Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007754.1 Hibiscus syriacus cultivar Beakdansim tig00110020_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: 3698414
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 15
Found at i:1179968 original size:273 final size:274
Alignment explanation
Indices: 1179446--1179981 Score: 819
Period size: 273 Copynumber: 2.0 Consensus size: 274
1179436 ATTTCGTGAG
* * * * * * * *
1179446 AAAAAATATTACAAGCTCGAAATCAAAGTAGGTAAGCTCTAATTCAAGATATTAAGGTGAGTGCA
1 AAAAAAGATTAAAAGCTAGAAATCAAAGGAGGTAAGCTCGAATTCAAGACATGAAGGTGAGTACA
* *
1179511 TTTCAAACTCTAAATGTTCCATAGATTTTCATGATGGTAATGCTTAGCATGACATATTTGGACGT
66 TTTCAAACTCTAAATGTTCCACAGATTTTCATAATGGTAATGCTTAGCATGACATATTTGGACGT
* * * *
1179576 TTATCTTAACATTAAATTAGGAAATAGGAAGAATTAACAAAATATCTCTAGATTTAAATAATGAA
131 TTATCTTAACATTAAATCAGGAAATAGAAAGAACTAACAAAATATCTCTAGATTTAAACAATGAA
*
1179641 TATTAGTGGTAAGAAATAAATACTATAGGATATAATTTTAAGAAAATATCCTAAGATTTTAGTAA
196 TATTAGTGGTAAGAAATAAATACTATACGATATAATTTTAAGAAAATATCCTAAGATTTTAGTAA
1179706 TTAAGGTGAGAAAA
261 TTAAGGTGAGAAAA
1179720 AAAAAAGATTAAAAGCTAGAAATCAAAGGA-GTAAGCTCGAATTC-AGAACATGAAGGTGAGTAC
1 AAAAAAGATTAAAAGCTAGAAATCAAAGGAGGTAAGCTCGAATTCAAG-ACATGAAGGTGAGTAC
* *
1179783 ATTTCAAACTCTAAATGTTCCACAGATTTTCATAATGGTGATGCTTAGCATGACCTATTTGGACG
65 ATTTCAAACTCTAAATGTTCCACAGATTTTCATAATGGTAATGCTTAGCATGACATATTTGGACG
* * **
1179848 TTTGTTTTAACATTTGATCAGGAAATAGAAAGAACTAACAAAATATCTCTAGATTTAAACAATGA
130 TTTATCTTAACATTAAATCAGGAAATAGAAAGAACTAACAAAATATCTCTAGATTTAAACAATGA
*
1179913 ATATTAGTGGTCAA-AAATAAATACTATATCG-TATAATTTTAAGAAAATGTCCTAAGATTTTAG
195 ATATTAGTGGT-AAGAAATAAATACTATA-CGATATAATTTTAAGAAAATATCCTAAGATTTTAG
1179976 TAATTA
258 TAATTA
1179982 CGAGTTAAAC
Statistics
Matches: 237, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
272 2 0.01
273 206 0.87
274 29 0.12
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.32
Consensus pattern (274 bp):
AAAAAAGATTAAAAGCTAGAAATCAAAGGAGGTAAGCTCGAATTCAAGACATGAAGGTGAGTACA
TTTCAAACTCTAAATGTTCCACAGATTTTCATAATGGTAATGCTTAGCATGACATATTTGGACGT
TTATCTTAACATTAAATCAGGAAATAGAAAGAACTAACAAAATATCTCTAGATTTAAACAATGAA
TATTAGTGGTAAGAAATAAATACTATACGATATAATTTTAAGAAAATATCCTAAGATTTTAGTAA
TTAAGGTGAGAAAA
Found at i:1186250 original size:44 final size:44
Alignment explanation
Indices: 1186153--1186308 Score: 188
Period size: 44 Copynumber: 3.5 Consensus size: 44
1186143 CGGTAAAGTA
* * * **
1186153 TTACCTAAAATATTATTTTTTA-CTGAAAATGTTAATATTGAGTG
1 TTACCTAAAACATTATTTTTTATCAG-AAATGTTAATATTAAACG
* **
1186197 ATATTTAAAACATTATTTTTTATCAGAAATGTTAATATTAAACG
1 TTACCTAAAACATTATTTTTTATCAGAAATGTTAATATTAAACG
*
1186241 TTACCTAAAACATTATTTTTCTATCAGAAATGTTAATAATAAACG
1 TTACCTAAAACATTATTTTT-TATCAGAAATGTTAATATTAAACG
* *
1186286 CTACCTAAAATATTATTTTTTAT
1 TTACCTAAAACATTATTTTTTAT
1186309 AATAAAATTA
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
44 53 0.55
45 43 0.45
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.44
Consensus pattern (44 bp):
TTACCTAAAACATTATTTTTTATCAGAAATGTTAATATTAAACG
Found at i:1186284 original size:45 final size:44
Alignment explanation
Indices: 1186202--1186308 Score: 178
Period size: 45 Copynumber: 2.4 Consensus size: 44
1186192 GAGTGATATT
* *
1186202 TAAAACATTATTTTTTATCAGAAATGTTAATATTAAACGTTACC
1 TAAAACATTATTTTTTATCAGAAATGTTAATAATAAACGCTACC
1186246 TAAAACATTATTTTTCTATCAGAAATGTTAATAATAAACGCTACC
1 TAAAACATTATTTTT-TATCAGAAATGTTAATAATAAACGCTACC
*
1186291 TAAAATATTATTTTTTAT
1 TAAAACATTATTTTTTAT
1186309 AATAAAATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 18 0.31
45 41 0.69
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (44 bp):
TAAAACATTATTTTTTATCAGAAATGTTAATAATAAACGCTACC
Found at i:1187271 original size:24 final size:24
Alignment explanation
Indices: 1187196--1187257 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
1187186 TTATATATAA
* *
1187196 ATATCAAAGTCTTGATAATAAAGT
1 ATATCAAAATCTTAATAATAAAGT
*
1187220 ACATCAAAATCTTAATAATAAAGT
1 ATATCAAAATCTTAATAATAAAGT
1187244 ATATCAAAATCTTA
1 ATATCAAAATCTTA
1187258 TTTAATATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.32
Consensus pattern (24 bp):
ATATCAAAATCTTAATAATAAAGT
Found at i:1189068 original size:43 final size:43
Alignment explanation
Indices: 1188996--1189089 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
1188986 GTTTAGGGGA
* * *
1188996 TTAATGGTTGTGTACTAGGGATTATGGTTTTAGTGTTTAGAAT
1 TTAAGGGTTATGTACTAGGGATTAGGGTTTTAGTGTTTAGAAT
* *
1189039 TTAAGGGTTATGTATTAGGGATTAGGGTTTTAGTTTTTAGAAT
1 TTAAGGGTTATGTACTAGGGATTAGGGTTTTAGTGTTTAGAAT
1189082 TT-AGGGTT
1 TTAAGGGTT
1189090 TAGGGTTTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 6 0.13
43 40 0.87
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (43 bp):
TTAAGGGTTATGTACTAGGGATTAGGGTTTTAGTGTTTAGAAT
Found at i:1189085 original size:22 final size:22
Alignment explanation
Indices: 1189021--1189090 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
1189011 TAGGGATTAT
*
1189021 GGTTTTAGTGTTTAGAATTTAAG
1 GGTTTTAGTTTTTAGAATTT-AG
* * *
1189044 GGTTAT-G-TATTAGGGA-TTAG
1 GGTTTTAGTTTTTA-GAATTTAG
1189064 GGTTTTAGTTTTTAGAATTTAG
1 GGTTTTAGTTTTTAGAATTTAG
1189086 GGTTT
1 GGTTT
1189091 AGGGTTTAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
20 7 0.19
21 8 0.22
22 16 0.44
23 5 0.14
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.49
Consensus pattern (22 bp):
GGTTTTAGTTTTTAGAATTTAG
Found at i:1190621 original size:60 final size:60
Alignment explanation
Indices: 1190538--1190663 Score: 227
Period size: 60 Copynumber: 2.1 Consensus size: 60
1190528 AATTAATGAC
* *
1190538 TTATA-ACAAAATGAGGCATCCATTTAATCCTACGTGTAAGTTCATCACTTTGCTTGATA
1 TTATAGACAAAATGAGGCACCCATTTAATCCTACGTGTAAGCTCATCACTTTGCTTGATA
1190597 TTATAGACAAAATGAGGCACCCATTTAATCCTACGTGTAAGCTCATCACTTTGCTTGATA
1 TTATAGACAAAATGAGGCACCCATTTAATCCTACGTGTAAGCTCATCACTTTGCTTGATA
1190657 TTATAGA
1 TTATAGA
1190664 AAACATGGTT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 5 0.08
60 59 0.92
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (60 bp):
TTATAGACAAAATGAGGCACCCATTTAATCCTACGTGTAAGCTCATCACTTTGCTTGATA
Found at i:1195190 original size:18 final size:17
Alignment explanation
Indices: 1195164--1195197 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1195154 TTTTCGTATG
1195164 ATTTAAATCAAGATTAAA
1 ATTTAAATCAA-ATTAAA
*
1195182 ATTTTAATCAAATTAA
1 ATTTAAATCAAATTAA
1195198 TTTAAGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTTAAATCAAATTAAA
Found at i:1198736 original size:64 final size:65
Alignment explanation
Indices: 1198619--1198778 Score: 170
Period size: 64 Copynumber: 2.5 Consensus size: 65
1198609 TTGTTTGAAG
* * ** *
1198619 GTGCATCGATGCACAGGTGTGCATCGATGCA-CTCTTTTAAAATAAAAAGATCGAATGCA-ATTA
1 GTGCATCGATGCAAAGGTATGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCATATTA
* *
1198682 GTGCATCGATGCATAAGGCATGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATTT
1 GTGCATCGATGCA-AAGGTATGCATCGATGCATCTCCATTAA-AATAAAAACATCGAATGCATAT
1198745 TA
64 TA
*
1198747 -TGCACCGATGCACAA-GTAGTGCATCGATGCAT
1 GTGCATCGATGCA-AAGGTA-TGCATCGATGCAT
1198779 ACCTTCATTA
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
63 15 0.18
64 60 0.73
65 7 0.09
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (65 bp):
GTGCATCGATGCAAAGGTATGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCATATTA
Found at i:1205991 original size:58 final size:57
Alignment explanation
Indices: 1205901--1206014 Score: 219
Period size: 58 Copynumber: 2.0 Consensus size: 57
1205891 CACTCCACAG
1205901 ACGCAGATGCTAGAACCCATAACCTTAAAAAGAACAACACTCTCTTTTACTAGTAAAT
1 ACGCAGATGCTAGAACCCATAACCTTAAAAAGAACAACACTCTCTTTTACTA-TAAAT
1205959 ACGCAGATGCTAGAACCCATAACCTTAAAAAGAACAACACTCTCTTTTACTATAAA
1 ACGCAGATGCTAGAACCCATAACCTTAAAAAGAACAACACTCTCTTTTACTATAAA
1206015 ATCGTTTAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 4 0.07
58 52 0.93
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.24
Consensus pattern (57 bp):
ACGCAGATGCTAGAACCCATAACCTTAAAAAGAACAACACTCTCTTTTACTATAAAT
Found at i:1215680 original size:18 final size:19
Alignment explanation
Indices: 1215659--1215705 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1215649 TTAAAATTAT
1215659 ATAAAAATATAATA-TTTC
1 ATAAAAATATAATATTTTC
* *
1215677 ATAAATATA-AATATTTTT
1 ATAAAAATATAATATTTTC
1215695 ATAAAAA-ATAA
1 ATAAAAATATAA
1215706 AATGTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAAATATAATATTTTC
Found at i:1215713 original size:18 final size:18
Alignment explanation
Indices: 1215655--1215715 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
1215645 TACTTTAAAA
*
1215655 TTATATAAAAATATAATAT
1 TTATA-AAAAATAAAATAT
* *
1215674 TTCAT-AAATATAAATATTT
1 TT-ATAAAAAATAAA-ATAT
*
1215693 TTATAAAAAATAAAATGT
1 TTATAAAAAATAAAATAT
1215711 TTATA
1 TTATA
1215716 TCTTATGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 17 0.50
19 15 0.44
20 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TTATAAAAAATAAAATAT
Found at i:1217611 original size:86 final size:87
Alignment explanation
Indices: 1217508--1217682 Score: 343
Period size: 86 Copynumber: 2.0 Consensus size: 87
1217498 TAGTTGGAGC
1217508 ATATTACATAAATAAAAAATTAAGAAAATATGCTCCAACTAGGTAATGACATGTGTCACCATTTA
1 ATATTACATAAATAAAAAATTAAGAAAATATGCTCCAACTAGGTAATGACATGTGTCACCATTTA
1217573 ATTGGAGATTAAA-TTATTTTA
66 ATTGGAGATTAAATTTATTTTA
1217594 ATATTACATAAATAAAAAATTAAGAAAATATGCTCCAACTAGGTAATGACATGTGTCACCATTTA
1 ATATTACATAAATAAAAAATTAAGAAAATATGCTCCAACTAGGTAATGACATGTGTCACCATTTA
1217659 ATTGGAGATTAAATTTATTTTA
66 ATTGGAGATTAAATTTATTTTA
1217681 AT
1 AT
1217683 TAAAATAAAT
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 78 0.89
87 10 0.11
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (87 bp):
ATATTACATAAATAAAAAATTAAGAAAATATGCTCCAACTAGGTAATGACATGTGTCACCATTTA
ATTGGAGATTAAATTTATTTTA
Found at i:1220500 original size:17 final size:17
Alignment explanation
Indices: 1220478--1220511 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1220468 TCATTGTCAA
1220478 TAATTAAAAAATATTAT
1 TAATTAAAAAATATTAT
*
1220495 TAATTAATAAATATTAT
1 TAATTAAAAAATATTAT
1220512 CTTGTAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTAAAAAATATTAT
Found at i:1220570 original size:18 final size:18
Alignment explanation
Indices: 1220530--1220567 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1220520 CACCCAGACT
1220530 ATTAAAAAAATAAAGAAA
1 ATTAAAAAAATAAAGAAA
*
1220548 ATTAAAGAAA-AAAGAAA
1 ATTAAAAAAATAAAGAAA
1220565 ATT
1 ATT
1220568 TAATTACACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (18 bp):
ATTAAAAAAATAAAGAAA
Found at i:1223761 original size:36 final size:34
Alignment explanation
Indices: 1223712--1223785 Score: 105
Period size: 34 Copynumber: 2.1 Consensus size: 34
1223702 AATATCGTCT
1223712 CTTTGTGTATGATTTTTTTTACGTTGATCTCGTTTTA
1 CTTTGTGTATGA-TTTTTTT-CGTTGATCTCG-TTTA
*
1223749 CTTT-TGTGTGATTTTTTTCGTTGATCTCGTTTA
1 CTTTGTGTATGATTTTTTTCGTTGATCTCGTTTA
1223782 CTTT
1 CTTT
1223786 CTTGTCTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
33 8 0.22
34 11 0.31
35 7 0.19
36 6 0.17
37 4 0.11
ACGTcount: A:0.11, C:0.12, G:0.16, T:0.61
Consensus pattern (34 bp):
CTTTGTGTATGATTTTTTTCGTTGATCTCGTTTA
Found at i:1225892 original size:13 final size:13
Alignment explanation
Indices: 1225874--1225937 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
1225864 AATAAATGAG
1225874 AAAAAATAATAAA
1 AAAAAATAATAAA
*
1225887 AAAAAATTATAAA
1 AAAAAATAATAAA
** *
1225900 ATTATTAATATTAAA
1 A--AAAAATAATAAA
*
1225915 ATAAAATAATAAA
1 AAAAAATAATAAA
*
1225928 ATAAAATAAT
1 AAAAAATAAT
1225938 TTTTTTAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
13 31 0.77
15 9 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAATAATAAA
Found at i:1227221 original size:391 final size:390
Alignment explanation
Indices: 1226490--1227272 Score: 1413
Period size: 391 Copynumber: 2.0 Consensus size: 390
1226480 GGGATTTATG
* *
1226490 TTCGGACGACGCTTATTTGTAATCCTGTAGATCTTCTTTGTTTTAGACTCTCGGGTTAGATTTAG
1 TTCGGACGACGCTTATTTGTAATCCTGTAGATCTTCTTTGCTTTAGACTCTCGGATTAGATTTAG
* * *
1226555 ATACGTAATTTGTATTCGGAGATAATTGTTTTACGTTGTTCGACTCTGATTTGCGATTGTCAATA
66 ATACGCAATTTGTATTCGGAGATAATTGTTTCACATTGTTCGACTCTGATTTGCGATTGTCAATA
* * *
1226620 GTCTTTCAATTGTTTCATCTCTGTGTGGTTCATTTTTAAATGTAATTAGATTTTTTCGTATATAT
131 GTCTTTCAATTGTTTCATCTCTGTGTGGTTCATTTTCAAATGTAATCAGATTTGTTCGTATATAT
1226685 ATTTTTGTTCGAATTTTTTGGACGTCTTTGTAGCCTTTTCCTTGTATAATCATTTATTGATCAAA
196 ATTTTTGTTCGAATTTTTTGGACGTCTTTGTAGCCTTTTCCTTGTATAATCATTTATTGATCAAA
*
1226750 GAGGTAATTGTTTTGTAATGATTATAAGAAAATGTCTTAATTATGTGTCTAATTCACGATTATAA
261 GAGGTAATTGTTTTGTAATGATTATAAGAAAATGTCTTAATTATGTGTATAATTCACGATTATAA
*
1226815 TTGTAAAACTTTATTGTAATTAATTTTAAATATTTTATTTTTTTATAATAAAACTAGTAATTTCT
326 TTGTAAAAATTTATTGTAATTAATTTTAAATATTTTA-TTTTTTATAATAAAACTAGTAATTTCT
1226880 A
390 A
* *
1226881 TTCGGATGACGCTTATTTGTTATCCTGTAGATCTTCTTTGCTTTAGACTCTCGGATTAGATTTAG
1 TTCGGACGACGCTTATTTGTAATCCTGTAGATCTTCTTTGCTTTAGACTCTCGGATTAGATTTAG
* *
1226946 ATACGCGATTTGTATTCGGAGATAATTGTTTCACATTGTTCGACTCTGATTTGCGATTGTCAGTA
66 ATACGCAATTTGTATTCGGAGATAATTGTTTCACATTGTTCGACTCTGATTTGCGATTGTCAATA
1227011 GTCTTTCAATTGTTTCATCTCTGTGTGGTTCATTTTCAAATGTAATCAGATTTGTTCGTATATAT
131 GTCTTTCAATTGTTTCATCTCTGTGTGGTTCATTTTCAAATGTAATCAGATTTGTTCGTATATAT
*
1227076 ATTTTTGTTCGAATTTTTTGGACGTCTTTGTAGCCTTTTCCTTGTATGATCATTTATTGATCAAA
196 ATTTTTGTTCGAATTTTTTGGACGTCTTTGTAGCCTTTTCCTTGTATAATCATTTATTGATCAAA
1227141 GAGGTAATTGTTTTGTAATGATTATAAGAAAATGTCTTAATTATGTGTATAATTCACGATTATAA
261 GAGGTAATTGTTTTGTAATGATTATAAGAAAATGTCTTAATTATGTGTATAATTCACGATTATAA
*
1227206 TTGTAAAAATTTATTGTAATTAATTTTAAATATTTTATTTTTTATAATAAAACTAGTTATTTCTA
326 TTGTAAAAATTTATTGTAATTAATTTTAAATATTTTATTTTTTATAATAAAACTAGTAATTTCTA
1227271 TT
1 TT
1227273 TGTGTAAAAA
Statistics
Matches: 376, Mismatches: 16, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
390 29 0.08
391 347 0.92
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.47
Consensus pattern (390 bp):
TTCGGACGACGCTTATTTGTAATCCTGTAGATCTTCTTTGCTTTAGACTCTCGGATTAGATTTAG
ATACGCAATTTGTATTCGGAGATAATTGTTTCACATTGTTCGACTCTGATTTGCGATTGTCAATA
GTCTTTCAATTGTTTCATCTCTGTGTGGTTCATTTTCAAATGTAATCAGATTTGTTCGTATATAT
ATTTTTGTTCGAATTTTTTGGACGTCTTTGTAGCCTTTTCCTTGTATAATCATTTATTGATCAAA
GAGGTAATTGTTTTGTAATGATTATAAGAAAATGTCTTAATTATGTGTATAATTCACGATTATAA
TTGTAAAAATTTATTGTAATTAATTTTAAATATTTTATTTTTTATAATAAAACTAGTAATTTCTA
Found at i:1227967 original size:30 final size:30
Alignment explanation
Indices: 1227931--1227987 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1227921 GGTTAATGGC
*
1227931 TTAAGGGGTTGACGGAGGATTGAATCTTGA
1 TTAAGGGGTTGACGAAGGATTGAATCTTGA
*
1227961 TTAAGGGGTTGACGAAGGATTGCATCT
1 TTAAGGGGTTGACGAAGGATTGAATCT
1227988 CCATTGAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.35, T:0.30
Consensus pattern (30 bp):
TTAAGGGGTTGACGAAGGATTGAATCTTGA
Found at i:1229804 original size:22 final size:22
Alignment explanation
Indices: 1229779--1229822 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1229769 CAATTTTTAT
1229779 AAGATATATTGAAAGAAAATAC
1 AAGATATATTGAAAGAAAATAC
1229801 AAGATATATTGAAAGAAAATAC
1 AAGATATATTGAAAGAAAATAC
1229823 GTCTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.23
Consensus pattern (22 bp):
AAGATATATTGAAAGAAAATAC
Found at i:1231902 original size:22 final size:23
Alignment explanation
Indices: 1231868--1231912 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1231858 CTCTGAAAGC
* *
1231868 TTTACAAATTTATTCT-TAAAAT
1 TTTAAAAACTTATTCTCTAAAAT
1231890 TTTAAAAACTTATTCTCTAAAAT
1 TTTAAAAACTTATTCTCTAAAAT
1231913 AAAATTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTAAAAACTTATTCTCTAAAAT
Found at i:1242331 original size:22 final size:23
Alignment explanation
Indices: 1242306--1242361 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1242296 TTAAATTTTT
*
1242306 TTAT-TAAATTTAAAAAATAAAA
1 TTATATAAATTTAAAAAAGAAAA
**
1242328 TTATATATGTTTAAAAAAGAAAA
1 TTATATAAATTTAAAAAAGAAAA
*
1242351 -CATATAAATTT
1 TTATATAAATTT
1242362 TGAAATAACC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
TTATATAAATTTAAAAAAGAAAA
Found at i:1243008 original size:19 final size:19
Alignment explanation
Indices: 1242984--1243028 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1242974 AAAAATCTTG
1242984 TTTTTATGTTGATTTTT-TA
1 TTTTTATGTTG-TTTTTATA
*
1243003 TTTTTATTTTGTTTTTATA
1 TTTTTATGTTGTTTTTATA
1243022 TTTTTAT
1 TTTTTAT
1243029 ATAAAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.78
Consensus pattern (19 bp):
TTTTTATGTTGTTTTTATA
Found at i:1243266 original size:24 final size:24
Alignment explanation
Indices: 1243231--1243287 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
1243221 ACAAACAAAT
*
1243231 TCATTTATTGACTCGATCATAAGC
1 TCATTTATTGACTCAATCATAAGC
* *
1243255 TCGTTTATTGACTCAATCATAAGT
1 TCATTTATTGACTCAATCATAAGC
1243279 TCATTTATT
1 TCATTTATT
1243288 CAGTTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.44
Consensus pattern (24 bp):
TCATTTATTGACTCAATCATAAGC
Found at i:1246087 original size:24 final size:23
Alignment explanation
Indices: 1246050--1246104 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
1246040 TAAAATTTGT
*
1246050 ATTAAA-AATTTAAGAATATAAA
1 ATTAAATATTTTAAGAATATAAA
* *
1246072 TTTATAATATTTTAAGAGTATAAA
1 ATTA-AATATTTTAAGAATATAAA
1246096 ATTAAATAT
1 ATTAAATAT
1246105 AAAGACAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.11
23 7 0.26
24 17 0.63
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (23 bp):
ATTAAATATTTTAAGAATATAAA
Found at i:1248327 original size:39 final size:39
Alignment explanation
Indices: 1248273--1248356 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
1248263 AACTAACACA
1248273 AACGAATGTATGTTTATGTTTGTTATTTAACTTTAACCG
1 AACGAATGTATGTTTATGTTTGTTATTTAACTTTAACCG
*
1248312 AACGAATGTATGTTTATGTTTGTTATTTAACTTTAACTG
1 AACGAATGTATGTTTATGTTTGTTATTTAACTTTAACCG
1248351 AACGAA
1 AACGAA
1248357 CATGAACTAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (39 bp):
AACGAATGTATGTTTATGTTTGTTATTTAACTTTAACCG
Found at i:1264536 original size:30 final size:31
Alignment explanation
Indices: 1264502--1264589 Score: 112
Period size: 30 Copynumber: 2.9 Consensus size: 31
1264492 CACGTTAATG
* * *
1264502 ATTTTTATTA-TATT-TTATGTGTTGTTTTAT
1 ATTTTTATGAGTATTATTATAT-TTGTATTAT
1264532 A-TTTTATGAGTATTATTATATTTGTATTAT
1 ATTTTTATGAGTATTATTATATTTGTATTAT
1264562 A-TTTTATGAGTATTATTATATTTGTATT
1 ATTTTTATGAGTATTATTATATTTGTATT
1264590 GTGTTTGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 7 0.13
30 41 0.77
31 5 0.09
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (31 bp):
ATTTTTATGAGTATTATTATATTTGTATTAT
Found at i:1264550 original size:19 final size:18
Alignment explanation
Indices: 1264505--1264584 Score: 66
Period size: 19 Copynumber: 4.7 Consensus size: 18
1264495 GTTAATGATT
*
1264505 TTTATTATATTTTATGTG
1 TTTATTATATTTTATGAG
*
1264523 TTGTTTTATATTTTATGAG
1 TT-TATTATATTTTATGAG
1264542 TATTATTATA--TT-T--G
1 T-TTATTATATTTTATGAG
1264556 --TATTATATTTTATGAG
1 TTTATTATATTTTATGAG
1264572 TATTATTATATTT
1 T-TTATTATATTT
1264585 GTATTGTGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 19
0.69 0.04 0.27
Matches are distributed among these distances:
11 7 0.14
13 2 0.04
14 2 0.04
16 2 0.04
17 2 0.04
18 2 0.04
19 31 0.63
20 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (18 bp):
TTTATTATATTTTATGAG
Found at i:1264558 original size:14 final size:14
Alignment explanation
Indices: 1264541--1264589 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1264531 TATTTTATGA
1264541 GTATTATTATATTT
1 GTATTATTATATTT
*
1264555 GTATTA-TATTTTAT
1 GTATTATTATATT-T
1264569 GAGTATTATTATATTT
1 --GTATTATTATATTT
1264585 GTATT
1 GTATT
1264590 GTGTTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 5 0.17
14 12 0.41
16 7 0.24
17 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (14 bp):
GTATTATTATATTT
Found at i:1269189 original size:19 final size:19
Alignment explanation
Indices: 1269159--1269204 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1269149 ATGAATCGAT
1269159 AAAAAAAT--TTAA-TTAA
1 AAAAAAATCATTAATTTAA
1269175 ATAAAAAATCATTAATTTAA
1 A-AAAAAATCATTAATTTAA
*
1269195 AAAGAAATCA
1 AAAAAAATCA
1269205 AACATGCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 7 0.28
19 12 0.48
20 5 0.20
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAAAATCATTAATTTAA
Found at i:1272943 original size:22 final size:23
Alignment explanation
Indices: 1272899--1272944 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1272889 ATATTTAATT
*
1272899 TATTGATAAATTGATAAATTAAA
1 TATTGATAAATTGATAAAATAAA
1272922 TATTGAT-AATTG-TAAAGATAAA
1 TATTGATAAATTGATAAA-ATAAA
1272944 T
1 T
1272945 TTAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 10 0.48
23 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (23 bp):
TATTGATAAATTGATAAAATAAA
Found at i:1274616 original size:22 final size:21
Alignment explanation
Indices: 1274567--1274616 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
1274557 GTTTAGGGCA
1274567 AACTATTTATTTAGTCACCAT
1 AACTATTTATTTAGTCACCAT
* *
1274588 -GCGATTTCATTTTAGTCA-CAT
1 AACTATTT-A-TTTAGTCACCAT
1274609 AACTATTT
1 AACTATTT
1274617 TTCTAAATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 5
0.71 0.13 0.16
Matches are distributed among these distances:
20 5 0.23
21 4 0.18
22 13 0.59
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.44
Consensus pattern (21 bp):
AACTATTTATTTAGTCACCAT
Found at i:1296112 original size:27 final size:23
Alignment explanation
Indices: 1296057--1296108 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1296047 TAATTACATG
1296057 TAATTATATATAATTACAAACTT
1 TAATTATATATAATTACAAACTT
*
1296080 TAATTATATATAATTACATACTT
1 TAATTATATATAATTACAAACTT
*
1296103 AAATTA
1 TAATTA
1296109 ATTAAACTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATTATATATAATTACAAACTT
Found at i:1297827 original size:15 final size:15
Alignment explanation
Indices: 1297807--1297836 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1297797 AGAGTGAATC
*
1297807 AAATTAATCATAATT
1 AAATTAATCAAAATT
1297822 AAATTAATCAAAATT
1 AAATTAATCAAAATT
1297837 TTTAATCATT
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:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAATCAAAATT
Found at i:1299254 original size:13 final size:13
Alignment explanation
Indices: 1299236--1299263 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1299226 ACGATCCAAC
1299236 TTTATTAAATATA
1 TTTATTAAATATA
1299249 TTTATTAAATATA
1 TTTATTAAATATA
1299262 TT
1 TT
1299264 AAATTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTATTAAATATA
Found at i:1305781 original size:29 final size:29
Alignment explanation
Indices: 1305746--1305827 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1305736 AAACTAAATT
*
1305746 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1305775 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
1305804 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1305828 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1310547 original size:29 final size:29
Alignment explanation
Indices: 1310512--1310593 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
1310502 AAACTAAATT
*
1310512 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1310541 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
*
1310570 GATATCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1310594 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:1315073 original size:52 final size:52
Alignment explanation
Indices: 1314998--1315105 Score: 207
Period size: 52 Copynumber: 2.1 Consensus size: 52
1314988 TTAATAATCA
1314998 ATCAAGTTGTGACATATGATCTTTAATAATGCCAATATCTTAAATAGTCAAT
1 ATCAAGTTGTGACATATGATCTTTAATAATGCCAATATCTTAAATAGTCAAT
*
1315050 ATCAAGTTGTGACATATGCTCTTTAATAATGCCAATATCTTAAATAGTCAAT
1 ATCAAGTTGTGACATATGATCTTTAATAATGCCAATATCTTAAATAGTCAAT
1315102 ATCA
1 ATCA
1315106 TGTAATACTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (52 bp):
ATCAAGTTGTGACATATGATCTTTAATAATGCCAATATCTTAAATAGTCAAT
Found at i:1315852 original size:21 final size:21
Alignment explanation
Indices: 1315801--1315853 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1315791 ATTATGACTA
1315801 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1315822 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1315843 TCGCAATGCGA
1 TCGCAATGCGA
1315854 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1315868 original size:20 final size:21
Alignment explanation
Indices: 1315843--1315894 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1315833 TTTTCCCAAT
*
1315843 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1315863 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1315884 TCGCAATGCGA
1 TCGCAATGCGA
1315895 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1315908 original size:20 final size:20
Alignment explanation
Indices: 1315883--1315977 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
1315873 AATTTGGAAA
* *
1315883 ATCGCAATGCGATACTGAC-T
1 ATCGCAACGCGATAAT-ACAT
*
1315903 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATAC-AT
**
1315924 ATCGCAACGCGATTCTGAC-T
1 ATCGCAACGCGATAAT-ACAT
*
1315944 ATCGCAACGAGATAATACAT
1 ATCGCAACGCGATAATACAT
*
1315964 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
1315978 TTTCAAAGCG
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.07
20 28 0.47
21 25 0.42
22 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATAATACAT
Found at i:1315978 original size:41 final size:41
Alignment explanation
Indices: 1315880--1315978 Score: 162
Period size: 41 Copynumber: 2.4 Consensus size: 41
1315870 GCGAATTTGG
* *
1315880 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATTCTGACTATCGCAACGAGATAATAC
*
1315921 AAAATCGCAACGCGATTCTGACTATCGCAACGAGATAATAC
1 AAAATCGCAATGCGATTCTGACTATCGCAACGAGATAATAC
*
1315962 ATAATCGCAATGCGATT
1 AAAATCGCAATGCGATT
1315979 TTCAAAGCGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAATCGCAATGCGATTCTGACTATCGCAACGAGATAATAC
Found at i:1316175 original size:22 final size:22
Alignment explanation
Indices: 1316150--1316200 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1316140 CTACGGCGAC
1316150 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
1316172 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
1316194 ATCCGTC
1 ATCCGTC
1316201 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1316595 original size:20 final size:19
Alignment explanation
Indices: 1316541--1316608 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
1316531 GAAACCGAGA
* **
1316541 ATCGCAACACGAAATGAGA
1 ATCGCAACGCGAAATGACT
*
1316560 ATCGCAACGACAAAATGACT
1 ATCGCAACG-CGAAATGACT
1316580 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
1316600 ATCGCAACG
1 ATCGCAACG
1316609 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 9 0.21
20 33 0.79
ACGTcount: A:0.41, C:0.25, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1316713 original size:32 final size:34
Alignment explanation
Indices: 1316657--1316726 Score: 108
Period size: 32 Copynumber: 2.1 Consensus size: 34
1316647 CAAATTCGCA
* *
1316657 TTGCGATTTTCATTTCCGCATTGCGATTTTCTCG
1 TTGCGATTTTCAATTCCGCATTGCGATTCTCTCG
1316691 TTGCGA-TTTCAATT-CGCATTGCGATTCTCTCG
1 TTGCGATTTTCAATTCCGCATTGCGATTCTCTCG
1316723 TTGC
1 TTGC
1316727 AATAGTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 21 0.62
33 7 0.21
34 6 0.18
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (34 bp):
TTGCGATTTTCAATTCCGCATTGCGATTCTCTCG
Found at i:1316751 original size:20 final size:20
Alignment explanation
Indices: 1316718--1316769 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1316708 ATTGCGATTC
*
1316718 TCTCGTTGCAATAGTCATTT
1 TCTCGTTGCGATAGTCATTT
1316738 TCGT-GTTGCGATAGTCATTT
1 TC-TCGTTGCGATAGTCATTT
1316758 TCTCGTTGCGAT
1 TCTCGTTGCGAT
1316770 TTTAAGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.44
Consensus pattern (20 bp):
TCTCGTTGCGATAGTCATTT
Found at i:1318116 original size:18 final size:18
Alignment explanation
Indices: 1318095--1318129 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1318085 CTCCACTTCG
1318095 AGAGCCATCACCTCACCC
1 AGAGCCATCACCTCACCC
1318113 AGAGCCATCACCTCACC
1 AGAGCCATCACCTCACC
1318130 TGATCGACCC
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:0.49, G:0.11, T:0.11
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:1318787 original size:33 final size:33
Alignment explanation
Indices: 1318740--1318832 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1318730 GGAAATGGCT
*
1318740 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1318773 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1318806 ATCGCAACGCGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
1318833 TGCGAATTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 42 0.74
34 15 0.26
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1318820 original size:14 final size:15
Alignment explanation
Indices: 1318755--1318821 Score: 68
Period size: 14 Copynumber: 4.4 Consensus size: 15
1318745 AATGTGAAAT
1318755 GAAAATCGCAACGAC
1 GAAAATCGCAACGAC
*
1318770 -AAAATCGCAATGCGAAAT
1 GAAAATCGCAA--CG--AC
1318788 GAAAATCGCAACGAC
1 GAAAATCGCAACGAC
1318803 -AAAATCGCAACG-C
1 GAAAATCGCAACGAC
1318816 GAAAAT
1 GAAAAT
1318822 GAAAATCGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
13 1 0.02
14 27 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.23
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.10
Consensus pattern (15 bp):
GAAAATCGCAACGAC
Found at i:1318826 original size:20 final size:19
Alignment explanation
Indices: 1318681--1318838 Score: 93
Period size: 20 Copynumber: 8.6 Consensus size: 19
1318671 TAGTTTACTT
* *
1318681 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1318701 TCGCAACGCGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
1318721 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
* *
1318741 TCGCAATGTGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1318760 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
1318774 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1318793 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1318807 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCG-AAATGAAAA
*
1318827 TCGCAATGCGAA
1 TCGCAACGCGAA
1318839 TTTAGTTTCG
Statistics
Matches: 109, Mismatches: 16, Indels: 27
0.72 0.11 0.18
Matches are distributed among these distances:
14 20 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 1 0.01
19 26 0.24
20 49 0.45
21 4 0.04
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1318865 original size:19 final size:19
Alignment explanation
Indices: 1318827--1318928 Score: 81
Period size: 19 Copynumber: 5.6 Consensus size: 19
1318817 AAAATGAAAA
* * *
1318827 TCGCAATGCGAATTTAGTT
1 TCGCATTGCGATTTTCGTT
1318846 TCGCATTGCGATTTGT-GTT
1 TCGCATTGCGATTT-TCGTT
* *
1318865 TCGCGTTACGATTTT-G--
1 TCGCATTGCGATTTTCGTT
*
1318881 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCGTT
* *
1318898 TCGCATTCCGATTTTCATT
1 TCGCATTGCGATTTTCGTT
1318917 TCGCATTGCGAT
1 TCGCATTGCGAT
1318929 AGCCATTTCT
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
14 9 0.13
16 3 0.04
17 3 0.04
18 2 0.03
19 51 0.74
20 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCGTT
Found at i:1318898 original size:20 final size:19
Alignment explanation
Indices: 1318875--1318971 Score: 77
Period size: 20 Copynumber: 4.9 Consensus size: 19
1318865 TCGCGTTACG
1318875 ATTTTGTCGTTGCGATTTTC
1 ATTTTG-CGTTGCGATTTTC
* * *
1318895 ATTTCGCATTCCGATTTTC
1 ATTTTGCGTTGCGATTTTC
* * ***
1318914 ATTTCGCATTGCGATAGCC
1 ATTTTGCGTTGCGATTTTC
**
1318933 ATTTCTGCGTTGCGATAGTC
1 ATTT-TGCGTTGCGATTTTC
1318953 ATTTTCGCGTTGCGATTTT
1 ATTTT-GCGTTGCGATTTT
1318972 AAGTTTCGTG
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
19 31 0.49
20 32 0.51
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
ATTTTGCGTTGCGATTTTC
Found at i:1318935 original size:19 final size:19
Alignment explanation
Indices: 1318893--1318968 Score: 80
Period size: 20 Copynumber: 3.9 Consensus size: 19
1318883 GTTGCGATTT
* **
1318893 TCATTTCGCATTCCGATTT
1 TCATTTCGCATTGCGATAG
1318912 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
* *
1318931 CCATTTCTGCGTTGCGATAG
1 TCATTTC-GCATTGCGATAG
*
1318951 TCATTTTCGCGTTGCGAT
1 TCA-TTTCGCATTGCGAT
1318969 TTTAAGTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
19 22 0.45
20 23 0.47
21 4 0.08
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.41
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1319381 original size:42 final size:42
Alignment explanation
Indices: 1319334--1319422 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
1319324 GACTCACCTG
* *
1319334 TCATCCCTCAAAAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAAAGTCCCCTCCAACCGTTCAAGAGGCCACTA
* * * *
1319376 TCATCCCTCAAGAGTCCGCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAAAGTCCCCTCCAACCGTTCAAGAGGCCACTA
1319418 TCATC
1 TCATC
1319423 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.40, G:0.15, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAAAGTCCCCTCCAACCGTTCAAGAGGCCACTA
Found at i:1319425 original size:21 final size:21
Alignment explanation
Indices: 1319357--1319432 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
1319347 GTCCCCTCCA
*
1319357 ATCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGGCCACTATC
** * * **
1319378 ATCCCTCAAGAGTCCGCTCCC
1 ATCGTTCAAGAGGCCACTATC
* *
1319399 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCCACTATC
*
1319420 ATCGTTGAAGAGG
1 ATCGTTCAAGAGG
1319433 TCCCTCCCAC
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.21
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCACTATC
Found at i:1319431 original size:42 final size:42
Alignment explanation
Indices: 1319334--1319442 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 42
1319324 GACTCACCTG
* * * *
1319334 TCATCCCTCAA-AAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCACTA
*
1319376 TCATCCCTCAAGA-GTCCGCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGGTCC-CTCCCACCGTTCAAGAGGCCACTA
** *
1319418 TCATCGTTGAAGAGGTCCCTCCCAC
1 TCATCCCTCAAGAGGTCCCTCCCAC
1319443 TATTCCAGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 2 0.04
42 50 0.88
43 5 0.09
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1320847 original size:14 final size:14
Alignment explanation
Indices: 1320828--1320863 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1320818 ATTGTTTAAT
1320828 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1320842 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1320856 TGATTTGT
1 TGATTTGT
1320864 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1321104 original size:19 final size:20
Alignment explanation
Indices: 1321061--1321113 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1321051 CGAAACTAAA
1321061 TTCGCATTGCGATTTTCATT
1 TTCGCATTGCGATTTTCATT
1321081 TTCGCATTGCGATTTTCA-T
1 TTCGCATTGCGATTTTCATT
1321100 TTCGCATTGCGATT
1 TTCGCATTGCGATT
1321114 CTCTCGTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (20 bp):
TTCGCATTGCGATTTTCATT
Found at i:1321143 original size:20 final size:20
Alignment explanation
Indices: 1321118--1321166 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1321108 GCGATTCTCT
1321118 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1321138 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
1321158 CGTTGCGAT
1 CGTTGCGAT
1321167 TTCCCCGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1321179 original size:54 final size:53
Alignment explanation
Indices: 1321081--1321188 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 53
1321071 GATTTTCATT
** *
1321081 TTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAA
1 TTCGCATTGCGATAGTCATTTCGCATTGCGATTCTCCCGTTGCGATAGTCAAA
* *
1321134 TTCGCGTTGCGATAGTCATTTTCGCGTTGCGATT-TCCCCGTTGCGATAGTCAAA
1 TTCGCATTGCGATAGTCA-TTTCGCATTGCGATTCT-CCCGTTGCGATAGTCAAA
1321188 T
1 T
1321189 GAATGTCTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
53 16 0.33
54 32 0.67
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (53 bp):
TTCGCATTGCGATAGTCATTTCGCATTGCGATTCTCCCGTTGCGATAGTCAAA
Found at i:1330224 original size:13 final size:13
Alignment explanation
Indices: 1330203--1330237 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1330193 CCCACTTACT
1330203 TTTCACTTTTCAC
1 TTTCACTTTTCAC
* *
1330216 TTTCTCTTTTTAC
1 TTTCACTTTTCAC
1330229 TTTCACTTT
1 TTTCACTTT
1330238 CTAGTTTCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTCACTTTTCAC
Found at i:1332883 original size:20 final size:20
Alignment explanation
Indices: 1332858--1332900 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1332848 TCTAAGAGCC
*
1332858 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
1332878 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
1332898 CAT
1 CAT
1332901 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:1335934 original size:24 final size:24
Alignment explanation
Indices: 1335900--1335949 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1335890 CTGAAACATC
1335900 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1335924 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1335948 AT
1 AT
1335950 GAAATTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1336705 original size:21 final size:21
Alignment explanation
Indices: 1336681--1336770 Score: 105
Period size: 21 Copynumber: 4.3 Consensus size: 21
1336671 GAAAATCGTA
*
1336681 TTGCGATTCTGTATTATCTCG
1 TTGCGATTCTGTATTATCGCG
*
1336702 TTGCGATAGTCAG-A--ATCGCG
1 TTGCGAT--TCTGTATTATCGCG
*
1336722 TTGCGATTTTGTATTATCGCG
1 TTGCGATTCTGTATTATCGCG
*
1336743 TTGCGATTTTGTATTATCGCG
1 TTGCGATTCTGTATTATCGCG
1336764 TTGCGAT
1 TTGCGAT
1336771 AGTCAATATC
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.03
19 1 0.02
20 12 0.20
21 41 0.68
22 1 0.02
23 3 0.05
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (21 bp):
TTGCGATTCTGTATTATCGCG
Found at i:1336809 original size:62 final size:62
Alignment explanation
Indices: 1336675--1336813 Score: 174
Period size: 62 Copynumber: 2.2 Consensus size: 62
1336665 AACTTTGAAA
* * * * ** *
1336675 ATCGTATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTTCAAAT
*
1336737 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCA-ATATCGCATTGCGATTTTCCAAAT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA-ATCGCATTGCGATTTT-CAAAT
1336800 -TCGCATTGCGATTT
1 ATCGCATTGCGATTT
1336814 ACTTATTCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
61 1 0.02
62 63 0.95
63 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (62 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCATTGCGATTTTCAAAT
Found at i:1336823 original size:20 final size:21
Alignment explanation
Indices: 1336779--1336830 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1336769 ATAGTCAATA
*
1336779 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1336800 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1336820 TCGCATTGCGA
1 TCGCATTGCGA
1336831 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1336872 original size:21 final size:22
Alignment explanation
Indices: 1336820--1336872 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1336810 ATTTACTTAT
1336820 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1336841 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1336862 TCGCATTGCGA
1 TCGCATTGCGA
1336873 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1348850 original size:21 final size:21
Alignment explanation
Indices: 1348781--1348840 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
1348771 AGGACGAGAG
*
1348781 CATTCATCAAGACGAGAATGT
1 CATTCATCAAGACGAGAATGC
1348802 CATTCATCAAGACGAGAATGC
1 CATTCATCAAGACGAGAATGC
1348823 CATTCATCAAGACGAGAA
1 CATTCATCAAGACGAGAA
1348841 GACCCTTCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (21 bp):
CATTCATCAAGACGAGAATGC
Found at i:1352932 original size:125 final size:125
Alignment explanation
Indices: 1352741--1352965 Score: 353
Period size: 125 Copynumber: 1.8 Consensus size: 125
1352731 CCCATAATTT
* *
1352741 TGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAATGAGCCTTACAATTTGAGGTGATGGGGC
1 TGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAATGAGCCTTACAATTTGAGATGATGAGGC
* * *
1352806 ATTTTGAAGGCCCGTACCAGTATGAGATAATGTTGGGGCGCGACTGAACCCACATCATGA
66 ATTTTGAAGGCCCGTACCAGAATAAAATAATGTTGGGGCGCGACTGAACCCACATCATGA
* ** *
1352866 TGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAATGAGCCTTATAATTTGAGAT-ATTGAGG
1 TGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAATGAGCCTTACAATTTGAGATGA-TGAGG
1352930 CATTTTGAAGGCCCGTACCAGAATAAAATAATGTTG
65 CATTTTGAAGGCCCGTACCAGAATAAAATAATGTTG
1352966 CGACATTAGT
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 1 0.01
125 89 0.99
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.24
Consensus pattern (125 bp):
TGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAATGAGCCTTACAATTTGAGATGATGAGGC
ATTTTGAAGGCCCGTACCAGAATAAAATAATGTTGGGGCGCGACTGAACCCACATCATGA
Found at i:1354305 original size:36 final size:36
Alignment explanation
Indices: 1354140--1354337 Score: 229
Period size: 36 Copynumber: 5.5 Consensus size: 36
1354130 GATTGGAGAA
*
1354140 AAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* *
1354176 AAACCATCTGAAGCCTTCACCGGAGAATAGTGGAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * *
1354212 AATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * * *
1354248 AAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * *
1354284 AAAGCATCTTAAGTCTTCACC--AAAAGTAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAA-TAGTGAAGC
* *
1354319 AGATCCATTTTAAGCCTTC
1 A-AACCATCTTAAGCCTTC
1354338 TCAGAAGAGT
Statistics
Matches: 139, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
34 2 0.01
35 10 0.07
36 127 0.91
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (36 bp):
AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
Found at i:1354334 original size:108 final size:107
Alignment explanation
Indices: 1354140--1354337 Score: 254
Period size: 108 Copynumber: 1.8 Consensus size: 107
1354130 GATTGGAGAA
* * *
1354140 AAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATA
1 AAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACC-GAAAATA
*
1354205 GTGGAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
65 GTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
* * * * *
1354248 AAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAAGCATCTTAAGTCTTCACC-AAAAGTA
1 AAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAA-TA
* * *
1354312 GTGAAGCAGATCCATTTTAAGCCTTC
65 GTGAAGCA-ATCAATCTGAAGCCTTC
1354338 TCAGAAGAGT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
106 3 0.04
107 9 0.12
108 64 0.84
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (107 bp):
AAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAATAG
TGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
Found at i:1354841 original size:53 final size:53
Alignment explanation
Indices: 1354718--1355546 Score: 991
Period size: 51 Copynumber: 15.8 Consensus size: 53
1354708 GAAGATATGC
* * *
1354718 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGGT-TC-
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* *
1354769 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGAGGTCT
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* *
1354822 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGGT-TC-
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* * *
1354873 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGGACCCGTTTGAAGAGAGGTCT
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
*
1354926 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* *
1354979 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGT-T
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* *
1355029 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGAGGTCT
1 -GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* ** * *
1355083 AAGTTCCATACTCCCTGGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTTT
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* *
1355134 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAGGAGCAAACCCGTTT-AA-AGATGT-T
1 GAGTTCCATACTCCCTAAAG-AA-A--GA---AGGAGCGAACCCGTTTGAAGAGATGTCT
*
1355191 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
1 -GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* *
1355245 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGT-T
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* * *
1355295 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTG-A-AGATGT-T
1 -GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* *
1355346 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGT-T
1 -GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* * *
1355397 CGAGTTCTATACTCCTTAAAGAAGGAAGGAGCGAACCCGTTTGAAGAGATGT-T
1 -GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* * ** * *
1355450 CGAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATATCT
1 -GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-AGATGTCT
* * * *
1355505 GAGTTCCATACTCCCTAGAGAAATAGGGAGCGAACCCATTTG
1 GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG
1355547 TTGAAGATTG
Statistics
Matches: 696, Mismatches: 54, Indels: 53
0.87 0.07 0.07
Matches are distributed among these distances:
50 2 0.00
51 323 0.46
52 12 0.02
53 268 0.39
54 46 0.07
55 3 0.00
56 1 0.00
57 3 0.00
58 35 0.05
59 2 0.00
60 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (53 bp):
GAGTTCCATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
Found at i:1354844 original size:104 final size:104
Alignment explanation
Indices: 1354718--1355546 Score: 1023
Period size: 104 Copynumber: 7.9 Consensus size: 104
1354708 GAAGATATGC
*
1354718 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGGTTCGAGTTCCATACTCC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGGTTCGAGTTCCATACTCC
* *
1354783 TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGAGGTCT
66 CTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* *
1354822 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGGTTCGAGTTCCATACTCC
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGGTTCGAGTTCCATACTCC
* * *
1354887 TTAAAGAAAGAAGGAGCGGACCCGTTTGAAGAGAGGTCT
66 CTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* * *
1354926 GAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTGAGTTCCATACT
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGGT-TC-GAGTTCCATACT
* *
1354991 CCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGT-T
64 CCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* *
1355029 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGAGGTCTAAGTTCCATAC
1 -GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAG-GTTC-GAGTTCCATAC
** * *
1355094 TCCCTGGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTTT
63 TCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* * *
1355134 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAGGAGCAAACCCGTTTAAAGATGTTCGAGTTCC
1 GAGTTCTATACTCCCTAAAG-AA-A--GA---AGGAGCGAACCCGTTTGAAGAGGTTCGAGTTCC
*
1355199 ATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
59 ATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* * * *
1355245 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--TGAAGAGATGTTCGAGTTCTATACT
1 GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAG--GTTCGAGTTCCATACT
* *
1355308 CCCTAAAGAAAGAGGGAGCGAACCCATTTG-A-AGATGT-T
64 CCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* * *
1355346 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTC
1 -GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGGTTCGAGTTCCATACTC
* *
1355411 CTTAAAGAAGGAAGGAGCGAACCCGTTTGAAGAGATGT-T
65 CCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
* ** **
1355450 CGAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATATCTGAGTTCCATA
1 -GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAG-AGGT-TC-GAGTTCCATA
* * * *
1355515 CTCCCTAGAGAAATAGGGAGCGAACCCATTTG
62 CTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG
1355547 TTGAAGATTG
Statistics
Matches: 646, Mismatches: 55, Indels: 45
0.87 0.07 0.06
Matches are distributed among these distances:
101 1 0.00
102 87 0.13
103 3 0.00
104 383 0.59
105 8 0.01
106 37 0.06
107 37 0.06
108 2 0.00
109 34 0.05
110 5 0.01
111 49 0.08
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (104 bp):
GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGGTTCGAGTTCCATACTCC
CTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT
Found at i:1355685 original size:108 final size:108
Alignment explanation
Indices: 1355546--1355811 Score: 371
Period size: 108 Copynumber: 2.5 Consensus size: 108
1355536 GAACCCATTT
* *
1355546 GTTGAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTTGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATT
1355609 GT-AGGTCTTATACTCTCT-GAGGATATAAGGG-GGAGACACGATA
66 GTGA-GTCTTATACTCTCTGGA-GATAT-AGGGAGGAGACACGATA
* * *
1355652 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATT
* * *
1355717 GTGAGTCTTATACTCTCTGGAGATATAGGGAGTAGACCCGATT
66 GTGAGTCTTATACTCTCTGGAGATATAGGGAGGAGACACGATA
* * *
1355760 GTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAAGGAGCAGACACG
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACG
1355812 TTTTCAAAAG
Statistics
Matches: 142, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
106 11 0.08
107 5 0.04
108 123 0.87
109 3 0.02
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (108 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGATGAAGATT
GTGAGTCTTATACTCTCTGGAGATATAGGGAGGAGACACGATA
Found at i:1355713 original size:55 final size:54
Alignment explanation
Indices: 1355523--1355858 Score: 339
Period size: 53 Copynumber: 6.2 Consensus size: 54
1355513 TACTCCCTAG
* *
1355523 AGAAATAGGGAGC-GA-ACCCATTTGTTGAAGATTGT-GGGTCTTATACTCTCTGA
1 AGAAATAGGGAGCAGACA-CGA-TTGTTGAAGATTGTCGAGTCTTATACTCTCTGA
* *
1355576 AGAAATAGGGAGCAGACACGATCGTTGAAGATTGTAG-GTCTTATACTCTCTGA
1 AGAAATAGGGAGCAGACACGATTGTTGAAGATTGTCGAGTCTTATACTCTCTGA
* * * *
1355629 GGATATAAGGG-GGAGACACGATAGTTGAAGATTGTTCGAGTCTTATACTCTCTGA
1 AGAAAT-AGGGAGCAGACACGATTGTTGAAGATTG-TCGAGTCTTATACTCTCTGA
* * * *
1355684 AGAAATAGGGGGCAGACGCGATTGATGAAGATTGT-GAGTCTTATACTCTCTGG
1 AGAAATAGGGAGCAGACACGATTGTTGAAGATTGTCGAGTCTTATACTCTCTGA
* * * *
1355737 AGATATAGGGAGTAGACCCGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGA
1 AGAAATAGGGAGCAGACACGATTGTTGAAGATTG-TCGAGTCTTATACTCTCTGA
* * * * *
1355792 AGGAATAAGGAGCAGACACG-TT-TTCAAAAGATTTTCGAGT-TCTATACTCCCTGA
1 AGAAATAGGGAGCAGACACGATTGTT--GAAGATTGTCGAGTCT-TATACTCTCTGA
*
1355846 AGAAAGAGGGAGC
1 AGAAATAGGGAGC
1355859 GAACCCGTAG
Statistics
Matches: 238, Mismatches: 33, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
53 116 0.49
54 45 0.19
55 77 0.32
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (54 bp):
AGAAATAGGGAGCAGACACGATTGTTGAAGATTGTCGAGTCTTATACTCTCTGA
Found at i:1360927 original size:27 final size:27
Alignment explanation
Indices: 1360827--1360956 Score: 102
Period size: 27 Copynumber: 4.7 Consensus size: 27
1360817 TTCTTTATAA
* *
1360827 TTTTATAAATTACAATAATACTATAACT
1 TTTTATAAATTATAATAA-AATATAACT
* * * *
1360855 TTTTAAAAATTATAGTAAAGAAGAAAACT
1 TTTTATAAATTATAAT-AA-AATATAACT
* * * *
1360884 TTTTAGAAAGTACAATAAAATATATCT
1 TTTTATAAATTATAATAAAATATAACT
*
1360911 TTTTATAAATTATAAT-AAATGAT-ATT
1 TTTTATAAATTATAATAAAAT-ATAACT
1360937 CTTTTATAAATTATAATAAA
1 -TTTTATAAATTATAATAAA
1360957 GAATAATTAT
Statistics
Matches: 79, Mismatches: 19, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
26 5 0.06
27 37 0.47
28 17 0.22
29 20 0.25
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (27 bp):
TTTTATAAATTATAATAAAATATAACT
Found at i:1360984 original size:30 final size:27
Alignment explanation
Indices: 1360883--1360987 Score: 97
Period size: 27 Copynumber: 3.8 Consensus size: 27
1360873 AGAAGAAAAC
* * * *
1360883 TTTTTAGAAAGTACAATAAAAT-ATATC
1 TTTTTATAAATTATAAT-AAATGATATT
1360910 TTTTTATAAATTATAATAAATGATATT
1 TTTTTATAAATTATAATAAATGATATT
*
1360937 CTTTTATAAATTATAATAAA-GAATAATT
1 TTTTTATAAATTATAATAAATG-AT-ATT
*
1360965 ATTTTTATAAAAATATAATAAAT
1 -TTTTTAT-AAATTATAATAAAT
1360988 ACCAAAATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
26 5 0.08
27 39 0.60
28 3 0.05
29 6 0.09
30 12 0.18
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (27 bp):
TTTTTATAAATTATAATAAATGATATT
Found at i:1367017 original size:18 final size:19
Alignment explanation
Indices: 1366994--1367030 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1366984 TCAGTAATCC
1366994 TATTCT-CTGATAATCTTT
1 TATTCTACTGATAATCTTT
1367012 TATTCTCACTGATAATCTT
1 TATTCT-ACTGATAATCTT
1367031 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.51
Consensus pattern (19 bp):
TATTCTACTGATAATCTTT
Found at i:1376066 original size:2 final size:2
Alignment explanation
Indices: 1376059--1376084 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1376049 TATAATTTTG
1376059 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
1376085 TTTCAACATT
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:1379368 original size:24 final size:24
Alignment explanation
Indices: 1379341--1379420 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
1379331 TTCGATTTGA
1379341 ATTTTGTTATGATACCTGACATGG
1 ATTTTGTTATGATACCTGACATGG
* * *
1379365 ATTTTGTTCTAATACCTGACCTGG
1 ATTTTGTTATGATACCTGACATGG
* * *
1379389 ATTTTGATATGATATCTGACATGA
1 ATTTTGTTATGATACCTGACATGG
*
1379413 ATTATGTT
1 ATTTTGTT
1379421 TTTCATTTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.44
Consensus pattern (24 bp):
ATTTTGTTATGATACCTGACATGG
Found at i:1381528 original size:13 final size:13
Alignment explanation
Indices: 1381498--1381554 Score: 84
Period size: 13 Copynumber: 4.6 Consensus size: 13
1381488 ACCCAGTCCG
1381498 ACCCGACCCGA-T
1 ACCCGACCCGACT
*
1381510 --CCGACCCAACT
1 ACCCGACCCGACT
1381521 ACCCGACCCGACT
1 ACCCGACCCGACT
1381534 ACCCGACCCGACT
1 ACCCGACCCGACT
1381547 ACCCGACC
1 ACCCGACC
1381555 TGATTGCCCG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
10 8 0.20
11 1 0.03
13 31 0.77
ACGTcount: A:0.25, C:0.54, G:0.14, T:0.07
Consensus pattern (13 bp):
ACCCGACCCGACT
Found at i:1383721 original size:24 final size:24
Alignment explanation
Indices: 1383694--1383761 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1383684 TTCGATTTGA
1383694 ATTTTGTTATGATACCTGACATGG
1 ATTTTGTTATGATACCTGACATGG
* * *
1383718 ATTTTGTTCTAATACCTGACCTGG
1 ATTTTGTTATGATACCTGACATGG
* * *
1383742 ATTCTGATATGATATCTGAC
1 ATTTTGTTATGATACCTGAC
1383762 CTGAATTATG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTTTGTTATGATACCTGACATGG
Found at i:1385866 original size:15 final size:15
Alignment explanation
Indices: 1385846--1385877 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1385836 GAACAGTTTT
1385846 GACCCGATCCGACCC
1 GACCCGATCCGACCC
1385861 GACCCGATCCGACCC
1 GACCCGATCCGACCC
1385876 GA
1 GA
1385878 TTGCCCGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.50, G:0.22, T:0.06
Consensus pattern (15 bp):
GACCCGATCCGACCC
Found at i:1385891 original size:18 final size:17
Alignment explanation
Indices: 1385870--1385903 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1385860 CGACCCGATC
*
1385870 CGACCCGATTGCCCGACT
1 CGACCCG-TTGACCGACT
1385888 CGACCCGTTGACCGAC
1 CGACCCGTTGACCGAC
1385904 CCGTTGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.15
Consensus pattern (17 bp):
CGACCCGTTGACCGACT
Found at i:1388041 original size:24 final size:24
Alignment explanation
Indices: 1388014--1388077 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
1388004 ATTTGAATTT
1388014 TGTTATGATACCTGACATGGATTC
1 TGTTATGATACCTGACATGGATTC
* *
1388038 TGTTATAATACCTGACCTGGATTC
1 TGTTATGATACCTGACATGGATTC
* *
1388062 TGATATGATATCTGAC
1 TGTTATGATACCTGAC
1388078 CTAAATTGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (24 bp):
TGTTATGATACCTGACATGGATTC
Found at i:1392341 original size:24 final size:24
Alignment explanation
Indices: 1392314--1392377 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
1392304 ATTTGAATTT
*
1392314 TGTTATGATGCCTGACATGGATTC
1 TGTTATGATACCTGACATGGATTC
* * *
1392338 TGTTCTAATACCTGACCTGGATTC
1 TGTTATGATACCTGACATGGATTC
* *
1392362 TGATATGATATCTGAC
1 TGTTATGATACCTGAC
1392378 CTGAATTATG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (24 bp):
TGTTATGATACCTGACATGGATTC
Found at i:1398899 original size:24 final size:24
Alignment explanation
Indices: 1398872--1398935 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
1398862 ATTTGAATTT
1398872 TGTTATGATACCTGACATGGATTC
1 TGTTATGATACCTGACATGGATTC
* *
1398896 TGTTTTAATACCTGACATGGATTC
1 TGTTATGATACCTGACATGGATTC
* *
1398920 TGATATGATATCTGAC
1 TGTTATGATACCTGAC
1398936 CTGAATTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (24 bp):
TGTTATGATACCTGACATGGATTC
Found at i:1398952 original size:24 final size:24
Alignment explanation
Indices: 1398865--1398952 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 24
1398855 ATTTTCGATT
*
1398865 TGAATTTTGTTATGATACCTGACA
1 TGAATTCTGTTATGATACCTGACA
* * *
1398889 TGGATTCTGTTTTAATACCTGACA
1 TGAATTCTGTTATGATACCTGACA
* * * *
1398913 TGGATTCTGATATGATATCTGACC
1 TGAATTCTGTTATGATACCTGACA
* *
1398937 TGAATTATGTTTTGAT
1 TGAATTCTGTTATGAT
1398953 TTTTTATATA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.43
Consensus pattern (24 bp):
TGAATTCTGTTATGATACCTGACA
Found at i:1414145 original size:13 final size:13
Alignment explanation
Indices: 1414124--1414153 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1414114 CCAGACACCG
*
1414124 AAGCGCTAAGCGA
1 AAGCACTAAGCGA
1414137 AAGCACTAAGCGA
1 AAGCACTAAGCGA
1414150 AAGC
1 AAGC
1414154 GCTCGCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.23, G:0.27, T:0.07
Consensus pattern (13 bp):
AAGCACTAAGCGA
Found at i:1428347 original size:29 final size:28
Alignment explanation
Indices: 1428314--1428368 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
1428304 TCCCAACACA
*
1428314 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCC-GGCGACCTTG
1428343 TAGGTCGCCATGCACTCCGGCGACCT
1 TAGGTCGCCATGCACTCCGGCGACCT
1428369 ACCCTCGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.13, C:0.38, G:0.29, T:0.20
Consensus pattern (28 bp):
TAGGTCGCCATGCACTCCGGCGACCTTG
Found at i:1428528 original size:18 final size:18
Alignment explanation
Indices: 1428505--1428540 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1428495 TTGTAGCTCG
1428505 CCGGAAGACATGGCGACC
1 CCGGAAGACATGGCGACC
*
1428523 CCGGAAGGCATGGCGACC
1 CCGGAAGACATGGCGACC
1428541 TACGACCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.33, G:0.36, T:0.06
Consensus pattern (18 bp):
CCGGAAGACATGGCGACC
Found at i:1441238 original size:1 final size:1
Alignment explanation
Indices: 1441232--1441256 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1441222 TTCATTTCCT
1441232 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1441257 GATAATGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1452915 original size:37 final size:37
Alignment explanation
Indices: 1452865--1452941 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
1452855 TGCATCTATA
1452865 AGTTTATACTTGGCTACACCTAATCCCTACATGCTTT
1 AGTTTATACTTGGCTACACCTAATCCCTACATGCTTT
* *
1452902 AGTTTATACTTGGCTACTCCTAATTCCTACATGCTTT
1 AGTTTATACTTGGCTACACCTAATCCCTACATGCTTT
1452939 AGT
1 AGT
1452942 ATCCAATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (37 bp):
AGTTTATACTTGGCTACACCTAATCCCTACATGCTTT
Found at i:1468138 original size:69 final size:67
Alignment explanation
Indices: 1468015--1468167 Score: 209
Period size: 69 Copynumber: 2.3 Consensus size: 67
1468005 ACCCATTCAA
* * *
1468015 GGGGGAACCGATA-CCCCCTCAACGAAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCC
1 GGGGGAACCGATACCCCCCTCAACGAAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCC
1468079 AGG
66 A-G
* * * *
1468082 GGGGGAACCGATACCCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGAGGAATCGATACCCC
1 GGGGGAACCGATACCCCCCTCAACG-AAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCC
1468147 CAG
65 CAG
*
1468150 GGGGGAACCGATTCCCCC
1 GGGGGAACCGATACCCCC
1468168 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
67 13 0.17
68 28 0.37
69 35 0.46
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (67 bp):
GGGGGAACCGATACCCCCCTCAACGAAATGAAATTCCAGAATGCTAGAGAGGAATCGATACCCCC
AG
Found at i:1468504 original size:29 final size:29
Alignment explanation
Indices: 1468470--1468541 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
1468460 CATATTATGA
**
1468470 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
1468499 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
1468528 TACATGACATGAAT
1 TACATGACATGAAT
1468542 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:1468598 original size:30 final size:31
Alignment explanation
Indices: 1468556--1468615 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
1468546 AGAAAAAGTT
*
1468556 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
1468587 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
1468616 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:1468862 original size:22 final size:23
Alignment explanation
Indices: 1468834--1468877 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1468824 TTATGGACAT
1468834 AATTCTAC-GGGCACTTCGGTGA
1 AATTCTACGGGGCACTTCGGTGA
1468856 AATTCTACGGGGCACTTCGGTG
1 AATTCTACGGGGCACTTCGGTG
1468878 CATTTATACG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (23 bp):
AATTCTACGGGGCACTTCGGTGA
Found at i:1468887 original size:23 final size:23
Alignment explanation
Indices: 1468834--1468887 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
1468824 TTATGGACAT
*
1468834 AATTCTAC-GGGCACTTCGGTGA
1 AATTATACGGGGCACTTCGGTGA
* *
1468856 AATTCTACGGGGCACTTCGGTGC
1 AATTATACGGGGCACTTCGGTGA
*
1468879 ATTTATACG
1 AATTATACG
1468888 AGCTGTGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 8 0.29
23 20 0.71
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
AATTATACGGGGCACTTCGGTGA
Found at i:1476549 original size:29 final size:29
Alignment explanation
Indices: 1476483--1476549 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
1476473 TTTGAGTCCG
*
1476483 TCGACTATTAAAAGTTACAAAATGATCAC
1 TCGACTATTAAAAGTTACAAAATGATAAC
* *
1476512 TTGATTATTAAAAGTTACAAAATGATAAC
1 TCGACTATTAAAAGTTACAAAATGATAAC
1476541 TCGACTATT
1 TCGACTATT
1476550 GATATGTTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (29 bp):
TCGACTATTAAAAGTTACAAAATGATAAC
Found at i:1485292 original size:27 final size:27
Alignment explanation
Indices: 1485255--1485309 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1485245 ATAATCAGTA
1485255 TATTTAATCATTTATTTATTTCTACAG
1 TATTTAATCATTTATTTATTTCTACAG
*
1485282 TATTTAATCATTTATTTATTTTTACAG
1 TATTTAATCATTTATTTATTTCTACAG
1485309 T
1 T
1485310 TTGAGTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.04, T:0.58
Consensus pattern (27 bp):
TATTTAATCATTTATTTATTTCTACAG
Found at i:1486385 original size:63 final size:68
Alignment explanation
Indices: 1486260--1486388 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 68
1486250 GAAACCATTA
* *
1486260 AAATTAAGTTTTGACCATCTTAAAATTTTCTGATTTAATTAATTTTTAAACATTATCGGTTTTAA
1 AAATTAAGTTTTGACCATCTTAAAATTTTCTGATTTAATTAATTTTTAAACATGATCAGTTTTAA
1486325 ATG
66 ATG
* * * *
1486328 AAATTAAGTTTTG-CC-TC-T-AACTTTTTTG-TTTAATTATTTTTTAGGACATGA-CAGTTTTA
1 AAATTAAGTTTTGACCATCTTAAAATTTTCTGATTTAATTAATTTTTA-AACATGATCAGTTTTA
1486387 AA
65 AA
1486389 ATTAATGAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
63 23 0.43
64 13 0.24
65 1 0.02
66 2 0.04
67 2 0.04
68 13 0.24
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (68 bp):
AAATTAAGTTTTGACCATCTTAAAATTTTCTGATTTAATTAATTTTTAAACATGATCAGTTTTAA
ATG
Found at i:1486976 original size:29 final size:32
Alignment explanation
Indices: 1486920--1486978 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1486910 TATCACCTCA
1486920 TTTTTCAACACCAACACCCATCATTCTATTTT
1 TTTTTCAACACCAACACCCATCATTCTATTTT
1486952 TTTTTCAACACC-A-ACCCATCA-TCTATT
1 TTTTTCAACACCAACACCCATCATTCTATT
1486979 GTTTCATGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 6 0.22
30 8 0.30
31 1 0.04
32 12 0.44
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (32 bp):
TTTTTCAACACCAACACCCATCATTCTATTTT
Found at i:1490565 original size:30 final size:31
Alignment explanation
Indices: 1490517--1490576 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
1490507 CCTTGTTGCA
1490517 TTTGCATATCGCATTTTGCAT-TCCATTTTG
1 TTTGCATATCGCATTTTGCATGTCCATTTTG
* *
1490547 TTTGCATATTTGCA-TTTGCATGTGCATTTT
1 TTTGCATA-TCGCATTTTGCATGTCCATTTT
1490577 TGAATCTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.52
Consensus pattern (31 bp):
TTTGCATATCGCATTTTGCATGTCCATTTTG
Found at i:1490611 original size:28 final size:29
Alignment explanation
Indices: 1490555--1490619 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
1490545 TGTTTGCATA
* * *
1490555 TTTGCATTTGCATGTGCATTTTTGAATC-
1 TTTGCATTTGCATGTACATCTGTGAATCT
*
1490583 TTTGCATTTGCATGTACATCTGTGTATCT
1 TTTGCATTTGCATGTACATCTGTGAATCT
1490612 TTTGCATT
1 TTTGCATT
1490620 AGTATATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 24 0.75
29 8 0.25
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (29 bp):
TTTGCATTTGCATGTACATCTGTGAATCT
Found at i:1492983 original size:77 final size:77
Alignment explanation
Indices: 1492888--1493447 Score: 653
Period size: 77 Copynumber: 7.3 Consensus size: 77
1492878 TTGTTTTTAA
* * * *
1492888 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATATAAGATTTTATTTTGCTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTTC-CTCGAAACAGAAGATTTTATCTCGCTTGAGATAG
*
1492953 TTTCACTCGAAAC
65 TTTCCCTCGAAAC
1492966 AGAAGA-TTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGTTT-CCTCGAAACAGAAGATTTTATCTCGCTTGAGATAG
* *
1493030 TTTCACTCGAAAT
65 TTTCCCTCGAAAC
* *
1493043 AGAA-ATTTTTATCTCGCTTGAGATAGATTCACTCGAAACAAAAGATTTTATCTCGCTTGAGATA
1 AGAAGA-TTTTATCTCGCTTGAGATAGTTTC-CTCGAAACAGAAGATTTTATCTCGCTTGAGATA
1493107 G-TTCCCTCGAAAC
64 GTTTCCCTCGAAAC
* * * *
1493120 AGAAGATTTTGTCGAAACACTCGC-TGAGATAGTTTCCCTCGAAACATAAGATTTTGTCTCACTT
1 AGAAGA-TTT-T----A-TCTCGCTTGAGATAGTTT-CCTCGAAACAGAAGATTTTATCTCGCTT
1493184 GAGATAGTTT-CCTCGAAAC
58 GAGATAGTTTCCCTCGAAAC
* * *
1493203 ATAAGATTTTATCTCACTTTAGATAGTTTCCTCGAAACAGAAGATTTTATCTCGCTTGAG-TAGT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGT
1493267 TTCCCTCGAAAC
66 TTCCCTCGAAAC
* *
1493279 A-AAGATTTTGTCTCGCTTGAGATAGTTTCCTCGAAACAGAAGATTTTGTCTCGCTTGAGATAGT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGT
*
1493343 TTCCCTAGAAAC
66 TTCCCTCGAAAC
* * ** * * *
1493355 AGAAGATTTTGTCTCGCTTGAG--A---CCCTATAAACAAAAGATTTTGTCTCGCTTGAGACAGT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGT
*
1493415 TTCCCTTGAAAC
66 TTCCCTCGAAAC
* *
1493427 A-AA-ATTTTGTCTCCCTTGAGA
1 AGAAGATTTTATCTCGCTTGAGA
1493448 CATTTTCTCT
Statistics
Matches: 431, Mismatches: 33, Indels: 43
0.85 0.07 0.08
Matches are distributed among these distances:
70 16 0.04
71 2 0.00
72 44 0.10
75 61 0.14
76 59 0.14
77 114 0.26
78 66 0.15
79 1 0.00
81 1 0.00
82 3 0.01
83 56 0.13
84 8 0.02
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (77 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGT
TTCCCTCGAAAC
Found at i:1492985 original size:38 final size:39
Alignment explanation
Indices: 1492888--1493447 Score: 659
Period size: 39 Copynumber: 14.6 Consensus size: 39
1492878 TTGTTTTTAA
* *
1492888 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
1492927 ATAAGATTTTATTTTGCTTGAGATAGTTTCACTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1492966 AGAAGA-TTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
1493004 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAT
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
1493043 AGAA-ATTTTTATCTCGCTTGAGATAGATTCACTCGAAAC
1 AGAAGA-TTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
1493082 AAAAGATTTTATCTCGCTTGAGATAG-TTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
1493120 AGAAGATTTTGTCGAAACACTCGC-TGAGATAGTTTCCCTCGAAAC
1 AGAAGA-TTT-T----A-TCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
1493165 ATAAGATTTTGTCTCACTTGAGATAGTTT-CCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
1493203 ATAAGATTTTATCTCACTTTAGATAGTTT-CCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1493241 AGAAGATTTTATCTCGCTTGAG-TAGTTTCCCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
1493279 A-AAGATTTTGTCTCGCTTGAGATAGTTT-CCTCGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
1493316 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTAGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* **
1493355 AGAAGATTTTGTCTCGCTTGAG--A----CCCTATAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * *
1493388 AAAAGATTTTGTCTCGCTTGAGACAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
1493427 A-AA-ATTTTGTCTCCCTTGAGA
1 AGAAGATTTTATCTCGCTTGAGA
1493448 CATTTTCTCT
Statistics
Matches: 467, Mismatches: 32, Indels: 46
0.86 0.06 0.08
Matches are distributed among these distances:
33 30 0.06
35 1 0.00
37 53 0.11
38 165 0.35
39 181 0.39
40 2 0.00
43 1 0.00
44 12 0.03
45 22 0.05
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:1493388 original size:33 final size:33
Alignment explanation
Indices: 1493236--1493411 Score: 147
Period size: 33 Copynumber: 4.9 Consensus size: 33
1493226 TAGTTTCCTC
* *
1493236 GAAACAGAAGATTTTATCTCGCTTGAGTAGTTTCCCTC
1 GAAACAGAAGATTTTGTCTCGCTTGAG-A----CCCTA
* *
1493274 GAAACA-AAGATTTTGTCTCGCTTGAGATAGTTTCCTC
1 GAAACAGAAGATTTTGTCTCGCTTGAG--A---CCCTA
1493311 GAAACAGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTA
1 GAAACAGAAGATTTTGTCTCGCTTGAG--A----CCCTA
1493350 GAAACAGAAGATTTTGTCTCGCTTGAGACCCTA
1 GAAACAGAAGATTTTGTCTCGCTTGAGACCCTA
* *
1493383 TAAACAAAAGATTTTGTCTCGCTTGAGAC
1 GAAACAGAAGATTTTGTCTCGCTTGAGAC
1493412 AGTTTCCCTT
Statistics
Matches: 127, Mismatches: 8, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
33 32 0.25
37 32 0.25
38 31 0.24
39 32 0.25
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (33 bp):
GAAACAGAAGATTTTGTCTCGCTTGAGACCCTA
Found at i:1493523 original size:15 final size:15
Alignment explanation
Indices: 1493503--1493594 Score: 60
Period size: 15 Copynumber: 5.4 Consensus size: 15
1493493 AAGTTTTGTC
1493503 TCCCTTGAGACAGTT
1 TCCCTTGAGACAGTT
1493518 TCCCTTGA-ACAAGTTTTGT
1 TCCCTTGAGAC-AG---T-T
1493537 CTCCCTTGAGACAGTT
1 -TCCCTTGAGACAGTT
*
1493553 TCCCTTGAAACAAGTTTT
1 TCCCTTGAGAC-AG--TT
1493571 GTCTCTCTTGAGACAGTT
1 -TC-C-CTTGAGACAGTT
1493589 TCCCTT
1 TCCCTT
1493595 AAAATGAATT
Statistics
Matches: 62, Mismatches: 2, Indels: 26
0.69 0.02 0.29
Matches are distributed among these distances:
14 2 0.03
15 23 0.37
16 4 0.06
17 3 0.05
18 5 0.08
19 3 0.05
20 13 0.21
21 9 0.15
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (15 bp):
TCCCTTGAGACAGTT
Found at i:1493543 original size:20 final size:20
Alignment explanation
Indices: 1493518--1493581 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1493508 TGAGACAGTT
1493518 TCCCTTGAACAAGTTTTGTC
1 TCCCTTGAACAAGTTTTGTC
1493538 TCCCTTGAGAC-AG---T-T-
1 TCCCTTGA-ACAAGTTTTGTC
1493553 TCCCTTGAAACAAGTTTTGTC
1 TCCCTTG-AACAAGTTTTGTC
*
1493574 TCTCTTGA
1 TCCCTTGA
1493582 GACAGTTTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 16
0.67 0.02 0.31
Matches are distributed among these distances:
15 9 0.26
16 4 0.11
17 1 0.03
19 1 0.03
20 12 0.34
21 8 0.23
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (20 bp):
TCCCTTGAACAAGTTTTGTC
Found at i:1493572 original size:36 final size:36
Alignment explanation
Indices: 1493480--1493636 Score: 219
Period size: 36 Copynumber: 4.3 Consensus size: 36
1493470 TTTGAAAACG
1493480 TCCCTTTGAAACAAAGTTTTGTCTCCCTTGAGACAGTT
1 TCCC-TTGAAAC-AAGTTTTGTCTCCCTTGAGACAGTT
1493518 TCCCTTG-AACAAGTTTTGTCTCCCTTGAGACAGTT
1 TCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTT
*
1493553 TCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAGTT
1 TCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTT
* * * *
1493589 TCCCTTAAAATGAA-TTTTTTCTCTCTTGAGACAGTT
1 TCCCTTGAAA-CAAGTTTTGTCTCCCTTGAGACAGTT
*
1493625 TCTCTTGAAACA
1 TCCCTTGAAACA
1493637 TCAATCTTTG
Statistics
Matches: 110, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
35 33 0.30
36 68 0.62
37 5 0.05
38 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (36 bp):
TCCCTTGAAACAAGTTTTGTCTCCCTTGAGACAGTT
Found at i:1494084 original size:44 final size:44
Alignment explanation
Indices: 1494018--1494222 Score: 153
Period size: 44 Copynumber: 4.6 Consensus size: 44
1494008 AACTGTTTGG
* * *
1494018 TCGATTCTATCACAGAAGGAGGTAGACCAGCACCAACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCACCAACATCTCGC
* * ***** *
1494062 TCGATTCCATCACAGAATGAGGTGGATC-GACATTTTTATTTTCGC
1 TCGATTCCATCACAGAAGGAGGTAGATCAG-CACCAACA-TCTCGC
* * * * ** * * *
1494107 TCAAATCCATCACAGAAGGAGTTGGATCAGCGGCAACTTTTTGC
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCACCAACATCTCGC
* * *
1494151 TCGATTCTATCACAGAATGAGGTAGATCAGCACCAACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTAGATCAGCACCAACATCTCGC
*
1494195 TCGATTCCATCACTA-AAGGAGGTGGATC
1 TCGATTCCATCAC-AGAAGGAGGTAGATC
1494223 GACCTTTTTA
Statistics
Matches: 119, Mismatches: 38, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
43 1 0.01
44 87 0.73
45 30 0.25
46 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (44 bp):
TCGATTCCATCACAGAAGGAGGTAGATCAGCACCAACATCTCGC
Found at i:1494245 original size:133 final size:133
Alignment explanation
Indices: 1494006--1494919 Score: 968
Period size: 133 Copynumber: 7.0 Consensus size: 133
1493996 AAGAGATTGT
* * * * *
1494006 TCAACTGTTTGGTCGATTCTATCACAGAAGGAGGTAGACCAGCACCAACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* *
1494071 TCACAGAATGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCACAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
1494136 GCG
131 GCG
* * * *
1494139 GCAACTTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
*
1494204 TCACTA-AAGGAGGTGGATCGACCTTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
66 TCAC-AGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
*
1494268 AGTG
130 AGCG
* * ** * *
1494272 TCAACTTTTAGCTCGATTCTACCACAGAAGGATATAGATCA-CTATCGACATATCGTTTGATTTC
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGC-ATCGACATCTCGTTCGA-TTC
*
1494336 CATCATAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT
64 CATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT
*
1494401 CA--T
129 CAGCG
* * * * *
1494404 TCAACTTTTTGCTAGATTATATCATAG-ATGAGGTAGATCAACATCGACATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* *
1494468 TCACA-AAGGAGGTGGATCGACATTTTTATTTT-GCTCAAATCCATCACAGAAGGAGTTGGATTA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
* *
1494531 TCA
131 GCG
* * * * *
1494534 CCAACATTTTGCTCGATTCTATCGCAAAAGGAGGTAGATCAGCATCGGCATCTCGTTCGATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
* *
1494599 TCACAGAAGGAGGTGGATCGACATTTTTA-TTTCACTCAAATCCATCGCAGAATGAGTTGGATAA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGAT--
* *
1494663 GCATCA
129 -CAGCG
* * * *
1494669 TCAACATTGTCATTTTTGCTCGATTCTATTACAGAAGGAGGAAGATCATCATCGACATCTCATTC
1 TC-A-A----C-TTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTC
* * *
1494734 GATTCCATCACAGAAGGAGATGGAT--AGA----TATTTT---T---AT-CA---CATAAGGAGT
59 GATTCCATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGT
*
1494783 TGGATCAACG
124 TGGATCAGCG
* * * * * * *
1494793 CCAACTTTTTGTTCGATTCTATCACAGAAAGAAGTAGATTAGCACCGACATCTCGTTCAATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
** * * **
1494858 TCACAGAATAAGATGTATTTACA----T-TTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
1494918 GC
131 GC
1494920 ATCATCAATA
Statistics
Matches: 666, Mismatches: 82, Indels: 71
0.81 0.10 0.09
Matches are distributed among these distances:
117 65 0.10
118 5 0.01
119 3 0.00
121 1 0.00
122 1 0.00
123 1 0.00
124 6 0.01
125 2 0.00
127 13 0.02
128 46 0.07
129 27 0.04
130 31 0.05
131 69 0.10
132 73 0.11
133 171 0.26
134 68 0.10
135 5 0.01
136 3 0.00
137 4 0.01
140 2 0.00
141 1 0.00
142 69 0.10
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (133 bp):
TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCATCGACATCTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
GCG
Found at i:1502778 original size:23 final size:23
Alignment explanation
Indices: 1502748--1502794 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1502738 ATTATTGTAC
*
1502748 TTTATAGTGATATATCATCATCA
1 TTTATAGTGATATATCAACATCA
1502771 TTTATAGTGATATATCAACATCA
1 TTTATAGTGATATATCAACATCA
1502794 T
1 T
1502795 ACGGATGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (23 bp):
TTTATAGTGATATATCAACATCA
Found at i:1513515 original size:37 final size:37
Alignment explanation
Indices: 1513428--1513520 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 37
1513418 GCATAATAGC
* **
1513428 ATAAAATTGTAAAATTAT-TAAAAAATTGGAAAATTT
1 ATAAAATTATAAAATTATATAAAAAATTGGAAAAGCT
* **
1513464 ATAAAAGTATTAAAATTATAT-AAAAATTGTTAAAGCT
1 ATAAAATTA-TAAAATTATATAAAAAATTGGAAAAGCT
1513501 ATGAAAATTATAAAATTATA
1 AT-AAAATTATAAAATTATA
1513521 GAAATCATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
36 7 0.15
37 33 0.70
38 7 0.15
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.35
Consensus pattern (37 bp):
ATAAAATTATAAAATTATATAAAAAATTGGAAAAGCT
Found at i:1513517 original size:8 final size:8
Alignment explanation
Indices: 1513504--1513546 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
1513494 TAAAGCTATG
1513504 AAAATTAT
1 AAAATTAT
1513512 AAAATTAT
1 AAAATTAT
*
1513520 AGAAATCAT
1 A-AAATTAT
1513529 AAAA-TAT
1 AAAATTAT
1513536 AAAAATTAT
1 -AAAATTAT
1513545 AA
1 AA
1513547 CATATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 2 0.07
8 18 0.60
9 10 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (8 bp):
AAAATTAT
Found at i:1513541 original size:16 final size:16
Alignment explanation
Indices: 1513481--1513551 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 16
1513471 TATTAAAATT
*
1513481 ATATAAAAATTGTTAAA
1 ATATAAAAATT-ATAAA
* *
1513498 GCTATGAAAATTATAAA
1 -ATATAAAAATTATAAA
* *
1513515 ATTATAGAAATCATAAA
1 A-TATAAAAATTATAAA
*
1513532 ATATAAAAATTATAAC
1 ATATAAAAATTATAAA
1513548 ATAT
1 ATAT
1513552 TATTTAAAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
16 16 0.38
17 17 0.40
18 9 0.21
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (16 bp):
ATATAAAAATTATAAA
Found at i:1514239 original size:23 final size:23
Alignment explanation
Indices: 1514209--1514254 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1514199 AGTCCAAAAT
1514209 GTGTAGGTTCCCCAGAACCATAC
1 GTGTAGGTTCCCCAGAACCATAC
1514232 GTGTAGGTTCCCCAGAACCATAC
1 GTGTAGGTTCCCCAGAACCATAC
1514255 ACACACCGTC
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:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (23 bp):
GTGTAGGTTCCCCAGAACCATAC
Found at i:1514426 original size:24 final size:24
Alignment explanation
Indices: 1514399--1514450 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1514389 AACGGATATA
1514399 TCAAAAATCAAAACATAAAT-CAGG
1 TCAAAAATCAAAACA-AAATCCAGG
* * *
1514423 TCAAATATCATATCAAAATCCAGG
1 TCAAAAATCAAAACAAAATCCAGG
1514447 TCAA
1 TCAA
1514451 GTATCATATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAATCCAGG
Found at i:1514455 original size:24 final size:24
Alignment explanation
Indices: 1514419--1514533 Score: 144
Period size: 24 Copynumber: 4.8 Consensus size: 24
1514409 AAACATAAAT
* *
1514419 CAGGTCAAATATCATATCAAAATC
1 CAGGTCAAGTATCATATCAGAATC
1514443 CAGGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
*
1514467 CAAGTCAAGTATCATATCAGAATC
1 CAGGTCAAGTATCATATCAGAATC
* *
1514491 CATGTC-AGATATCAGAT-ATGAATC
1 CAGGTCAAG-TATCATATCA-GAATC
*
1514515 CATGTCAAGTATCATATCA
1 CAGGTCAAGTATCATATCA
1514534 TAATTCAAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
23 3 0.04
24 75 0.93
25 3 0.04
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (24 bp):
CAGGTCAAGTATCATATCAGAATC
Found at i:1514553 original size:48 final size:48
Alignment explanation
Indices: 1514462--1514556 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
1514452 TATCATATCA
** *
1514462 GAATCCAAGTCAAGTATCATATCAGAATCCATGTCAGATATCAGATAT
1 GAATCCAAGTCAAGTATCATATCAGAATCCAAATCAGAAATCAGATAT
* * *
1514510 GAATCCATGTCAAGTATCATATCATAATTCAAATC-GAAAATCAGATA
1 GAATCCAAGTCAAGTATCATATCAGAATCCAAATCAG-AAATCAGATA
1514557 AAATATTCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
47 1 0.03
48 39 0.98
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (48 bp):
GAATCCAAGTCAAGTATCATATCAGAATCCAAATCAGAAATCAGATAT
Done.