Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 7 of 17
Found at i:1206892 original size:20 final size:21
Alignment explanation
Indices: 1206854--1206893 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1206844 CAAATGAGAA
*
1206854 TGATGTGGCAAAATGGAATGAC
1 TGATGTGG-AAAATAGAATGAC
1206876 TGATGTGG-AAATAGAATG
1 TGATGTGGAAAATAGAATG
1206894 GTGGTAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.25
Consensus pattern (21 bp):
TGATGTGGAAAATAGAATGAC
Found at i:1211536 original size:145 final size:145
Alignment explanation
Indices: 1211273--1211562 Score: 580
Period size: 145 Copynumber: 2.0 Consensus size: 145
1211263 CACTGAATCT
1211273 GTGACAAAGATCAGCTTCAAACTCATGACATGTTACATGGTGTTTCTGCATGATATAACCATCAA
1 GTGACAAAGATCAGCTTCAAACTCATGACATGTTACATGGTGTTTCTGCATGATATAACCATCAA
1211338 ACTAGATTTCTACTTTGCTTGTTAAATACATAGTAACTGCCTCCACTCTCTGCTCAACAGGAACA
66 ACTAGATTTCTACTTTGCTTGTTAAATACATAGTAACTGCCTCCACTCTCTGCTCAACAGGAACA
1211403 CTACAAATAGAAAAA
131 CTACAAATAGAAAAA
1211418 GTGACAAAGATCAGCTTCAAACTCATGACATGTTACATGGTGTTTCTGCATGATATAACCATCAA
1 GTGACAAAGATCAGCTTCAAACTCATGACATGTTACATGGTGTTTCTGCATGATATAACCATCAA
1211483 ACTAGATTTCTACTTTGCTTGTTAAATACATAGTAACTGCCTCCACTCTCTGCTCAACAGGAACA
66 ACTAGATTTCTACTTTGCTTGTTAAATACATAGTAACTGCCTCCACTCTCTGCTCAACAGGAACA
1211548 CTACAAATAGAAAAA
131 CTACAAATAGAAAAA
1211563 TATTTCAGGC
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (145 bp):
GTGACAAAGATCAGCTTCAAACTCATGACATGTTACATGGTGTTTCTGCATGATATAACCATCAA
ACTAGATTTCTACTTTGCTTGTTAAATACATAGTAACTGCCTCCACTCTCTGCTCAACAGGAACA
CTACAAATAGAAAAA
Found at i:1214180 original size:2 final size:2
Alignment explanation
Indices: 1214173--1214204 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1214163 CTCAATTGAC
1214173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1214205 GTAACCAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1221105 original size:69 final size:66
Alignment explanation
Indices: 1220991--1221125 Score: 211
Period size: 69 Copynumber: 2.0 Consensus size: 66
1220981 GAGCAAACTT
1220991 TTGACTAATATGCTCAAGGAAGGATTTTTATTGGACTCAGGAAGCAATGGCAAACA-TTGAAGAA
1 TTGACTAATATGCTCAAGGAAGGATTTTTATTGGACTCAGGAAGCAATGGC--ACATTTGAAGAA
1221055 TTG
64 TTG
1221058 TTGACTAATATGCTCAAGGAATAAGGA-TTTTATTGGACTCAGGAAGCAATGGCACATTTGAAGA
1 TTGACTAATATGCTCAAGG---AAGGATTTTTATTGGACTCAGGAAGCAATGGCACATTTGAAGA
1221122 ATTG
63 ATTG
1221126 AAACAAGTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
67 22 0.34
68 11 0.17
69 26 0.41
70 5 0.08
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (66 bp):
TTGACTAATATGCTCAAGGAAGGATTTTTATTGGACTCAGGAAGCAATGGCACATTTGAAGAATT
G
Found at i:1227308 original size:30 final size:29
Alignment explanation
Indices: 1227274--1227336 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
1227264 ATTTTAAAAA
1227274 ATTAAATTTTAATCATTTATGTATTAATTT
1 ATTAAATTTTAATCATTTATGTA-TAATTT
* * * *
1227304 ATTAAGTTTTGATCATTTATTTATGATTT
1 ATTAAATTTTAATCATTTATGTATAATTT
1227333 ATTA
1 ATTA
1227337 TTTATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.57
Consensus pattern (29 bp):
ATTAAATTTTAATCATTTATGTATAATTT
Found at i:1227549 original size:22 final size:22
Alignment explanation
Indices: 1227521--1227564 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1227511 TTTGGATATG
*
1227521 AATTTTAAGTATATGATTTAAT
1 AATTTTAAATATATGATTTAAT
* *
1227543 AATTTTAAATTTATGTTTTAAT
1 AATTTTAAATATATGATTTAAT
1227565 TATAATCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
AATTTTAAATATATGATTTAAT
Found at i:1234623 original size:2 final size:2
Alignment explanation
Indices: 1234616--1234655 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1234606 TGAGATACAA
1234616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1234656 GTAAATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1237150 original size:52 final size:52
Alignment explanation
Indices: 1237088--1237248 Score: 122
Period size: 50 Copynumber: 3.2 Consensus size: 52
1237078 ATTTTTTTAT
* * *
1237088 TCGATTCGAGTTTATGAAACTACAATTTGAAGCCAATTCGAGTTGAATTTTC
1 TCGAGTCGAGTTTATGAAAATACAATTTGAAGACAATTCGAGTTGAATTTTC
* * ** ** *
1237140 TCGAGTCGAG--TA-AAAAAT-CTATTTTCCGAA-TTAAGCCGAGTT---TTTTAT
1 TCGAGTCGAGTTTATGAAAATAC-AATTT--GAAGACAATTCGAGTTGAATTTT-C
* *
1237188 TCGATTCGAGTTTATGAAATTACAATTTGAAGACAATTCGAGTTGAATTTTC
1 TCGAGTCGAGTTTATGAAAATACAATTTGAAGACAATTCGAGTTGAATTTTC
1237240 TCGAGTCGA
1 TCGAGTCGA
1237249 ATTAAAAAAA
Statistics
Matches: 78, Mismatches: 19, Indels: 24
0.64 0.16 0.20
Matches are distributed among these distances:
47 4 0.05
48 10 0.13
49 11 0.14
50 20 0.26
51 11 0.14
52 18 0.23
53 4 0.05
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (52 bp):
TCGAGTCGAGTTTATGAAAATACAATTTGAAGACAATTCGAGTTGAATTTTC
Found at i:1237185 original size:100 final size:102
Alignment explanation
Indices: 1237080--1237276 Score: 335
Period size: 100 Copynumber: 2.0 Consensus size: 102
1237070 TGAACTTAAT
*
1237080 TTTTTTATTCGATTCGAGTTTATGAAACTACAATTTGAAGCCAATTCGAGTTGAATTTTCTCGAG
1 TTTTTTATTCGATTCGAGTTTATGAAACTACAATTTGAAGACAATTCGAGTTGAATTTTCTCGAG
1237145 TCG-AGT-AAAAAATCTATTTTCCGAATTAAGCCGAG
66 TCGAAGTAAAAAAATCTATTTTCCGAATTAAGCCGAG
*
1237180 TTTTTTATTCGATTCGAGTTTATGAAATTACAATTTGAAGACAATTCGAGTTGAATTTTCTCGAG
1 TTTTTTATTCGATTCGAGTTTATGAAACTACAATTTGAAGACAATTCGAGTTGAATTTTCTCGAG
* **
1237245 TCGAATTAAAAAAATCTATTTTTTGAATTAAG
66 TCGAAGTAAAAAAATCTATTTTCCGAATTAAG
1237277 TGCAGTTTTA
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
100 66 0.73
101 2 0.02
102 22 0.24
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (102 bp):
TTTTTTATTCGATTCGAGTTTATGAAACTACAATTTGAAGACAATTCGAGTTGAATTTTCTCGAG
TCGAAGTAAAAAAATCTATTTTCCGAATTAAGCCGAG
Found at i:1251550 original size:58 final size:58
Alignment explanation
Indices: 1251478--1251591 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 58
1251468 AGTAATCGCA
* * * *
1251478 CAAACACAATCATAGAGCAAAGGGTAGAAAAACAGAGATCATTTCTGAATCAGATCCC
1 CAAACAAAAGCATAGAGCAAAGGGTAGAAAAACAGAGAGCATTTCTGAACCAGATCCC
** *
1251536 CAAACAAAAGCATAGTTCAAAGGGTAGAAGAACAGAGAGCATTTCTGAACCAGATC
1 CAAACAAAAGCATAGAGCAAAGGGTAGAAAAACAGAGAGCATTTCTGAACCAGATC
1251592 TCCATCATTC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (58 bp):
CAAACAAAAGCATAGAGCAAAGGGTAGAAAAACAGAGAGCATTTCTGAACCAGATCCC
Found at i:1253295 original size:37 final size:37
Alignment explanation
Indices: 1253219--1253295 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
1253209 TTTTTATATT
*
1253219 TTTAATTTTGTAAAAATAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAATAATTATATAAATATTATCAA
* *
1253256 TTTAATTTTTTAAAGAA-AA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AATAATTATATAAATATTAT-CAA
1253293 TTT
1 TTT
1253296 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 20 0.57
38 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAATAATTATATAAATATTATCAA
Found at i:1254088 original size:30 final size:32
Alignment explanation
Indices: 1254042--1254118 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
1254032 TTTAAATAGT
*
1254042 TATTATATTTTATATT-AAT-ATATTTATGTAAA
1 TATTAT-TTTT-TATTAAATAATATTTATATAAA
*
1254074 TATTATTTTTTATTAAATAATATTTATATAAT
1 TATTATTTTTTATTAAATAATATTTATATAAA
1254106 TATTATTTATTTA
1 TATTATTT-TTTA
1254119 GAATTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 4 0.10
31 7 0.17
32 25 0.62
33 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (32 bp):
TATTATTTTTTATTAAATAATATTTATATAAA
Found at i:1254092 original size:17 final size:18
Alignment explanation
Indices: 1254064--1254098 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1254054 TATTAATATA
*
1254064 TTTATGTAAATATTATTT
1 TTTATGTAAATAATATTT
1254082 TTTAT-TAAATAATATTT
1 TTTATGTAAATAATATTT
1254099 ATATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTATGTAAATAATATTT
Found at i:1254275 original size:17 final size:17
Alignment explanation
Indices: 1254253--1254306 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1254243 AATGTTAATA
1254253 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1254270 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1254287 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1254304 TTT
1 TTT
1254307 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1255598 original size:128 final size:128
Alignment explanation
Indices: 1255370--1255668 Score: 544
Period size: 128 Copynumber: 2.3 Consensus size: 128
1255360 GAGGTATGGA
*
1255370 TATCATTGCCCTATTATGTCACTCATGTCTCTCGGGGACACTATTCATATCAGTACCTATTATTT
1 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTT
* *
1255435 CTCAGGGGACTTGAAGGTGCGTTCCCGGGGGCGCGCCTTCTATTATTTTATCAGAGAATATGT
66 CTCAGGGGACTTGAAGGAGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGT
*
1255498 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTATTCATATCAGTACCTATTATTT
1 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTT
* *
1255563 CTTAGGGGACTTGAAGGAGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGT
66 CTCAGGGGACTTGAAGGAGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGT
1255626 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTA
1 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTA
1255669 GATGGATTGT
Statistics
Matches: 164, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 164 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (128 bp):
TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTT
CTCAGGGGACTTGAAGGAGCGTTCCCGGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGT
Found at i:1256097 original size:34 final size:34
Alignment explanation
Indices: 1256058--1256164 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
1256048 TAAGTTGAAA
* *
1256058 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
1256092 TTTAATTTTAAATTTCGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
1256126 TTTTATTTTAAATTTTGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
1256160 TTTAA
1 TTTAA
1256165 AAACATTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:1256702 original size:21 final size:21
Alignment explanation
Indices: 1256672--1256807 Score: 204
Period size: 21 Copynumber: 6.5 Consensus size: 21
1256662 TATGGTATAA
*
1256672 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
1256693 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1256714 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1256735 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1256756 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
1256777 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1256798 AACCCTGCGG
1 AACCCTGCGG
1256808 AGATGGCATA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
20 6 0.06
21 95 0.89
22 6 0.06
ACGTcount: A:0.21, C:0.26, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1256831 original size:42 final size:42
Alignment explanation
Indices: 1256672--1256807 Score: 229
Period size: 42 Copynumber: 3.2 Consensus size: 42
1256662 TATGGTATAA
* *
1256672 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1256714 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
1 AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
*
1256756 AACCCTGCGGGCTCGGAATGTAACCCT-GCGGGCTCGGAATGT
1 AACCCTGCGGGCTCGGAATGTAA-CCTGGCGGGCTAGGAATGT
1256798 AACCCTGCGG
1 AACCCTGCGG
1256808 AGATGGCATA
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
42 87 0.97
43 3 0.03
ACGTcount: A:0.21, C:0.26, G:0.35, T:0.18
Consensus pattern (42 bp):
AACCCTGCGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGT
Found at i:1256837 original size:21 final size:21
Alignment explanation
Indices: 1256811--1256879 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
1256801 CCTGCGGAGA
1256811 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGTGGGCT
1256832 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGTGGGCT
* *
1256853 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGTGGGCT
*
1256874 GGGCAT
1 TGGCAT
1256880 GTACCCCTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.20, C:0.13, G:0.41, T:0.26
Consensus pattern (21 bp):
TGGCATATGAACTGGTGGGCT
Found at i:1265926 original size:18 final size:18
Alignment explanation
Indices: 1265903--1265939 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1265893 AGTACTGAAA
1265903 TTTCCAAAGTTAATGTTT
1 TTTCCAAAGTTAATGTTT
*
1265921 TTTCCAAAGTTGATGTTT
1 TTTCCAAAGTTAATGTTT
1265939 T
1 T
1265940 CAATTGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (18 bp):
TTTCCAAAGTTAATGTTT
Found at i:1266820 original size:36 final size:36
Alignment explanation
Indices: 1266768--1266839 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
1266758 ACTAAATTCT
*
1266768 GCCTTTGTAAATCCGATCGCAATGTCGACAATGGCA
1 GCCTATGTAAATCCGATCGCAATGTCGACAATGGCA
*
1266804 GCCTATGTAAATCCGATCGTAATGTCGACAATGGCA
1 GCCTATGTAAATCCGATCGCAATGTCGACAATGGCA
1266840 ACGGCAACGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (36 bp):
GCCTATGTAAATCCGATCGCAATGTCGACAATGGCA
Found at i:1267141 original size:20 final size:20
Alignment explanation
Indices: 1267116--1267169 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1267106 AATTGGGAAA
1267116 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1267136 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
1267156 ATCGCAATGCGATA
1 ATCGCAATGCGATA
1267170 ATACAAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1267179 original size:61 final size:62
Alignment explanation
Indices: 1267113--1267230 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 62
1267103 GCGAATTGGG
* * * *
1267113 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTAC-T-ATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA-ATACATAATCGCAATGCGATAATAC
* *
1267174 AAAATCGCAACGAGATACTGACTTTCGCAACGTGATAATACATAATCGCAATGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATACATAATCGCAATGCGAT
1267231 TTTCAAAGCG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
60 3 0.06
61 33 0.67
62 13 0.27
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (62 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATACATAATCGCAATGCGATAATAC
Found at i:1267190 original size:21 final size:20
Alignment explanation
Indices: 1267156--1267224 Score: 50
Period size: 21 Copynumber: 3.4 Consensus size: 20
1267146 GATACTTACT
* *
1267156 ATCGCAATGCGATAATACAAA
1 ATCGCAACGAGATAATAC-AA
* *
1267177 ATCGCAACGAGATACTGAC-T
1 ATCGCAACGAGATAAT-ACAA
* *
1267197 TTCGCAACGTGATAATACATA
1 ATCGCAACGAGATAATACA-A
1267218 ATCGCAA
1 ATCGCAA
1267225 TGCGATTTTC
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
19 2 0.06
20 13 0.36
21 19 0.53
22 2 0.06
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATAATACAA
Found at i:1267202 original size:41 final size:41
Alignment explanation
Indices: 1267136--1267224 Score: 115
Period size: 41 Copynumber: 2.2 Consensus size: 41
1267126 GATACTGACT
* * * *
1267136 ATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAACGAGATACTGACTATCGCAACGCGATAATACAAA
* * *
1267177 ATCGCAACGAGATACTGACTTTCGCAACGTGATAATACATA
1 ATCGCAACGAGATACTGACTATCGCAACGCGATAATACAAA
1267218 ATCGCAA
1 ATCGCAA
1267225 TGCGATTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (41 bp):
ATCGCAACGAGATACTGACTATCGCAACGCGATAATACAAA
Found at i:1267424 original size:22 final size:22
Alignment explanation
Indices: 1267396--1267439 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1267386 CACTCTCTCA
1267396 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1267418 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1267440 TATCTCCATC
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:1267748 original size:20 final size:20
Alignment explanation
Indices: 1267694--1267752 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1267684 GCGATTCTCT
**
1267694 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1267714 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1267734 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1267753 AGAAACTATT
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:1269078 original size:18 final size:17
Alignment explanation
Indices: 1269057--1269100 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1269047 TCCACTTCGG
*
1269057 GAGCCATCACATCGCCCA
1 GAGCCATCACATC-ACCA
* *
1269075 GAGCTATCACCTCACCA
1 GAGCCATCACATCACCA
1269092 GAGCCATCA
1 GAGCCATCA
1269101 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.30, C:0.41, G:0.16, T:0.14
Consensus pattern (17 bp):
GAGCCATCACATCACCA
Found at i:1269658 original size:32 final size:32
Alignment explanation
Indices: 1269620--1269708 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
1269610 ACGGATGGCT
1269620 ATCGCAATGCGAAATGAAAATCGCAACGAC-AA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1269652 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
1269684 ATCGCAACGCGAAATGAAATCGCAA
1 ATCGCAATGCGAAATGAAATCGCAA
1269709 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 13 0.24
32 42 0.76
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:1269744 original size:14 final size:14
Alignment explanation
Indices: 1269725--1269782 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1269715 TTGTGTTTCG
1269725 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1269739 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1269755 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1269771 CGTTGCGATTTT
1 CGTTGCGATTTT
1269783 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1269763 original size:32 final size:33
Alignment explanation
Indices: 1269720--1269798 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1269710 GCGATTTGTG
*
1269720 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1269752 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1269785 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1269799 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1269818 original size:21 final size:20
Alignment explanation
Indices: 1269785--1269839 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
1269775 GCGATTTTCA
*
1269785 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
1269805 TTTCCGCGTTGCGATAGTCAT
1 TTT-CGCGTTGCGATAGCCAT
*
1269826 TTTCGTGTTGCGAT
1 TTTCGCGTTGCGAT
1269840 TTTAAATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:1269837 original size:20 final size:20
Alignment explanation
Indices: 1269792--1269858 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
1269782 TCATTTCGCA
* *
1269792 TTGCGATAGCCATTTTCCGCG
1 TTGCGATAGTCATTTT-CGTG
1269813 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGTG
** * *
1269833 TTGCGATTTTAAATTTCGTG
1 TTGCGATAGTCATTTTCGTG
1269853 TTGCGA
1 TTGCGA
1269859 AAGTAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGTG
Found at i:1269865 original size:20 final size:20
Alignment explanation
Indices: 1269812--1269865 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1269802 CATTTTCCGC
* *
1269812 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTAAATTTCGT
**
1269832 GTTGCGATTTTAAATTTCGT
1 GTTGCGATAGTAAATTTCGT
*
1269852 GTTGCGAAAGTAAA
1 GTTGCGATAGTAAA
1269866 ATTCTTCTTC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (20 bp):
GTTGCGATAGTAAATTTCGT
Found at i:1271579 original size:14 final size:14
Alignment explanation
Indices: 1271560--1271595 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1271550 ATTGTTTAAT
1271560 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1271574 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1271588 TGATTTGT
1 TGATTTGT
1271596 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:1271703 original size:20 final size:20
Alignment explanation
Indices: 1271678--1271716 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1271668 ATGTTGAAGG
1271678 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
1271698 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
1271717 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:1271774 original size:19 final size:19
Alignment explanation
Indices: 1271722--1271767 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1271712 GCAACGAGAG
1271722 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1271741 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1271760 AATCGCAA
1 AATCGCAA
1271768 CGAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1271854 original size:20 final size:20
Alignment explanation
Indices: 1271812--1271881 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
1271802 GCGATTTTGT
* * *
1271812 CGTTACGATAGTCA-TTTCA
1 CGTTGCGATAGCCATTTTCG
1271831 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1271851 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1271871 CGTTGCGATAG
1 CGTTGCGATAG
1271882 TCAAATGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 12 0.26
20 35 0.74
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:1272119 original size:20 final size:20
Alignment explanation
Indices: 1272094--1272144 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1272084 AAATGATTGC
1272094 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
1272114 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
*
1272134 CTTTCACAACG
1 CTTTCGCAACG
1272145 AGATAATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:1272920 original size:24 final size:24
Alignment explanation
Indices: 1272886--1272939 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1272876 GTATTCGAAA
*
1272886 TTTGATCTTGGTAAATACCCGGAC
1 TTTGATATTGGTAAATACCCGGAC
* * *
1272910 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTAAATACCCGGAC
1272934 TTTGAT
1 TTTGAT
1272940 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTAAATACCCGGAC
Found at i:1273131 original size:12 final size:12
Alignment explanation
Indices: 1273114--1273138 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1273104 ATATAATCCT
1273114 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1273126 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1273138 G
1 G
1273139 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1275459 original size:33 final size:33
Alignment explanation
Indices: 1275412--1275539 Score: 177
Period size: 33 Copynumber: 3.8 Consensus size: 33
1275402 GGAAATTACT
* *
1275412 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAGA
* * *
1275445 ATCGCAATGTGAAATGAAAAATCGCAACGCTAA-T
1 ATCGCAATGCGAAATG-AAAATCGCAACG-AAAGA
*
1275479 TTCGCAATGCGAAATGAAAATCGCAACGAAAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAGA
1275512 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1275540 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
32 2 0.02
33 53 0.65
34 26 0.32
35 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAGA
Found at i:1275526 original size:67 final size:66
Alignment explanation
Indices: 1275413--1275546 Score: 223
Period size: 67 Copynumber: 2.0 Consensus size: 66
1275403 GAAATTACTA
* * *
1275413 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGTGAAATGAAAAATCGCAACGCTAA
1 TCGCAATACGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATG-AAAATCGCAACGCGAA
1275478 TT
65 TT
*
1275480 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATACGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1275545 T
66 T
1275546 T
1 T
1275547 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 18 0.29
67 45 0.71
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (66 bp):
TCGCAATACGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1275542 original size:19 final size:19
Alignment explanation
Indices: 1275412--1275543 Score: 87
Period size: 19 Copynumber: 7.7 Consensus size: 19
1275402 GGAAATTACT
*
1275412 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1275431 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1275445 ATCGCAATGTGAAATGAAAA
1 ATCGCAATGCGAAATG-AAA
* *
1275465 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1275479 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1275498 ATCGCAA--CGAAA-G--A
1 ATCGCAATGCGAAATGAAA
1275512 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1275531 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1275544 TTTAATTTCG
Statistics
Matches: 86, Mismatches: 11, Indels: 32
0.67 0.09 0.25
Matches are distributed among these distances:
14 26 0.30
15 1 0.01
16 10 0.12
17 8 0.09
18 3 0.03
19 29 0.34
20 9 0.10
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1275561 original size:19 final size:19
Alignment explanation
Indices: 1275548--1275600 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
1275538 CGCGAATTTA
1275548 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1275567 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1275586 ATTTCGCGTTGCGAT
1 ATTTCGCGTTGCGAT
1275601 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:1275726 original size:14 final size:14
Alignment explanation
Indices: 1275707--1275743 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1275697 CATCAATTAA
1275707 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1275721 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1275735 ACAAATCAA
1 ACAAATCAA
1275744 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:1277156 original size:42 final size:42
Alignment explanation
Indices: 1277094--1277263 Score: 145
Period size: 41 Copynumber: 4.1 Consensus size: 42
1277084 GTGAATCGGA
* *
1277094 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1277136 CTCTTG-ACGGTGGGAGGGGACTC-TCGAGGAATGATAGAGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAAGG-ATGACAGTGGC
* * * * * * *
1277177 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAAGGATGACAGTGGC
* *
1277219 CTCTTGAACGGT-GGAGGGGACTC-TCGAGGAATGATAG-GGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAAGG-ATGACAGTGGC
1277259 CTCTT
1 CTCTT
1277264 CAATGATAGG
Statistics
Matches: 100, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
40 15 0.15
41 41 0.41
42 41 0.41
43 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.24
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAAGGATGACAGTGGC
Found at i:1277235 original size:83 final size:81
Alignment explanation
Indices: 1277124--1277295 Score: 310
Period size: 83 Copynumber: 2.1 Consensus size: 81
1277114 CCTCTTCAAC
1277124 GATGACAGTGGCCTCTTGACGGTGGGAGGGGACTCTCGAGGAATGATAGAGGCCTCTTCAATGAT
1 GATGACAGTGGCCTCTTGACGGTGGGAGGGGACTCTCGAGGAATGATAG-GGCCTCTTCAATGAT
1277189 AGGAGTGGACTCTTGAGG
65 AGGA-TGGACTCTTGAGG
1277207 GATGACAGTGGCCTCTTGAACGGT-GGAGGGGACTCTCGAGGAATGATAGGGCCTCTTCAATGAT
1 GATGACAGTGGCCTCTTG-ACGGTGGGAGGGGACTCTCGAGGAATGATAGGGCCTCTTCAATGAT
1277271 AGGATGGACTCTTGAGG
65 AGGATGGACTCTTGAGG
1277288 GATGACAG
1 GATGACAG
1277296 ACGAGTCGGG
Statistics
Matches: 88, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
81 21 0.24
82 19 0.22
83 43 0.49
84 5 0.06
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.23
Consensus pattern (81 bp):
GATGACAGTGGCCTCTTGACGGTGGGAGGGGACTCTCGAGGAATGATAGGGCCTCTTCAATGATA
GGATGGACTCTTGAGG
Found at i:1277280 original size:40 final size:42
Alignment explanation
Indices: 1277148--1277292 Score: 170
Period size: 42 Copynumber: 3.5 Consensus size: 42
1277138 CTTGACGGTG
*
1277148 GGAGGGGACTCTCGAGGAATGATAGAGGCCTCTTCAATGATA
1 GGAGTGGACTCTCGAGGAATGATAGAGGCCTCTTCAATGATA
* * * * * * *
1277190 GGAGTGGACTCTTGAGGGATGACAGTGGCCTCTTGAACGGT-
1 GGAGTGGACTCTCGAGGAATGATAGAGGCCTCTTCAATGATA
*
1277231 GGAGGGGACTCTCGAGGAATGATAG-GGCCTCTTCAATGATA
1 GGAGTGGACTCTCGAGGAATGATAGAGGCCTCTTCAATGATA
* *
1277272 GGA-TGGACTCTTGAGGGATGA
1 GGAGTGGACTCTCGAGGAATGA
1277293 CAGACGAGTC
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
40 27 0.32
41 24 0.29
42 33 0.39
ACGTcount: A:0.25, C:0.16, G:0.37, T:0.23
Consensus pattern (42 bp):
GGAGTGGACTCTCGAGGAATGATAGAGGCCTCTTCAATGATA
Found at i:1277639 original size:94 final size:86
Alignment explanation
Indices: 1277512--1277694 Score: 267
Period size: 94 Copynumber: 2.0 Consensus size: 86
1277502 ATCTTTCAAA
* *
1277512 ACTTCAACCAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAG
1 ACTTCAACCAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG-TTAG
1277577 CAGAATTGGCAGCAACCGAATAAATTT
61 CAGAATTGGCAGCAACCGAAT-AATTT
1277604 ACTTCAAACCAAAGACAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTAGCAG
1 ACTTC-AACCAAAGACAAA-AAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTAGCAG
*
1277669 TATTGGCAGCAACCGAATAATTT
64 AATTGGCAGCAACCGAATAATTT
1277692 ACT
1 ACT
1277695 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
88 8 0.09
89 24 0.28
90 8 0.09
92 5 0.06
93 13 0.15
94 28 0.33
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (86 bp):
ACTTCAACCAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTAGCAGAA
TTGGCAGCAACCGAATAATTT
Found at i:1278106 original size:9 final size:9
Alignment explanation
Indices: 1278092--1278119 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1278082 GATGGCTCTC
1278092 GAAGTGGAG
1 GAAGTGGAG
1278101 GAAGTGGAG
1 GAAGTGGAG
1278110 GAAGTGGAG
1 GAAGTGGAG
1278119 G
1 G
1278120 CTGCTCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.57, T:0.11
Consensus pattern (9 bp):
GAAGTGGAG
Found at i:1279345 original size:39 final size:34
Alignment explanation
Indices: 1279302--1279391 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 34
1279292 TCTTTTGGTT
* *
1279302 GAAATGAAAATCGCAACGAGATAAAGAGAATTGCAACGC
1 GAAATGAAAATCGCAACG-G----AGAGAATCGCAACAC
**
1279341 GAAATGACTATCGCAAC-GAGAGAATCGCAACAC
1 GAAATGAAAATCGCAACGGAGAGAATCGCAACAC
1279374 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
1279392 CGAAATGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
33 28 0.64
37 1 0.02
39 15 0.34
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (34 bp):
GAAATGAAAATCGCAACGGAGAGAATCGCAACAC
Found at i:1279358 original size:19 final size:19
Alignment explanation
Indices: 1279302--1279446 Score: 121
Period size: 19 Copynumber: 8.1 Consensus size: 19
1279292 TCTTTTGGTT
*
1279302 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* * *
1279321 GATAAAGAGAATTGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1279341 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
1279358 G--A-GAGAATCGCAACAC
1 GAAATGAAAATCGCAACGC
1279374 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1279393 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1279410 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1279426 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1279445 GA
1 GA
1279447 TTTTGGTTCG
Statistics
Matches: 100, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.19
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 54 0.54
20 15 0.15
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1279371 original size:33 final size:33
Alignment explanation
Indices: 1279326--1279391 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1279316 AACGAGATAA
* * **
1279326 AGAGAATTGCAACGCGAAATGACTATCGCAACG
1 AGAGAATCGCAACACGAAATGAAAATCGCAACG
1279359 AGAGAATCGCAACACGAAATGAAAATCGCAACG
1 AGAGAATCGCAACACGAAATGAAAATCGCAACG
1279392 CGAAATGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
AGAGAATCGCAACACGAAATGAAAATCGCAACG
Found at i:1279394 original size:52 final size:52
Alignment explanation
Indices: 1279334--1279446 Score: 190
Period size: 52 Copynumber: 2.2 Consensus size: 52
1279324 AAAGAGAATT
**
1279334 GCAACGCGAAATGACTATCGCAACGAGAGAATCGCAACACGAAATGAAAATC
1 GCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACACGAAATGAAAATC
*
1279386 GCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACACGAAATGAAAATC
*
1279438 GCAATGCGA
1 GCAACGCGA
1279447 TTTTGGTTCG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (52 bp):
GCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACACGAAATGAAAATC
Found at i:1279880 original size:22 final size:22
Alignment explanation
Indices: 1279824--1279880 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
1279814 TGGTTGTGAG
**
1279824 GGATTTCGCCGGCGATGGGGAC
1 GGATTTCGCCGTAGATGGGGAC
** **
1279846 GGAAATCTTCGTAGATGGGGAC
1 GGATTTCGCCGTAGATGGGGAC
1279868 GGATTTCGCCGTA
1 GGATTTCGCCGTA
1279881 AAGAGTTAGA
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.39, T:0.23
Consensus pattern (22 bp):
GGATTTCGCCGTAGATGGGGAC
Found at i:1280063 original size:20 final size:20
Alignment explanation
Indices: 1280038--1280090 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1280028 GCGCTATGTA
1280038 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
**
1280058 AATCGCGTTAAGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1280078 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1280091 TTTTGTATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1280124 original size:20 final size:20
Alignment explanation
Indices: 1280099--1280152 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1280089 GATTTTGTAT
1280099 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1280119 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1280139 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1280153 TTCCCAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1280164 original size:20 final size:20
Alignment explanation
Indices: 1280141--1280191 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1280131 ATAGTCAGTA
*
1280141 TCGCATTGCGATTTCCCAAT
1 TCGCATTGCGATTTACCAAT
* **
1280161 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
1280181 TCGCATTGCGA
1 TCGCATTGCGA
1280192 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:1280262 original size:21 final size:21
Alignment explanation
Indices: 1280222--1280262 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1280212 ACTGTAGACC
**
1280222 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1280243 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1280263 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1283845 original size:15 final size:15
Alignment explanation
Indices: 1283825--1283871 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
1283815 AAATGGAAAG
*
1283825 ACAGAACAGAACAGA
1 ACAGAACAGAACGGA
1283840 ACAGAACAGAACGGA
1 ACAGAACAGAACGGA
*
1283855 ACAGAACGGAACGGA
1 ACAGAACAGAACGGA
1283870 AC
1 AC
1283872 GGAGTTGTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.53, C:0.21, G:0.26, T:0.00
Consensus pattern (15 bp):
ACAGAACAGAACGGA
Found at i:1283874 original size:5 final size:5
Alignment explanation
Indices: 1283825--1283871 Score: 67
Period size: 5 Copynumber: 9.4 Consensus size: 5
1283815 AAATGGAAAG
* * *
1283825 ACAGA ACAGA ACAGA ACAGA ACAGA ACGGA ACAGA ACGGA ACGGA AC
1 ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA ACAGA AC
1283872 GGAGTTGTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.53, C:0.21, G:0.26, T:0.00
Consensus pattern (5 bp):
ACAGA
Found at i:1284259 original size:30 final size:30
Alignment explanation
Indices: 1284218--1284274 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1284208 CTATAGTTCG
*
1284218 AATGAAGGTCGTCAGGTGGTCTGGGCGACC
1 AATGAAAGTCGTCAGGTGGTCTGGGCGACC
*
1284248 AATGAAAGTCGTCGGGTGGTCTGGGCG
1 AATGAAAGTCGTCAGGTGGTCTGGGCG
1284275 CCATGCCGTT
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:0.19, C:0.18, G:0.42, T:0.21
Consensus pattern (30 bp):
AATGAAAGTCGTCAGGTGGTCTGGGCGACC
Found at i:1284484 original size:50 final size:50
Alignment explanation
Indices: 1284421--1284522 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
1284411 TTTATCCTAT
1284421 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1284471 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1284521 TT
1 TT
1284523 CAATAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
Found at i:1287541 original size:20 final size:20
Alignment explanation
Indices: 1287516--1287566 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
1287506 CACGGAATGT
*
1287516 AAGATTATCAGTG-GAAATAA
1 AAGATTACCAGTGTG-AATAA
1287536 AAGATTACCAGTGTGAATAA
1 AAGATTACCAGTGTGAATAA
1287556 AAGATTACCAG
1 AAGATTACCAG
1287567 GGAATAGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.24
Consensus pattern (20 bp):
AAGATTACCAGTGTGAATAA
Found at i:1289476 original size:2 final size:2
Alignment explanation
Indices: 1289469--1289520 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1289459 TGTATCTGTG
1289469 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1289511 TA TA TA TA TA
1 TA TA TA TA TA
1289521 ATGGCTTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1291033 original size:15 final size:15
Alignment explanation
Indices: 1291013--1291043 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1291003 TACACTATTT
*
1291013 TTTGCACTGTTCGAA
1 TTTGCACTATTCGAA
1291028 TTTGCACTATTCGAA
1 TTTGCACTATTCGAA
1291043 T
1 T
1291044 AGTGTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (15 bp):
TTTGCACTATTCGAA
Found at i:1295835 original size:64 final size:65
Alignment explanation
Indices: 1295656--1295815 Score: 259
Period size: 65 Copynumber: 2.5 Consensus size: 65
1295646 GATTTAATTG
*
1295656 AACATCGAATGCATTTGATGCATCAATGCACATACCATGCATCGATGCACTCAGGGTTTTATAAA
1 AACATCGAATGCATTTGATGCATCAATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
* * *
1295721 AACATCGAATGTATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTT-TCAA
1 AACATCGAATGCATTTGATGCATCAATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
* *
1295785 AACATCGAATGCATTTTATGCATTAATGCAC
1 AACATCGAATGCATTTGATGCATCAATGCAC
1295816 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 30 0.34
65 57 0.66
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCAATGCACATACCATGCATCGATGCACTCAGGCTTTTATAAA
Found at i:1304413 original size:19 final size:19
Alignment explanation
Indices: 1304389--1304440 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1304379 AATGCATTTG
1304389 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1304408 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
1304427 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1304441 TCAGGCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:1304439 original size:83 final size:83
Alignment explanation
Indices: 1304323--1304485 Score: 206
Period size: 83 Copynumber: 2.0 Consensus size: 83
1304313 TATTCAAAGG
* * *
1304323 CATGCACCGATGCATCAAACTATGCATCGATGCAC-CGATGATTTAATT-GAACATCGAATGCAT
1 CATGCACCGATGCATCAAACCATGCATCGATGCACTC-AGGATTT--TTAAAACATCGAATGCAT
1304386 TTGATGCATCGATGCACATAC
63 TTGATGCATCGATGCACATAC
* * *
1304407 CATGCATCGATGCA-CATACCATGCATCGATGCACTCAGGCTTTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCATCAAACCATGCATCGATGCACTCAGGATTTTT-AAAACATCGAATGCATTT
*
1304471 TATGCATCGATGCAC
65 GATGCATCGATGCAC
1304486 TCTTAGTGCA
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
81 2 0.03
83 53 0.77
84 14 0.20
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (83 bp):
CATGCACCGATGCATCAAACCATGCATCGATGCACTCAGGATTTTTAAAACATCGAATGCATTTG
ATGCATCGATGCACATAC
Found at i:1306899 original size:6 final size:6
Alignment explanation
Indices: 1306888--1306957 Score: 52
Period size: 6 Copynumber: 10.8 Consensus size: 6
1306878 TGATAAGTCG
* * *
1306888 AATTAA AATTAACA AATTAA AATAAAAA AATGAAA ACATTTA AAT-AA
1 AATTAA AATT-A-A AATTAA AAT--TAA AAT-TAA A-ATTAA AATTAA
1306935 AATTAA AATTAA AATTAA AATTA
1 AATTAA AATTAA AATTAA AATTA
1306958 TGTTGTCTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
5 4 0.08
6 29 0.55
7 8 0.15
8 12 0.23
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (6 bp):
AATTAA
Found at i:1309074 original size:21 final size:21
Alignment explanation
Indices: 1309032--1309074 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1309022 TTTCTGGGCT
*
1309032 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
1309053 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
1309074 A
1 A
1309075 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1310049 original size:103 final size:103
Alignment explanation
Indices: 1309618--1310038 Score: 779
Period size: 103 Copynumber: 4.1 Consensus size: 103
1309608 GTAGAGGGTC
1309618 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1309683 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1309721 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1309786 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
1309824 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGATACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1309889 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1309927 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
1309992 TTGATCATTGGTATATGTATATGATTCGTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1310030 TATGTGGTC
1 TATGTGGTC
1310039 TTTATGGACA
Statistics
Matches: 312, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 312 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1310091 original size:23 final size:23
Alignment explanation
Indices: 1310058--1310120 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
1310048 ATTATTATAT
1310058 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1310081 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
1310104 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
1310121 ATATGAGCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1315273 original size:21 final size:21
Alignment explanation
Indices: 1315231--1315273 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1315221 TTTCTGGGCT
*
1315231 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
1315252 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
1315273 A
1 A
1315274 ACAAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1315326 original size:20 final size:20
Alignment explanation
Indices: 1315301--1315338 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1315291 GAATGCTAGA
*
1315301 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
1315321 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
1315339 TAAAAAAAAG
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:1315996 original size:103 final size:103
Alignment explanation
Indices: 1315817--1316240 Score: 812
Period size: 103 Copynumber: 4.1 Consensus size: 103
1315807 GTAGAGGGTC
1315817 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1315882 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1315920 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1315985 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1316023 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1316088 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
1316126 TATGTGGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1316191 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1316229 TATGTGGTCCTT
1 TATGTGGTCCTT
1316241 ATGGACATTA
Statistics
Matches: 316, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 316 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1316293 original size:23 final size:23
Alignment explanation
Indices: 1316258--1316301 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1316248 TTATTATATG
*
1316258 GCACTACGGTGCAATTCTACGCA
1 GCACTACGATGCAATTCTACGCA
*
1316281 GCACTCCGATGCAATTCTACG
1 GCACTACGATGCAATTCTACG
1316302 TGGAACTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (23 bp):
GCACTACGATGCAATTCTACGCA
Found at i:1320690 original size:103 final size:103
Alignment explanation
Indices: 1320465--1320682 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
1320455 GTCGAGGGTC
1320465 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
1320530 TTGATCCTTGGCATATGTATATGATTTTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1320568 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1320633 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1320671 TATGTGGTCCTT
1 TATGTGGTCCTT
1320683 ATAGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1320765 original size:23 final size:23
Alignment explanation
Indices: 1320689--1320766 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
1320679 CCTTATAGAC
* *
1320689 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
1320713 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
1320736 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
1320759 ATTATATG
1 ATTATATG
1320767 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:1324280 original size:18 final size:18
Alignment explanation
Indices: 1324254--1324288 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1324244 TCATTTTTAC
*
1324254 TCTTTCTCTATTCCTTTT
1 TCTTCCTCTATTCCTTTT
*
1324272 TCTTCCTCTATTTCTTT
1 TCTTCCTCTATTCCTTT
1324289 CTCTATTTAT
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:0.06, C:0.29, G:0.00, T:0.66
Consensus pattern (18 bp):
TCTTCCTCTATTCCTTTT
Found at i:1334321 original size:37 final size:37
Alignment explanation
Indices: 1334270--1334361 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
1334260 CTTTTACCTG
*
1334270 ATAAAGACTCCTAATAAAATTGCAT-AACAGTTGCCTA
1 ATAAAGACTCCTAATAAAATTGAATAAAC-GTTGCCTA
* *
1334307 TTAAAGACTCCTAATAAAGTTGAATAAACGTTGCCTA
1 ATAAAGACTCCTAATAAAATTGAATAAACGTTGCCTA
1334344 ATAAA-ACTCCTAATAAAA
1 ATAAAGACTCCTAATAAAA
1334362 ATAAACTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 12 0.24
37 34 0.69
38 3 0.06
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (37 bp):
ATAAAGACTCCTAATAAAATTGAATAAACGTTGCCTA
Found at i:1342817 original size:32 final size:32
Alignment explanation
Indices: 1342765--1342851 Score: 115
Period size: 32 Copynumber: 2.8 Consensus size: 32
1342755 GCTACTTAGA
*
1342765 ACATAGGT-ATAT-TGTCCATATGTCTCAAAAG
1 ACATAGGTAAT-TCTGTCCATATGTCCCAAAAG
* *
1342796 ACATATGTAATTCTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCAAAAG
*
1342828 ACATAGGTAATTCTATCCATATGT
1 ACATAGGTAATTCTGTCCATATGT
1342852 TCCGTAGAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
31 8 0.16
32 41 0.84
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (32 bp):
ACATAGGTAATTCTGTCCATATGTCCCAAAAG
Found at i:1342864 original size:32 final size:32
Alignment explanation
Indices: 1342779--1342869 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
1342769 AGGTATATTG
* * * *
1342779 TCCATATGTCTCAAAAGACATATGTAATTCTG
1 TCCATATGTCCCGAAAGACATAGGTAATTCTA
1342811 TCCATATGTCCCGAAAGACATAGGTAATTCTA
1 TCCATATGTCCCGAAAGACATAGGTAATTCTA
* *
1342843 TCCATATGTTCCG-TAGAACATAGGTAA
1 TCCATATGTCCCGAAAG-ACATAGGTAA
1342870 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 2 0.04
32 50 0.96
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (32 bp):
TCCATATGTCCCGAAAGACATAGGTAATTCTA
Found at i:1343643 original size:24 final size:20
Alignment explanation
Indices: 1343590--1343666 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
1343580 TTCCCTTTGA
*
1343590 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
1343610 AGTGCATCGATGCATTCCTTAAC
1 AGTGCATCGATGCATT-C-T-AC
* * *
1343633 ATGTGCATCGATGCACTATCC
1 A-GTGCATCGATGCATTCTAC
1343654 A-TGCATCGATGCA
1 AGTGCATCGATGCA
1343667 CTATCCATGC
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 12 0.24
20 15 0.31
21 3 0.06
22 2 0.04
23 3 0.06
24 14 0.29
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1343660 original size:19 final size:19
Alignment explanation
Indices: 1343636--1343680 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1343626 CCTTAACATG
1343636 TGCATCGATGCACTATCCA
1 TGCATCGATGCACTATCCA
1343655 TGCATCGATGCACTATCCA
1 TGCATCGATGCACTATCCA
1343674 TGCATCG
1 TGCATCG
1343681 GTACACAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
TGCATCGATGCACTATCCA
Found at i:1351296 original size:60 final size:61
Alignment explanation
Indices: 1351199--1351345 Score: 140
Period size: 60 Copynumber: 2.4 Consensus size: 61
1351189 TGGGGATCAA
** ** * *
1351199 TTTAGAATGCAT-GTCATAGTTTGGGGATGCAATTAAAA-AGTTCAAAAGTTTGAGAACT-AC
1 TTTAGAATG-ATAGTCATAGTTTAAGGATAAAACTAAAATA-TTCAAAAGTTTAAGAACTAAC
* * * *
1351259 TTTAGAATGATAGTCATAGTTTAAGGATAAAACTAAAATATTTAAAAGTTTAAGGATTAAT
1 TTTAGAATGATAGTCATAGTTTAAGGATAAAACTAAAATATTCAAAAGTTTAAGAACTAAC
* *
1351320 TTTA-AATGAAAGTCATATTTTAAGGA
1 TTTAGAATGATAGTCATAGTTTAAGGA
1351346 CACGTGATGT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
59 2 0.03
60 64 0.89
61 6 0.08
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (61 bp):
TTTAGAATGATAGTCATAGTTTAAGGATAAAACTAAAATATTCAAAAGTTTAAGAACTAAC
Found at i:1353083 original size:70 final size:70
Alignment explanation
Indices: 1352996--1353135 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
1352986 ATGTCATCTA
1352996 TAATCAAGGCGAAAATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTCCGATTTCCACCAGGAAT
1 TAATCAAGGCGAAAATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTCCGATTTCCACCAGGAAT
1353061 GCCTC
66 GCCTC
1353066 TAATCAAGGCGAAAATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTCCGATTTCCACCAGGAAT
1 TAATCAAGGCGAAAATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTCCGATTTCCACCAGGAAT
1353131 GCCTC
66 GCCTC
1353136 GGTGTCGCCA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.19
Consensus pattern (70 bp):
TAATCAAGGCGAAAATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTCCGATTTCCACCAGGAAT
GCCTC
Found at i:1354739 original size:6 final size:7
Alignment explanation
Indices: 1354723--1354751 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1354713 ATTTCTAGTG
1354723 TTTTAAT
1 TTTTAAT
1354730 TTTTAAT
1 TTTTAAT
1354737 TTTTAA-
1 TTTTAAT
1354743 TTTTAAT
1 TTTTAAT
1354750 TT
1 TT
1354752 AATATGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTAAT
Found at i:1354746 original size:13 final size:14
Alignment explanation
Indices: 1354723--1354751 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1354713 ATTTCTAGTG
1354723 TTTTAATTTTTAAT
1 TTTTAATTTTTAAT
1354737 TTTTAA-TTTTAAT
1 TTTTAATTTTTAAT
1354750 TT
1 TT
1354752 AATATGATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTAATTTTTAAT
Found at i:1354967 original size:38 final size:38
Alignment explanation
Indices: 1354924--1354996 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
1354914 TTGAATGATT
1354924 TAAAAAGCTCCAAAATCCATAAATTCTAACCTTAATTA
1 TAAAAAGCTCCAAAATCCATAAATTCTAACCTTAATTA
1354962 TAAAAAGCTCCAAAATCCATAAATTCTAACCTTAA
1 TAAAAAGCTCCAAAATCCATAAATTCTAACCTTAA
1354997 CCTCTCTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.48, C:0.22, G:0.03, T:0.27
Consensus pattern (38 bp):
TAAAAAGCTCCAAAATCCATAAATTCTAACCTTAATTA
Found at i:1355892 original size:5 final size:5
Alignment explanation
Indices: 1355873--1355916 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
1355863 GATCATTCGT
*
1355873 TTTTA ATTTA TTTTTA TTTTA --TTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1355917 ATATAGTCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 3 0.09
5 27 0.79
6 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:1355902 original size:13 final size:13
Alignment explanation
Indices: 1355884--1355908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1355874 TTTAATTTAT
1355884 TTTTATTTTATTA
1 TTTTATTTTATTA
1355897 TTTTATTTTATT
1 TTTTATTTTATT
1355909 TTATTTTAAT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:1355962 original size:20 final size:20
Alignment explanation
Indices: 1355909--1355962 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
1355899 TTATTTTATT
* *
1355909 TTATTTTAATATAGTCACTA
1 TTATTTTAATTTAGCCACTA
*
1355929 TTAGTTTTTGATTTAGCCACTA
1 TTA--TTTTAATTTAGCCACTA
1355951 TTATTTTAATTT
1 TTATTTTAATTT
1355963 TTTTCATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.56
Consensus pattern (20 bp):
TTATTTTAATTTAGCCACTA
Found at i:1356216 original size:30 final size:29
Alignment explanation
Indices: 1356165--1356262 Score: 99
Period size: 30 Copynumber: 3.3 Consensus size: 29
1356155 GTCTATGTTT
* *
1356165 TTTTC-CTATTATAGTCCTTTAAATTTATG
1 TTTTCGCTATTTTAG-CCTTTAAGTTTATG
*
1356194 TTTTCGCTATTTTAGCCTTTTAAGTTTCTG
1 TTTTCGCTATTTTAGCC-TTTAAGTTTATG
* * *
1356224 TTTTTGCCATTTTAATCCTTTAAGTTTATG
1 TTTTCGCTATTTT-AGCCTTTAAGTTTATG
*
1356254 TTTTTGCTA
1 TTTTCGCTA
1356263 GATCTCTTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
29 7 0.12
30 48 0.83
31 3 0.05
ACGTcount: A:0.18, C:0.14, G:0.10, T:0.57
Consensus pattern (29 bp):
TTTTCGCTATTTTAGCCTTTAAGTTTATG
Found at i:1362762 original size:22 final size:23
Alignment explanation
Indices: 1362719--1362762 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1362709 CATTATATAT
1362719 AATATATTATAATTAAATGATAA
1 AATATATTATAATTAAATGATAA
1362742 AATATATT-TAA-TAAATAGATA
1 AATATATTATAATTAAAT-GATA
1362763 GTACTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 7 0.35
23 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (23 bp):
AATATATTATAATTAAATGATAA
Found at i:1365106 original size:32 final size:32
Alignment explanation
Indices: 1365005--1365111 Score: 112
Period size: 31 Copynumber: 3.4 Consensus size: 32
1364995 TAGGTCCTGA
* **
1365005 AGAACCTAGGTAA-ATTGTCCATATGTTCTTT
1 AGAACATAGGTAATATTGTCCATATGTTCCGT
* * *
1365036 AGAACATAGGT-ATACTGTTCATATGTCCCG-
1 AGAACATAGGTAATATTGTCCATATGTTCCGT
* *
1365066 AAAGACATAGGTAATTTTGTCCATATGTTCCGT
1 AGA-ACATAGGTAATATTGTCCATATGTTCCGT
1365099 AGAACATAGGTAA
1 AGAACATAGGTAA
1365112 ACCCTCGACT
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
30 3 0.05
31 30 0.50
32 25 0.42
33 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (32 bp):
AGAACATAGGTAATATTGTCCATATGTTCCGT
Found at i:1366014 original size:20 final size:20
Alignment explanation
Indices: 1365989--1366043 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1365979 CGAAATTCCC
1365989 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCACCCCTTA
**
1366009 ATGCATCGACACACCCCTTA
1 ATGCATCGATGCACCCCTTA
*
1366029 ATGCATCAATGCACC
1 ATGCATCGATGCACC
1366044 TTCAAATTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.36, G:0.13, T:0.22
Consensus pattern (20 bp):
ATGCATCGATGCACCCCTTA
Found at i:1369587 original size:24 final size:23
Alignment explanation
Indices: 1369560--1369617 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
1369550 ATATGGGAGT
*
1369560 GAAGAGGAAGGAGGAGATGGAAAG
1 GAAGA-GAAGGAGGAGAGGGAAAG
* *
1369584 GAAGAAAGAGGAGGAGAGGGAGAG
1 GAAGAGA-AGGAGGAGAGGGAAAG
1369608 GAAGAAGAAG
1 GAAG-AGAAG
1369618 TTGGAGAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.04
24 25 0.89
25 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (23 bp):
GAAGAGAAGGAGGAGAGGGAAAG
Found at i:1372804 original size:54 final size:54
Alignment explanation
Indices: 1372719--1372823 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
1372709 TTATATTGAA
* * * * *
1372719 AGATGCACATACTTACACCGCTGTAAGTATGTGTTGAGTGTTACATTTTTTTAG
1 AGATGCACATACTTACACCGATGTAACTATGTGTTAAGTATTACACTTTTTTAG
*
1372773 AGATGTACATACTTACACCGATGTAACTATGTGTTAAGTATTACACTTTTT
1 AGATGCACATACTTACACCGATGTAACTATGTGTTAAGTATTACACTTTTT
1372824 GGAAGATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (54 bp):
AGATGCACATACTTACACCGATGTAACTATGTGTTAAGTATTACACTTTTTTAG
Found at i:1372852 original size:54 final size:54
Alignment explanation
Indices: 1372725--1372844 Score: 152
Period size: 54 Copynumber: 2.2 Consensus size: 54
1372715 TGAAAGATGC
* * * * ** *
1372725 ACATACTTACACCGCTGTAAGTATGTGTTGAGTGTTACATTTTTTTAGAGATGT
1 ACATACTTACACCGATGTAACTATGTGTTAAGTATTACATTTTTGGAGAGATAT
1372779 ACATACTTACACCGATGTAACTATGTGTTAAGTATTACACTTTTTGGA-AGATAT
1 ACATACTTACACCGATGTAACTATGTGTTAAGTATTACA-TTTTTGGAGAGATAT
*
1372833 ACGTACTTACAC
1 ACATACTTACAC
1372845 TGGTGTAAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 51 0.89
55 6 0.11
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (54 bp):
ACATACTTACACCGATGTAACTATGTGTTAAGTATTACATTTTTGGAGAGATAT
Found at i:1376104 original size:18 final size:18
Alignment explanation
Indices: 1376083--1376127 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1376073 AAGATTGAAG
1376083 AAAGTGAAAGTTGAAGCA
1 AAAGTGAAAGTTGAAGCA
* * *
1376101 AAAGAGGAAGTTGAATCA
1 AAAGTGAAAGTTGAAGCA
1376119 AAACGTGAA
1 AAA-GTGAA
1376128 TTATGTCATC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.51, C:0.07, G:0.27, T:0.16
Consensus pattern (18 bp):
AAAGTGAAAGTTGAAGCA
Found at i:1378737 original size:147 final size:149
Alignment explanation
Indices: 1378544--1378839 Score: 569
Period size: 147 Copynumber: 2.0 Consensus size: 149
1378534 CTAAGGAATT
1378544 GCAGACTACCAAGTTAAGATTGTAACCAACAATCCACCTTCCTGATTCATCACGAATCAGTCCAG
1 GCAGACTACCAAGTTAAGATTGTAACCAACAATCCACCTTCCTGATTCATCACGAATCAGTCCAG
*
1378609 CAACCCTAGCAGCACCAGTTTTCCCTAGAGA-C-CCCGGCTACACTCAACCTCACCATATTTGAA
66 CAACCCTAGCAGCACCAGGTTTCCCTAGAGACCTCCCGGCTACACTCAACCTCACCATATTTGAA
1378672 GCAAAAAGTGCTGAAGATA
131 GCAAAAAGTGCTGAAGATA
1378691 GCAGACTACCAAGTTAAGATTGTAACCAACAATCCACCTTCCTGATTCATCACGAATCAGTCCAG
1 GCAGACTACCAAGTTAAGATTGTAACCAACAATCCACCTTCCTGATTCATCACGAATCAGTCCAG
1378756 CAACCCTAGCAGCACCAGGTTTCCCTAGAGACCTCCCGGCTACACTCAACCTCACCATATTTGAA
66 CAACCCTAGCAGCACCAGGTTTCCCTAGAGACCTCCCGGCTACACTCAACCTCACCATATTTGAA
1378821 GCAAAAAGTGCTGAAGATA
131 GCAAAAAGTGCTGAAGATA
1378840 ATGATGTCTC
Statistics
Matches: 146, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
147 95 0.65
148 1 0.01
149 50 0.34
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (149 bp):
GCAGACTACCAAGTTAAGATTGTAACCAACAATCCACCTTCCTGATTCATCACGAATCAGTCCAG
CAACCCTAGCAGCACCAGGTTTCCCTAGAGACCTCCCGGCTACACTCAACCTCACCATATTTGAA
GCAAAAAGTGCTGAAGATA
Found at i:1388257 original size:21 final size:21
Alignment explanation
Indices: 1388212--1388257 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1388202 TCATCAAGTT
** * *
1388212 TTATTAAATTGTTGTCTTGGT
1 TTATTAAATTGTAATCATGGG
1388233 TTATTAAATTGTAATCATGGG
1 TTATTAAATTGTAATCATGGG
1388254 TTAT
1 TTAT
1388258 AATGATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.52
Consensus pattern (21 bp):
TTATTAAATTGTAATCATGGG
Found at i:1389510 original size:18 final size:18
Alignment explanation
Indices: 1389487--1389529 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1389477 ATATGGTGTC
1389487 GTGCCTGTTGGGGTGTTG
1 GTGCCTGTTGGGGTGTTG
1389505 GTGCCTGTTGGGGTGTTG
1 GTGCCTGTTGGGGTGTTG
1389523 GTGCCTG
1 GTGCCTG
1389530 GGTTCATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.00, C:0.14, G:0.49, T:0.37
Consensus pattern (18 bp):
GTGCCTGTTGGGGTGTTG
Found at i:1393096 original size:14 final size:14
Alignment explanation
Indices: 1393067--1393100 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1393057 CCCTAAATCA
*
1393067 TAAATTATAAATCC
1 TAAATTATAAACCC
*
1393081 TAAATTCTAAACCC
1 TAAATTATAAACCC
1393095 TAAATT
1 TAAATT
1393101 GTACTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAATTATAAACCC
Found at i:1394353 original size:23 final size:23
Alignment explanation
Indices: 1394335--1394395 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
1394325 CTCGTATAAA
1394335 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1394358 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1394381 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1394396 TATAAGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1394748 original size:25 final size:25
Alignment explanation
Indices: 1394720--1394781 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1394710 CTTAATGCAT
*
1394720 ATAATATGAATTCATGTCATGTATC
1 ATAATATGAATTCATATCATGTATC
* **
1394745 ATAATATGAAATGTTATCATGTATC
1 ATAATATGAATTCATATCATGTATC
*
1394770 AAAATATTGAAT
1 ATAATA-TGAAT
1394782 CTAGACTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 26 0.87
26 4 0.13
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (25 bp):
ATAATATGAATTCATATCATGTATC
Found at i:1395065 original size:19 final size:20
Alignment explanation
Indices: 1395020--1395074 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1395010 TTAATGAAGG
*
1395020 TATGCATCGATGCACCACAC
1 TATGCATCGATGCACTACAC
* *
1395040 CATGCATCGATGCACTAC-T
1 TATGCATCGATGCACTACAC
1395059 TATGCATCGATGCACT
1 TATGCATCGATGCACT
1395075 GATGACATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (20 bp):
TATGCATCGATGCACTACAC
Found at i:1401256 original size:23 final size:23
Alignment explanation
Indices: 1401238--1401298 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
1401228 CTCGTATAAA
1401238 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1401261 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1401284 TGCACC-ATAGTGCCA
1 TGCACCGA-AGTGCCA
1401299 TATAAGATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1401565 original size:31 final size:30
Alignment explanation
Indices: 1401521--1401580 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
1401511 TATTATATAG
1401521 ACATATAATTTCCAT-ACCTTTATCACATAA
1 ACATATAATTTCCATCA-CTTTATCACATAA
*
1401551 ACATATCATGTTCCATCACTTTATCACATA
1 ACATATAAT-TTCCATCACTTTATCACATA
1401581 GCTTATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 18 0.67
32 1 0.04
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
ACATATAATTTCCATCACTTTATCACATAA
Found at i:1403948 original size:11 final size:11
Alignment explanation
Indices: 1403932--1404006 Score: 73
Period size: 11 Copynumber: 6.6 Consensus size: 11
1403922 TAACCTGACT
1403932 TCGAGCTTCAA
1 TCGAGCTTCAA
*
1403943 TCGAGCTTGAA
1 TCGAGCTTCAA
1403954 TCGAGC-TCAAA
1 TCGAGCTTC-AA
*
1403965 GTCGAGCTTGAA
1 -TCGAGCTTCAA
*
1403977 TTGAGC-TCAAAA
1 TCGAGCTTC--AA
1403989 TCGAGCTTCAA
1 TCGAGCTTCAA
1404000 TCGAGCT
1 TCGAGCT
1404007 AAGTCTTGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
10 2 0.04
11 32 0.62
12 15 0.29
13 3 0.06
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTCAA
Found at i:1403972 original size:23 final size:23
Alignment explanation
Indices: 1403941--1404006 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
1403931 TTCGAGCTTC
1403941 AATCGAGCTTGAATCGAGCTCAA
1 AATCGAGCTTGAATCGAGCTCAA
* *
1403964 AGTCGAGCTTGAATTGAGCTCAA
1 AATCGAGCTTGAATCGAGCTCAA
*
1403987 AATCGAGCTTCAATCGAGCT
1 AATCGAGCTTGAATCGAGCT
1404007 AAGTCTTGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (23 bp):
AATCGAGCTTGAATCGAGCTCAA
Found at i:1404484 original size:12 final size:12
Alignment explanation
Indices: 1404467--1404491 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1404457 CAGTTAAAAA
1404467 AAATAATATTTT
1 AAATAATATTTT
1404479 AAATAATATTTT
1 AAATAATATTTT
1404491 A
1 A
1404492 TTTAAAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:1408549 original size:20 final size:21
Alignment explanation
Indices: 1408513--1408561 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1408503 AAATATTCAC
1408513 GTTTCAATAGTCATTTTATCT
1 GTTTCAATAGTCATTTTATCT
1408534 GTTT-AATA-TCATTTTTAT-T
1 GTTTCAATAGTCA-TTTTATCT
1408553 GTGTTCAAT
1 GT-TTCAAT
1408562 TATTTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.55
Consensus pattern (21 bp):
GTTTCAATAGTCATTTTATCT
Found at i:1413509 original size:15 final size:15
Alignment explanation
Indices: 1413489--1413519 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1413479 CAACAAATAG
1413489 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1413504 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1413519 A
1 A
1413520 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1413693 original size:18 final size:19
Alignment explanation
Indices: 1413670--1413713 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1413660 CCAGTAATCC
*
1413670 TATTCCCA-GGTAATCTTT
1 TATTCCCATGGTAATCTTA
*
1413688 TATTCCTATTGGTAATCTTA
1 TATTCCCA-TGGTAATCTTA
1413708 TATTCC
1 TATTCC
1413714 GTGATCCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTA
Found at i:1458484 original size:20 final size:20
Alignment explanation
Indices: 1458459--1458498 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1458449 AGCAACAGAA
*
1458459 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
1458479 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
1458499 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:1458527 original size:53 final size:52
Alignment explanation
Indices: 1458455--1458583 Score: 242
Period size: 53 Copynumber: 2.5 Consensus size: 52
1458445 AATTAGCAAC
1458455 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1458506 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1458559 AGAATAAAAACTGATTCTATCTAAT
1 AGAATAAAAACTGATTCTATCTAAT
1458584 ATTTAATTTA
Statistics
Matches: 76, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
51 5 0.07
52 25 0.33
53 46 0.61
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:1458541 original size:20 final size:21
Alignment explanation
Indices: 1458512--1458551 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1458502 TAATAGAATA
*
1458512 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
1458533 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
1458552 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Done.