1277314 CTAAATAATTATTATAAAATCATTATTA
1 -TAAATCATTATTAT-AAATCATTATTA
*
1277342 T-AATGATTATTATCAAATCATTACTAAATCA
1 TAAATCATTATTAT-AAATCATTA-T---T-A
*
1277373 TCAAATCATTAAATATTTAAATCATTA-T-
1 T-AAATCATT--AT-TATAAATCATTATTA
* *
1277401 TAAATCATTTTTAT-AATGATTATTA
1 TAAATCATTATTATAAATCATTATTA
* *
1277426 CTAAATTATTATTAT-AATGATTATTA
1 -TAAATCATTATTATAAATCATTATTA
* *
1277452 TCAAATCATTACTAT-AATGATTATTA
1 T-AAATCATTATTATAAATCATTATTA
*
1277478 TCAAATCATTACTAAATCATCAAATCATTAAATATT
1 T-AAATCATTA-T---T-AT-AAATCATT--AT-TA
*
1277514 TAAATCATTA-T-TAAATCATTTTTA
1 TAAATCATTATTATAAATCATTATTA
*
1277538 T-AATGATTATTACTAAATCATTATTA
1 TAAATCATTATTA-TAAATCATTATTA
* *
1277564 T-AATGATTATTATCAAATCATTACTA
1 TAAATCATTATTAT-AAATCATTATTA
*
1277590 T-AATGATTATTATCAAATCATTA
1 TAAATCATTATTAT-AAATCATTA
1277613 CTAAATCATC
Statistics
Matches: 262, Mismatches: 21, Indels: 74
0.73 0.06 0.21
Matches are distributed among these distances:
21 3 0.01
22 5 0.02
23 20 0.08
24 12 0.05
25 13 0.05
26 140 0.53
27 18 0.07
28 5 0.02
30 4 0.02
31 4 0.02
33 12 0.05
35 22 0.08
36 4 0.02
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
TAAATCATTATTATAAATCATTATTA
Found at i:1277309 original size:11 final size:11
Alignment explanation
Indices: 1277289--1277324 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1277279 ATAAATCATT
1277289 ATTA-TAAATA
1 ATTACTAAATA
1277299 ATTACTAAATA
1 ATTACTAAATA
*
1277310 ATAACTAAATA
1 ATTACTAAATA
1277321 ATTA
1 ATTA
1277325 TTATAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (11 bp):
ATTACTAAATA
Found at i:1277485 original size:124 final size:124
Alignment explanation
Indices: 1277261--1277670 Score: 682
Period size: 124 Copynumber: 3.3 Consensus size: 124
1277251 CTCATTTGTT
* * * * *
1277261 ATATATTAAATCATTATTATAAATCATTATTATAA--ATAATTACTAAATAATAACTA-AATAAT
1 ATAT-TTAAATCATTA-T-TAAATCATTTTTATAATGATTATTACTAAATAATTATTATAATGAT
* *
1277323 TATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAA
63 TATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAA
*
1277385 ATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATTATTATTATAATGATTAT
1 ATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATAATTATTATAATGATTAT
1277450 TATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAA
66 TATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAA
*
1277509 ATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTAT
1 ATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATAATTATTATAATGATTAT
1277574 TATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAA
66 TATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAA
*
1277633 ATATTTAAATCATTTTTAAATCATTTTTATAATGATTA
1 ATATTTAAATCATTATTAAATCATTTTTATAATGATTA
1277671 ATAAATACAT
Statistics
Matches: 273, Mismatches: 10, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
121 15 0.05
122 1 0.00
123 28 0.10
124 229 0.84
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (124 bp):
ATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATAATTATTATAATGATTAT
TATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAA
Found at i:1277652 original size:11 final size:11
Alignment explanation
Indices: 1277636--1277661 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1277626 TCATTAAATA
1277636 TTTAAATCATT
1 TTTAAATCATT
1277647 TTTAAATCATT
1 TTTAAATCATT
1277658 TTTA
1 TTTA
1277662 TAATGATTAA
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:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTAAATCATT
Found at i:1280542 original size:26 final size:24
Alignment explanation
Indices: 1280486--1280542 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
1280476 TAATAAACCT
*
1280486 ATAATGATTTGATAATTACTATTA
1 ATAATGATTTGATAATTAATATTA
*
1280510 ATTTAATGATTTGATATTTAATGATTTA
1 A--TAATGATTTGATAATTAAT-A-TTA
1280538 ATAAT
1 ATAAT
1280543 AATATGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
24 1 0.04
26 21 0.78
27 1 0.04
28 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (24 bp):
ATAATGATTTGATAATTAATATTA
Found at i:1281405 original size:27 final size:29
Alignment explanation
Indices: 1281349--1281409 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 29
1281339 ATTTTTTATA
1281349 TAATATAATATATAACTTAAACTAACAAC
1 TAATATAATATATAACTTAAACTAACAAC
1281378 TAATAT-A-ATATAACTT-AACTAACAAAC
1 TAATATAATATATAACTTAAACTAAC-AAC
1281405 TAATA
1 TAATA
1281410 ATTTATACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 7 0.23
27 17 0.55
28 1 0.03
29 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (29 bp):
TAATATAATATATAACTTAAACTAACAAC
Found at i:1281416 original size:27 final size:27
Alignment explanation
Indices: 1281353--1281416 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1281343 TTTATATAAT
1281353 ATAATATATAACTTAAACTAACAACTA
1 ATAATATATAACTTAAACTAACAACTA
1281380 AT-ATAATATAACTT-AACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAAC-AACTA
*
1281407 ATAATTTATA
1 ATAATATATA
1281417 CTAACAAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 9 0.27
27 22 0.67
28 2 0.06
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (27 bp):
ATAATATATAACTTAAACTAACAACTA
Found at i:1281420 original size:21 final size:20
Alignment explanation
Indices: 1281387--1281434 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
1281377 CTAATATAAT
1281387 ATAACTTAACTAACAAACTA
1 ATAACTTAACTAACAAACTA
*
1281407 ATAATTTATACTAACAAACTA
1 ATAACTTA-ACTAACAAACTA
1281428 ATTAACT
1 A-TAACT
1281435 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 13 0.54
22 4 0.17
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAACTTAACTAACAAACTA
Found at i:1281990 original size:25 final size:25
Alignment explanation
Indices: 1281936--1281993 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1281926 GTTCCCACGT
* *
1281936 CCCATGCACAGCATGCATCTGCATG
1 CCCATGCACAGCATGCATCTCCATC
* *
1281961 GCCATGCACAGCATGCATC-CCCTCC
1 CCCATGCACAGCATGCATCTCCAT-C
1281986 CCCATGCA
1 CCCATGCA
1281994 TTCCCACGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.22, C:0.43, G:0.17, T:0.17
Consensus pattern (25 bp):
CCCATGCACAGCATGCATCTCCATC
Found at i:1282084 original size:29 final size:29
Alignment explanation
Indices: 1282052--1282131 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
1282042 TCCACCTTGG
*
1282052 AGGTCGCCCGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
*
1282081 AGGTCGCCTGGATTGCATGGCGACCTCTA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
1282110 AGGTCGCCTGGATTGCATGGCG
1 AGGTCGCCTGGATTGCATGGCG
1282132 TCCTATGGCG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:1282600 original size:60 final size:62
Alignment explanation
Indices: 1282474--1282613 Score: 169
Period size: 60 Copynumber: 2.3 Consensus size: 62
1282464 CATATACCTT
* * *** * * * *
1282474 GGGATAAAAATGAAATGTTCAAAAAATTTGGTGACTCAATTTATAATGAAGATCATATTTTG
1 GGGATGAAATTGAAATGTTCAAAAAATTTGAAAACTCAATTTAGAATGAAGATCATAATCTA
1282536 GGGATGAAATTGAAATGTTC-AAAAATTTGAAAACT-AATTTAGAATGATA-ATCATAATCTA
1 GGGATGAAATTGAAATGTTCAAAAAATTTGAAAACTCAATTTAGAATGA-AGATCATAATCTA
1282596 GGGATGAAATTGAAATGT
1 GGGATGAAATTGAAATGT
1282614 ATAAAAGTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
60 37 0.54
61 13 0.19
62 18 0.26
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.32
Consensus pattern (62 bp):
GGGATGAAATTGAAATGTTCAAAAAATTTGAAAACTCAATTTAGAATGAAGATCATAATCTA
Found at i:1282632 original size:60 final size:59
Alignment explanation
Indices: 1282474--1282634 Score: 164
Period size: 60 Copynumber: 2.6 Consensus size: 59
1282464 CATATACCTT
* * * * * *
1282474 GGGATAAAAATGAAATGTTCAAAAAATTTGGTGACTCAATTTATAATGAAGATCATATTTTG
1 GGGATGAAATTGAAATGTTC-AAAAATTTGGT-ACT-AATTTAGAATGAAGATCATAATCTA
**
1282536 GGGATGAAATTGAAATGTTCAAAAATTTGAAAACTAATTTAGAATGATA-ATCATAATCTA
1 GGGATGAAATTGAAATGTTCAAAAATTTG-GTACTAATTTAGAATGA-AGATCATAATCTA
*
1282596 GGGATGAAATTGAAATGTAT-AAAAGTTTTGGTACTAATT
1 GGGATGAAATTGAAATGT-TCAAAA-ATTTGGTACTAATT
1282635 CAAAATAATG
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
60 48 0.57
61 18 0.21
62 18 0.21
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.34
Consensus pattern (59 bp):
GGGATGAAATTGAAATGTTCAAAAATTTGGTACTAATTTAGAATGAAGATCATAATCTA
Found at i:1282649 original size:60 final size:60
Alignment explanation
Indices: 1282536--1282650 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
1282526 TCATATTTTG
* * *
1282536 GGGATGAAATTGAAATGTTCAAAAATTTGAAAACTAATTTAGAATGATAATCATAATCTA
1 GGGATGAAATTGAAATGTTCAAAAATTTGAAAACTAATTCAAAATAATAATCATAATCTA
* ** *
1282596 GGGATGAAATTGAAATGTAT-AAAAGTTTTG-GTACTAATTCAAAATAATGATCATA
1 GGGATGAAATTGAAATGT-TCAAAA-ATTTGAAAACTAATTCAAAATAATAATCATA
1282651 CTTGAAAGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 41 0.89
61 5 0.11
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (60 bp):
GGGATGAAATTGAAATGTTCAAAAATTTGAAAACTAATTCAAAATAATAATCATAATCTA
Found at i:1295045 original size:2 final size:2
Alignment explanation
Indices: 1295038--1295063 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1295028 TTAGAACTCA
1295038 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1295064 TATTTAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1297179 original size:16 final size:18
Alignment explanation
Indices: 1297158--1297191 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1297148 ATTTCTTATT
1297158 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1297174 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1297192 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1297334 original size:21 final size:21
Alignment explanation
Indices: 1297310--1297352 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1297300 TATTACCTTA
1297310 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1297331 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
1297352 A
1 A
1297353 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:1297370 original size:35 final size:35
Alignment explanation
Indices: 1297321--1297406 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
1297311 ATTGAAGTAT
** * *
1297321 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
1297356 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
1297391 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
1297407 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:1297589 original size:29 final size:29
Alignment explanation
Indices: 1297537--1297594 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1297527 GCAAATGGAA
* *
1297537 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGTTT
1297566 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT
1297595 CAGAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGTTT
Found at i:1301189 original size:20 final size:20
Alignment explanation
Indices: 1301164--1301201 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1301154 TATTTAATTA
1301164 AAATTTATATATGATTTTTT
1 AAATTTATATATGATTTTTT
*
1301184 AAATTTATCTATGATTTT
1 AAATTTATATATGATTTT
1301202 ATCATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (20 bp):
AAATTTATATATGATTTTTT
Found at i:1310184 original size:6 final size:6
Alignment explanation
Indices: 1310167--1310200 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1310157 GAATCCGATA
* *
1310167 ATGACG ACGACG ATGACG ATGACG ATGAAG ATGA
1 ATGACG ATGACG ATGACG ATGACG ATGACG ATGA
1310201 TGACAAGTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.32, T:0.15
Consensus pattern (6 bp):
ATGACG
Found at i:1311907 original size:18 final size:18
Alignment explanation
Indices: 1311886--1311950 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
1311876 ATTATTATTA
1311886 TTGTTGTTGTTGTTATCG
1 TTGTTGTTGTTGTTATCG
* *
1311904 TTGTTGTTGCTGTAATCG
1 TTGTTGTTGTTGTTATCG
* * *
1311922 TCGTCGTTGTTGTTATTG
1 TTGTTGTTGTTGTTATCG
1311940 TTGTTGTTGTT
1 TTGTTGTTGTT
1311951 ATCTAAAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.06, C:0.08, G:0.28, T:0.58
Consensus pattern (18 bp):
TTGTTGTTGTTGTTATCG
Found at i:1313563 original size:6 final size:6
Alignment explanation
Indices: 1313554--1313607 Score: 90
Period size: 6 Copynumber: 9.0 Consensus size: 6
1313544 TATTCACTTC
* *
1313554 CCATAT CCATTT CCATTT GCATTT CCATTT CCATTT CCATTT CCATTT
1 CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT
1313602 CCATTT
1 CCATTT
1313608 GCTGATCTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.19, C:0.31, G:0.02, T:0.48
Consensus pattern (6 bp):
CCATTT
Found at i:1315826 original size:77 final size:79
Alignment explanation
Indices: 1315713--1315865 Score: 213
Period size: 78 Copynumber: 2.0 Consensus size: 79
1315703 TTATTATTTT
* *
1315713 TTTAATATTTTTGATAAAGCGTTATGCAAAACA-TTTTTTTCTACCGAAAATATTAATATTGGGC
1 TTTAATATTTTCGATAAAGCGTTATCCAAAACATTTTTTTTCTACCGAAAATATTAATATTGGGC
1315777 TCTACC-GAAAATG
66 TCTACCAGAAAATG
* * * *
1315790 TTTAATATTTTCGGTAAAGCGTTA-CCTAAAATATTTTTTTTCTACTGAAAATGTTAATATTGGG
1 TTTAATATTTTCGATAAAGCGTTATCC-AAAACATTTTTTTTCTACCGAAAATATTAATATTGGG
*
1315854 TTCTACCAGAAA
65 CTCTACCAGAAA
1315866 TTAGTTAGTG
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
76 1 0.02
77 27 0.41
78 34 0.52
79 4 0.06
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (79 bp):
TTTAATATTTTCGATAAAGCGTTATCCAAAACATTTTTTTTCTACCGAAAATATTAATATTGGGC
TCTACCAGAAAATG
Found at i:1318623 original size:22 final size:22
Alignment explanation
Indices: 1318594--1318636 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1318584 CGACCCGAAA
*
1318594 TATTAATAAAAATATT-ATTTT
1 TATTAATAAAAACATTGATTTT
1318615 TATTCAATAAAAACATTGATTT
1 TATT-AATAAAAACATTGATTT
1318637 AATTGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTAATAAAAACATTGATTTT
Found at i:1330989 original size:2 final size:2
Alignment explanation
Indices: 1330982--1331008 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1330972 CTTATTTTTA
1330982 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1331009 ATGAAATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1331700 original size:24 final size:24
Alignment explanation
Indices: 1331622--1331716 Score: 82
Period size: 24 Copynumber: 4.0 Consensus size: 24
1331612 ATGAGAATTG
* *
1331622 AATAAATGAGTTTATAAATGAGTC
1 AATAAACGAGCTTATAAATGAGTC
* * * **
1331646 TATAAACAAACTTATAAATGACCC
1 AATAAACGAGCTTATAAATGAGTC
* *
1331670 AACAAACGAGCTTATAAATGTGTC
1 AATAAACGAGCTTATAAATGAGTC
* **
1331694 GATAAACGAGCCAATAAATGAGT
1 AATAAACGAGCTTATAAATGAGT
1331717 TTGCTCATTA
Statistics
Matches: 52, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (24 bp):
AATAAACGAGCTTATAAATGAGTC
Found at i:1337290 original size:334 final size:334
Alignment explanation
Indices: 1336680--1337515 Score: 1390
Period size: 334 Copynumber: 2.5 Consensus size: 334
1336670 ATTGTTTTCT
1336680 TGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTCAGT
1 TGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTCAGT
* *
1336745 CTTGACTTCCTCTAGAGATTCTTGCAGAT-AATCACCTTAGATTCAACTTCCTTTAGGCCATCCT
66 CTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTATCCT
*
1336809 TCAACCGAGTTTCTTCCTCCTTGAACTCAGAAGCCTCTTGAATGACACTCTGCAACTCAGTTTCT
131 TCAACC-AGTTTCTTCCTCCTTG-ACTCAGAAGCCTCCTGAATGACACTCTGCAACTCAGTTTCT
* * *
1336874 TTAGCCAACAAACTCTCCTCTAGTTTCATGCTCTCAGCCTTGACTTTCTCTAGAGCTTCTTGCAG
194 TTAGCCAACAAACTCTCCTCTAATTTCATGCTCTCAGCCTCGACTTCCTCTAGAGCTTCTTGCAG
*
1336939 ATAAATCACCTTAGATTCAACTTCCTTTAGGCTATCCTTCAACCGAGTTTCTTCCTCCTTGGACT
259 ATAAATCACCTTAGATTCAACTTCCTTTAAGCTATCCTTCAACCGAGTTTCTTCCTCCTTGGACT
1337004 CAGAAGCCTCC
324 CAGAAGCCTCC
*
1337015 TGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCCCCTTTAATTTCATGCTCTCAGT
1 TGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTCAGT
* *
1337080 CTTGACTTCCTCTAGTGCTTCTTGCAGATAAATCACTTTAGATTCAACTTCCTTTAGGCTATCCT
66 CTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTATCCT
* *
1337145 TCAACC-GTTTCTTCCCCCTTCGATTCAGAAGCCTCCTGAATGACACTCTGCAACTCAGTTTCTT
131 TCAACCAGTTTCTTCCTCCTT-GACTCAGAAGCCTCCTGAATGACACTCTGCAACTCAGTTTCTT
** * * * *
1337209 TATTCAACAAACTCTCCTTTAATTTCATGCTCTCGGTCTCGACTTCCTCTAGAGCTTCTTGCCGA
195 TAGCCAACAAACTCTCCTCTAATTTCATGCTCTCAGCCTCGACTTCCTCTAGAGCTTCTTGCAGA
1337274 TAAATCACCTTAGATTCAACTTCCTTTAAGCTATCCTTCAACCGAGTTTCTTCCTCCTTGGACTC
260 TAAATCACCTTAGATTCAACTTCCTTTAAGCTATCCTTCAACCGAGTTTCTTCCTCCTTGGACTC
* *
1337339 ATAAGCCTCT
325 AGAAGCCTCC
* *
1337349 TGAATGACACTCTGCAACTC-GTTTTCTTTATCCAACAAACTATCCTTTAATTTCATGCTTTCAG
1 TGAATGACACTCTGCAACTCAG-TTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTCAG
1337413 TCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTATCC
65 TCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTATCC
*
1337478 TTCAACCGAGCTTCTTCCTCCTTGGACTCAGAAGCCTC
130 TTCAACC-AGTTTCTTCCTCCTT-GACTCAGAAGCCTC
1337516 TTCCTCAGAT
Statistics
Matches: 467, Mismatches: 29, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
333 1 0.00
334 310 0.66
335 92 0.20
336 64 0.14
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.36
Consensus pattern (334 bp):
TGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTCAGT
CTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTATCCT
TCAACCAGTTTCTTCCTCCTTGACTCAGAAGCCTCCTGAATGACACTCTGCAACTCAGTTTCTTT
AGCCAACAAACTCTCCTCTAATTTCATGCTCTCAGCCTCGACTTCCTCTAGAGCTTCTTGCAGAT
AAATCACCTTAGATTCAACTTCCTTTAAGCTATCCTTCAACCGAGTTTCTTCCTCCTTGGACTCA
GAAGCCTCC
Found at i:1337516 original size:168 final size:168
Alignment explanation
Indices: 1336677--1337517 Score: 1420
Period size: 168 Copynumber: 5.0 Consensus size: 168
1336667 TTCATTGTTT
1336677 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
* *
1336742 AGTCTTGACTTCCTCTAGAGATTCTTGCAGAT-AATCACCTTAGATTCAACTTCCTTTAGGCCAT
66 AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
*
1336806 CCTTCAACCGAGTTTCTTCCTCCTTGAACTCAGAAGCC
131 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
* * *
1336844 TCTTGAATGACACTCTGCAACTCAGTTTCTTTAGCCAACAAACTCTCCTCTAGTTTCATGCTCTC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
* *
1336909 AGCCTTGACTTTCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
66 AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
1336974 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
131 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
* *
1337012 TCCTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCCCCTTTAATTTCATGCTCTC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
* *
1337077 AGTCTTGACTTCCTCTAGTGCTTCTTGCAGATAAATCACTTTAGATTCAACTTCCTTTAGGCTAT
66 AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
* * *
1337142 CCTTCAACC--GTTTCTTCCCCCTTCGATTCAGAAGCC
131 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
* *
1337178 TCCTGAATGACACTCTGCAACTCAGTTTCTTTATTCAACAAACTCTCCTTTAATTTCATGCTCTC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
* * * *
1337243 GGTCTCGACTTCCTCTAGAGCTTCTTGCCGATAAATCACCTTAGATTCAACTTCCTTTAAGCTAT
66 AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
*
1337308 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCATAAGCC
131 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
* *
1337346 TCTTGAATGACACTCTGCAACTC-GTTTTCTTTATCCAACAAACTATCCTTTAATTTCATGCTTT
1 TCTTGAATGACACTCTGCAACTCAG-TTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCT
1337410 CAGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTA
65 CAGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTA
*
1337475 TCCTTCAACCGAGCTTCTTCCTCCTTGGACTCAGAAGCC
130 TCCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
1337514 TCTT
1 TCTT
1337518 CCTCAGATTG
Statistics
Matches: 628, Mismatches: 42, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
166 155 0.25
167 92 0.15
168 381 0.61
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.36
Consensus pattern (168 bp):
TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTCTCCTTTAATTTCATGCTCTC
AGTCTTGACTTCCTCTAGAGCTTCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
Found at i:1346299 original size:23 final size:24
Alignment explanation
Indices: 1346273--1346324 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1346263 GATAAAAGCA
1346273 TTATCAGTAATA-ATTAATTATT-T
1 TTAT-AGTAATAGATTAATTATTAT
* *
1346296 TTATATTAATAGTTTAATTATTAT
1 TTATAGTAATAGATTAATTATTAT
1346320 TTATA
1 TTATA
1346325 TGGTGATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.24
23 13 0.52
24 6 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
TTATAGTAATAGATTAATTATTAT
Found at i:1346415 original size:15 final size:15
Alignment explanation
Indices: 1346380--1346429 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1346370 TAACTGAGCG
*
1346380 TAAATATAAAAATAT
1 TAAATATAAAATTAT
*
1346395 TAAA-ATAAAATATTTT
1 TAAATAT-AAA-ATTAT
1346411 TAAATATAAAATTAT
1 TAAATATAAAATTAT
1346426 TAAA
1 TAAA
1346430 AGTTATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.07
15 15 0.52
16 10 0.34
17 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAATATAAAATTAT
Found at i:1354725 original size:17 final size:17
Alignment explanation
Indices: 1354703--1354736 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1354693 AATCTTAAAC
1354703 CACTTAACAAGTTTAGG
1 CACTTAACAAGTTTAGG
1354720 CACTTAACAAGTTTAGG
1 CACTTAACAAGTTTAGG
1354737 GACCTTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (17 bp):
CACTTAACAAGTTTAGG
Found at i:1360735 original size:31 final size:31
Alignment explanation
Indices: 1360700--1360772 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
1360690 CGGTCAAGTC
* *
1360700 ATTATAAAATAATTATTAAAATTTTTAAATT
1 ATTATAAAATAATTATTAAAATTATTAAACT
* *
1360731 ATTATAAAATAATTATTCAACTTATTAAACT
1 ATTATAAAATAATTATTAAAATTATTAAACT
*
1360762 ATTACAAAATA
1 ATTATAAAATA
1360773 GTCTTTAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.42
Consensus pattern (31 bp):
ATTATAAAATAATTATTAAAATTATTAAACT
Found at i:1366305 original size:11 final size:12
Alignment explanation
Indices: 1366289--1366319 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1366279 ATAAAATTGC
1366289 AAATCTATTT-T
1 AAATCTATTTGT
1366300 AAATCTATTTGT
1 AAATCTATTTGT
1366312 AAATCTAT
1 AAATCTAT
1366320 ATTTTTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (12 bp):
AAATCTATTTGT
Found at i:1372632 original size:2 final size:2
Alignment explanation
Indices: 1372625--1372655 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1372615 TGAAGTCTTC
1372625 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 A
1372656 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1375506 original size:11 final size:11
Alignment explanation
Indices: 1375492--1375550 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
1375482 ATATGTTATA
1375492 AATATTAAACG
1 AATATTAAACG
* *
1375503 AATA-CATCACG
1 AATATTA-AACG
*
1375514 AATATTAAATG
1 AATATTAAACG
* *
1375525 AATATT-CACA
1 AATATTAAACG
1375535 AATATTAAACG
1 AATATTAAACG
1375546 AATAT
1 AATAT
1375551 ATATATACGA
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
10 8 0.23
11 26 0.74
12 1 0.03
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.29
Consensus pattern (11 bp):
AATATTAAACG
Found at i:1375538 original size:21 final size:21
Alignment explanation
Indices: 1375491--1375550 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
1375481 AATATGTTAT
*
1375491 AAATATTAAACGAATACATCAC
1 AAATATTAAACGAATA-TTCAC
* *
1375513 GAATATTAAATGAATATTCAC
1 AAATATTAAACGAATATTCAC
1375534 AAATATTAAACGAATAT
1 AAATATTAAACGAATAT
1375551 ATATATACGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 19 0.58
22 14 0.42
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (21 bp):
AAATATTAAACGAATATTCAC
Found at i:1379859 original size:14 final size:14
Alignment explanation
Indices: 1379837--1379899 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
1379827 AAACTGTGCA
* *
1379837 GAAAATTAAAAGCT
1 GAAATTTAAAGGCT
1379851 GAAATTTAAAGGTCT
1 GAAATTTAAAGG-CT
* * *
1379866 GAAATGTAAATGTT
1 GAAATTTAAAGGCT
* *
1379880 AAAATTTAAAGGCA
1 GAAATTTAAAGGCT
1379894 GAAATT
1 GAAATT
1379900 GAAGATGCAG
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
14 25 0.68
15 12 0.32
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (14 bp):
GAAATTTAAAGGCT
Found at i:1379869 original size:15 final size:15
Alignment explanation
Indices: 1379849--1379891 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1379839 AAATTAAAAG
1379849 CTGAAATTTAAAGGT
1 CTGAAATTTAAAGGT
* *
1379864 CTGAAATGTAAATGT
1 CTGAAATTTAAAGGT
*
1379879 -TAAAATTTAAAGG
1 CTGAAATTTAAAGG
1379892 CAGAAATTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.33
Consensus pattern (15 bp):
CTGAAATTTAAAGGT
Found at i:1382753 original size:22 final size:22
Alignment explanation
Indices: 1382725--1382772 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1382715 TTTAATCTTT
1382725 TCTTTGCATGGTCATTGTGTGA
1 TCTTTGCATGGTCATTGTGTGA
1382747 TCTTTGCATGGTCATTGTGTGA
1 TCTTTGCATGGTCATTGTGTGA
1382769 TCTT
1 TCTT
1382773 AAGCGGCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (22 bp):
TCTTTGCATGGTCATTGTGTGA
Found at i:1387594 original size:59 final size:59
Alignment explanation
Indices: 1387510--1387631 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 59
1387500 TCAATAATTT
* * * ** * *
1387510 TCAACTATTTGATAATAAACGCTCATACCCCTACATACGTGGTACTCGAACCTGAGAGC
1 TCAACTATATGATAATAAACACTCATACCACTACATACCCGGGACTCGAAACTGAGAGC
* * * *
1387569 TCAATTATATGATAATAAACACTCATATCACTGCATACCCGGGACTCGAAACTGGGAGC
1 TCAACTATATGATAATAAACACTCATACCACTACATACCCGGGACTCGAAACTGAGAGC
1387628 TCAA
1 TCAA
1387632 GATATAACAA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (59 bp):
TCAACTATATGATAATAAACACTCATACCACTACATACCCGGGACTCGAAACTGAGAGC
Found at i:1389270 original size:14 final size:15
Alignment explanation
Indices: 1389240--1389276 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1389230 ATAAATTAGT
1389240 TAAAA-ATTTAAAGA
1 TAAAATATTTAAAGA
*
1389254 TAAATTATTTAAA-A
1 TAAAATATTTAAAGA
1389268 TAAAATATT
1 TAAAATATT
1389277 AATTACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAAGA
Found at i:1398753 original size:7 final size:7
Alignment explanation
Indices: 1398741--1398881 Score: 53
Period size: 7 Copynumber: 20.3 Consensus size: 7
1398731 GAACCCTAAC
1398741 CCTAAAA
1 CCTAAAA
*
1398748 CCTAAAT
1 CCTAAAA
* *
1398755 CATAAAC
1 CCTAAAA
1398762 CCT-AAA
1 CCTAAAA
1398768 CCT-AAA
1 CCTAAAA
1398774 CTCT-AAA
1 C-CTAAAA
1398781 CCATAAATA
1 CC-TAAA-A
*
1398790 -AT-AAA
1 CCTAAAA
*
1398795 CCTTAAA
1 CCTAAAA
*
1398802 CCATAAAT
1 CC-TAAAA
*
1398810 CCTAAAT
1 CCTAAAA
*
1398817 CCTAAAT
1 CCTAAAA
* *
1398824 TC-AATA
1 CCTAAAA
*
1398830 CCCAAAA
1 CCTAAAA
1398837 CCCTAAAA
1 -CCTAAAA
1398845 CCTAAAA
1 CCTAAAA
*
1398852 CCTAAAT
1 CCTAAAA
**
1398859 TTTAAAA
1 CCTAAAA
1398866 CCCT-AAA
1 -CCTAAAA
1398873 CCTAAAA
1 CCTAAAA
1398880 CC
1 CC
1398882 CTAATTCCCA
Statistics
Matches: 102, Mismatches: 21, Indels: 22
0.70 0.14 0.15
Matches are distributed among these distances:
5 1 0.01
6 19 0.19
7 67 0.66
8 14 0.14
9 1 0.01
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.21
Consensus pattern (7 bp):
CCTAAAA
Found at i:1398764 original size:21 final size:20
Alignment explanation
Indices: 1398738--1398822 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
1398728 GATGAACCCT
*
1398738 AACCCTAAAACCTAAATCATA
1 AACCATAAAACCTAAATC-TA
*
1398759 AACCCT-AAACCTAAACTCTA
1 AACCATAAAACCTAAA-TCTA
* *
1398779 AACCATAAATA-ATAAACCTTA
1 AACCATAAA-ACCTAAATC-TA
*
1398800 AACCATAAATCCTAAATCCTA
1 AACCATAAAACCTAAAT-CTA
1398821 AA
1 AA
1398823 TTCAATACCC
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
20 17 0.33
21 33 0.63
22 2 0.04
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (20 bp):
AACCATAAAACCTAAATCTA
Found at i:1398770 original size:20 final size:20
Alignment explanation
Indices: 1398738--1398787 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1398728 GATGAACCCT
1398738 AACCCTAAAACCTAAA-TCATA
1 AACCCT-AAACCTAAACTC-TA
1398759 AACCCTAAACCTAAACTCTA
1 AACCCTAAACCTAAACTCTA
*
1398779 AACCATAAA
1 AACCCTAAA
1398788 TAATAAACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (20 bp):
AACCCTAAACCTAAACTCTA
Found at i:1398808 original size:14 final size:13
Alignment explanation
Indices: 1398745--1398787 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1398735 CCTAACCCTA
*
1398745 AAACCTAAATCAT
1 AAACCTAAACCAT
1398758 AAACCCTAAACC-T
1 AAA-CCTAAACCAT
1398771 AAACTCTAAACCAT
1 AAAC-CTAAACCAT
1398785 AAA
1 AAA
1398788 TAATAAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.04
13 14 0.54
14 11 0.42
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (13 bp):
AAACCTAAACCAT
Found at i:1398882 original size:14 final size:14
Alignment explanation
Indices: 1398833--1398885 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
1398823 TTCAATACCC
1398833 AAAACCCTAAAACCT
1 AAAACCCT-AAACCT
**
1398848 AAAA-CCTAAATTTT
1 AAAACCCTAAA-CCT
1398862 AAAACCCTAAACCT
1 AAAACCCTAAACCT
1398876 AAAACCCTAA
1 AAAACCCTAA
1398886 TTCCCAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 3 0.09
14 19 0.59
15 10 0.31
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAACCCTAAACCT
Found at i:1398894 original size:28 final size:28
Alignment explanation
Indices: 1398831--1398905 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
1398821 AATTCAATAC
1398831 CCAAAACCCTAAAACCTAAAACCTAAATT
1 CCAAAACCCT-AAACCTAAAACCTAAATT
**
1398860 TTAAAACCCTAAACCTAAAACCCT-AATT
1 CCAAAACCCTAAACCTAAAA-CCTAAATT
* * *
1398888 CCCAAACCATAAATCTAA
1 CCAAAACCCTAAACCTAA
1398906 TTATGTGATA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 27 0.71
29 11 0.29
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (28 bp):
CCAAAACCCTAAACCTAAAACCTAAATT
Found at i:1407330 original size:59 final size:59
Alignment explanation
Indices: 1407258--1407379 Score: 172
Period size: 59 Copynumber: 2.1 Consensus size: 59
1407248 TCAATAATTT
* * * * *
1407258 TCAACTATTTGATAATAAACGCTCATACCCCTACATACGTGGTACTCGAACCTGAGAGC
1 TCAACTATATGATAATAAACACTCATACCCCTACATACCTGATACTCGAAACTGAGAGC
* * *
1407317 TCAACTATATGATAATAAACACTCATATCCCTGCATACCTGATACTCGAAACTGGGAGC
1 TCAACTATATGATAATAAACACTCATACCCCTACATACCTGATACTCGAAACTGAGAGC
1407376 TCAA
1 TCAA
1407380 GGTATAACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.25
Consensus pattern (59 bp):
TCAACTATATGATAATAAACACTCATACCCCTACATACCTGATACTCGAAACTGAGAGC
Found at i:1409011 original size:14 final size:15
Alignment explanation
Indices: 1408980--1409016 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1408970 ATAAATTAGT
1408980 TAAAA-ATTTAAAAG
1 TAAAATATTTAAAAG
*
1408994 TAAATTATTTAAAA-
1 TAAAATATTTAAAAG
1409008 TAAAATATT
1 TAAAATATT
1409017 AACTACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAAAG
Found at i:1410522 original size:18 final size:18
Alignment explanation
Indices: 1410499--1410618 Score: 135
Period size: 18 Copynumber: 7.0 Consensus size: 18
1410489 TCCTAAACTC
*
1410499 GAGTCCCTAAGCCTTAAA
1 GAGTCCCTAAGCCTTAAT
1410517 GAGTCCCTAAGCCTTAAT
1 GAGTCCCTAAGCCTTAAT
1410535 GAGTCCCTAAGCCTTAAT
1 GAGTCCCTAAGCCTTAAT
*
1410553 GAGTCCCTAAGCC-TAGT
1 GAGTCCCTAAGCCTTAAT
* * * *
1410570 G-G-ACCGAA-TCGT-A-
1 GAGTCCCTAAGCCTTAAT
*
1410583 GAGTCCCTAAGCCTAAAT
1 GAGTCCCTAAGCCTTAAT
1410601 GAGTCCCTAAGCCTTAAT
1 GAGTCCCTAAGCCTTAAT
1410619 CATTTGAGGG
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.01
14 2 0.02
15 9 0.11
16 2 0.02
17 5 0.06
18 65 0.77
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (18 bp):
GAGTCCCTAAGCCTTAAT
Found at i:1412512 original size:14 final size:14
Alignment explanation
Indices: 1412495--1412525 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1412485 GTTTTCGTCT
1412495 TGTGAATTTCATGG
1 TGTGAATTTCATGG
1412509 TGTGAATTTCATGG
1 TGTGAATTTCATGG
1412523 TGT
1 TGT
1412526 TATAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.29, T:0.45
Consensus pattern (14 bp):
TGTGAATTTCATGG
Found at i:1420040 original size:6 final size:6
Alignment explanation
Indices: 1420031--1420057 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1420021 TATATACATA
1420031 TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TAT
1420058 TGGTGTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:1421724 original size:201 final size:202
Alignment explanation
Indices: 1421359--1421769 Score: 709
Period size: 201 Copynumber: 2.0 Consensus size: 202
1421349 TCAAATTATA
* *
1421359 ATTTTTTAAGTCGATTGAGCATGATCATACTGATTAATATCAAGGTTGTTAGAAAGAGGTTTGAT
1 ATTTTTTAAGTCAATTGAGCATCATCATACTGATTAATATCAAGGTTGTTAGAAAGAGGTTTGAT
* * *
1421424 AATGAGATCCGTTAATTGCTTAAGTGGTTAATAATGCTTATATTATCTCACTCTATGTGGATTAT
66 AATGAGATCCATTAATTGATTAAGTGGTCAATAATGCTTATATTATCTCACTCTATGTGGATTAT
* *
1421489 AATCTCGACATTTGTTTTAAACAAAAT-AAAAAAAATCATAATTTCCTGAGAAATTTTCAAAAAA
131 AATATCGACATTTGTTTTAAACAAAATAAAAAAAAATCATAATTTCCTAAGAAATTTTCAAAAAA
1421553 TCCCTTC
196 TCCCTTC
*
1421560 ATTTTTTACGTCAATTGAGCATCATCATACTGATTAATATCAAGGTTGTTAGAAAGAGGTTTGAT
1 ATTTTTTAAGTCAATTGAGCATCATCATACTGATTAATATCAAGGTTGTTAGAAAGAGGTTTGAT
*
1421625 AGTGAGATCCATTAATTGATTAAGTGGTCAATAATGCTTATATTATCTCACTCTATGTGGATTA-
66 AATGAGATCCATTAATTGATTAAGTGGTCAATAATGCTTATATTATCTCACTCTATGTGGATTAT
1421689 AATATCGACATTTGTTTTAAACAAAATATAAAAAAAAATCATAATTTCCTAAGAAATTTTCAAAA
131 AATATCGACATTTGTTTTAAAC-AAA-ATAAAAAAAAATCATAATTTCCTAAGAAATTTTCAAAA
1421754 AATCCCTTC
194 AATCCCTTC
1421763 ATTTTTT
1 ATTTTTT
1421770 CCATGCCCAA
Statistics
Matches: 198, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
200 21 0.11
201 125 0.63
202 2 0.01
203 50 0.25
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (202 bp):
ATTTTTTAAGTCAATTGAGCATCATCATACTGATTAATATCAAGGTTGTTAGAAAGAGGTTTGAT
AATGAGATCCATTAATTGATTAAGTGGTCAATAATGCTTATATTATCTCACTCTATGTGGATTAT
AATATCGACATTTGTTTTAAACAAAATAAAAAAAAATCATAATTTCCTAAGAAATTTTCAAAAAA
TCCCTTC
Found at i:1423772 original size:41 final size:41
Alignment explanation
Indices: 1423727--1423808 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
1423717 GAAGCAGTAT
1423727 CCGTTTGCACCCTATAAACTATTTTTATATACTTTTTAGAA
1 CCGTTTGCACCCTATAAACTATTTTTATATACTTTTTAGAA
* *
1423768 CCGTTTGCACCCTATAGACTTTTTTTATATACTTTTTAGAA
1 CCGTTTGCACCCTATAAACTATTTTTATATACTTTTTAGAA
1423809 TTGTTAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.45
Consensus pattern (41 bp):
CCGTTTGCACCCTATAAACTATTTTTATATACTTTTTAGAA
Found at i:1424480 original size:11 final size:11
Alignment explanation
Indices: 1424451--1424495 Score: 81
Period size: 11 Copynumber: 4.0 Consensus size: 11
1424441 ATTTAGTAAA
1424451 AAAATAGATTT
1 AAAATAGATTT
1424462 ACAAATAGATTT
1 A-AAATAGATTT
1424474 AAAATAGATTT
1 AAAATAGATTT
1424485 AAAATAGATTT
1 AAAATAGATTT
1424496 GCAATTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (11 bp):
AAAATAGATTT
Found at i:1424480 original size:23 final size:22
Alignment explanation
Indices: 1424451--1424495 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
1424441 ATTTAGTAAA
1424451 AAAATAGATTTACAAATAGATTT
1 AAAATAGATTTA-AAATAGATTT
1424474 AAAATAGATTTAAAATAGATTT
1 AAAATAGATTTAAAATAGATTT
1424496 GCAATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (22 bp):
AAAATAGATTTAAAATAGATTT
Found at i:1431866 original size:2 final size:2
Alignment explanation
Indices: 1431859--1431884 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1431849 TTATTCACAA
1431859 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1431885 TGATCCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1434433 original size:29 final size:29
Alignment explanation
Indices: 1434409--1434469 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
1434399 TTAAATATAT
1434409 ATATT-CTAAAATTATTTATAAAAATAAC
1 ATATTCCTAAAATTATTTATAAAAATAAC
** *
1434437 ATATTCCTACTATTATTTATGAAAATAAC
1 ATATTCCTAAAATTATTTATAAAAATAAC
1434466 ATAT
1 ATAT
1434470 AGATATGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.41
Consensus pattern (29 bp):
ATATTCCTAAAATTATTTATAAAAATAAC
Found at i:1435766 original size:28 final size:27
Alignment explanation
Indices: 1435734--1435799 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
1435724 TTAAAACTAT
*
1435734 ATTTATTTTTGTTTAACTTATTAAATAA
1 ATTTATTTTT-CTTAACTTATTAAATAA
* *
1435762 TTTTATTTTATCTTAATTTATTAAATAA
1 ATTTATTTT-TCTTAACTTATTAAATAA
*
1435790 ATTTGTTTTT
1 ATTTATTTTT
1435800 ATTTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
27 1 0.03
28 30 0.94
29 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (27 bp):
ATTTATTTTTCTTAACTTATTAAATAA
Found at i:1435944 original size:30 final size:31
Alignment explanation
Indices: 1435884--1435948 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1435874 ATATATTTAA
1435884 ATATTTTACTATTAATTTAATATAAAAATAT
1 ATATTTTACTATTAATTTAATATAAAAATAT
* * *
1435915 ATATTTTACTCTTATTTTAA-ATTAAAATAT
1 ATATTTTACTATTAATTTAATATAAAAATAT
1435945 ATAT
1 ATAT
1435949 AATATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 13 0.42
31 18 0.58
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.51
Consensus pattern (31 bp):
ATATTTTACTATTAATTTAATATAAAAATAT
Found at i:1436026 original size:29 final size:29
Alignment explanation
Indices: 1435970--1436049 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
1435960 ATATTTTTAA
* *
1435970 AAGTTAAGATAATAA-AAAATATAATTTT
1 AAGTAAAGATAAGAATAAAATATAATTTT
* * *
1435998 AATTTGAA-ATAAGAATAAAATATATTTTT
1 AA-GTAAAGATAAGAATAAAATATAATTTT
1436027 AAGTAAAGATAAGAATAAAATAT
1 AAGTAAAGATAAGAATAAAATAT
1436050 TATATATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 11 0.26
29 32 0.74
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (29 bp):
AAGTAAAGATAAGAATAAAATATAATTTT
Found at i:1436234 original size:30 final size:30
Alignment explanation
Indices: 1436200--1436287 Score: 108
Period size: 29 Copynumber: 3.0 Consensus size: 30
1436190 ACATTAAAAT
1436200 AAAAATAAAATAAATTTAATAAATTAAGAC
1 AAAAATAAAATAAATTTAATAAATTAAGAC
* * *
1436230 AAAAATAAAA-ATATTTAATAAGTTAAAAC
1 AAAAATAAAATAAATTTAATAAATTAAGAC
* *
1436259 AAAAATAAAGATAATTTTAA-AATTTAAGA
1 AAAAATAAA-ATAAATTTAATAAATTAAGA
1436288 TATATAACTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
29 25 0.51
30 18 0.37
31 6 0.12
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (30 bp):
AAAAATAAAATAAATTTAATAAATTAAGAC
Found at i:1436480 original size:11 final size:11
Alignment explanation
Indices: 1436464--1436492 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1436454 AAATAAATCT
1436464 ATTAAATTAAA
1 ATTAAATTAAA
1436475 ATTAAATTAAA
1 ATTAAATTAAA
1436486 A-TAAATT
1 ATTAAATT
1436493 TAGTCTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTAAATTAAA
Found at i:1436594 original size:31 final size:31
Alignment explanation
Indices: 1436559--1436625 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
1436549 ATTTGTAGGT
*
1436559 AAATTTATTTTAATTTATTAAAATTAGGATC
1 AAATTTATTTTAATTTATTAAAACTAGGATC
*
1436590 AAATTTATTTTAATTTATTAAAACTATGATC
1 AAATTTATTTTAATTTATTAAAACTAGGATC
1436621 AAATT
1 AAATT
1436626 GAAAGAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (31 bp):
AAATTTATTTTAATTTATTAAAACTAGGATC
Found at i:1437099 original size:17 final size:18
Alignment explanation
Indices: 1437077--1437128 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
1437067 ATAGTATGTT
1437077 ATATTTTAATATAAAA-A
1 ATATTTTAATATAAAATA
*
1437094 ATATTTAAATATTTAAAATA
1 ATATTTTAATA--TAAAATA
*
1437114 ATATTATTAAAATAA
1 ATATT-TTAATATAA
1437129 TTATAGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 10 0.36
19 8 0.29
20 6 0.21
21 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTTTAATATAAAATA
Found at i:1437465 original size:3 final size:3
Alignment explanation
Indices: 1437457--1437481 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1437447 TATGAATTTG
1437457 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1437482 AAAAGGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1444371 original size:10 final size:9
Alignment explanation
Indices: 1444342--1444371 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1444332 CCCCAAAAGC
1444342 TTTCTAATT
1 TTTCTAATT
1444351 TTTCTAATT
1 TTTCTAATT
*
1444360 TTTCTCATT
1 TTTCTAATT
1444369 TTT
1 TTT
1444372 ATAAATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTCTAATT
Found at i:1447929 original size:14 final size:14
Alignment explanation
Indices: 1447870--1447930 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
1447860 ATGTTTATAA
1447870 TTTAGAGTTTAA-AT
1 TTTAGA-TTTAAGAT
1447884 TTGTA-ATTTAAGAT
1 TT-TAGATTTAAGAT
*
1447898 TTTAGGATTAAAGA-
1 TTTA-GATTTAAGAT
*
1447912 TTTAGATTTGAGAT
1 TTTAGATTTAAGAT
1447926 TTTAG
1 TTTAG
1447931 TATTCAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 14 0.36
14 16 0.41
15 9 0.23
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (14 bp):
TTTAGATTTAAGAT
Found at i:1448156 original size:2 final size:2
Alignment explanation
Indices: 1448149--1448186 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1448139 GATTAATTAA
1448149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1448187 GAATTTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1449360 original size:2 final size:2
Alignment explanation
Indices: 1449353--1449380 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1449343 TAATTAATGA
1449353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1449381 TCTTAAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.