Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008703.1 Hibiscus syriacus cultivar Beakdansim tig00111742_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: 1275178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:954938 original size:2 final size:2
Alignment explanation
Indices: 954933--954957 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
954923 TTTTCTGATA
954933 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 A
954958 ATTAAATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:958570 original size:21 final size:21
Alignment explanation
Indices: 958544--958583 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
958534 TCACAATAAC
* *
958544 ATATTAAATTTAATGAAAAAT
1 ATATTAAATTAAATCAAAAAT
958565 ATATTAAATTAAATCAAAA
1 ATATTAAATTAAATCAAAA
958584 TAAAATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (21 bp):
ATATTAAATTAAATCAAAAAT
Found at i:959041 original size:38 final size:38
Alignment explanation
Indices: 958984--959056 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
958974 GTATTAACGA
* * *
958984 TATTTTGTTCTGTAAATGTTTTATACGGTTTTCTGTGG
1 TATTTTGATATGTAAATGTTTTATACAGTTTTCTGTGG
*
959022 TATTTTGATATGTATATGTTTTATACAGTTTTCTG
1 TATTTTGATATGTAAATGTTTTATACAGTTTTCTG
959057 ACATATGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.19, C:0.07, G:0.18, T:0.56
Consensus pattern (38 bp):
TATTTTGATATGTAAATGTTTTATACAGTTTTCTGTGG
Found at i:964412 original size:44 final size:44
Alignment explanation
Indices: 964364--964492 Score: 168
Period size: 44 Copynumber: 2.9 Consensus size: 44
964354 TTGGAGGAAG
* *
964364 TTTCTGAAGGCTCCTTTGCTATTTTCAAGGGTAAGACCTTACAA
1 TTTCTGAAGGCTCCTTTGCTATATACAAGGGTAAGACCTTACAA
* * * *
964408 TTTCTGAAGGCTCATTTGCTATGTGCAAGGGTAAGACCTTACCA
1 TTTCTGAAGGCTCCTTTGCTATATACAAGGGTAAGACCTTACAA
* * * *
964452 TTTCTGAAAGTTCCTCTGCAATATACAAGGGTAAGACCTTA
1 TTTCTGAAGGCTCCTTTGCTATATACAAGGGTAAGACCTTA
964493 ATGCTTTCTG
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
TTTCTGAAGGCTCCTTTGCTATATACAAGGGTAAGACCTTACAA
Found at i:968743 original size:2 final size:2
Alignment explanation
Indices: 968736--968771 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
968726 TATTTAATAA
968736 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
968772 TCATTGGGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:976739 original size:80 final size:77
Alignment explanation
Indices: 976636--976786 Score: 180
Period size: 76 Copynumber: 1.9 Consensus size: 77
976626 AGTAAGTAAC
* *
976636 CATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATATATAATTCAGAA-TAATTAA
1 CATTAAAAGAATGTAATTCAGATTACAAATC-TTTAA--G-TATATATAATT-AGAATTAATTAA
976700 ATAAGATTTTAAATAAA
61 ATAAGATTTTAAATAAA
* * * * *
976717 CATT-AAAGATTGTAATTCAGATTATAAATCTTTAAGTATATTTAATTTGAATTAATTAAATAAT
1 CATTAAAAGAATGTAATTCAGATTACAAATCTTTAAGTATATATAATTAGAATTAATTAAATAAG
976781 ATTTTA
66 ATTTTA
976787 TTTATTAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
75 3 0.05
76 27 0.44
77 1 0.02
79 5 0.08
80 22 0.35
81 4 0.06
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (77 bp):
CATTAAAAGAATGTAATTCAGATTACAAATCTTTAAGTATATATAATTAGAATTAATTAAATAAG
ATTTTAAATAAA
Found at i:990681 original size:3 final size:3
Alignment explanation
Indices: 990668--990718 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
990658 TAAAAGAAAA
* * *
990668 AAT AA- AAT AAT AAT AAT AAT AAT AAT ACT AGT TA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
990714 AAT AA
1 AAT AA
990719 CGAAATATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
2 3 0.07
3 38 0.93
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:990724 original size:20 final size:20
Alignment explanation
Indices: 990682--990725 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
990672 AAATAATAAT
* ***
990682 AATAATAATAATACTAGTTA
1 AATAATAATAATAATAACGA
990702 AATAATAATAATAATAACGA
1 AATAATAATAATAATAACGA
990722 AATA
1 AATA
990726 TCCATGTGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (20 bp):
AATAATAATAATAATAACGA
Found at i:992256 original size:2 final size:2
Alignment explanation
Indices: 992251--992298 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
992241 AATATATCAA
992251 AT 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 AT
992293 AT AT AT
1 AT AT AT
992299 TATTTTCGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:994048 original size:46 final size:46
Alignment explanation
Indices: 993961--994048 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
993951 TCTAATCAAC
* * * *
993961 ATGTTTTTTCTCATTTGCTTATTGTTGTATATAACTTTTTTTCTTT
1 ATGTTTTTTATCATTTGCTTATTGCTGTATAAAACTCTTTTTCTTT
994007 ATGTTTTTTATCATTTGCTTATTGCTGTA-ACAAACTCTTTTT
1 ATGTTTTTTATCATTTGCTTATTGCTGTATA-AAACTCTTTTT
994049 TTTGTTTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 1 0.03
46 36 0.97
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.60
Consensus pattern (46 bp):
ATGTTTTTTATCATTTGCTTATTGCTGTATAAAACTCTTTTTCTTT
Found at i:997398 original size:24 final size:24
Alignment explanation
Indices: 997371--997481 Score: 116
Period size: 24 Copynumber: 4.6 Consensus size: 24
997361 GACTGTTTTA
* *
997371 TCTGATTTCTGATTTGAATTTTGT
1 TCTGATTTCTGATATGAATTCTGT
997395 TCTGATTTCTGATATGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* *
997419 TTTGATTTCTGATCT-AGATTCTGT
1 TCTGATTTCTGATATGA-ATTCTGT
* * * *
997443 TCTAATATCTTATCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* *
997467 TTTGATTTTTGATAT
1 TCTGATTTCTGATAT
997482 CTCCGTTTAC
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
23 1 0.01
24 69 0.97
25 1 0.01
ACGTcount: A:0.20, C:0.11, G:0.14, T:0.55
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:997427 original size:48 final size:48
Alignment explanation
Indices: 997373--997479 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 48
997363 CTGTTTTATC
* * * *
997373 TGATTTCTGAT-TTGAATTTTGTTCTGATTTCTGATATGAATTCTGTTT
1 TGATTTCTGATCTAG-ATTCTGTTCTAATATCTGATATGAATTCTGTTT
* *
997421 TGATTTCTGATCTAGATTCTGTTCTAATATCTTATCTGAATTCTGTTT
1 TGATTTCTGATCTAGATTCTGTTCTAATATCTGATATGAATTCTGTTT
*
997469 TGATTTTTGAT
1 TGATTTCTGAT
997480 ATCTCCGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 49 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.55
Consensus pattern (48 bp):
TGATTTCTGATCTAGATTCTGTTCTAATATCTGATATGAATTCTGTTT
Found at i:997428 original size:12 final size:12
Alignment explanation
Indices: 997373--997431 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
997363 CTGTTTTATC
997373 TGATTTCTGATT
1 TGATTTCTGATT
997385 TGAATTT-TG-TT
1 TG-ATTTCTGATT
*
997396 CTGATTTCTGATA
1 -TGATTTCTGATT
* *
997409 TGAATTCTGTTT
1 TGATTTCTGATT
997421 TGATTTCTGAT
1 TGATTTCTGAT
997432 CTAGATTCTG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
11 6 0.16
12 26 0.70
13 5 0.14
ACGTcount: A:0.19, C:0.08, G:0.17, T:0.56
Consensus pattern (12 bp):
TGATTTCTGATT
Found at i:1001536 original size:24 final size:24
Alignment explanation
Indices: 1001509--1001603 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
1001499 TTTTTTATTT
1001509 GAATTATGTTCTGATTTCTGATAG
1 GAATTATGTTCTGATTTCTGATAG
* * *
1001533 GAATTCTATTATGATTTCTGATATG
1 GAATTATGTTCTGATTTCTGATA-G
* **
1001558 G-ATTATGTTCTGATATCTGATCT
1 GAATTATGTTCTGATTTCTGATAG
* * *
1001581 GAATTCTGTTTTGATTTATGATA
1 GAATTATGTTCTGATTTCTGATA
1001604 TCTCCGTTTA
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
23 1 0.02
24 52 0.95
25 2 0.04
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.48
Consensus pattern (24 bp):
GAATTATGTTCTGATTTCTGATAG
Found at i:1001585 original size:48 final size:48
Alignment explanation
Indices: 1001511--1001604 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 48
1001501 TTTTATTTGA
* *
1001511 ATTATGTTCTGATTTCTGATAGGAATTCTATTATGATTTCTGATATGG
1 ATTATGTTCTGATATCTGATAGGAATTCTATTATGATTTATGATATGG
** * *
1001559 ATTATGTTCTGATATCTGATCTGAATTCTGTTTTGATTTATGATAT
1 ATTATGTTCTGATATCTGATAGGAATTCTATTATGATTTATGATAT
1001605 CTCCGTTTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (48 bp):
ATTATGTTCTGATATCTGATAGGAATTCTATTATGATTTATGATATGG
Found at i:1001791 original size:13 final size:13
Alignment explanation
Indices: 1001773--1001797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1001763 AGTGTTATGT
1001773 TTTTAAAAATATA
1 TTTTAAAAATATA
1001786 TTTTAAAAATAT
1 TTTTAAAAATAT
1001798 TTGTATATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAAAATATA
Found at i:1013272 original size:54 final size:54
Alignment explanation
Indices: 1013164--1013391 Score: 276
Period size: 54 Copynumber: 4.2 Consensus size: 54
1013154 TTTTCAAAGA
* * * * * *
1013164 TTTCTTGACATGTTGTTCCAATGAATTTTTAAAGAAACTAAGCTTGATCTTTAGGAG
1 TTTCTTG--ATGTT-TTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGG
* * * * * *
1013221 TTTTTTGATATTTTCAAATGGATTTTTAAAGGAGATAAGTCTAATTTTTAGGGG
1 TTTCTTGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGG
* *
1013275 TTTCTTGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGC
1 TTTCTTGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGG
* * *
1013329 TTTATTGATGTTTTCAAGTGAATTTTTAAAGAAGCTAAACCTAATTTTTAGGGG
1 TTTCTTGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGG
1013383 TTTCTTGAT
1 TTTCTTGAT
1013392 TATAATTGTA
Statistics
Matches: 145, Mismatches: 26, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
54 135 0.93
55 4 0.03
57 6 0.04
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.43
Consensus pattern (54 bp):
TTTCTTGATGTTTTCAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGG
Found at i:1015090 original size:117 final size:116
Alignment explanation
Indices: 1014854--1015212 Score: 409
Period size: 117 Copynumber: 3.1 Consensus size: 116
1014844 GGATAAACCA
* * *
1014854 ATCAACATTTCCAATTGAAGGGTTCGTAATGAGAATAACTCATCAAATGAGGGACAAAAAGTTCA
1 ATCAACATTTCCAA-TGAA-GGTTCATAATGAGAATAACTCATCTAATGAGGGACAAGAAGTTCA
* * * *** *
1014919 TAATAAGAAGAACTTGTTCAACCTTAACTCGATTCCATCATTGAAGGAGGTGG
64 TAATAAGAAGAAATTGTTCAACCTTAGCTCTATTCCATCACAAAAGGAGATGG
* * *
1014972 ATCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCTAATGAGGGATAAGAAGTTCAT
1 ATCAACATTTCCAATGAAG-GTTCATAATGAGAATAACTCATCTAATGAGGGACAAGAAGTTCAT
* * *
1015037 AATGAA-AAGAAATTGTTCTACCTTAGCTCTATTCCATCACAAAATGATATGG
65 AAT-AAGAAGAAATTGTTCAACCTTAGCTCTATTCCATCACAAAAGGAGATGG
* * * * *
1015089 ATCAACATTTCCAATGAAGGTTTCATAATTAGAAGAACTCGTCTGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGAAGG-TTCATAATGAGAATAACTCATCTAATGAGGGACAAGAAGTTCAT
* * *
1015154 AATAAGAAGAATTTGTTCAACCTTAGCT-TGATTTCATCACATAAA-GAGTTGG
65 AATAAGAAGAAATTGTTCAACCTTAGCTCT-ATTCCATCACA-AAAGGAGATGG
*
1015206 AACAACA
1 ATCAACA
1015213 ACAATACTTG
Statistics
Matches: 206, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
116 5 0.02
117 183 0.89
118 18 0.09
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (116 bp):
ATCAACATTTCCAATGAAGGTTCATAATGAGAATAACTCATCTAATGAGGGACAAGAAGTTCATA
ATAAGAAGAAATTGTTCAACCTTAGCTCTATTCCATCACAAAAGGAGATGG
Found at i:1017834 original size:13 final size:14
Alignment explanation
Indices: 1017815--1017846 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1017805 CCCTAGTGTT
1017815 TAAAACTTGAAAAA
1 TAAAACTTGAAAAA
1017829 -AAAACTTGAAAAA
1 TAAAACTTGAAAAA
1017842 TAAAA
1 TAAAA
1017847 AGGGACAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (14 bp):
TAAAACTTGAAAAA
Found at i:1022222 original size:3 final size:3
Alignment explanation
Indices: 1022207--1022238 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1022197 AAACTATCTA
*
1022207 ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1022239 ATTTATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1026984 original size:43 final size:42
Alignment explanation
Indices: 1026914--1027011 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
1026904 ATTTAATAAT
* *
1026914 AATAATATA-TCTATAATCATTTATTACATGTTAAACTATTAA
1 AATAATATATTTTATAATAATTTATTACATGTTAAACTATT-A
* ** *
1026956 AATAATATATTTTATAATAATTGT-TTACATTTTTTATTATTA
1 AATAATATATTTTATAATAATT-TATTACATGTTAAACTATTA
*
1026998 AAGAATATATTTTA
1 AATAATATATTTTA
1027012 ACATTATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
42 23 0.49
43 23 0.49
44 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (42 bp):
AATAATATATTTTATAATAATTTATTACATGTTAAACTATTA
Found at i:1031226 original size:18 final size:18
Alignment explanation
Indices: 1031203--1031319 Score: 119
Period size: 18 Copynumber: 6.5 Consensus size: 18
1031193 CTGTGTCACA
1031203 AATGATAATCGTGCTTCC
1 AATGATAATCGTGCTTCC
1031221 AATGATAATCGTGCTTCC
1 AATGATAATCGTGCTTCC
* ** *
1031239 AATGGTCGTCGTCCTTCC
1 AATGATAATCGTGCTTCC
* *
1031257 TACGATAATCGTGCTTCC
1 AATGATAATCGTGCTTCC
* *
1031275 AATGATCATCGTGCTTCT
1 AATGATAATCGTGCTTCC
* *
1031293 TACGATAATCG-GACTTCC
1 AATGATAATCGTG-CTTCC
*
1031311 TATGATAAT
1 AATGATAAT
1031320 TGTGGTTTTT
Statistics
Matches: 79, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
17 1 0.01
18 78 0.99
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (18 bp):
AATGATAATCGTGCTTCC
Found at i:1031264 original size:36 final size:36
Alignment explanation
Indices: 1031203--1031316 Score: 131
Period size: 36 Copynumber: 3.2 Consensus size: 36
1031193 CTGTGTCACA
* * * *
1031203 AATGATAATCGTGCTTCCAATGATAATCGTGCTTCC
1 AATGATCATCGTCCTTCCTACGATAATCGTGCTTCC
* *
1031239 AATGGTCGTCGTCCTTCCTACGATAATCGTGCTTCC
1 AATGATCATCGTCCTTCCTACGATAATCGTGCTTCC
* *
1031275 AATGATCATCGTGCTTCTTACGATAATCG-GACTTCC
1 AATGATCATCGTCCTTCCTACGATAATCGTG-CTTCC
*
1031311 TATGAT
1 AATGAT
1031317 AATTGTGGTT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
35 1 0.02
36 65 0.98
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (36 bp):
AATGATCATCGTCCTTCCTACGATAATCGTGCTTCC
Found at i:1031310 original size:54 final size:54
Alignment explanation
Indices: 1031206--1031319 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
1031196 TGTCACAAAT
* * ** **
1031206 GATAATCGTGCTTCCAATGATAATCGTGCTTCCAATGGTCGTCGTCCTTCCTAC
1 GATAATCGTGCTTCCAATGATAATCGTGCTTCCAACGATAATCGGACTTCCTAC
* ** *
1031260 GATAATCGTGCTTCCAATGATCATCGTGCTTCTTACGATAATCGGACTTCCTAT
1 GATAATCGTGCTTCCAATGATAATCGTGCTTCCAACGATAATCGGACTTCCTAC
1031314 GATAAT
1 GATAAT
1031320 TGTGGTTTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (54 bp):
GATAATCGTGCTTCCAATGATAATCGTGCTTCCAACGATAATCGGACTTCCTAC
Found at i:1033915 original size:14 final size:14
Alignment explanation
Indices: 1033896--1033925 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1033886 TTAAAGATTC
1033896 AGTTAGAGTCTGTT
1 AGTTAGAGTCTGTT
1033910 AGTTAGAGTCTGTT
1 AGTTAGAGTCTGTT
1033924 AG
1 AG
1033926 GCTTAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (14 bp):
AGTTAGAGTCTGTT
Found at i:1040265 original size:32 final size:32
Alignment explanation
Indices: 1040224--1040284 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1040214 ATGGTCGACT
* *
1040224 GTTGACCAGAACTTTGACCACCGTTGACCACA
1 GTTGACCAGAACATTGACCACAGTTGACCACA
*
1040256 GTTGACCAGAACATTGACCGCAGTTGACC
1 GTTGACCAGAACATTGACCACAGTTGACC
1040285 GAGCATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (32 bp):
GTTGACCAGAACATTGACCACAGTTGACCACA
Found at i:1042725 original size:48 final size:48
Alignment explanation
Indices: 1042673--1042764 Score: 112
Period size: 48 Copynumber: 1.9 Consensus size: 48
1042663 TTCGACTTGA
*
1042673 ATTCTGTTCTCATACATGACCTGAATTCTGTTATGATTTCTGATCTGG
1 ATTCTGTTATCATACATGACCTGAATTCTGTTATGATTTCTGATCTGG
* * ** * * *
1042721 ATTCTGTTATGATATATGTTCTGAATTCTTTTTTGATTTTTGAT
1 ATTCTGTTATCATACATGACCTGAATTCTGTTATGATTTCTGAT
1042765 ATCTCTGTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 36 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (48 bp):
ATTCTGTTATCATACATGACCTGAATTCTGTTATGATTTCTGATCTGG
Found at i:1042757 original size:24 final size:24
Alignment explanation
Indices: 1042670--1042749 Score: 88
Period size: 24 Copynumber: 3.3 Consensus size: 24
1042660 ATTTTCGACT
* * * *
1042670 TGAATTCTGTTCTCATACATGACC
1 TGAATTCTGTTATGATATATGATC
* *
1042694 TGAATTCTGTTATGATTTCTGATC
1 TGAATTCTGTTATGATATATGATC
* *
1042718 TGGATTCTGTTATGATATATGTTC
1 TGAATTCTGTTATGATATATGATC
1042742 TGAATTCT
1 TGAATTCT
1042750 TTTTTGATTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46
Consensus pattern (24 bp):
TGAATTCTGTTATGATATATGATC
Found at i:1044077 original size:13 final size:13
Alignment explanation
Indices: 1044061--1044085 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1044051 ATATCATATT
1044061 AAAAAGAAAAAAC
1 AAAAAGAAAAAAC
1044074 AAAAAGAAAAAA
1 AAAAAGAAAAAA
1044086 GCTCAAGACA
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:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAC
Found at i:1044720 original size:23 final size:23
Alignment explanation
Indices: 1044694--1044738 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1044684 TTGATCACAT
*
1044694 CATAAGTAAAGAAGATGTATCAA
1 CATAAGTAAAGAAAATGTATCAA
1044717 CATAAGTAAAGAAAATGTATCA
1 CATAAGTAAAGAAAATGTATCA
1044739 GCCTGAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (23 bp):
CATAAGTAAAGAAAATGTATCAA
Found at i:1046480 original size:24 final size:24
Alignment explanation
Indices: 1046428--1046543 Score: 157
Period size: 24 Copynumber: 4.9 Consensus size: 24
1046418 ATCATAATTT
*
1046428 ATGTCAAGTATCATATCA-AATCC
1 ATGTCAAGTATCAGATCAGAATCC
*
1046451 AGGTCAAGTAAT-AGATCAGAATCC
1 ATGTCAAGT-ATCAGATCAGAATCC
*
1046475 AAGTCAAGTATCAGATCAGAATCC
1 ATGTCAAGTATCAGATCAGAATCC
*
1046499 ATGTC-AGATATAAGATCAGAATCC
1 ATGTCAAG-TATCAGATCAGAATCC
1046523 ATGTCAAGTATCAGATCAGAA
1 ATGTCAAGTATCAGATCAGAA
1046544 ATCAAATCGA
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
23 17 0.21
24 63 0.77
25 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (24 bp):
ATGTCAAGTATCAGATCAGAATCC
Found at i:1051341 original size:24 final size:24
Alignment explanation
Indices: 1051314--1051434 Score: 129
Period size: 24 Copynumber: 5.0 Consensus size: 24
1051304 TATATCAAAC
* * *
1051314 ATCAAATCATAATTCATGTCAAGT
1 ATCAGATCAAAATCCATGTCAAGT
* *
1051338 ATCATATCAAAATCCAGGTCAAGT
1 ATCAGATCAAAATCCATGTCAAGT
* * *
1051362 AAT-TGATCAGAATCCAAGTCAAGT
1 -ATCAGATCAAAATCCATGTCAAGT
1051386 ATCAGATCAAAATCCATGTC-AGAT
1 ATCAGATCAAAATCCATGTCAAG-T
*
1051410 ATCAGATCAGAATCCATGTCAAGT
1 ATCAGATCAAAATCCATGTCAAGT
1051434 A
1 A
1051435 CAAATTAGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
23 4 0.05
24 73 0.90
25 4 0.05
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (24 bp):
ATCAGATCAAAATCCATGTCAAGT
Found at i:1051447 original size:24 final size:25
Alignment explanation
Indices: 1051328--1051447 Score: 119
Period size: 24 Copynumber: 5.0 Consensus size: 25
1051318 AATCATAATT
*
1051328 CATGTCAAGTATCATATCA-AAATC
1 CATGTCAAGTATCAGATCAGAAATC
* *
1051352 CAGGTCAAGTAAT-TGATCAG-AATC
1 CATGTCAAGT-ATCAGATCAGAAATC
*
1051376 CAAGTCAAGTATCAGATCA-AAATC
1 CATGTCAAGTATCAGATCAGAAATC
1051400 CATGTC-AGATATCAGATCAG-AATC
1 CATGTCAAG-TATCAGATCAGAAATC
* *
1051424 CATGTCAAGTA-CAAATTAGAAATC
1 CATGTCAAGTATCAGATCAGAAATC
1051448 AAATCGAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
23 10 0.12
24 66 0.82
25 4 0.05
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (25 bp):
CATGTCAAGTATCAGATCAGAAATC
Found at i:1062598 original size:41 final size:41
Alignment explanation
Indices: 1062544--1062623 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
1062534 TGTCCTCCGC
* *
1062544 GACCGTTATTATATGACCGCGCATAGCGGTAAATGCGAGGT
1 GACCATTATTATATGACCGCACATAGCGGTAAATGCGAGGT
1062585 GACCATTATTATATGACCGCACATAGCGGTAAATGCGAG
1 GACCATTATTATATGACCGCACATAGCGGTAAATGCGAG
1062624 CGACCGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (41 bp):
GACCATTATTATATGACCGCACATAGCGGTAAATGCGAGGT
Found at i:1065889 original size:2 final size:2
Alignment explanation
Indices: 1065882--1065911 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1065872 AAAATATTAA
*
1065882 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1065912 TAGGGTTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1066166 original size:27 final size:26
Alignment explanation
Indices: 1066127--1066179 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1066117 GTCCATTTCT
1066127 TAATATCG-AAAAATAAATAAATATTAA
1 TAATATCGAAAAAAT-AATAAA-ATTAA
1066154 TAATAT-GATAAAAATAATAAAATTAA
1 TAATATCGA-AAAAATAATAAAATTAA
1066180 ATATATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 6 0.25
27 12 0.50
28 6 0.25
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (26 bp):
TAATATCGAAAAAATAATAAAATTAA
Found at i:1066305 original size:2 final size:2
Alignment explanation
Indices: 1066298--1066327 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1066288 AAATAAAGAA
*
1066298 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1066328 GACTAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1066343 original size:130 final size:130
Alignment explanation
Indices: 1066099--1066343 Score: 277
Period size: 129 Copynumber: 1.9 Consensus size: 130
1066089 GAAAATGACT
*
1066099 TCTAGTTGCTTTAAGACAGTCCATTTCTTAATATCGAAAAATAAATAAATATTAATAATATGATA
1 TCTAGTTGCTTTAAGACAGTCCATTTCTTAATATCGAAAAATAAATAAATATTAATAATATAATA
* * * * *
1066164 AAAATAATAAAATTAAATATATAATTTTTATTATATTTATTTATTTAAAATACCAGAATAGGACA
66 AAAATAATAAAATTAAATATATAATATTTATTATACTAATATATATAAAATACCAGAATAGGACA
* * * *
1066229 TCTAGTTGCTTTAAGACTG-CCCTTTCTTAATATAC-AAAAATAAATAAATATT-ATTATTTAAA
1 TCTAGTTGCTTTAAGACAGTCCATTTCTTAATAT-CGAAAAATAAATAAATATTAATAATAT-AA
* * *
1066291 TAAAGA-AATATATATATATATATATATATATTTA-TATGACTAATATA-ATAAAA
64 TAAAAATAATA-AAAT-TAAATATATA-ATATTTATTAT-ACTAATATATATAAAA
1066344 ATAAAATAAT
Statistics
Matches: 96, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
128 9 0.09
129 39 0.41
130 36 0.38
131 12 0.12
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (130 bp):
TCTAGTTGCTTTAAGACAGTCCATTTCTTAATATCGAAAAATAAATAAATATTAATAATATAATA
AAAATAATAAAATTAAATATATAATATTTATTATACTAATATATATAAAATACCAGAATAGGACA
Found at i:1067737 original size:3 final size:3
Alignment explanation
Indices: 1067729--1067791 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
1067719 TATTTATTTA
* * **
1067729 AAT AAT AAT AAT TAT -AT ATAT AAT ATAT AAT AAT AAT GAT AAT TTT
1 AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT
1067775 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
1067792 AATGAAATGA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:1067743 original size:18 final size:18
Alignment explanation
Indices: 1067716--1067759 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1067706 TTGGGCCTTT
* *
1067716 TAATATTTATTTAAATAA
1 TAATAATTATATAAATAA
*
1067734 TAATAATTATATATATAA
1 TAATAATTATATAAATAA
1067752 TATATAAT
1 TA-ATAAT
1067760 AATAATGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATAATTATATAAATAA
Found at i:1067982 original size:45 final size:45
Alignment explanation
Indices: 1067918--1068201 Score: 433
Period size: 45 Copynumber: 6.3 Consensus size: 45
1067908 GATGGAAATG
*
1067918 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
1067963 TTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
1068008 TTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * *
1068053 TTGAAAGCATCATGCACTGAAGGGTTTACATATGACCCGAAGGCTTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG--TT
* * *
1068100 TTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * *
1068145 TTGACAGCATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
1068190 TTGAAAATATCA
1 TTGAAAACATCA
1068202 AAAAGCTCCC
Statistics
Matches: 216, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
45 177 0.82
47 39 0.18
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:1068148 original size:92 final size:92
Alignment explanation
Indices: 1067918--1068191 Score: 453
Period size: 92 Copynumber: 3.0 Consensus size: 92
1067908 GATGGAAATG
* * *
1067918 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGA
1 TTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGA
*
1067983 AGGGCTTACGGATGACCCGAAGG--TT
66 AGGGCTTACAGATGACCCGAAGGCTTT
1068008 TTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGA
1 TTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGA
* *
1068073 AGGGTTTACATATGACCCGAAGGCTTT
66 AGGGCTTACAGATGACCCGAAGGCTTT
* * *
1068100 TTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGACAGCATCATGCACTGA
1 TTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGA
1068165 AGGGCTTACAGATGACCCGAAGGCTTT
66 AGGGCTTACAGATGACCCGAAGGCTTT
1068192 GAAAATATCA
Statistics
Matches: 171, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
90 82 0.48
92 89 0.52
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.23
Consensus pattern (92 bp):
TTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGA
AGGGCTTACAGATGACCCGAAGGCTTT
Found at i:1068162 original size:137 final size:135
Alignment explanation
Indices: 1067918--1068201 Score: 451
Period size: 137 Copynumber: 2.1 Consensus size: 135
1067908 GATGGAAATG
1067918 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGA
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGA
*
1067983 AGGGCTTACGGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGA
66 AGGGCTTACGGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGA
*
1068048 AGGTT
131 AGGCT
* ** * *
1068053 TTGAAAGCATCATGCACTGAAGGGTTTACATATGACCCGAAGGCTTTTTGAAAACATCCTGCACT
1 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TTTTGAAAACATCATGCACT
* * *
1068118 GCAGGGCTTACGGATGACCCGAAGGTTTTGACAGCATCATGCACTGAAGGGCTTACAGATGACCC
64 GAAGGGCTTACGGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
1068183 GAAGGCT
129 GAAGGCT
*
1068190 TTGAAAATATCA
1 TTGAAAACATCA
1068202 AAAAGCTCCC
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
135 39 0.29
137 96 0.71
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (135 bp):
TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGA
AGGGCTTACGGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGA
AGGCT
Found at i:1068237 original size:76 final size:76
Alignment explanation
Indices: 1068135--1068329 Score: 297
Period size: 76 Copynumber: 2.6 Consensus size: 76
1068125 TTACGGATGA
* * *
1068135 CCCGAAGG--TTTTGACAGCATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAAT
*
1068198 ATCAAAAAGCT
66 ATCAAAAACCT
* * *
1068209 CCCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCAAAGGCTTTGAAAAT
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAAT
1068274 ATCAAAAACCT
66 ATCAAAAACCT
*
1068285 -CCTAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1068330 TGGGAAATAG
Statistics
Matches: 108, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
74 8 0.07
75 41 0.38
76 59 0.55
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.23
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGCTTTGAAAAT
ATCAAAAACCT
Found at i:1069020 original size:22 final size:22
Alignment explanation
Indices: 1068965--1069021 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
1068955 AATAAAGATT
*
1068965 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1068987 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1069009 TCATCTTTGAAGA
1 TCATCTTTGAAGA
1069022 ATGTAGATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1070498 original size:75 final size:75
Alignment explanation
Indices: 1070370--1070538 Score: 221
Period size: 75 Copynumber: 2.3 Consensus size: 75
1070360 GATATAGGTC
* * * *
1070370 TTCAGCATGCCTCAACATTGGCTAATACAAATGTTCAAAATACATCAACATTCCTGATTCTGATT
1 TTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTAATTATGATT
*
1070435 GAAAGGGGCT
66 GAAAAGGGCT
* *** *
1070445 TTCAGCATACCCCAACATTGGCTAATACAAACGTTCAAAATGTGTCAATATTCCTAATTATGATT
1 TTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTAATTATGATT
1070510 GAAAAGGGCT
66 GAAAAGGGCT
* * *
1070520 GTCAACATGCCCCAGCATT
1 TTCAGCATGCCCCAACATT
1070539 TGTTTCTTGT
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 80 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTGGCTAATACAAACGTTCAAAATACATCAACATTCCTAATTATGATT
GAAAAGGGCT
Found at i:1073726 original size:6 final size:6
Alignment explanation
Indices: 1073715--1073841 Score: 107
Period size: 6 Copynumber: 20.8 Consensus size: 6
1073705 TATTTATTTA
*
1073715 AATAAT AATAAT AATAAT AAT-AT ATATAAT ATATAAT AATAAT GATAAT
1 AATAAT AATAAT AATAAT AATAAT A-ATAAT A-ATAAT AATAAT AATAAT
** **
1073764 TTTAAT TTTAAT AATAAT -ATATAT AAT-AT ATATAAT ATATAAT AATAAT
1 AATAAT AATAAT AATAAT AATA-AT AATAAT A-ATAAT A-ATAAT AATAAT
* ** *
1073813 GATAAT TTTAAT AATACT AATAAT AATAA
1 AATAAT AATAAT AATAAT AATAAT AATAA
1073842 AATGAAATGA
Statistics
Matches: 103, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
5 9 0.09
6 72 0.70
7 22 0.21
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.41
Consensus pattern (6 bp):
AATAAT
Found at i:1073729 original size:9 final size:9
Alignment explanation
Indices: 1073715--1073841 Score: 107
Period size: 9 Copynumber: 13.9 Consensus size: 9
1073705 TATTTATTTA
1073715 AATAATAAT
1 AATAATAAT
1073724 AATAATAAT
1 AATAATAAT
1073733 AAT-ATATAT
1 AATAATA-AT
1073742 AATATATAAT
1 AATA-ATAAT
*
1073752 AATAATGAT
1 AATAATAAT
**
1073761 AATTTTAAT
1 AATAATAAT
**
1073770 TTTAATAAT
1 AATAATAAT
1073779 AAT-ATATAT
1 AATAATA-AT
1073788 AAT-ATATAT
1 AATAATA-AT
1073797 AATATATAAT
1 AATA-ATAAT
*
1073807 AATAATGAT
1 AATAATAAT
**
1073816 AATTTTAAT
1 AATAATAAT
*
1073825 AATACTAAT
1 AATAATAAT
1073834 AATAATAA
1 AATAATAA
1073842 AATGAAATGA
Statistics
Matches: 95, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
8 6 0.06
9 71 0.75
10 12 0.13
11 6 0.06
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.41
Consensus pattern (9 bp):
AATAATAAT
Found at i:1073776 original size:46 final size:49
Alignment explanation
Indices: 1073726--1073828 Score: 158
Period size: 49 Copynumber: 2.2 Consensus size: 49
1073716 ATAATAATAA
* **
1073726 TAATAATAATATATAT-A-ATATATAATA-ATAATGATAATTTTAATTT
1 TAATAATAATATATATAATATATATAATATATAATAATAATGATAATTT
1073772 TAATAATAATATATATAATATATATAATATATAATAATAATGATAATTT
1 TAATAATAATATATATAATATATATAATATATAATAATAATGATAATTT
1073821 TAATAATA
1 TAATAATA
1073829 CTAATAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
46 16 0.31
47 1 0.02
48 10 0.20
49 24 0.47
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (49 bp):
TAATAATAATATATATAATATATATAATATATAATAATAATGATAATTT
Found at i:1073793 original size:55 final size:55
Alignment explanation
Indices: 1073717--1073841 Score: 207
Period size: 55 Copynumber: 2.3 Consensus size: 55
1073707 TTTATTTAAA
1073717 TAATAATAATAATAATAATATATATAATATATAATAATAATGATAATTTTAATTT
1 TAATAATAATAATAATAATATATATAATATATAATAATAATGATAATTTTAATTT
**
1073772 TAATAATAAT-ATATATAATATATATAATATATAATAATAATGATAATTTTAATAA
1 TAATAATAATAATA-ATAATATATATAATATATAATAATAATGATAATTTTAATTT
*
1073827 TACTAATAATAATAA
1 TAATAATAATAATAA
1073842 AATGAAATGA
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
54 3 0.05
55 59 0.91
56 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (55 bp):
TAATAATAATAATAATAATATATATAATATATAATAATAATGATAATTTTAATTT
Found at i:1079031 original size:128 final size:128
Alignment explanation
Indices: 1078803--1079054 Score: 450
Period size: 128 Copynumber: 2.0 Consensus size: 128
1078793 TTTTCACATC
* * *
1078803 AAGCCGAGCTAAATCAAAAATGATTTGATTGAAGACATTTACGTGTTGCACCAAATCATGATCAA
1 AAGCCGAGCAAAATCAAAAACGATTTGATTGAAGACATTCACGTGTTGCACCAAATCATGATCAA
* *
1078868 CCTACATCTTCATCCCATACAACCGCTGTTTTAGATACAGTTTAGTCGTTAAGGATTTGATTG
66 CCTACATCTTCAGCCCATACAACCGCTGTTTTAGATACAATTTAGTCGTTAAGGATTTGATTG
*
1078931 AAGCCGAGCAAAATCAAAAACGATTTGATTGAAGACATTCACGTGTTGCACCAAATCATGATCAT
1 AAGCCGAGCAAAATCAAAAACGATTTGATTGAAGACATTCACGTGTTGCACCAAATCATGATCAA
1078996 CCTACATCTTCAGCCCATACAACCGCTGTTTTAGATACAATTTAGTCGTTAAGGATTTG
66 CCTACATCTTCAGCCCATACAACCGCTGTTTTAGATACAATTTAGTCGTTAAGGATTTG
1079055 GACATAAACT
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
128 118 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (128 bp):
AAGCCGAGCAAAATCAAAAACGATTTGATTGAAGACATTCACGTGTTGCACCAAATCATGATCAA
CCTACATCTTCAGCCCATACAACCGCTGTTTTAGATACAATTTAGTCGTTAAGGATTTGATTG
Found at i:1079315 original size:15 final size:15
Alignment explanation
Indices: 1079295--1079332 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1079285 ACCCTGACCA
1079295 TCGAATTTCGCAACT
1 TCGAATTTCGCAACT
*
1079310 TCGAATTTTGCAACT
1 TCGAATTTCGCAACT
1079325 TCGAATTT
1 TCGAATTT
1079333 GGCTCTTGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (15 bp):
TCGAATTTCGCAACT
Found at i:1081979 original size:33 final size:34
Alignment explanation
Indices: 1081927--1081998 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 34
1081917 ATAGTGTTAT
*
1081927 ATATATTTTAAAAATATTATT-TAGTATATTTTAA
1 ATATATTTTAAAAATATTATTATAGTA-ATATTAA
* *
1081961 ATATCTTTT-AAAATATTATTATATTAATATTAA
1 ATATATTTTAAAAATATTATTATAGTAATATTAA
1081994 ATATA
1 ATATA
1081999 AATAATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 21 0.64
34 12 0.36
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (34 bp):
ATATATTTTAAAAATATTATTATAGTAATATTAA
Found at i:1082064 original size:30 final size:30
Alignment explanation
Indices: 1082025--1082095 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
1082015 ATTAATAATT
1082025 TAATATTATTTATATGAAATTAATAAATAA
1 TAATATTATTTATATGAAATTAATAAATAA
*
1082055 TATTATTATTTATATGAAATTAATAAATAA
1 TAATATTATTTATATGAAATTAATAAATAA
1082085 TAATATTATTT
1 TAATATTATTT
1082096 TAATAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
TAATATTATTTATATGAAATTAATAAATAA
Found at i:1084335 original size:19 final size:20
Alignment explanation
Indices: 1084311--1084366 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
1084301 TTCATTATCC
1084311 TATTATTAGTTGGTTATT-AT
1 TATTATTAGTT-GTTATTCAT
*
1084331 T-TTATTTGTTTGTT-TTCAT
1 TATTATTAG-TTGTTATTCAT
1084350 TATTATTAGTTGTTATT
1 TATTATTAGTTGTTATT
1084367 TGTCAATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 2 0.07
19 17 0.57
20 11 0.37
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.66
Consensus pattern (20 bp):
TATTATTAGTTGTTATTCAT
Found at i:1085065 original size:30 final size:29
Alignment explanation
Indices: 1085016--1085073 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
1085006 TGAATAAATT
* * *
1085016 GAAAGTTTGGTGGCTAAAGTATAAATTTTG
1 GAAAGTTTGGAGACCAAAGTAT-AATTTTG
*
1085046 GAAAGTTTGGAGACCAAAGTGTAATTTT
1 GAAAGTTTGGAGACCAAAGTATAATTTT
1085074 AAAAAGTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (29 bp):
GAAAGTTTGGAGACCAAAGTATAATTTTG
Found at i:1087401 original size:23 final size:23
Alignment explanation
Indices: 1087371--1087418 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1087361 ATATCTACAT
1087371 TATCTAGTTGAAATGCACTAAAA
1 TATCTAGTTGAAATGCACTAAAA
1087394 TATCTAGTTGAAATGCACTAAAA
1 TATCTAGTTGAAATGCACTAAAA
1087417 TA
1 TA
1087419 ATAGTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (23 bp):
TATCTAGTTGAAATGCACTAAAA
Found at i:1087430 original size:23 final size:23
Alignment explanation
Indices: 1087375--1087430 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1087365 CTACATTATC
* *
1087375 TAGTTGAAATGCACTAAAATATC
1 TAGTTAAAATGCACTAAAATATA
*
1087398 TAGTTGAAATGCACTAAAATA-A
1 TAGTTAAAATGCACTAAAATATA
1087420 TAGTATAAAAT
1 TAGT-TAAAAT
1087431 TGGAATGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 4 0.13
23 26 0.87
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.30
Consensus pattern (23 bp):
TAGTTAAAATGCACTAAAATATA
Found at i:1087464 original size:20 final size:18
Alignment explanation
Indices: 1087426--1087461 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1087416 ATAATAGTAT
1087426 AAAATTGGAATGCATATA
1 AAAATTGGAATGCATATA
1087444 AAAATTGGAATGCATATA
1 AAAATTGGAATGCATATA
1087462 TAACCCCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.28
Consensus pattern (18 bp):
AAAATTGGAATGCATATA
Found at i:1089110 original size:59 final size:59
Alignment explanation
Indices: 1089018--1089270 Score: 380
Period size: 59 Copynumber: 4.3 Consensus size: 59
1089008 ACGGTCAACT
* * * *
1089018 TTTACACAAATATCACCCTAACATAAATTAATTACGTATTAGACACCCTTTTAAAAATA
1 TTTACAAAAATAGCACCTTAACAGAAATTAATTACGTATTAGACACCCTTTTAAAAATA
* * *
1089077 TTTACAAAAATAGCAACTTAACAGAAATTAATTACGTAGTAGGCACCCTTTTAAAAATA
1 TTTACAAAAATAGCACCTTAACAGAAATTAATTACGTATTAGACACCCTTTTAAAAATA
* * * * *
1089136 TTTACAAAAATATCACCTTAACAGAAATTAATTACGCATTAGATAACATTTTAAAAATA
1 TTTACAAAAATAGCACCTTAACAGAAATTAATTACGTATTAGACACCCTTTTAAAAATA
* *
1089195 TTTACAAAAATAGCACCTTAATAGAAATTAATTACGTATTAGACACCTTTTTAAAAATA
1 TTTACAAAAATAGCACCTTAACAGAAATTAATTACGTATTAGACACCCTTTTAAAAATA
1089254 TTTACAAAAATAGCACC
1 TTTACAAAAATAGCACC
1089271 CGAGTTTTTT
Statistics
Matches: 173, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 173 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.31
Consensus pattern (59 bp):
TTTACAAAAATAGCACCTTAACAGAAATTAATTACGTATTAGACACCCTTTTAAAAATA
Found at i:1093358 original size:59 final size:59
Alignment explanation
Indices: 1093288--1093457 Score: 268
Period size: 59 Copynumber: 2.9 Consensus size: 59
1093278 TCACCCTAAT
*
1093288 AGAAATTAATTACGTATTAGGCACCCTTTTACAAATATTTACAAAAATAGCAACTTAAC
1 AGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAGCAACTTAAC
* * * * *
1093347 AGAAATTAATTATGTATTAGACACCCTTTTAAAAATATTTACAAAAATACCACCTTAAT
1 AGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAGCAACTTAAC
* *
1093406 AGAAATTAATTACGTTTTAGGCACTCTTTTAAAAATATTTACAAAAATAGCA
1 AGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAGCA
1093458 CCCGATTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 100 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.33
Consensus pattern (59 bp):
AGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAGCAACTTAAC
Found at i:1097593 original size:59 final size:59
Alignment explanation
Indices: 1097508--1097636 Score: 195
Period size: 59 Copynumber: 2.2 Consensus size: 59
1097498 ACTTTTACGC
* * *
1097508 AAATATCACCCTAATAGAAATTAATTACGTATTAGACACCCTTTTAAAAGTATTTACAA
1 AAATACCACCCTAACAGAAATTAATTACGTATTAGACACCCTTTTAAAAATATTTACAA
* * *
1097567 AAATACCACCTTAACAGAAATTAATTACGTTTTAGACACTCTTTTAAAAATATTTACAA
1 AAATACCACCCTAACAGAAATTAATTACGTATTAGACACCCTTTTAAAAATATTTACAA
*
1097626 AAATAGCACCC
1 AAATACCACCC
1097637 GAGTTTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (59 bp):
AAATACCACCCTAACAGAAATTAATTACGTATTAGACACCCTTTTAAAAATATTTACAA
Found at i:1097685 original size:18 final size:18
Alignment explanation
Indices: 1097659--1097701 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1097649 ACAAATCACA
* *
1097659 AGTCAGGTCAACGGTTCG
1 AGTCGGGTCAACGGGTCG
1097677 AGTCGGGTCAACGGGTCG
1 AGTCGGGTCAACGGGTCG
*
1097695 GGTCGGG
1 AGTCGGG
1097702 CTTTCAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.21, G:0.44, T:0.19
Consensus pattern (18 bp):
AGTCGGGTCAACGGGTCG
Found at i:1101774 original size:59 final size:59
Alignment explanation
Indices: 1101704--1101873 Score: 277
Period size: 59 Copynumber: 2.9 Consensus size: 59
1101694 TCACCCTAAT
*
1101704 AGAAATTAATTACGTATTAGGCACCCTTTTAAAAATATTTACAAAAATAGCAACTTAAC
1 AGAAATTAATTACGTATTAGACACCCTTTTAAAAATATTTACAAAAATAGCAACTTAAC
* *
1101763 AGAAATTAATTACGTATTAGACACCCTTTTAAAAATATTTACAAAAATACCACCTTAAC
1 AGAAATTAATTACGTATTAGACACCCTTTTAAAAATATTTACAAAAATAGCAACTTAAC
* * **
1101822 AGAAATTAATTACATTTTAGACAATCTTTTAAAAATATTTACAAAAATAGCA
1 AGAAATTAATTACGTATTAGACACCCTTTTAAAAATATTTACAAAAATAGCA
1101874 CCCGAGTTTT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 103 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (59 bp):
AGAAATTAATTACGTATTAGACACCCTTTTAAAAATATTTACAAAAATAGCAACTTAAC
Found at i:1104274 original size:27 final size:27
Alignment explanation
Indices: 1104236--1104302 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
1104226 TGTCTTCGTG
1104236 TCAATGTGAATTTGGATTTAAGTTGAA
1 TCAATGTGAATTTGGATTTAAGTTGAA
1104263 TCAATGTGAATTTGGATTTAAGTTGAA
1 TCAATGTGAATTTGGATTTAAGTTGAA
1104290 TCAATGTGAATTT
1 TCAATGTGAATTT
1104303 TTAAGGATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (27 bp):
TCAATGTGAATTTGGATTTAAGTTGAA
Found at i:1104483 original size:13 final size:14
Alignment explanation
Indices: 1104467--1104504 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
1104457 TCCTTTTATC
1104467 TATTTATTT-TAAA
1 TATTTATTTATAAA
1104480 TATTTATTTGATAAA
1 TATTTATTT-ATAAA
1104495 TCATTTATTT
1 T-ATTTATTT
1104505 CTTTTAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
15 5 0.23
16 8 0.36
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (14 bp):
TATTTATTTATAAA
Found at i:1107950 original size:24 final size:24
Alignment explanation
Indices: 1107894--1107959 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
1107884 GGGTTTTGTT
* * *
1107894 GGTTGAGAGCAGAAAAGATGGGTA
1 GGTTGTGAGCAGAAGAGAAGGGTA
1107918 GGTTGTGAGCAGAAGAGAAGGGTA
1 GGTTGTGAGCAGAAGAGAAGGGTA
* *
1107942 GGTTTTGAGAAG-AGAGAA
1 GGTTGTGAGCAGAAGAGAA
1107960 AAATGGCAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 6 0.16
24 31 0.84
ACGTcount: A:0.36, C:0.03, G:0.42, T:0.18
Consensus pattern (24 bp):
GGTTGTGAGCAGAAGAGAAGGGTA
Found at i:1126741 original size:9 final size:9
Alignment explanation
Indices: 1126727--1126789 Score: 72
Period size: 9 Copynumber: 6.8 Consensus size: 9
1126717 ATCGTTTGCA
1126727 TTCTTTCTT
1 TTCTTTCTT
1126736 TTCTTTCTT
1 TTCTTTCTT
1126745 TCTCTTTCTT
1 T-TCTTTCTT
1126755 TCTCTTTCTT
1 T-TCTTTCTT
* * *
1126765 TTATCTATT
1 TTCTTTCTT
*
1126774 TTCTTTATT
1 TTCTTTCTT
1126783 TTCTTTC
1 TTCTTTC
1126790 CTATTTTTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
9 28 0.60
10 19 0.40
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:1126752 original size:10 final size:10
Alignment explanation
Indices: 1126728--1126765 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
1126718 TCGTTTGCAT
1126728 TCTTTCTTT-
1 TCTTTCTTTC
1126737 TCTTTCTTTC
1 TCTTTCTTTC
1126747 TCTTTCTTTC
1 TCTTTCTTTC
1126757 TCTTTCTTT
1 TCTTTCTTT
1126766 TATCTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TCTTTCTTTC
Found at i:1126795 original size:21 final size:19
Alignment explanation
Indices: 1126769--1126808 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1126759 TTTCTTTTAT
*
1126769 CTATTTTCTTTATTTTCTTTC
1 CTATTTT-TGTATTTT-TTTC
1126790 CTATTTTTGTATTTTTTTC
1 CTATTTTTGTATTTTTTTC
1126809 TATATCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 7 0.39
21 7 0.39
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (19 bp):
CTATTTTTGTATTTTTTTC
Found at i:1130958 original size:17 final size:17
Alignment explanation
Indices: 1130936--1130971 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1130926 TTGAATTTTG
1130936 AGTTTAAATTCCTAATA
1 AGTTTAAATTCCTAATA
1130953 AGTTTAAATTCCTAATA
1 AGTTTAAATTCCTAATA
1130970 AG
1 AG
1130972 CCTTTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (17 bp):
AGTTTAAATTCCTAATA
Found at i:1139855 original size:20 final size:21
Alignment explanation
Indices: 1139826--1139886 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
1139816 TCCTTTGTTG
1139826 TATTTACATTTTGCAT-TTTA
1 TATTTACATTTTGCATCTTTA
* *
1139846 TATTTCCATTTTTGCATCTTTC
1 TATTTACA-TTTTGCATCTTTA
*
1139868 TATTTGCA-TTTGCATCTTT
1 TATTTACATTTTGCATCTTT
1139887 GCATTAGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 18 0.50
21 8 0.22
22 10 0.28
ACGTcount: A:0.18, C:0.16, G:0.07, T:0.59
Consensus pattern (21 bp):
TATTTACATTTTGCATCTTTA
Found at i:1139896 original size:20 final size:20
Alignment explanation
Indices: 1139856--1139896 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1139846 TATTTCCATT
*
1139856 TTTGCATCTTTCTATTTGCA
1 TTTGCATCTTTCTATTAGCA
1139876 TTTGCATCTTTGC-ATTAGCA
1 TTTGCATCTTT-CTATTAGCA
1139896 T
1 T
1139897 ATTGAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.17, C:0.20, G:0.12, T:0.51
Consensus pattern (20 bp):
TTTGCATCTTTCTATTAGCA
Found at i:1142195 original size:133 final size:133
Alignment explanation
Indices: 1142051--1142359 Score: 395
Period size: 133 Copynumber: 2.3 Consensus size: 133
1142041 AATAGTAATA
*
1142051 AAGCAAATCAAGCTTGATTCAATCTTCTATAAAGAGTAGTGAAGTGGATCAAAGTTTTTCAAGTC
1 AAGCAAATCAAGTTTGATTCAATCTTCTATAAAGAGTAGTGAAGTGGATCAAAGTTTTTCAAGTC
* * * * * *
1142116 TGATCTCCCCTGAAGAGTAGTAG-AGCATATCCTCCTTCTTTCAGATTTGGTCTTCCTGAAAAGT
66 TGATCTCCCCTAAAGAGTAGT-GTAGCAGATCCTCCTTCTTTCAGAGTTGATCTTCATGAAAAGC
*
1142180 AGTG
130 AATG
* * ** * *** *
1142184 AAGCAAATCAAGTTTGATTAAATCCTCCCTAAAGAATAACAAAGTGGATCAAAGTTTTTCGAGTC
1 AAGCAAATCAAGTTTGATTCAATCTTCTATAAAGAGTAGTGAAGTGGATCAAAGTTTTTCAAGTC
* *
1142249 TGATCTCCCCTAAAGAGTAGTGTAGTAGATCCTCCTTCTTTCAGAGTTGATCTTCATGAAGAGCA
66 TGATCTCCCCTAAAGAGTAGTGTAGCAGATCCTCCTTCTTTCAGAGTTGATCTTCATGAAAAGCA
1142314 ATG
131 ATG
* * * *
1142317 ATGCAAATAAAGTTTGATTCAATCTTCTATGAAGAGCAGTGAA
1 AAGCAAATCAAGTTTGATTCAATCTTCTATAAAGAGTAGTGAA
1142360 ATAAATCAAA
Statistics
Matches: 144, Mismatches: 31, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
132 1 0.01
133 143 0.99
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (133 bp):
AAGCAAATCAAGTTTGATTCAATCTTCTATAAAGAGTAGTGAAGTGGATCAAAGTTTTTCAAGTC
TGATCTCCCCTAAAGAGTAGTGTAGCAGATCCTCCTTCTTTCAGAGTTGATCTTCATGAAAAGCA
ATG
Found at i:1144602 original size:13 final size:13
Alignment explanation
Indices: 1144584--1144614 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1144574 ACTCAAGTGA
1144584 TTTATTTACTTTT
1 TTTATTTACTTTT
1144597 TTTATTTACTTTT
1 TTTATTTACTTTT
1144610 TTTAT
1 TTTAT
1144615 AGTTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTACTTTT
Found at i:1147265 original size:4 final size:4
Alignment explanation
Indices: 1147256--1147462 Score: 76
Period size: 4 Copynumber: 51.2 Consensus size: 4
1147246 AAAAGGTAAG
* * *
1147256 AAAT AAAT AAAT ATAT AAATT AAAAT GAAG AAA- AAAT AAATT AAAT AAA-
1 AAAT AAAT AAAT AAAT AAA-T -AAAT AAAT AAAT AAAT AAA-T AAAT AAAT
* * * * * * *
1147305 AGAT AAGAT AAAG AAAG CAA- AGAT AAA- ATAGT AAGT AAAAT AAAT AAA-
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT A-AAT AAAT AAAT
* * *
1147353 AAAT ATATAT AAA- AAAT AAAG AAA- ACAAT ATAT AAAT ATAT AAATT
1 AAAT A-A-AT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAA-T
* * *
1147399 AAAC AAAT AAAT AAA- ATAAT AAAA AAAT AAA- AAAT ATAT ATAAT AAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT
1147447 AAA- AACAT AAA- AAAT A
1 AAAT AA-AT AAAT AAAT A
1147463 GTAAATATAT
Statistics
Matches: 154, Mismatches: 25, Indels: 48
0.68 0.11 0.21
Matches are distributed among these distances:
3 23 0.15
4 98 0.64
5 27 0.18
6 6 0.04
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1147307 original size:21 final size:21
Alignment explanation
Indices: 1147256--1147429 Score: 68
Period size: 21 Copynumber: 7.9 Consensus size: 21
1147246 AAAAGGTAAG
* *
1147256 AAATAAATAAATATATAAATTA
1 AAATAAAGAAA-AAATAAATTA
*
1147278 AAATGAAGAAAAAATAAATT-
1 AAATAAAGAAAAAATAAATTA
* * *
1147298 AAATAAAAGATAAGATAAA-GA
1 AAAT-AAAGAAAAAATAAATTA
** * *
1147319 AAGCAAAGATAAAATAGTAAGTA
1 AAATAAAGAAAAAATA--AATTA
* *
1147342 AAATAAATAAAAAATATATATAAA
1 AAATAAAGAAAAAATA-A-AT-TA
* *
1147366 AAATAAAGAAAACAATATATAA
1 AAATAAAGAAAA-AATAAATTA
*
1147388 ATATATAAATTAAACAAATAAA-TA
1 A-A-ATAAA-GAAA-AAATAAATTA
1147412 AAATAATA-AAAAAATAAA
1 AAATAA-AGAAAAAATAAA
1147430 AAATATATAT
Statistics
Matches: 117, Mismatches: 22, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
20 22 0.19
21 24 0.21
22 20 0.17
23 19 0.16
24 19 0.16
25 12 0.10
26 1 0.01
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAAAAATAAATTA
Found at i:1147312 original size:26 final size:30
Alignment explanation
Indices: 1147246--1147312 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 30
1147236 GTGTTAGATA
*
1147246 AAAAGGTAAGAAATAAATAAATATATAAAT
1 AAAAGATAAGAAATAAATAAATATATAAAT
*
1147276 TAAA-ATGAAGAAA-AAAT-AA-AT-TAAAT
1 AAAAGAT-AAGAAATAAATAAATATATAAAT
1147302 AAAAGATAAGA
1 AAAAGATAAGA
1147313 TAAAGAAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
26 12 0.38
27 4 0.12
28 2 0.06
29 5 0.16
30 9 0.28
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (30 bp):
AAAAGATAAGAAATAAATAAATATATAAAT
Found at i:1147377 original size:24 final size:25
Alignment explanation
Indices: 1147340--1147449 Score: 111
Period size: 24 Copynumber: 4.4 Consensus size: 25
1147330 AAATAGTAAG
1147340 TAAAATAAATAAAAAATATATATAA
1 TAAAATAAATAAAAAATATATATAA
*
1147365 -AAAATAAAGAAAACAATATATAAATATA
1 TAAAATAAATAAAA-AATATAT--ATA-A
* * *
1147393 TAAATTAAACAAATAAATA-AAATAA
1 TAAAATAAATAAA-AAATATATATAA
1147418 TAAAA-AAATAAAAAATATATATAA
1 TAAAATAAATAAAAAATATATATAA
1147442 T-AAATAAA
1 TAAAATAAA
1147450 AACATAAAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
23 8 0.11
24 27 0.39
25 12 0.17
26 3 0.04
27 3 0.04
28 2 0.03
29 14 0.20
30 1 0.01
ACGTcount: A:0.73, C:0.02, G:0.01, T:0.25
Consensus pattern (25 bp):
TAAAATAAATAAAAAATATATATAA
Found at i:1147388 original size:57 final size:56
Alignment explanation
Indices: 1147289--1147429 Score: 137
Period size: 57 Copynumber: 2.5 Consensus size: 56
1147279 AATGAAGAAA
* * * * *
1147289 AAATAAATTAAATAA-AAGATAAGATAAAGAAAGCAAAGATAAA-ATAGTAAGTAAAAT
1 AAATAAATAAAATAATAA-A-AAAATAAAGAAAACAAAGATAAATATA-TAAATAAAAC
* *
1147346 AAAT-AA-AAAATATATATAAAAAATAAAGAAAACAATATATAAATATATAAATTAAAC
1 AAATAAATAAAATA-ATA-AAAAAATAAAGAAAACAA-AGATAAATATATAAATAAAAC
1147403 AAATAAATAAAATAATAAAAAAATAAA
1 AAATAAATAAAATAATAAAAAAATAAA
1147430 AAATATATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
55 5 0.07
56 17 0.24
57 33 0.47
58 9 0.13
59 6 0.09
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21
Consensus pattern (56 bp):
AAATAAATAAAATAATAAAAAAATAAAGAAAACAAAGATAAATATATAAATAAAAC
Found at i:1147421 original size:33 final size:31
Alignment explanation
Indices: 1147342--1147432 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 31
1147332 ATAGTAAGTA
*
1147342 AAATAAATAAAA-AAT--ATATATAAAAAAT
1 AAATAAATAAAATAATAAATATATAAAAAAC
* *
1147370 AAAGAAA-ACAATATATAAATATATAAATTAAAC
1 AAATAAATAAAATA-ATAAATATATAAA--AAAC
* *
1147403 AAATAAATAAAATAATAAAAAAATAAAAAA
1 AAATAAATAAAATAATAAATATATAAAAAA
1147433 TATATATAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
27 3 0.06
28 7 0.14
29 2 0.04
31 12 0.24
33 20 0.41
34 5 0.10
ACGTcount: A:0.75, C:0.02, G:0.01, T:0.22
Consensus pattern (31 bp):
AAATAAATAAAATAATAAATATATAAAAAAC
Found at i:1147472 original size:35 final size:36
Alignment explanation
Indices: 1147340--1147460 Score: 102
Period size: 36 Copynumber: 3.2 Consensus size: 36
1147330 AAATAGTAAG
* *
1147340 TAAAATAAATAAAAAATATATATAAAAAATAAAGAAAA
1 TAAAA-AAATAAAAAATATATATAATAAATAAA-ATAA
* * * *
1147378 CAATATATAAATATATAAAT-TAAACAAATAAATAAAATAA
1 TAA-A-A-AAATA-AAAAATATATA-TAATAAATAAAATAA
1147418 TAAAAAAATAAAAAATATATATAATAAATAAAA-ACA
1 TAAAAAAATAAAAAATATATATAATAAATAAAATA-A
1147454 TAAAAAA
1 TAAAAAA
1147461 TAGTAAATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
35 1 0.01
36 24 0.36
37 8 0.12
38 3 0.04
39 2 0.03
40 15 0.22
41 14 0.21
ACGTcount: A:0.74, C:0.02, G:0.01, T:0.23
Consensus pattern (36 bp):
TAAAAAAATAAAAAATATATATAATAAATAAAATAA
Found at i:1148124 original size:37 final size:38
Alignment explanation
Indices: 1148074--1148180 Score: 137
Period size: 37 Copynumber: 2.9 Consensus size: 38
1148064 ATGCCTGTGG
*
1148074 ATCCTATTTTTAGGAGTTTGAATCATAGT-AGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAAACTCT
* **
1148111 ATCCTATTTTTAGGAGTTTAAATGGTAGTAAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAAACTCT
* * *
1148149 ATCTTA-TTTTAGGAGTTTGAATCCTATTAAAA
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAA
1148181 CTTTAACATT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
37 48 0.80
38 12 0.20
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (38 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAAACTCT
Found at i:1148992 original size:34 final size:34
Alignment explanation
Indices: 1148946--1149060 Score: 178
Period size: 34 Copynumber: 3.4 Consensus size: 34
1148936 AAGGTCTTGG
*
1148946 GTTTCAAGAGAAACATTTTCAAAGGTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
* * *
1148980 GTTTAAAGAGAAACAATTTCAAAGATTATTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
1149014 GTTTCAAGAGAAACAATTTCAAAGG-TTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
*
1149047 GTTTTAAGAGAAAC
1 GTTTCAAGAGAAAC
1149061 TGTCACAAGG
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 20 0.27
34 53 0.73
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (34 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTGT
Found at i:1149164 original size:67 final size:72
Alignment explanation
Indices: 1149044--1149604 Score: 332
Period size: 73 Copynumber: 8.0 Consensus size: 72
1149034 AAAGGTTTTT
* * * *
1149044 TGTGTTTTAAGAGAAACTGTCACAAGGGAGGC-AAACTTTTGTTTCAACAGAAACATAT-TC-A-
1 TGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC-TTTGTTTCAACAGAAAC-TATCTCAAG
**
1149105 A-AG-ATTA
64 AGAGAAAAA
** *
1149112 -GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAACAGAAACTATCTCAAGAG
1149176 AGACAAAA
66 AGA-AAAA
* * * * * * *
1149184 TTTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGTTCCAAAAGAAACTATCTTAAGGG
1 TGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAACAGAAACTATCTCAAGAG
1149249 AGATAAAA
66 AGA-AAAA
* * * * ** *
1149257 TTTGTTTCAAGAAAAACAGAT-TC-A-A-AG-----ATTTTGTTTCAAGGGAAACTGTCTCAAGA
1 TGTGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAACTTTGTTTCAACAGAAACTATCTCAAGA
1149313 GAGACAAAA
65 GAGA-AAAA
* * ** * *
1149322 TTTGTTTCAAG-GACAACTGTCTCAAGAGAGACAAAACTTTGCTTCAAGGGAAACTGTTTCAAGA
1 TGTGTTTCAAGAGA-AACTGTCTCAAGAGAGACAAAACTTTGTTTCAACAGAAACTATCTCAAGA
1149386 GAGACAAAA
65 GAGA-AAAA
* * * * * * * * *
1149395 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAATTGTCTTAAGGG
1 TGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAACAGAAACTATCTCAAGAG
*
1149460 AGATGAAA
66 AGA-AAAA
* * * * ** *
1149468 TTTATTTCAAG-GAAAACATAT-TC-A-A-AG-----ATTTTGTTTCAAGGGAAACTGTCTCAAG
1 TGTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAACTTTGTTTCAACAGAAACTATCTCAAG
1149523 AGAGACAAAA
64 AGAGA-AAAA
* * * * * * *
1149533 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTTGTTTCAAGAAAAACTGTGTCAAGAG
1 TGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAACAGAAACTATCTCAAGAG
1149597 AGACAAAA
66 AGA-AAAA
1149605 CTTTGTTTTG
Statistics
Matches: 398, Mismatches: 63, Indels: 60
0.76 0.12 0.12
Matches are distributed among these distances:
64 5 0.01
65 90 0.23
66 5 0.01
67 46 0.12
68 9 0.02
69 1 0.00
70 6 0.02
71 2 0.01
72 38 0.10
73 191 0.48
74 5 0.01
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (72 bp):
TGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAACAGAAACTATCTCAAGAG
AGAAAAA
Found at i:1149200 original size:36 final size:36
Alignment explanation
Indices: 1149113--1149612 Score: 496
Period size: 36 Copynumber: 14.1 Consensus size: 36
1149103 CAAAGATTAG
1149113 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
1149150 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1149186 TGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * * *
1149223 AGTTCCAAAAGAAACTATCTTAAGGGAGATAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1149259 TGTTTCAAGAAAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
1149288 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1149324 TGTTTCAAG-GACAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGA-AACTGTCTCAAGAGAGACAAAA-TT
* * *
1149361 TGCTTCAAGGGAAACTGTTTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1149397 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * * **
1149434 AGTTCCAAAAGAAATTGTCTTAAGGGAGATGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1149470 TATTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
1149499 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1149535 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1149571 TGTTTCAAGAAAAACTGTGTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
1149608 TGTTT
1 TGTTT
1149613 TGAGTAAATT
Statistics
Matches: 382, Mismatches: 55, Indels: 52
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.01
29 36 0.09
30 3 0.01
31 2 0.01
32 4 0.01
33 4 0.01
35 5 0.01
36 193 0.51
37 130 0.34
38 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1149309 original size:138 final size:138
Alignment explanation
Indices: 1149148--1149411 Score: 408
Period size: 138 Copynumber: 1.9 Consensus size: 138
1149138 GAGACAAAAC
1149148 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGA-AACTGTCTCAAAAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-GACAACTGTCTCAAAAG
* *
1149212 AGACAAAACTTAG-TTCCAAAAGAAACTATCTT-AAGGGAGATAAAATTTGTTTCAAGAAAAACA
65 AGACAAAACTTAGCTT-CAAAAGAAACTAT-TTCAAGAGAGACAAAATTTGTTTCAAGAAAAACA
1149275 GATTCAAAGAT
128 GATTCAAAGAT
*
1149286 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGACAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGACAACTGTCTCAAAAGA
* ** * *
1149351 GACAAAACTTTGCTTCAAGGGAAACTGTTTCAAGAGAGACAAAATTTGTTTCAAGAGAAAC
66 GACAAAACTTAGCTTCAAAAGAAACTATTTCAAGAGAGACAAAATTTGTTTCAAGAAAAAC
1149412 TGTCTCAAGA
Statistics
Matches: 115, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
137 4 0.03
138 109 0.95
139 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (138 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGACAACTGTCTCAAAAGA
GACAAAACTTAGCTTCAAAAGAAACTATTTCAAGAGAGACAAAATTTGTTTCAAGAAAAACAGAT
TCAAAGAT
Found at i:1149360 original size:211 final size:210
Alignment explanation
Indices: 1149113--1149612 Score: 831
Period size: 211 Copynumber: 2.4 Consensus size: 210
1149103 CAAAGATTAG
1149113 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
*
1149178 ACAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAAACTTAGTTCCAAAAGAAACTATCT
65 ACAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGAGAAAAAACTTAGTTCCAAAAGAAACTATCT
*
1149243 TAAGGGAGATAAAATTTGTTTCAAGAAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCT
130 TAAGGGAGATAAAATTTATTTCAAGAAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCT
1149308 CAAGAGAGACAAAATT
195 CAAGAGAGACAAAATT
* *
1149324 TGTTTCAAGGACAACTGTCTCAAGAGAGACAAAACTTTGCTTCAAGGGAAACTGTTTCAAGAGAG
1 TGTTTCAAGGA-AACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
* * *
1149389 ACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAACTTAGTTCCAAAAGAAATTGTCT
65 ACAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGAGAAAAAACTTAGTTCCAAAAGAAACTATCT
* * *
1149454 TAAGGGAGATGAAATTTATTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCT
130 TAAGGGAGATAAAATTTATTTCAAGAAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCT
1149519 CAAGAGAGACAAAATT
195 CAAGAGAGACAAAATT
* ** *
1149535 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTTGTTTCAAGAAAAACTGTGTCAAGAGAG
1 TGTTTCAA-GGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1149599 ACAAAACTTTGTTT
65 ACAAAA-TTTGTTT
1149613 TGAGTAAATT
Statistics
Matches: 271, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
210 34 0.13
211 234 0.86
212 3 0.01
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (210 bp):
TGTTTCAAGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
CAAAATTTGTTTCAAGAGAAACTGTCTCAAAAGAGAAAAAACTTAGTTCCAAAAGAAACTATCTT
AAGGGAGATAAAATTTATTTCAAGAAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTC
AAGAGAGACAAAATT
Found at i:1149580 original size:21 final size:21
Alignment explanation
Indices: 1149518--1149580 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
1149508 GGAAACTGTC
1149518 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* * *
1149539 TCAAG-G-G---AAA-CTATC
1 TCAAGAGAGACAAAATTTGTT
1149554 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
1149575 TCAAGA
1 TCAAGA
1149581 AAAACTGTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 1 0.03
19 1 0.03
20 4 0.13
21 13 0.43
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:1149631 original size:37 final size:36
Alignment explanation
Indices: 1149497--1149637 Score: 153
Period size: 36 Copynumber: 3.9 Consensus size: 36
1149487 ATTCAAAGAT
*
1149497 TTTGTTTCAAGGGAAACT-GTCTCAAGAGAGACAAAA
1 TTTGTTTCAA-GAAAACTAGTCTCAAGAGAGACAAAA
*
1149533 TTTGTTTCAAGGGAAACTA-TCTCAAGAGAGACAAAA
1 TTTGTTTCAA-GAAAACTAGTCTCAAGAGAGACAAAA
*
1149569 TTTGTTTCAAGAAAAACT-GTGTCAAGAGAGACAAAA
1 TTTGTTTCAAG-AAAACTAGTCTCAAGAGAGACAAAA
** * * *
1149605 CTTTGTTTTGAGTAAATTAGTCTCAAGCGAGAC
1 -TTTGTTTCAAGAAAACTAGTCTCAAGAGAGAC
1149638 GACCCCTTGT
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
35 1 0.01
36 70 0.76
37 21 0.23
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAAAACTAGTCTCAAGAGAGACAAAA
Found at i:1150436 original size:20 final size:20
Alignment explanation
Indices: 1150411--1150450 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1150401 TTCTTTCTCT
1150411 TTTATTTTCAAAGTTCTGAA
1 TTTATTTTCAAAGTTCTGAA
1150431 TTTATTTTCAAAGTTCTGAA
1 TTTATTTTCAAAGTTCTGAA
1150451 AATATCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTATTTTCAAAGTTCTGAA
Found at i:1151385 original size:14 final size:13
Alignment explanation
Indices: 1151331--1151422 Score: 62
Period size: 14 Copynumber: 6.9 Consensus size: 13
1151321 ATGAGTCTTG
1151331 TCTTTTTTTTCTTC
1 TCTTTTTTTT-TTC
* ** *
1151345 ACTTTTTCCTTTG
1 TCTTTTTTTTTTC
* *
1151358 T-TTTTATTTCTC
1 TCTTTTTTTTTTC
1151370 TCTTTTTTATTTTC
1 TCTTTTTT-TTTTC
*
1151384 TCTTTGCTTTTTTC
1 TCTTT-TTTTTTTC
*
1151398 T-TTGTTTTTTTC
1 TCTTTTTTTTTTC
1151410 TCTTTTTCTTTTT
1 TCTTTTT-TTTTT
1151423 GTTCTGATTG
Statistics
Matches: 57, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
12 15 0.26
13 13 0.23
14 27 0.47
15 2 0.04
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (13 bp):
TCTTTTTTTTTTC
Found at i:1154502 original size:5 final size:4
Alignment explanation
Indices: 1154481--1154692 Score: 73
Period size: 4 Copynumber: 51.8 Consensus size: 4
1154471 AAAAGGTAAG
*
1154481 AAAT AAAT AAAT AAATT AAATT AAAAT AAAG AAA- AAAT AAATT AAAT
1 AAAT AAAT AAAT AAA-T AAA-T -AAAT AAAT AAAT AAAT AAA-T AAAT
* * * * * * *
1154528 AAA- AGAT AAGAT AAAG AAAG CAA- AGAT AAA- ATAGT AAGT AAAAT AAAT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT -AAAT AAAT
* * * * *
1154576 AAA- AAA- AATAT ATAT ATAT AAAAT AAA- GAA- AAAT ATAT AAAT ATAT
1 AAAT AAAT AA-AT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
1154622 AAAT AAAAC AAAT AAAAC AAAT AAAT AAA- AAAT AAAT AAAA ATAAT AAAA
1 AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT
*
1154672 ATAAT ATAT ATAAT AAAT AAA
1 A-AAT AAAT A-AAT AAAT AAA
1154693 AACAAAAAAA
Statistics
Matches: 160, Mismatches: 28, Indels: 40
0.70 0.12 0.18
Matches are distributed among these distances:
3 19 0.12
4 100 0.62
5 38 0.24
6 3 0.02
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1154542 original size:21 final size:21
Alignment explanation
Indices: 1154481--1154530 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 21
1154471 AAAAGGTAAG
*
1154481 AAATAAATAAATAAATTAAATTA
1 AAATAAAGAAA-AAA-TAAATTA
1154504 AAATAAAGAAAAAATAAATT-
1 AAATAAAGAAAAAATAAATTA
1154524 AAATAAA
1 AAATAAA
1154531 AGATAAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.27
21 6 0.23
22 3 0.12
23 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
AAATAAAGAAAAAATAAATTA
Found at i:1154619 original size:27 final size:23
Alignment explanation
Indices: 1154570--1154694 Score: 109
Period size: 22 Copynumber: 5.5 Consensus size: 23
1154560 AGTAAGTAAA
1154570 ATAAATAAAAAAAATATATATAT
1 ATAAATAAAAAAAATATATATAT
1154593 ATAAAATAAAGAAAAATATATAAATAT
1 AT-AAATAAA-AAAAATATAT--ATAT
* * * *
1154620 ATAAATAAAACAAATA-AAACAA
1 ATAAATAAAAAAAATATATATAT
*
1154642 ATAAATAAAAAATAA-ATA-A-AA
1 ATAAATAAAAAA-AATATATATAT
*
1154663 AT-AATAAAAATAATATATATA-
1 ATAAATAAAAAAAATATATATAT
1154684 ATAAATAAAAA
1 ATAAATAAAAA
1154695 CAAAAAAATA
Statistics
Matches: 86, Mismatches: 6, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.02
20 11 0.13
21 7 0.08
22 24 0.28
23 5 0.06
24 8 0.09
25 16 0.19
26 7 0.08
27 6 0.07
ACGTcount: A:0.74, C:0.02, G:0.01, T:0.24
Consensus pattern (23 bp):
ATAAATAAAAAAAATATATATAT
Found at i:1154634 original size:25 final size:25
Alignment explanation
Indices: 1154570--1154714 Score: 107
Period size: 25 Copynumber: 6.1 Consensus size: 25
1154560 AGTAAGTAAA
*
1154570 ATAAATAAAAAAAATATATATATAT
1 ATAAATAAAAAAAATATATAAATAT
1154595 A-AAATAAAGAAAAATATATAAATAT
1 ATAAATAAA-AAAAATATATAAATAT
*
1154620 ATAAATAAAACAAATA-A-AACA-A-
1 ATAAATAAAAAAAATATATAA-ATAT
*
1154642 ATAAATAAAAAATAA-ATAAAAATA-
1 ATAAATAAAAAA-AATATATAAATAT
* * *
1154666 AT-AA-AAATAATATATAT-AATAA
1 ATAAATAAAAAAAATATATAAATAT
1154688 ATAAA-AACAAAAAA-ATAGTAAATAT
1 ATAAATAA-AAAAAATATA-TAAATAT
1154713 AT
1 AT
1154715 GTATAAATTA
Statistics
Matches: 98, Mismatches: 9, Indels: 26
0.74 0.07 0.20
Matches are distributed among these distances:
21 5 0.05
22 22 0.22
23 16 0.16
24 19 0.19
25 29 0.30
26 7 0.07
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.24
Consensus pattern (25 bp):
ATAAATAAAAAAAATATATAAATAT
Found at i:1154676 original size:9 final size:9
Alignment explanation
Indices: 1154567--1154688 Score: 65
Period size: 9 Copynumber: 13.2 Consensus size: 9
1154557 AATAGTAAGT
1154567 AAAATAAATA
1 AAAAT-AATA
*
1154577 AAAAAAATA
1 AAAATAATA
* *
1154586 TATAT-ATA
1 AAAATAATA
*
1154594 TAAAATAAAGA
1 -AAAAT-AATA
1154605 AAAAT-ATA
1 AAAATAATA
*
1154613 TAAAT-ATA
1 AAAATAATA
*
1154621 TAAATAA-A
1 AAAATAATA
1154629 ACAAATAA-A
1 A-AAATAATA
1154638 ACAAATAAATAA
1 A-AAAT-AAT-A
1154650 AAAATAAATA
1 AAAAT-AATA
1154660 AAAATAATA
1 AAAATAATA
1154669 AAAATAATA
1 AAAATAATA
* *
1154678 TATATAATA
1 AAAATAATA
1154687 AA
1 AA
1154689 TAAAAACAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
8 18 0.20
9 44 0.48
10 17 0.19
11 10 0.11
12 2 0.02
ACGTcount: A:0.74, C:0.02, G:0.01, T:0.24
Consensus pattern (9 bp):
AAAATAATA
Found at i:1154690 original size:55 final size:57
Alignment explanation
Indices: 1154566--1154704 Score: 158
Period size: 55 Copynumber: 2.4 Consensus size: 57
1154556 AAATAGTAAG
* *
1154566 TAAAATAAATAAAAAAAATATATATATATAAAATAAAGAAAAATATATAAATATATAAA
1 TAAAATAAATAAAACAAATA-A-ATATATAAAATAAAGAAAAATATAAAAATATATAAA
* * *
1154625 TAAAACAAATAAAACAAATAAATA-A-AAAATAAATAAAAATAATAAAAATA-ATATA
1 TAAAATAAATAAAACAAATAAATATATAAAATAAAGAAAAAT-ATAAAAATATATAAA
* *
1154680 TATAATAAATAAAAACAAAAAAATA
1 TAAAATAAAT-AAAACAAATAAATA
1154705 GTAAATATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
55 26 0.37
56 22 0.31
57 3 0.04
58 1 0.01
59 18 0.26
ACGTcount: A:0.74, C:0.02, G:0.01, T:0.23
Consensus pattern (57 bp):
TAAAATAAATAAAACAAATAAATATATAAAATAAAGAAAAATATAAAAATATATAAA
Found at i:1154704 original size:27 final size:27
Alignment explanation
Indices: 1154568--1154714 Score: 107
Period size: 27 Copynumber: 5.0 Consensus size: 27
1154558 ATAGTAAGTA
* *
1154568 AAATAAATAAAAAAAATATATATATAT
1 AAATAAAAAAAAAAAATATAAATATAT
* *
1154595 AAA-ATAAAGAAAAATATATAAATATAT
1 AAATA-AAAAAAAAAAATATAAATATAT
* *
1154622 AAATAAAACAAATAAAACAAATAAATAAAAAAT
1 AAATAAAA-AAA-AAAA-ATATAAAT---ATAT
*
1154655 AAATAAAAATAATAAAAATAATATATATAAT
1 AAATAAAAA-AA-AAAAAT-ATAAATAT-AT
1154686 AAATAAAAACAAAAAAATAGTAAATATAT
1 AAATAAAAA-AAAAAAATA-TAAATATAT
1154715 GTATAAATTA
Statistics
Matches: 95, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
26 1 0.01
27 27 0.28
28 3 0.03
29 6 0.06
30 20 0.21
31 13 0.14
32 2 0.02
33 23 0.24
ACGTcount: A:0.73, C:0.02, G:0.01, T:0.24
Consensus pattern (27 bp):
AAATAAAAAAAAAAAATATAAATATAT
Found at i:1154732 original size:92 final size:92
Alignment explanation
Indices: 1154567--1154747 Score: 224
Period size: 92 Copynumber: 2.0 Consensus size: 92
1154557 AATAGTAAGT
* * *
1154567 AAAATAAATAAAAAAAATATATATATATAAAATAAAGAAAAATATATAAATATATAAATAAAACA
1 AAAATAAATAAAAAAAATATATATATATAAAAAAAACAAAAAAATATAAATATATAAATAAAACA
1154632 AATAAAACAAATAAATAAAAAATAAATA
66 AATAAAACAAAT-AATAAAAAATAAATA
* **
1154660 AAAAT-AATAAAAATAATATATATA-ATAAATAAAAACAAAAAAATAGTAAATATATGTAT-AAA
1 AAAATAAATAAAAAAAATATATATATATAAA-AAAAACAAAAAAATA-TAAATATATAAATAAAA
** * *
1154722 TTAATGAAACAGATAATAAAAAATAA
64 CAAATAAAACAAATAATAAAAAATAA
1154748 CATATATATA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
91 17 0.22
92 43 0.57
93 16 0.21
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (92 bp):
AAAATAAATAAAAAAAATATATATATATAAAAAAAACAAAAAAATATAAATATATAAATAAAACA
AATAAAACAAATAATAAAAAATAAATA
Found at i:1155369 original size:37 final size:37
Alignment explanation
Indices: 1155319--1155430 Score: 161
Period size: 37 Copynumber: 3.0 Consensus size: 37
1155309 ATGCTTGTGG
*
1155319 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* * *
1155356 ATCCTATTTTTAGGAGTTTAAATCCTAGTAAAACTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* * *
1155393 ATTCTATTTTTAGGAGTTTGAATCGTAATAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1155430 A
1 A
1155431 ACGTTATGTT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:1159765 original size:15 final size:15
Alignment explanation
Indices: 1159702--1159785 Score: 82
Period size: 15 Copynumber: 5.6 Consensus size: 15
1159692 TATCAGTTTA
1159702 TATTATTATATATAT
1 TATTATTATATATAT
* *
1159717 TATTAACTATATATGT
1 TATT-ATTATATATAT
* **
1159733 TTTTATTATATACGT
1 TATTATTATATATAT
1159748 TATTATTATATATAT
1 TATTATTATATATAT
1159763 TA-TATTA-ATAATAT
1 TATTATTATAT-ATAT
*
1159777 TAGTATTAT
1 TATTATTAT
1159786 TAAATAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
13 2 0.04
14 11 0.19
15 32 0.56
16 12 0.21
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (15 bp):
TATTATTATATATAT
Found at i:1166466 original size:20 final size:20
Alignment explanation
Indices: 1166441--1166480 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1166431 GATTATTAAA
*
1166441 TCATTTTCTTTTTCTTGATC
1 TCATTTTCTTTTTCTCGATC
1166461 TCATTTTCTTTTTCTCGATC
1 TCATTTTCTTTTTCTCGATC
1166481 ATAATAATTA
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:0.10, C:0.23, G:0.05, T:0.62
Consensus pattern (20 bp):
TCATTTTCTTTTTCTCGATC
Found at i:1171105 original size:43 final size:43
Alignment explanation
Indices: 1171034--1171140 Score: 108
Period size: 43 Copynumber: 2.5 Consensus size: 43
1171024 CGTTTCAGCA
* * * * *
1171034 AAGGTAAGACTTTACTATTTCTGTAGGCTAC-TCCTCTATGTGC
1 AAGGGAAGACCTTACCATTTATATAGGCT-CTTCCTCTATGTGC
** *
1171077 AAGGGAAGACCTTACCATTTATATAGGCTCTTTTTCTATTTGC
1 AAGGGAAGACCTTACCATTTATATAGGCTCTTCCTCTATGTGC
*
1171120 AAGGGTAAGAACTTACCATTT
1 AAGGG-AAGACCTTACCATTT
1171141 TTGCAGGCTC
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
42 1 0.02
43 38 0.72
44 14 0.26
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (43 bp):
AAGGGAAGACCTTACCATTTATATAGGCTCTTCCTCTATGTGC
Found at i:1171149 original size:44 final size:44
Alignment explanation
Indices: 1171058--1171173 Score: 117
Period size: 44 Copynumber: 2.7 Consensus size: 44
1171048 CTATTTCTGT
* * * * *
1171058 AGGCTACTCCTCTATGTGCAAGGG-AAGACCTTACCATTTATAT
1 AGGCTCCTCTTCTATTTGCAAGGGTAAGAACTTACCATTTATAC
* * * *
1171101 AGGCTCTTTTTCTATTTGCAAGGGTAAGAACTTACCATTTTTGC
1 AGGCTCCTCTTCTATTTGCAAGGGTAAGAACTTACCATTTATAC
* **
1171145 AGGCTCCTCTGCTATTTATAAGGGTAAGA
1 AGGCTCCTCTTCTATTTGCAAGGGTAAGA
1171174 CTTTATCACT
Statistics
Matches: 58, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
43 19 0.33
44 39 0.67
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (44 bp):
AGGCTCCTCTTCTATTTGCAAGGGTAAGAACTTACCATTTATAC
Found at i:1171252 original size:39 final size:39
Alignment explanation
Indices: 1171189--1171305 Score: 128
Period size: 39 Copynumber: 3.0 Consensus size: 39
1171179 TCACTTTCCG
*
1171189 CAGGCTCCTCTA-CTTTGTGTTCAGGGTAATTCCTTACTA
1 CAGGCTCCTC-AGCTTTGTGCTCAGGGTAATTCCTTACTA
* * *
1171228 TAGGCTCCTCAGCTTTATGCTCAGGGTAAGTCCTTACTA
1 CAGGCTCCTCAGCTTTGTGCTCAGGGTAATTCCTTACTA
* ** * * *
1171267 CAGGCTTCTGTGCTTTGTGCACAGGGTTATCCCTTACTA
1 CAGGCTCCTCAGCTTTGTGCTCAGGGTAATTCCTTACTA
1171306 GGTGTGCAGG
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 1 0.02
39 63 0.98
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.36
Consensus pattern (39 bp):
CAGGCTCCTCAGCTTTGTGCTCAGGGTAATTCCTTACTA
Found at i:1177143 original size:44 final size:44
Alignment explanation
Indices: 1177068--1177224 Score: 165
Period size: 44 Copynumber: 3.6 Consensus size: 44
1177058 TGACTTGTAT
* * * *
1177068 GACCTTACCATTTTTGCA-ACTCCTATACTATGTGCAAAGGTAA
1 GACCTTACCGTTTTAGCAGGCTCCTATACTATGTGCAAGGGTAA
* * *
1177111 CACCTTACCGTTTTAGCAGGCTCCTTTTCTATGTGCAAGGGTAA
1 GACCTTACCGTTTTAGCAGGCTCCTATACTATGTGCAAGGGTAA
* * * *
1177155 GACCTTACCGTTTCT-GCATGCTCATCTGCTATGTGCAAGGGTAA
1 GACCTTACCGTTT-TAGCAGGCTCCTATACTATGTGCAAGGGTAA
* *
1177199 GACCTTATCGCTTTCAGCAGGCTCCT
1 GACCTTACCG-TTTTAGCAGGCTCCT
1177225 CGACTTTATT
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
43 15 0.16
44 67 0.71
45 12 0.13
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (44 bp):
GACCTTACCGTTTTAGCAGGCTCCTATACTATGTGCAAGGGTAA
Found at i:1180225 original size:17 final size:17
Alignment explanation
Indices: 1180203--1180252 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
1180193 TTCAGGGAAG
1180203 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* * *
1180220 TTGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
1180237 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
1180253 ATAACACATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:1181981 original size:19 final size:19
Alignment explanation
Indices: 1181959--1181996 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1181949 CCTCAAGAAA
1181959 TTTAAAGAAAAGCAAGAGC
1 TTTAAAGAAAAGCAAGAGC
1181978 TTTAAAGAAAAGCAAGAGC
1 TTTAAAGAAAAGCAAGAGC
1181997 AGTAAAAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (19 bp):
TTTAAAGAAAAGCAAGAGC
Found at i:1182002 original size:19 final size:19
Alignment explanation
Indices: 1181961--1182002 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1181951 TCAAGAAATT
**
1181961 TAAAGAAAAGCAAGAGCTT
1 TAAAGAAAAGCAAGAGCAG
1181980 TAAAGAAAAGCAAGAGCAG
1 TAAAGAAAAGCAAGAGCAG
1181999 TAAA
1 TAAA
1182003 AGGCAAGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.10, G:0.21, T:0.12
Consensus pattern (19 bp):
TAAAGAAAAGCAAGAGCAG
Found at i:1187108 original size:17 final size:17
Alignment explanation
Indices: 1187088--1187130 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1187078 TTTAGGGAAG
*
1187088 TAGTTCATTAATTAAAA
1 TAGTTCATTAATCAAAA
*
1187105 TAGTTCATTCATCAAAA
1 TAGTTCATTAATCAAAA
*
1187122 TAATTCATT
1 TAGTTCATT
1187131 TACTAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATCAAAA
Found at i:1190311 original size:17 final size:17
Alignment explanation
Indices: 1190291--1190340 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
1190281 TTTAGGGAAG
*
1190291 TAGTTAATTAATTAAAC
1 TAGTTCATTAATTAAAC
*
1190308 TAGTTCATTAATCAAAC
1 TAGTTCATTAATTAAAC
*
1190325 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
1190341 TTAACTCTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:1193800 original size:21 final size:18
Alignment explanation
Indices: 1193775--1193817 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
1193765 AACTATCTAG
1193775 TTCATTTAGAGAAGTAGTTCA
1 TTCATTTA-A-AA-TAGTTCA
1193796 TTCA-TTAAAATAGTTCA
1 TTCATTTAAAATAGTTCA
1193813 TTCAT
1 TTCAT
1193818 CAAACTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.52
18 2 0.10
19 1 0.05
20 3 0.14
21 4 0.19
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (18 bp):
TTCATTTAAAATAGTTCA
Found at i:1193809 original size:17 final size:17
Alignment explanation
Indices: 1193789--1193838 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
1193779 TTTAGAGAAG
1193789 TAGTTCATTCATTAAAA
1 TAGTTCATTCATTAAAA
* *
1193806 TAGTTCATTCATCAAAC
1 TAGTTCATTCATTAAAA
1193823 TAGTTCAATT-ATTAAA
1 TAGTTC-ATTCATTAAA
1193839 TTAACTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 26 0.90
18 3 0.10
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTCATTAAAA
Found at i:1196260 original size:21 final size:18
Alignment explanation
Indices: 1196233--1196277 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
1196223 AATGAGAGTT
*
1196233 AAAAAAGACATTGAGAGCAA
1 AAAAAAGAAATTG-GAG-AA
1196253 AGAAAAAGAAATTGGAGAA
1 A-AAAAAGAAATTGGAGAA
1196272 AAAAAA
1 AAAAAA
1196278 TTGAAAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 3 0.13
20 4 0.17
21 11 0.48
ACGTcount: A:0.67, C:0.04, G:0.20, T:0.09
Consensus pattern (18 bp):
AAAAAAGAAATTGGAGAA
Found at i:1200827 original size:17 final size:17
Alignment explanation
Indices: 1200807--1200856 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
1200797 TTGAGGGAAG
1200807 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
1200824 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
1200841 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
1200857 TTTACTCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:1202873 original size:35 final size:35
Alignment explanation
Indices: 1202827--1202898 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1202817 TGGAGGTGAC
*
1202827 GCCCAAAATGATAGAGGTGCACCAAACTTGCAAAT
1 GCCCAAAATGATAGAGGTACACCAAACTTGCAAAT
*
1202862 GCCCAAAATGATGGAGGTACACCAAACTTGCAAAT
1 GCCCAAAATGATAGAGGTACACCAAACTTGCAAAT
1202897 GC
1 GC
1202899 AAAACATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.17
Consensus pattern (35 bp):
GCCCAAAATGATAGAGGTACACCAAACTTGCAAAT
Found at i:1203335 original size:21 final size:21
Alignment explanation
Indices: 1203311--1203355 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1203301 CGAAGAAAAA
*
1203311 GAAATTGGAGTT-AAAAAGATT
1 GAAAGTGGAGTTGAAAAA-ATT
*
1203332 GAAAGTGTAGTTGAAAAAATT
1 GAAAGTGGAGTTGAAAAAATT
1203353 GAA
1 GAA
1203356 GCAGAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.24, T:0.27
Consensus pattern (21 bp):
GAAAGTGGAGTTGAAAAAATT
Found at i:1205963 original size:16 final size:17
Alignment explanation
Indices: 1205932--1205965 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
1205922 GGGGTCTTCT
1205932 TTTAAAAATCAAAATAAA
1 TTTAAAAA-CAAAATAAA
1205950 TTTAAAAA-AAAATAAA
1 TTTAAAAACAAAATAAA
1205966 ACATGGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
TTTAAAAACAAAATAAA
Found at i:1210989 original size:24 final size:24
Alignment explanation
Indices: 1210934--1210991 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1210924 CACCAAAGTG
* *
1210934 CCACGCAGAATTTGTCCTGAAGGA
1 CCACGTAGAATTTGTCCAGAAGGA
** **
1210958 CCGTGTAGAATTTGTCCAGATTGA
1 CCACGTAGAATTTGTCCAGAAGGA
1210982 CCACGTAGAA
1 CCACGTAGAA
1210992 ATGCCTTGAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCAGAAGGA
Done.