Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008981.1 Hibiscus syriacus cultivar Beakdansim tig00112343_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: 1473337
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 5 of 7
Found at i:961151 original size:8 final size:8
Alignment explanation
Indices: 961106--961162 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
961096 TTGGTATTCA
961106 TTATTTTT
1 TTATTTTT
*
961114 TTCTTTTAT
1 TTATTTT-T
* *
961123 TTATTATA
1 TTATTTTT
* * *
961131 TTGTATCT
1 TTATTTTT
961139 TTATTTTT
1 TTATTTTT
961147 TTATTTTT
1 TTATTTTT
961155 TTATTTTT
1 TTATTTTT
961163 AACAATTCTG
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
8 30 0.83
9 6 0.17
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.79
Consensus pattern (8 bp):
TTATTTTT
Found at i:961394 original size:78 final size:78
Alignment explanation
Indices: 961304--961460 Score: 305
Period size: 78 Copynumber: 2.0 Consensus size: 78
961294 TTTGGTTGCT
*
961304 ATTTTTGTTTATTCTTTTTTTTAGGGTTTGATATCGCTTCGACTGATCAAGATGGACATTATTTG
1 ATTTTTGTTTATTCTTTTTTCTAGGGTTTGATATCGCTTCGACTGATCAAGATGGACATTATTTG
961369 TTACCATGCTAGG
66 TTACCATGCTAGG
961382 ATTTTTGTTTATTCTTTTTTCTAGGGTTTGATATCGCTTCGACTGATCAAGATGGACATTATTTG
1 ATTTTTGTTTATTCTTTTTTCTAGGGTTTGATATCGCTTCGACTGATCAAGATGGACATTATTTG
961447 TTACCATGCTAGG
66 TTACCATGCTAGG
961460 A
1 A
961461 CCATCAGATT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (78 bp):
ATTTTTGTTTATTCTTTTTTCTAGGGTTTGATATCGCTTCGACTGATCAAGATGGACATTATTTG
TTACCATGCTAGG
Found at i:963305 original size:30 final size:30
Alignment explanation
Indices: 963269--963328 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
963259 TTTATAGGCC
963269 ACTAACGAAAGGACAAGAAAGAGATTATTA
1 ACTAACGAAAGGACAAGAAAGAGATTATTA
*
963299 ACTAACGAAAGGACAAGCAAGAGATTATTA
1 ACTAACGAAAGGACAAGAAAGAGATTATTA
963329 TACTGTGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.12, G:0.20, T:0.17
Consensus pattern (30 bp):
ACTAACGAAAGGACAAGAAAGAGATTATTA
Found at i:970043 original size:55 final size:53
Alignment explanation
Indices: 969954--970063 Score: 157
Period size: 55 Copynumber: 2.0 Consensus size: 53
969944 TAAACTTGTC
* *
969954 AAAGAGCTTATTTATGCACTGTAGTTGACTAATAGAATGTGTTTTTAGGAGATAT
1 AAAGAGCTTATTTATGCACTGTAGTTGACTAATAG--TATGTATTTAGGAGATAT
* * *
970009 AAAGGGCTTATTTATGCATTGTAGTTTACTAATAGTATGTATTTAGGAGATAT
1 AAAGAGCTTATTTATGCACTGTAGTTGACTAATAGTATGTATTTAGGAGATAT
970062 AA
1 AA
970064 GTTAATCGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 18 0.36
55 32 0.64
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (53 bp):
AAAGAGCTTATTTATGCACTGTAGTTGACTAATAGTATGTATTTAGGAGATAT
Found at i:970110 original size:33 final size:33
Alignment explanation
Indices: 970068--970135 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
970058 ATATAAGTTA
*
970068 ATCGGAATATGTGATAGAAGGAGAGATTTCTCG
1 ATCGAAATATGTGATAGAAGGAGAGATTTCTCG
* * *
970101 ATCGAAATATTTGATAGAATGAGAGATTTTTCG
1 ATCGAAATATGTGATAGAAGGAGAGATTTCTCG
970134 AT
1 AT
970136 ATATCTCCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.32
Consensus pattern (33 bp):
ATCGAAATATGTGATAGAAGGAGAGATTTCTCG
Found at i:977631 original size:13 final size:13
Alignment explanation
Indices: 977613--977659 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
977603 AGATCCCAAA
977613 TTAATTTTAAAGG
1 TTAATTTTAAAGG
977626 TTAATTTTTTAAA--
1 TTAA--TTTTAAAGG
977639 TTAATTTTAAAGG
1 TTAATTTTAAAGG
977652 TTAATTTT
1 TTAATTTT
977660 TTCATCCGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 7 0.23
13 16 0.53
15 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (13 bp):
TTAATTTTAAAGG
Found at i:977639 original size:26 final size:26
Alignment explanation
Indices: 977610--977661 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
977600 CGTAGATCCC
977610 AAATTAATTTTAAAGGTTAATTTTTT
1 AAATTAATTTTAAAGGTTAATTTTTT
977636 AAATTAATTTTAAAGGTTAATTTTTT
1 AAATTAATTTTAAAGGTTAATTTTTT
977662 CATCCGTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (26 bp):
AAATTAATTTTAAAGGTTAATTTTTT
Found at i:984280 original size:15 final size:15
Alignment explanation
Indices: 984260--984289 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
984250 TTATGCAGCT
*
984260 TGGAGCATTTCTGGC
1 TGGAGCATTACTGGC
984275 TGGAGCATTACTGGC
1 TGGAGCATTACTGGC
984290 AGAAACAAAT
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:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (15 bp):
TGGAGCATTACTGGC
Found at i:989325 original size:31 final size:31
Alignment explanation
Indices: 989287--989361 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
989277 CAAAAAAACA
989287 TAAGATATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATATGGTCACTTTCGTTTTTATTTAAT
* *
989318 TAAGATATGATCATTTTCGTTTTTATTTAAT
1 TAAGATATGGTCACTTTCGTTTTTATTTAAT
*
989349 TAAGATGTGGTCA
1 TAAGATATGGTCA
989362 TCACGGGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCGTTTTTATTTAAT
Found at i:989524 original size:27 final size:26
Alignment explanation
Indices: 989484--989566 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
989474 ATAAATTTTA
*
989484 ATATAAATAAATATTTTTAAATTTAGTT-
1 ATATAAA-AAATATTTTT-AA-TAAGTTC
*
989512 A-ATAATAAAATATATTTAATAAGTTC
1 ATATAA-AAAATATTTTTAATAAGTTC
*
989538 ATATAAAAAATATTTTT--TAAGTTA
1 ATATAAAAAATATTTTTAATAAGTTC
989562 ATATA
1 ATATA
989567 TATTTAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
24 11 0.23
25 5 0.10
26 13 0.27
27 17 0.35
28 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.45
Consensus pattern (26 bp):
ATATAAAAAATATTTTTAATAAGTTC
Found at i:989550 original size:24 final size:24
Alignment explanation
Indices: 989481--989566 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 24
989471 TAAATAAATT
*
989481 TTAATATAAATAAATATTTTTAAATTTAG
1 TTAATATAAA-AAATA--TTT-AA-TAAG
*
989510 TTAATAATAAAATATATTTAATAAG
1 TTAAT-ATAAAAAATATTTAATAAG
* **
989535 TTCATATAAAAAATATTTTTTAAG
1 TTAATATAAAAAATATTTAATAAG
989559 TTAATATA
1 TTAATATA
989567 TATTTAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
24 23 0.47
25 7 0.14
26 2 0.04
27 3 0.06
29 9 0.18
30 5 0.10
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.45
Consensus pattern (24 bp):
TTAATATAAAAAATATTTAATAAG
Found at i:994352 original size:11 final size:12
Alignment explanation
Indices: 994312--994355 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
994302 TATTTAAACG
*
994312 GGTATTGGGCCA
1 GGTATTGGGTCA
*
994324 GGTATTGGGTCG
1 GGTATTGGGTCA
994336 GGTATTGGGTC-
1 GGTATTGGGTCA
994347 GGTATTGGG
1 GGTATTGGG
994356 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:994354 original size:23 final size:24
Alignment explanation
Indices: 994310--994355 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
994300 ATTATTTAAA
994310 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
994334 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
994356 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:994850 original size:5 final size:5
Alignment explanation
Indices: 994842--994867 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
994832 AATATAACTT
994842 GGTCG GGTCG GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTCG GGTCG GGTCG G
994868 ATAAGTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.62, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:1010111 original size:13 final size:13
Alignment explanation
Indices: 1010093--1010117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1010083 CACTATATAT
1010093 ATTTTTTTTGGGC
1 ATTTTTTTTGGGC
1010106 ATTTTTTTTGGG
1 ATTTTTTTTGGG
1010118 GCCTGCACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.04, G:0.24, T:0.64
Consensus pattern (13 bp):
ATTTTTTTTGGGC
Found at i:1014841 original size:61 final size:61
Alignment explanation
Indices: 1014768--1014884 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
1014758 ACCATTTTGC
*
1014768 AACTTTTAATAGTCGAGGGACTTAACAAAATAACA-CTCTATAGTCAAAGGACTATTTTTTT
1 AACTTTTAATAGTCGAGAGACTTAACAAAATAACATC-CTATAGTCAAAGGACTATTTTTTT
* * * *
1014829 AACTTTTAATAGTCGAGAGACTTAACAAAGTAATATCCTATAGTCGAGGGACTATT
1 AACTTTTAATAGTCGAGAGACTTAACAAAATAACATCCTATAGTCAAAGGACTATT
1014885 GTATACTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
61 49 0.98
62 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (61 bp):
AACTTTTAATAGTCGAGAGACTTAACAAAATAACATCCTATAGTCAAAGGACTATTTTTTT
Found at i:1015182 original size:27 final size:27
Alignment explanation
Indices: 1015127--1015183 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1015117 CAAAATATTT
* *
1015127 TTATTTTATATATTTAATATTAATATA
1 TTATTTAATATATTTAATATAAATATA
1015154 TTATTTAATATCATTTTAATA-AAAT-TA
1 TTATTTAATAT-A-TTTAATATAAATATA
1015181 TTA
1 TTA
1015184 ATTATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 15 0.58
28 4 0.15
29 7 0.27
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
TTATTTAATATATTTAATATAAATATA
Found at i:1015587 original size:20 final size:20
Alignment explanation
Indices: 1015567--1015605 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1015557 ATATTAAATA
1015567 AATTATT-TTAATATTTTAT
1 AATTATTATTAATATTTTAT
*
1015586 AATTATTATTATTATTTTAT
1 AATTATTATTAATATTTTAT
1015606 TAATAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTATTATTAATATTTTAT
Found at i:1015619 original size:21 final size:20
Alignment explanation
Indices: 1015578--1015623 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1015568 ATTATTTTAA
* * *
1015578 TATTTTATAATTATTATTAT
1 TATTTTATAATAAATAATAT
1015598 TATTTTATTAATAAATAATAT
1 TATTTTA-TAATAAATAATAT
1015619 TATTT
1 TATTT
1015624 ATTGTATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTTATAATAAATAATAT
Found at i:1015726 original size:14 final size:14
Alignment explanation
Indices: 1015707--1015741 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1015697 TAAACACCAT
1015707 AAAATGATTTTT-AG
1 AAAATG-TTTTTCAG
1015721 AAAATGTTTTTCAG
1 AAAATGTTTTTCAG
1015735 AAAATGT
1 AAAATGT
1015742 AATTTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.40
Consensus pattern (14 bp):
AAAATGTTTTTCAG
Found at i:1018992 original size:64 final size:63
Alignment explanation
Indices: 1018895--1019035 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
1018885 CATATTCAAT
* * *
1018895 GTGCATCGATGCACTCTTTAAAGAAGAAACATTGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATTGAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * * * *
1018958 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATTGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATTGAAGGCAATTGGTGCATCGATGCATAGGTA
1019022 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1019036 ATGTTAAAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 18 0.27
64 49 0.73
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATTGAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:1027349 original size:20 final size:19
Alignment explanation
Indices: 1027312--1027360 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
1027302 TATTTTATGA
1027312 ATCGATGCACGTACCATGC
1 ATCGATGCACGTACCATGC
1027331 ATCGATGCACAAG-ACCATGC
1 ATCGATGCAC--GTACCATGC
1027351 ATCGATGCAC
1 ATCGATGCAC
1027361 TCAGGCTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.36
20 17 0.61
21 1 0.04
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (19 bp):
ATCGATGCACGTACCATGC
Found at i:1028301 original size:23 final size:21
Alignment explanation
Indices: 1028274--1028328 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
1028264 TAGTCTAATA
1028274 ATATTATAAAAATTCCTTAAAAT
1 ATATTATAAAAATT--TTAAAAT
*
1028297 ATATTTATTAATAATTTTAAAAT
1 ATA-TTA-TAAAAATTTTAAAAT
*
1028320 ATAATATAA
1 ATATTATAA
1028329 TATTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 3 0.11
22 2 0.07
23 13 0.46
24 3 0.11
25 7 0.25
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTATAAAAATTTTAAAAT
Found at i:1028529 original size:22 final size:20
Alignment explanation
Indices: 1028477--1028530 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
1028467 ATTATTCTAA
*
1028477 TATTTTTAAAATAATAATAT
1 TATTTTTATAATAATAATAT
1028497 TAAGTTTTTATAATAAATAATAT
1 T-A-TTTTTATAAT-AATAATAT
1028520 TATTTATTATA
1 TATTT-TTATA
1028531 TTTTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.14
22 15 0.52
23 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TATTTTTATAATAATAATAT
Found at i:1031162 original size:33 final size:33
Alignment explanation
Indices: 1031124--1031277 Score: 130
Period size: 33 Copynumber: 4.6 Consensus size: 33
1031114 GAGGCTTGGC
* *
1031124 GAAGAGGAGCATGAAGGAGCAAGCAAACACGAA
1 GAAGAGGAGCAGGAAGAAGCAAGCAAACACGAA
* * * *
1031157 GAAGAGGAGCTGGATGAAACAGGCAAACACGAA
1 GAAGAGGAGCAGGAAGAAGCAAGCAAACACGAA
* * * * * *
1031190 GAGGAGGAACAGGATGAAGGAAGTAAACATGAA
1 GAAGAGGAGCAGGAAGAAGCAAGCAAACACGAA
* * *
1031223 GAGGAGCAGCAGGAAGAAGGAAGCAAACACAATGAA
1 GAAGAGGAGCAGGAAGAAGCAAGCAAACAC---GAA
1031259 GAAGAGGAGCCA-GAAGAAG
1 GAAGAGGAG-CAGGAAGAAG
1031278 TGCAGGGAGA
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
33 77 0.80
36 17 0.18
37 2 0.02
ACGTcount: A:0.48, C:0.12, G:0.35, T:0.05
Consensus pattern (33 bp):
GAAGAGGAGCAGGAAGAAGCAAGCAAACACGAA
Found at i:1031880 original size:69 final size:69
Alignment explanation
Indices: 1031750--1031880 Score: 190
Period size: 69 Copynumber: 1.9 Consensus size: 69
1031740 AAGCCAATGG
* * * * *
1031750 TGATGAAAACAAGTCTGAAGCGAAGGATGATGAAGGTAAACACTCTGAAGGTGGTAGTTCCTCTA
1 TGATGAAAACAAGTCAGAAGCGAAGGATGATGAAGGTAAACACTCCGAAAGTGATAATTCCTCTA
1031815 ATAA
66 ATAA
* * *
1031819 TGATGAAAACAAGTCAGAAGTGAAGGTTGATGAAGGTAAACGCTCCGAAAGTGATAATTCCT
1 TGATGAAAACAAGTCAGAAGCGAAGGATGATGAAGGTAAACACTCCGAAAGTGATAATTCCT
1031881 TGAATGTCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (69 bp):
TGATGAAAACAAGTCAGAAGCGAAGGATGATGAAGGTAAACACTCCGAAAGTGATAATTCCTCTA
ATAA
Found at i:1034138 original size:14 final size:14
Alignment explanation
Indices: 1034116--1034146 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1034106 ATTCTGAGAC
1034116 GAAACTTTATGTTA
1 GAAACTTTATGTTA
*
1034130 GAAATTTTATGTTA
1 GAAACTTTATGTTA
1034144 GAA
1 GAA
1034147 TTTGACAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (14 bp):
GAAACTTTATGTTA
Found at i:1035862 original size:12 final size:12
Alignment explanation
Indices: 1035834--1035870 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1035824 TTTAGTAATC
*
1035834 CCCGACCCGATTA
1 CCCGGCCCGA-TA
1035847 CCCGGCCCGATA
1 CCCGGCCCGATA
1035859 CCCGGCCCGATA
1 CCCGGCCCGATA
1035871 AATATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.11
Consensus pattern (12 bp):
CCCGGCCCGATA
Found at i:1035958 original size:42 final size:40
Alignment explanation
Indices: 1035883--1035971 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 40
1035873 TATTAAAAAT
*
1035883 AATTATTATATATATATATAATATTAATAAATTTAATTTA
1 AATTAATATATATATATATAATATTAATAAATTTAATTTA
*
1035923 AATTAATATATATATATAT-AT-TT-ATATATTTAATTTA
1 AATTAATATATATATATATAATATTAATAAATTTAATTTA
1035960 AA-T-ATATATATA
1 AATTAATATATATA
1035972 CCCGGCCCGA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
35 9 0.19
36 1 0.02
37 15 0.32
38 2 0.04
39 2 0.04
40 18 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
AATTAATATATATATATATAATATTAATAAATTTAATTTA
Found at i:1036050 original size:20 final size:20
Alignment explanation
Indices: 1036013--1036050 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1036003 ATGCTAAACA
* *
1036013 GTTTTCCCCGTTTCCCCGCG
1 GTTTTCCCCGATTACCCGCG
1036033 GTTTTCCCCGATTACCCG
1 GTTTTCCCCGATTACCCG
1036051 ATGGGGATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.42, G:0.18, T:0.34
Consensus pattern (20 bp):
GTTTTCCCCGATTACCCGCG
Found at i:1044753 original size:7 final size:7
Alignment explanation
Indices: 1044741--1044821 Score: 69
Period size: 7 Copynumber: 11.7 Consensus size: 7
1044731 CCAAATCCTA
1044741 AAACCCT
1 AAACCCT
1044748 AAACCCT
1 AAACCCT
*
1044755 AAAACTCT
1 -AAACCCT
*
1044763 AAATCC-
1 AAACCCT
1044769 AAA-CCT
1 AAACCCT
**
1044775 AAAATCT
1 AAACCCT
*
1044782 CAAACTCT
1 -AAACCCT
1044790 AAACCCT
1 AAACCCT
1044797 AAACCCT
1 AAACCCT
1044804 AAACCC-
1 AAACCCT
*
1044810 AAACCCC
1 AAACCCT
1044817 AAACC
1 AAACC
1044822 ATAGCCATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
5 2 0.03
6 12 0.19
7 37 0.59
8 12 0.19
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCCT
Found at i:1044773 original size:21 final size:21
Alignment explanation
Indices: 1044748--1044815 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 21
1044738 CTAAAACCCT
1044748 AAACCCTAAAACTCTAAATCC
1 AAACCCTAAAACTCTAAATCC
*
1044769 AAA-CCTAAAA-TCTCAAACTCT
1 AAACCCTAAAACTCT-AAA-TCC
* *
1044790 AAACCCT-AAACCCTAAACCC
1 AAACCCTAAAACTCTAAATCC
1044810 AAACCC
1 AAACCC
1044816 CAAACCATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 14 0.36
22 5 0.13
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (21 bp):
AAACCCTAAAACTCTAAATCC
Found at i:1044800 original size:14 final size:14
Alignment explanation
Indices: 1044741--1044821 Score: 69
Period size: 15 Copynumber: 5.9 Consensus size: 14
1044731 CCAAATCCTA
1044741 AAACCCTAAACCCT
1 AAACCCTAAACCCT
* *
1044755 AAAACTCTAAATCC-
1 -AAACCCTAAACCCT
**
1044769 AAA-CCTAAAATCT
1 AAACCCTAAACCCT
*
1044782 CAAACTCTAAACCCT
1 -AAACCCTAAACCCT
1044797 AAACCCTAAACCC-
1 AAACCCTAAACCCT
*
1044810 AAACCCCAAACC
1 AAACCCTAAACC
1044822 ATAGCCATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
12 6 0.11
13 14 0.26
14 15 0.28
15 18 0.34
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (14 bp):
AAACCCTAAACCCT
Found at i:1044812 original size:27 final size:26
Alignment explanation
Indices: 1044741--1044813 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
1044731 CCAAATCCTA
*
1044741 AAACCCTAAACCCTAAAACTCTAAATCC
1 AAACCCTAAACCC--AAACTCTAAACCC
*
1044769 AAA-CCTAAAATCTCAAACTCTAAACCC
1 AAACCCT-AAA-CCCAAACTCTAAACCC
1044796 TAAACCCTAAACCCAAAC
1 -AAACCCTAAACCCAAAC
1044814 CCCAAACCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 21 0.55
28 12 0.32
29 5 0.13
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.16
Consensus pattern (26 bp):
AAACCCTAAACCCAAACTCTAAACCC
Found at i:1052237 original size:20 final size:19
Alignment explanation
Indices: 1052212--1052251 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1052202 AAAGTTCGTA
1052212 TTTTTAAAACATAAATATAT
1 TTTTTAAAA-ATAAATATAT
*
1052232 TTTTTAAAAATAAATTTAT
1 TTTTTAAAAATAAATATAT
1052251 T
1 T
1052252 ACCCCTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTTAAAAATAAATATAT
Found at i:1061857 original size:20 final size:21
Alignment explanation
Indices: 1061817--1061863 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1061807 AATGAAACAG
*
1061817 AAAATTTTATGCAATACAAAC
1 AAAATTATATGCAATACAAAC
* *
1061838 AGAATTATATG-AATAGAAAC
1 AAAATTATATGCAATACAAAC
1061858 AAAATT
1 AAAATT
1061864 GTTATATAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAATTATATGCAATACAAAC
Found at i:1063666 original size:24 final size:25
Alignment explanation
Indices: 1063629--1063683 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
1063619 CATAATCTAA
*
1063629 AAAAATATTATATTATTAAAATGAC
1 AAAAATACTATATTATTAAAATGAC
*
1063654 AAAAATACT-TATTATTAAAATGAT
1 AAAAATACTATATTATTAAAATGAC
1063678 AAAAAT
1 AAAAAT
1063684 GTTACATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (25 bp):
AAAAATACTATATTATTAAAATGAC
Found at i:1074139 original size:32 final size:32
Alignment explanation
Indices: 1074073--1074142 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1074063 TTTAAAAAAT
* *
1074073 AATTTAGAATATTAATGTGAAATAATTTATTA
1 AATTTAAAATATTAATGTGAAATAATTTAATA
*
1074105 AATTTAAAATATT-ATGGTAGAAA-AGTTTAATA
1 AATTTAAAATATTAAT-GT-GAAATAATTTAATA
1074137 AATTTA
1 AATTTA
1074143 TAATTTAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 2 0.06
32 27 0.82
33 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (32 bp):
AATTTAAAATATTAATGTGAAATAATTTAATA
Found at i:1075116 original size:2 final size:2
Alignment explanation
Indices: 1075111--1075137 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1075101 TATTTTTTAA
1075111 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
1075138 ATTCTAAAAT
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:1082706 original size:25 final size:23
Alignment explanation
Indices: 1082662--1082712 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
1082652 GTAGGTGTCA
1082662 ATTATTTTTAAAATAATATTTCT
1 ATTATTTTTAAAATAATATTTCT
* *
1082685 ATTATTCTTTAGAAATATTATTTTT
1 ATTATT-TTTA-AAATAATATTTCT
1082710 ATT
1 ATT
1082713 TTTATCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 4 0.17
25 14 0.58
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTATTTTTAAAATAATATTTCT
Found at i:1082916 original size:54 final size:54
Alignment explanation
Indices: 1082830--1082950 Score: 215
Period size: 54 Copynumber: 2.2 Consensus size: 54
1082820 ATCAAAGTGT
* *
1082830 AAATTTACCATTACATTACCTTCATATATCTAGATTCAAAAGGACTAAACTTGC
1 AAATTTATCATTACATTACCGTCATATATCTAGATTCAAAAGGACTAAACTTGC
*
1082884 AAATTTATCATTACATTACCGTCATATCTCTAGATTCAAAAGGACTAAACTTGC
1 AAATTTATCATTACATTACCGTCATATATCTAGATTCAAAAGGACTAAACTTGC
1082938 AAATTTATCATTA
1 AAATTTATCATTA
1082951 AGATAATTGA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (54 bp):
AAATTTATCATTACATTACCGTCATATATCTAGATTCAAAAGGACTAAACTTGC
Found at i:1086788 original size:123 final size:123
Alignment explanation
Indices: 1086629--1086875 Score: 494
Period size: 123 Copynumber: 2.0 Consensus size: 123
1086619 TCTGGAACAA
1086629 GAATACAGAATCAACGATGTTTTCTAAGGGAAAAAAAAGTTGAAAAAACATGATCAAAATGAAAG
1 GAATACAGAATCAACGATGTTTTCTAAGGGAAAAAAAAGTTGAAAAAACATGATCAAAATGAAAG
1086694 TTGAGCAACCTGATCTGCATTTTCATCAGATGCTAATACGATGATGGGCTGATGGCAC
66 TTGAGCAACCTGATCTGCATTTTCATCAGATGCTAATACGATGATGGGCTGATGGCAC
1086752 GAATACAGAATCAACGATGTTTTCTAAGGGAAAAAAAAGTTGAAAAAACATGATCAAAATGAAAG
1 GAATACAGAATCAACGATGTTTTCTAAGGGAAAAAAAAGTTGAAAAAACATGATCAAAATGAAAG
1086817 TTGAGCAACCTGATCTGCATTTTCATCAGATGCTAATACGATGATGGGCTGATGGCAC
66 TTGAGCAACCTGATCTGCATTTTCATCAGATGCTAATACGATGATGGGCTGATGGCAC
1086875 G
1 G
1086876 TGCTTTTGAG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 124 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (123 bp):
GAATACAGAATCAACGATGTTTTCTAAGGGAAAAAAAAGTTGAAAAAACATGATCAAAATGAAAG
TTGAGCAACCTGATCTGCATTTTCATCAGATGCTAATACGATGATGGGCTGATGGCAC
Found at i:1098088 original size:2 final size:2
Alignment explanation
Indices: 1098037--1098069 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1098027 TACTCTCAAT
1098037 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 T
1098070 GTTAGCATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1098249 original size:2 final size:2
Alignment explanation
Indices: 1098242--1098270 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1098232 ATCGTATCTC
1098242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1098271 GCTCCTGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1102410 original size:2 final size:2
Alignment explanation
Indices: 1102399--1102427 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1102389 TGTCAAATAA
1102399 AT AT -T 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
1102428 GAAAGTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1104582 original size:16 final size:16
Alignment explanation
Indices: 1104561--1104594 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1104551 TTATTATTCA
*
1104561 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1104577 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1104593 CG
1 CG
1104595 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:1109560 original size:18 final size:18
Alignment explanation
Indices: 1109537--1109571 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1109527 AACCCTACCT
1109537 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
1109555 AAAATATTATTTTTATT
1 AAAATAATATATTTATT
1109572 CAATAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:1110668 original size:16 final size:17
Alignment explanation
Indices: 1110647--1110681 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1110637 CTTATAATGA
1110647 TTCGAG-TTCAAATTTT
1 TTCGAGCTTCAAATTTT
*
1110663 TTCGAGCTTCAAGTTTT
1 TTCGAGCTTCAAATTTT
1110680 TT
1 TT
1110682 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.51
Consensus pattern (17 bp):
TTCGAGCTTCAAATTTT
Found at i:1112247 original size:6 final size:6
Alignment explanation
Indices: 1112236--1112269 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1112226 CAAAGAAAAG
* *
1112236 AGAAAC AGAAAC AGAAAC AGAAAA AGAAAA AGAA
1 AGAAAC AGAAAC AGAAAC AGAAAC AGAAAC AGAA
1112270 TACATCTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.74, C:0.09, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAC
Found at i:1112253 original size:12 final size:12
Alignment explanation
Indices: 1112229--1112269 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1112219 CCTTTGGCAA
1112229 AGAAAAGAGAAAC
1 AGAAAA-AGAAAC
*
1112242 AGAAACAGAAAC
1 AGAAAAAGAAAC
*
1112254 AGAAAAAGAAAA
1 AGAAAAAGAAAC
1112266 AGAA
1 AGAA
1112270 TACATCTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAAAC
Found at i:1113563 original size:16 final size:16
Alignment explanation
Indices: 1113542--1113575 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1113532 TCTAAGGATG
*
1113542 TTTCGAGTTCAAATTT
1 TTTCGAGCTCAAATTT
*
1113558 TTTCGAGCTCCAATTT
1 TTTCGAGCTCAAATTT
1113574 TT
1 TT
1113576 ATTTTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.50
Consensus pattern (16 bp):
TTTCGAGCTCAAATTT
Found at i:1118008 original size:27 final size:27
Alignment explanation
Indices: 1117977--1118033 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1117967 ATGAAAGATG
*
1117977 TATGACTGGAAAGAAATGTTATATGAT
1 TATGACTGAAAAGAAATGTTATATGAT
*
1118004 TATGACTGAAAATAAATGTTATATGAT
1 TATGACTGAAAAGAAATGTTATATGAT
1118031 TAT
1 TAT
1118034 TCTATCAGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.37
Consensus pattern (27 bp):
TATGACTGAAAAGAAATGTTATATGAT
Found at i:1120702 original size:16 final size:16
Alignment explanation
Indices: 1120657--1120712 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
1120647 CAGCTTTATC
*
1120657 ATGCATGTATATATGT
1 ATGCATGTATATATAT
1120673 ATGCATGTATATATAT
1 ATGCATGTATATATAT
* **
1120689 AT--ATATATGCATAT
1 ATGCATGTATATATAT
1120703 ATGCATGTAT
1 ATGCATGTAT
1120713 GTATGCATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 11 0.33
16 22 0.67
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (16 bp):
ATGCATGTATATATAT
Found at i:1128889 original size:28 final size:26
Alignment explanation
Indices: 1128854--1128914 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 26
1128844 AACAAAATTC
*
1128854 AATTAATGTGTT-TATACATTATATAAA
1 AATTAATGT-TTAAATACATTATA-AAA
1128881 AATATAATGTTTAAATACATTATAAAA
1 AAT-TAATGTTTAAATACATTATAAAA
1128908 AATTAAT
1 AATTAAT
1128915 ATGGTATACT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 4 0.13
27 11 0.35
28 16 0.52
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (26 bp):
AATTAATGTTTAAATACATTATAAAA
Found at i:1133687 original size:27 final size:27
Alignment explanation
Indices: 1133657--1133740 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 27
1133647 ATTAACATAA
1133657 ATTTTTTTATTTTATCTTATAAAATAT
1 ATTTTTTTATTTTATCTTATAAAATAT
**
1133684 ATTTTAGTA-TTTA-CTTAATTTAAAA-AT
1 ATTTTTTTATTTTATCTT-A--TAAAATAT
*
1133711 A-TTTTAT-TTTTAT-TTA-AAAATAT
1 ATTTTTTTATTTTATCTTATAAAATAT
1133734 ATTTTTT
1 ATTTTTT
1133741 ATGTTAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 17
0.67 0.07 0.25
Matches are distributed among these distances:
22 4 0.09
23 3 0.07
24 4 0.09
25 4 0.09
26 15 0.33
27 10 0.22
28 5 0.11
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (27 bp):
ATTTTTTTATTTTATCTTATAAAATAT
Found at i:1133756 original size:19 final size:19
Alignment explanation
Indices: 1133701--1133749 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 19
1133691 TATTTACTTA
*
1133701 ATTTAAAAATATTTTATTTTT
1 ATTTAAAAATA-TAT-TTTTT
1133722 ATTTAAAAATATATTTTTT
1 ATTTAAAAATATATTTTTT
1133741 ATGTTAAAA
1 AT-TTAAAA
1133750 TTCATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 8 0.31
21 11 0.42
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
ATTTAAAAATATATTTTTT
Found at i:1134615 original size:20 final size:20
Alignment explanation
Indices: 1134590--1134682 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
1134580 TTTTCCCAAT
1134590 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1134610 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1134630 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* * *
1134651 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1134672 TCGCAATGCGA
1 TCGCAATGCGA
1134683 TACTGACTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 27 0.46
21 32 0.54
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1134632 original size:41 final size:41
Alignment explanation
Indices: 1134587--1134682 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
1134577 CGATTTTCCC
*
1134587 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1134628 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
*
1134669 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1134683 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGA
Found at i:1134695 original size:41 final size:41
Alignment explanation
Indices: 1134609--1134743 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
1134599 GAATAAGTAA
* * * *
1134609 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
1134650 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
1134691 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
1134732 TTCGCAACGCGA
1 ATCGCAACGCGA
1134744 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:1134696 original size:20 final size:20
Alignment explanation
Indices: 1134671--1134764 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1134661 AATTGAGAAA
*
1134671 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1134691 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1134712 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1134732 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1134752 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1134765 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1135324 original size:19 final size:19
Alignment explanation
Indices: 1135286--1135352 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1135276 TTCGAGAATG
*
1135286 AAAATCGCAAAGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1135306 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1135325 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1135344 AAAATCGCA
1 AAAATCGCA
1135353 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1135370 original size:19 final size:19
Alignment explanation
Indices: 1135348--1135512 Score: 134
Period size: 19 Copynumber: 9.1 Consensus size: 19
1135338 GAAACCAAAA
*
1135348 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1135367 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1135386 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1135405 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1135419 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1135438 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
1135452 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
1135471 TCCGCGTTGCAATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1135491 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1135511 TC
1 TC
1135513 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 18, Indels: 24
0.73 0.11 0.15
Matches are distributed among these distances:
14 18 0.16
16 4 0.03
17 5 0.04
19 60 0.52
20 28 0.24
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1135404 original size:38 final size:33
Alignment explanation
Indices: 1135353--1135487 Score: 144
Period size: 33 Copynumber: 3.9 Consensus size: 33
1135343 CAAAATCGCA
*
1135353 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA--TTC---TCTCG
1135391 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* ** *
1135424 TCGCGATAGTCATTTCGCGTTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
1135457 TTGCGATAGTCATTTCCGCGTTGCAATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
1135488 ATTATCTCGT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 47 0.53
34 14 0.16
36 3 0.03
38 25 0.28
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1135489 original size:20 final size:20
Alignment explanation
Indices: 1135466--1135512 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1135456 ATTGCGATAG
1135466 TCATTTCCGCGTTGCAATTC
1 TCATTTCCGCGTTGCAATTC
* * *
1135486 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCAATTC
1135506 TCATTTC
1 TCATTTC
1135513 AACCAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.15, C:0.26, G:0.13, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCAATTC
Found at i:1137573 original size:42 final size:42
Alignment explanation
Indices: 1137513--1137635 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1137503 GCCCGACTCG
* * *
1137513 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1137555 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1137597 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1137636 CCTGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1137593 original size:21 final size:21
Alignment explanation
Indices: 1137569--1137635 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1137559 TCATTCCTCG
1137569 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1137590 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1137611 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1137632 AGAG
1 AGAG
1137636 CCTGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1139012 original size:14 final size:14
Alignment explanation
Indices: 1138993--1139028 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1138983 ATTGTTTAAT
1138993 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
* *
1139007 TGATTTGTACAAGT
1 TGATTTGTAAAAGG
1139021 TGATTTGT
1 TGATTTGT
1139029 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:0.28, C:0.03, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1139229 original size:19 final size:19
Alignment explanation
Indices: 1139207--1139324 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
1139197 CGAAATTAAA
1139207 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1139226 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1139241 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1139259 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1139274 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1139292 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1139311 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1139325 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1139253 original size:33 final size:33
Alignment explanation
Indices: 1139211--1139304 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
1139201 ATTAAATTCG
1139211 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1139244 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1139277 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1139305 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1141615 original size:12 final size:12
Alignment explanation
Indices: 1141598--1141622 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1141588 TCTTCGGGGA
1141598 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1141610 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1141622 C
1 C
1141623 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1142438 original size:14 final size:14
Alignment explanation
Indices: 1142419--1142455 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1142409 CATCAATTAA
1142419 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1142433 ACAAATCATCTTTT
1 ACAAATCAACATTT
1142447 ACAAATCAA
1 ACAAATCAA
1142456 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1144348 original size:19 final size:19
Alignment explanation
Indices: 1144323--1144440 Score: 124
Period size: 19 Copynumber: 6.5 Consensus size: 19
1144313 CGAAACTTAA
1144323 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAC
* *
1144342 TATCGCAACGCGGAAATGGC
1 AATCGCAACGC-GAAATGAC
* * *
1144362 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAC
1144381 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
*
1144399 AATCGCAA--CGACA--A-
1 AATCGCAACGCGAAATGAC
1144413 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
1144431 AATCGCAACG
1 AATCGCAACG
1144441 ACAAAATCGC
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
14 9 0.11
16 8 0.09
18 19 0.22
19 32 0.38
20 17 0.20
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:1144367 original size:39 final size:38
Alignment explanation
Indices: 1144324--1144397 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
1144314 GAAACTTAAA
**
1144324 ATCGCAACGCGAAATGACTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAATGAAAATCGCAACGC-GAAATGGCT
*
1144363 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATG
1144398 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 6 0.19
39 26 0.81
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGGCT
Found at i:1144417 original size:14 final size:14
Alignment explanation
Indices: 1144398--1144454 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
1144388 ACGCGAAATG
1144398 AAATCGCAACGACA
1 AAATCGCAACGACA
*
1144412 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
1144428 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
1144444 AAATCGCAACG
1 AAATCGCAACG
1144455 CGAAACACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:1144420 original size:32 final size:32
Alignment explanation
Indices: 1144379--1144459 Score: 162
Period size: 32 Copynumber: 2.5 Consensus size: 32
1144369 ATGCGAAATG
1144379 AAAATCGCAACGCGAAATGAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAATCGCAACGAC
1144411 AAAATCGCAACGCGAAATGAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAATCGCAACGAC
1144443 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
1144460 CACAAATCGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.48, C:0.25, G:0.19, T:0.09
Consensus pattern (32 bp):
AAAATCGCAACGCGAAATGAAATCGCAACGAC
Found at i:1144488 original size:19 final size:17
Alignment explanation
Indices: 1144466--1144560 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 17
1144456 GAAACACAAA
1144466 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
1144485 TCGCGTTGCGA-TT--TG
1 TCGC-TTGCGATTTCATT
1144500 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
1144516 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
1144532 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
1144549 TCGCATTGCGAT
1 TCGC-TTGCGAT
1144561 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
13 6 0.10
14 8 0.13
15 7 0.11
16 8 0.13
17 6 0.10
18 10 0.16
19 16 0.26
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:1144504 original size:13 final size:14
Alignment explanation
Indices: 1144488--1144544 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1144478 TTTCATTTCG
1144488 CGTTGCGA-TTTGT
1 CGTTGCGATTTTGT
*
1144501 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1144517 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1144533 CGTTGCGATTTT
1 CGTTGCGATTTT
1144545 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.22
14 14 0.38
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1144532 original size:32 final size:33
Alignment explanation
Indices: 1144471--1144560 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1144461 ACAAATCGCA
1144471 TTGCGATTTTCATTTCGCGTTGCGA-TTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1144503 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
1144535 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
1144561 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 18 0.33
32 19 0.35
33 18 0.33
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:1144579 original size:20 final size:19
Alignment explanation
Indices: 1144545--1144599 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1144535 TTGCGATTTT
*
1144545 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1144564 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1144584 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1144600 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1145098 original size:18 final size:18
Alignment explanation
Indices: 1145072--1145116 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1145062 GTCGATCAGA
*
1145072 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
1145090 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
1145108 TGATGGCTC
1 TGATGGCTC
1145117 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:1146461 original size:20 final size:20
Alignment explanation
Indices: 1146436--1146473 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1146426 AATAGTTTCT
1146436 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1146456 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1146474 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1146761 original size:22 final size:22
Alignment explanation
Indices: 1146736--1146779 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1146726 GATTTAGATA
1146736 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1146758 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1146780 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1146992 original size:20 final size:20
Alignment explanation
Indices: 1146967--1147060 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1146957 GATTATGTAT
1146967 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1146987 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1147007 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1147028 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1147048 TATCGCATTGCGA
1 TATCGCGTTGCGA
1147061 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1147032 original size:41 final size:42
Alignment explanation
Indices: 1146987--1147122 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
1146977 CGAAAGTCAG
* * * *
1146987 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
1147028 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
1147070 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
1147111 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
1147123 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:1147061 original size:20 final size:20
Alignment explanation
Indices: 1146947--1147061 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1146937 CGCTTTGAAA
*
1146947 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1146968 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1146988 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1147008 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1147029 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1147049 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1147062 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1147094 original size:20 final size:20
Alignment explanation
Indices: 1147050--1147142 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
1147040 ATAGTCAGTA
*
1147050 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
1147071 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
1147091 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
1147112 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
1147132 TCGCATTGCGA
1 TCGCATTGCGA
1147143 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:1147123 original size:41 final size:41
Alignment explanation
Indices: 1147050--1147145 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
1147040 ATAGTCAGTA
* *
1147050 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1147091 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1147132 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1147146 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1148608 original size:21 final size:21
Alignment explanation
Indices: 1148562--1148610 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1148552 AAATTTCTAT
* *
1148562 TATTTTATTTATATATAAATA
1 TATTATATATATATATAAATA
*
1148583 CATTATATATATATATTAAA-A
1 TATTATATATATATA-TAAATA
1148604 TATTATA
1 TATTATA
1148611 AAAATATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTATATATATATATAAATA
Found at i:1148628 original size:26 final size:24
Alignment explanation
Indices: 1148589--1148656 Score: 91
Period size: 26 Copynumber: 2.7 Consensus size: 24
1148579 AATACATTAT
*
1148589 ATATATATATTAAAATATTATAAAA
1 ATATA-ATTTTAAAATATTATAAAA
*
1148614 ATATTTAATTTTAAAAAATTATAAAA
1 ATA--TAATTTTAAAATATTATAAAA
1148640 ATATAATTTTAAAATAT
1 ATATAATTTTAAAATAT
1148657 AAAATAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 13 0.34
25 3 0.08
26 20 0.53
27 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATAATTTTAAAATATTATAAAA
Found at i:1148663 original size:26 final size:25
Alignment explanation
Indices: 1148608--1148670 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
1148598 TTAAAATATT
**
1148608 ATAAAAATATTTAATTTTAAAAAATT
1 ATAAAAATA-TTAATTTTAAAAAAAA
1148634 ATAAAAATA-TAATTTTAAAATATAAA
1 ATAAAAATATTAATTTTAAAA-A-AAA
1148660 ATAAAAA-ATTA
1 ATAAAAATATTA
1148671 TAAAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 11 0.34
25 2 0.06
26 19 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAAAAATATTAATTTTAAAAAAAA
Found at i:1149603 original size:75 final size:77
Alignment explanation
Indices: 1149403--1149605 Score: 263
Period size: 76 Copynumber: 2.7 Consensus size: 77
1149393 GTTGAACAGA
* * *
1149403 GGGGAATCGGTACCCCCT-TGGGGGGAATCGGTTCCCTCCGAGC-ATACTGGAATTCTCGGAACA
1 GGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAAT-CTGGAAATCTCGGAACA
** *
1149466 AAAACTGTTTAGG
65 AAAACCATTCAGG
* * *
1149479 GGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC-C
1 GGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAACAA
1149542 AAACCATTCA-G
66 AAACCATTCAGG
**
1149553 GGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTATGAGCAATCTGGAA
1 GGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAA
1149606 TTTTTGGCTT
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
74 21 0.19
75 36 0.32
76 53 0.47
77 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (77 bp):
GGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAACAA
AAACCATTCAGG
Found at i:1158150 original size:76 final size:77
Alignment explanation
Indices: 1157984--1158184 Score: 289
Period size: 76 Copynumber: 2.6 Consensus size: 77
1157974 AACAGAGGGC
* * * *
1157984 AATCGGTACCCCCT-TGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACAAAAAC
1 AATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAAAAAC
** *
1158048 TGTTTAGGGGGG
66 CATTCAGGGGGG
* *
1158060 AATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGC-CAAAC
1 AATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAAAAAC
1158124 CATTCAGGGGGG
66 CATTCAGGGGGG
* *
1158136 AATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 AATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
1158185 TTTTTGGCTT
Statistics
Matches: 113, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
76 72 0.64
77 41 0.36
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (77 bp):
AATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAACAAAAAC
CATTCAGGGGGG
Found at i:1160015 original size:21 final size:21
Alignment explanation
Indices: 1159989--1160032 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1159979 TTACTTTTCT
1159989 CCTCT-CTCTCCCCCCCCCCAC
1 CCTCTCCTCT-CCCCCCCCCAC
*
1160010 CCTCTCCTCTCTCCCCCCCAC
1 CCTCTCCTCTCCCCCCCCCAC
1160031 CC
1 CC
1160033 ACGGGAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.05, C:0.75, G:0.00, T:0.20
Consensus pattern (21 bp):
CCTCTCCTCTCCCCCCCCCAC
Found at i:1160022 original size:26 final size:25
Alignment explanation
Indices: 1159986--1160034 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
1159976 CCTTTACTTT
*
1159986 TCTCCTCTCTCTCCCCCCCCCCACCC
1 TCTCCTCTCTC-CCCCCCACCCACCC
1160012 TCTCCTCTCTCCCCCCCACCCAC
1 TCTCCTCTCTCCCCCCCACCCAC
1160035 GGGAATCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.06, C:0.71, G:0.00, T:0.22
Consensus pattern (25 bp):
TCTCCTCTCTCCCCCCCACCCACCC
Found at i:1165676 original size:22 final size:22
Alignment explanation
Indices: 1165651--1165723 Score: 146
Period size: 22 Copynumber: 3.3 Consensus size: 22
1165641 AATGGAATCA
1165651 TTCAACACTGAATGTTGAACCG
1 TTCAACACTGAATGTTGAACCG
1165673 TTCAACACTGAATGTTGAACCG
1 TTCAACACTGAATGTTGAACCG
1165695 TTCAACACTGAATGTTGAACCG
1 TTCAACACTGAATGTTGAACCG
1165717 TTCAACA
1 TTCAACA
1165724 TTCAGCGCGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (22 bp):
TTCAACACTGAATGTTGAACCG
Found at i:1166539 original size:19 final size:19
Alignment explanation
Indices: 1166509--1166562 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
1166499 GCTAGATTGA
1166509 GTATTAAGCCTAACAATAAT
1 GTATT-AGCCTAACAATAAT
1166529 GTATTAGCCTAACAATAAT
1 GTATTAGCCTAACAATAAT
*
1166548 GTATTAGACTAACAA
1 GTATTAGCCTAACAA
1166563 AGATTGGGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 28 0.85
20 5 0.15
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (19 bp):
GTATTAGCCTAACAATAAT
Found at i:1168208 original size:161 final size:161
Alignment explanation
Indices: 1168026--1168345 Score: 613
Period size: 161 Copynumber: 2.0 Consensus size: 161
1168016 GGGTAATTAA
1168026 TCTCATTTCAGGATGATATCTTTTTATGCATATTCACTGTTGTTCATCATTGCTTTAAATCAACT
1 TCTCATTTCAGGATGATATCTTTTTATGCATATTCACTGTTGTTCATCATTGCTTTAAATCAACT
*
1168091 ATTACCATGTTTGCATTTCGGTGGCCTTATGCTTTTGGTGTTATTAACCAGTCTTAGTCTAGGCA
66 ATTACCATGTTTGCATTTCGGTGGCCTTATGCTTTTGGTGTTATTAACCAGTCTTAGACTAGGCA
1168156 CGTAGTAGATGTATCTATGCTAGGATAGTAT
131 CGTAGTAGATGTATCTATGCTAGGATAGTAT
1168187 TCTCATTTCAGGATGATATCTTTTTATGCATATTCACTGTTGTTCATCATTGCTTTAAATCAACT
1 TCTCATTTCAGGATGATATCTTTTTATGCATATTCACTGTTGTTCATCATTGCTTTAAATCAACT
* *
1168252 ATTACCATGTTTGCATTTCGGTGGCCTTATGCTTTTGGTGTTATTAACCGGTCTTAGAGTAGGCA
66 ATTACCATGTTTGCATTTCGGTGGCCTTATGCTTTTGGTGTTATTAACCAGTCTTAGACTAGGCA
1168317 CGTAGTAGATGTATCTATGCTAGGATAGT
131 CGTAGTAGATGTATCTATGCTAGGATAGT
1168346 TGATTTGGCT
Statistics
Matches: 156, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 156 1.00
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (161 bp):
TCTCATTTCAGGATGATATCTTTTTATGCATATTCACTGTTGTTCATCATTGCTTTAAATCAACT
ATTACCATGTTTGCATTTCGGTGGCCTTATGCTTTTGGTGTTATTAACCAGTCTTAGACTAGGCA
CGTAGTAGATGTATCTATGCTAGGATAGTAT
Found at i:1171600 original size:20 final size:21
Alignment explanation
Indices: 1171575--1171667 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1171565 TTTTCCCAAT
*
1171575 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1171595 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1171616 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1171636 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1171657 TCGCAATGCGA
1 TCGCAATGCGA
1171668 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1171681 original size:20 final size:20
Alignment explanation
Indices: 1171656--1171770 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1171646 AATTGGGAAA
*
1171656 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1171676 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* * *
1171697 ATCACAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1171717 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1171737 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1171757 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1171771 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1171682 original size:41 final size:41
Alignment explanation
Indices: 1171575--1171667 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1171565 TTTTCCCAAT
1171575 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1171616 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1171657 TCGCAATGCGA
1 TCGCAATGCGA
1171668 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1171986 original size:22 final size:22
Alignment explanation
Indices: 1171958--1172001 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1171948 CACTCTCTCA
1171958 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1171980 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1172002 TATCTATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1172316 original size:20 final size:20
Alignment explanation
Indices: 1172262--1172320 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1172252 GCGATTATCT
**
1172262 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1172282 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1172302 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1172321 AGAACTATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1173659 original size:18 final size:18
Alignment explanation
Indices: 1173638--1173682 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1173628 TCCACTTCGG
*
1173638 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1173656 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1173674 GAGCCATCA
1 GAGCCATCA
1173683 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1174218 original size:19 final size:20
Alignment explanation
Indices: 1174164--1174230 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1174154 TAGTTTACTT
* *
1174164 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1174184 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1174204 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1174223 TCGCAACG
1 TCGCAACG
1174231 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1174238 original size:14 final size:14
Alignment explanation
Indices: 1174219--1174276 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1174209 ATGCGAAATG
1174219 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1174233 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1174249 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
1174265 AAAATCGTAACG
1 AAAATCGCAACG
1174277 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1174261 original size:32 final size:33
Alignment explanation
Indices: 1174203--1174293 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1174193 GGAAATGGCT
1174203 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1174236 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1174268 ATCGTAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1174294 TGCTATCTGG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1176139 original size:14 final size:14
Alignment explanation
Indices: 1176120--1176155 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1176110 ATTGTTTAAT
1176120 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1176134 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1176148 TGATTTGT
1 TGATTTGT
1176156 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:1176281 original size:14 final size:14
Alignment explanation
Indices: 1176262--1176315 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1176252 CGAAATGGCT
1176262 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
1176276 ATCGCAATGTGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1176295 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1176309 ATCGCAA
1 ATCGCAA
1176316 TGCGATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 18 0.55
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.33
ACGTcount: A:0.48, C:0.19, G:0.20, T:0.13
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1176308 original size:19 final size:19
Alignment explanation
Indices: 1176272--1176308 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1176262 ATCGCAACGA
* *
1176272 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAACGAGAAAT
1176291 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
1176309 ATCGCAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.14, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:1176333 original size:33 final size:33
Alignment explanation
Indices: 1176243--1176320 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
1176233 AAAACAGACT
* ***
1176243 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
1176276 ATCGCAATGTGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1176309 ATCGCAATGCGA
1 ATCGCAATGCGA
1176321 TTTTCATTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:1176364 original size:20 final size:20
Alignment explanation
Indices: 1176339--1176376 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1176329 TCGCATTGCG
*
1176339 ATTTTCTCATTGCGATAGCC
1 ATTTTCGCATTGCGATAGCC
*
1176359 ATTTTCGCGTTGCGATAG
1 ATTTTCGCATTGCGATAG
1176377 TCAAATGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTTTCGCATTGCGATAGCC
Found at i:1177710 original size:19 final size:19
Alignment explanation
Indices: 1177688--1177746 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1177678 GGAAATTACT
1177688 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1177707 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1177721 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1177740 ATCGCAA
1 ATCGCAA
1177747 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1177892 original size:14 final size:14
Alignment explanation
Indices: 1177873--1177909 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1177863 CATCAATTAA
1177873 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1177887 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1177901 ACAAATCAA
1 ACAAATCAA
1177910 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1181433 original size:14 final size:14
Alignment explanation
Indices: 1181414--1181450 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1181404 GGAAATGACT
*
1181414 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
1181428 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1181442 ATCGCAACG
1 ATCGCAACG
1181451 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1181478 original size:47 final size:48
Alignment explanation
Indices: 1181390--1181483 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 48
1181380 ACGAGATAAT
* * *
1181390 GAGAATCGCAACGCGGAAATGACTATCGCAACGATAGAATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACGA
*
1181438 GAGAATCGCAACGC-GAAATGACTATCGCGACCAGACAATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACG
1181484 CGAAATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 28 0.67
48 14 0.33
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (48 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACGA
Found at i:1181496 original size:19 final size:19
Alignment explanation
Indices: 1181474--1181544 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
1181464 GCGACCAGAC
1181474 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1181493 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
1181513 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1181532 AATCGCAATGCGA
1 AATCGCAACGCGA
1181545 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 30 0.62
20 18 0.38
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1181498 original size:33 final size:33
Alignment explanation
Indices: 1181427--1181539 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 33
1181417 GCAACGATAG
* * *
1181427 AATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
1181460 TATCGCGACCAGACAATCGCAACGCGAAATGAA
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
1181493 AATCGCAACCGCGAAATAAAAATCGCAACGCGAAATGAA
1 AATCGCAA-C-C---A-GACAATCGCAACGCGAAATGAA
1181532 AATCGCAA
1 AATCGCAA
1181540 TGCGATTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 34 0.52
34 1 0.02
35 1 0.02
38 1 0.02
39 28 0.43
ACGTcount: A:0.44, C:0.25, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACCAGACAATCGCAACGCGAAATGAA
Found at i:1181507 original size:20 final size:19
Alignment explanation
Indices: 1181365--1181544 Score: 120
Period size: 20 Copynumber: 10.1 Consensus size: 19
1181355 TCTTTTGGTT
*
1181365 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1181384 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1181404 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1181422 G--AT-AGAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1181436 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1181452 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1181470 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1181485 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1181505 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1181524 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1181543 GA
1 GA
1181545 TTTTTGTTTC
Statistics
Matches: 132, Mismatches: 15, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
14 31 0.23
15 4 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.33
20 45 0.34
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1181562 original size:19 final size:19
Alignment explanation
Indices: 1181540--1181606 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
1181530 AAAATCGCAA
*
1181540 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
* *
1181559 TGCGTTTTTTATTTCTCGT
1 TGCGATTTTTATTTCGCGT
* **
1181578 TACGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1181598 TGCGATTTT
1 TGCGATTTT
1181607 CATTCTCGAA
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
19 26 0.72
20 10 0.28
ACGTcount: A:0.10, C:0.16, G:0.21, T:0.52
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1182147 original size:20 final size:20
Alignment explanation
Indices: 1182122--1182174 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1182112 GCGCTATGTA
1182122 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1182142 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1182162 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1182175 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Done.