Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008973.1 Hibiscus syriacus cultivar Beakdansim tig00112319_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: 2070395
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:982472 original size:20 final size:20
Alignment explanation
Indices: 982444--982517 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
982434 TGATAGTCAG
*
982444 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
982464 AATCGCATTGCGATTTTCCAG-
1 ATTCGCATTGCGA-TTTAC-GT
*
982485 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
982505 ATTCGCATTGCGA
1 ATTCGCATTGCGA
982518 ATTAGGAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 27 0.61
21 15 0.34
22 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:982538 original size:21 final size:21
Alignment explanation
Indices: 982514--982559 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
982504 TATTCGCATT
982514 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
982535 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
982556 GCGA
1 GCGA
982560 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:983247 original size:28 final size:28
Alignment explanation
Indices: 983214--983268 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
983204 ACTGTTCTTC
983214 ACTTTTCTCGGTTCTCATCATTTCTTTA
1 ACTTTTCTCGGTTCTCATCATTTCTTTA
983242 ACTTTTCTCGGTTCTCATCATTTCTTT
1 ACTTTTCTCGGTTCTCATCATTTCTTT
983269 CTCCATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.13, C:0.25, G:0.07, T:0.55
Consensus pattern (28 bp):
ACTTTTCTCGGTTCTCATCATTTCTTTA
Found at i:989365 original size:13 final size:12
Alignment explanation
Indices: 989347--989384 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
989337 AATGCCTAGG
989347 TTCTGTTTGGGTT
1 TTCTG-TTGGGTT
*
989360 TTCTGTTAGGTT
1 TTCTGTTGGGTT
989372 TTCTGTTGGGTT
1 TTCTGTTGGGTT
989384 T
1 T
989385 ATGATTTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.03, C:0.08, G:0.29, T:0.61
Consensus pattern (12 bp):
TTCTGTTGGGTT
Found at i:990161 original size:51 final size:51
Alignment explanation
Indices: 990106--990236 Score: 172
Period size: 51 Copynumber: 2.6 Consensus size: 51
990096 GCAACAGATT
* * *
990106 GTGGTGTTGAGGGTGATGGAGATGGTGTTCAAGTTACTGCTATAACATAAG
1 GTGGTCTTGAGGGTGATGGAGATGGTGTTCAAGCTACTGCTATAACAGAAG
* * * * * * *
990157 GTGGTCTTGAGGGTGATAGAGATGTTGTTGAAGCTACTGTTGTAGCAGAGG
1 GTGGTCTTGAGGGTGATGGAGATGGTGTTCAAGCTACTGCTATAACAGAAG
990208 GTGGTCTTGAGGGTGATGGAGATGGTGTT
1 GTGGTCTTGAGGGTGATGGAGATGGTGTT
990237 ACAGCAGAGG
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.21, C:0.07, G:0.40, T:0.32
Consensus pattern (51 bp):
GTGGTCTTGAGGGTGATGGAGATGGTGTTCAAGCTACTGCTATAACAGAAG
Found at i:993366 original size:30 final size:30
Alignment explanation
Indices: 993305--993375 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
993295 TTCGTTTTAA
* *
993305 TTCATTATCATTCACTTCACATTTCAAACT
1 TTCATTCTCTTTCACTTCACATTTCAAACT
* *
993335 TTCATTCTCTTTCACTTCGC-TTTGCATACT
1 TTCATTCTCTTTCACTTCACATTT-CAAACT
*
993365 TTCACTCTCTT
1 TTCATTCTCTT
993376 CCAACGTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 3 0.09
30 32 0.91
ACGTcount: A:0.20, C:0.30, G:0.03, T:0.48
Consensus pattern (30 bp):
TTCATTCTCTTTCACTTCACATTTCAAACT
Found at i:994212 original size:116 final size:116
Alignment explanation
Indices: 994003--994233 Score: 435
Period size: 116 Copynumber: 2.0 Consensus size: 116
993993 AAGCTATAGA
994003 ACAATGATCAAGGGTTATGAATAACCCATTCATAAAATCTATAAAATTCAGCTGGAAACTTGCAC
1 ACAATGATCAAGGGTTATGAATAACCCATTCATAAAATCTATAAAATTCAGCTGGAAACTTGCAC
*
994068 AAACCCTAACAATTAAAGAAAAATTATTTGAAAATCCATTAAAAAATAAGG
66 AAACCCTAACAATTAAAGAAAAAATATTTGAAAATCCATTAAAAAATAAGG
*
994119 ACAATGTTCAAGGGTTATGAATAACCCATTCATAAAATCTATAAAATTCAGCTGGAAACTTGCAC
1 ACAATGATCAAGGGTTATGAATAACCCATTCATAAAATCTATAAAATTCAGCTGGAAACTTGCAC
*
994184 AAACCCTAACAATTAAAGAAAAAATATTTGAAAATCCATTCAAAAATAAG
66 AAACCCTAACAATTAAAGAAAAAATATTTGAAAATCCATTAAAAAATAAG
994234 AAAATCCACA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 112 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (116 bp):
ACAATGATCAAGGGTTATGAATAACCCATTCATAAAATCTATAAAATTCAGCTGGAAACTTGCAC
AAACCCTAACAATTAAAGAAAAAATATTTGAAAATCCATTAAAAAATAAGG
Found at i:996477 original size:20 final size:20
Alignment explanation
Indices: 996431--996479 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
996421 TTGTCTTCTT
*
996431 TCTTCTCCCAAAAGCTCTCA
1 TCTTCTTCCAAAAGCTCTCA
996451 TCTTCTTCCAAAAGCTCTCA
1 TCTTCTTCCAAAAGCTCTCA
996471 TCTTCTTCC
1 TCTTCTTCC
996480 TTAGTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.39, G:0.04, T:0.37
Consensus pattern (20 bp):
TCTTCTTCCAAAAGCTCTCA
Found at i:998412 original size:14 final size:16
Alignment explanation
Indices: 998375--998427 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 16
998365 TGCAATCACC
*
998375 CATATCACACATATAT
1 CATATCATACATATAT
*
998391 CATGTCATACA-AT-T
1 CATATCATACATATAT
998405 CATATCATACATCATAT
1 CATATCATACAT-ATAT
998422 ACATAT
1 -CATAT
998428 ATTACATACA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 11 0.37
15 2 0.07
16 11 0.37
17 1 0.03
18 5 0.17
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (16 bp):
CATATCATACATATAT
Found at i:998563 original size:23 final size:23
Alignment explanation
Indices: 998537--998603 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
998527 CACCACAGCT
*
998537 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
998560 CGTAGAATTGCACTGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
998583 CGTAGAAATGCACCGAAGTGC
1 CGTAGAAATGCACCGAAGTGC
998604 TATATAAGGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1012862 original size:95 final size:95
Alignment explanation
Indices: 1012699--1012888 Score: 281
Period size: 95 Copynumber: 2.0 Consensus size: 95
1012689 TCTTCATTCT
* * * * * * *
1012699 ATTAGTGTATCATTTGAATGCTTCTAACTTTAGAGTTTGAGTAGTAAAGCATGTATGCACATTCA
1 ATTAGTGTACCATTGGAATGCTTCTAACTTTAAAGTTTGACTAGTAAAACATGCATGAACATTCA
* *
1012764 TGGTAGATTCTTGTGATATGTGTTATTAGC
66 TGGTAGATTATTGTGATATATGTTATTAGC
*
1012794 ATTAGTGTGCCATTGGAATGCTTCTAACTTTAAAGTTTGACTAGTAAAACATGCATGAACATTCA
1 ATTAGTGTACCATTGGAATGCTTCTAACTTTAAAGTTTGACTAGTAAAACATGCATGAACATTCA
*
1012859 TGGTAGATTATTGTGATATATTTTATTAGC
66 TGGTAGATTATTGTGATATATGTTATTAGC
1012889 GTCTTTAAAG
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.40
Consensus pattern (95 bp):
ATTAGTGTACCATTGGAATGCTTCTAACTTTAAAGTTTGACTAGTAAAACATGCATGAACATTCA
TGGTAGATTATTGTGATATATGTTATTAGC
Found at i:1013322 original size:18 final size:18
Alignment explanation
Indices: 1013301--1013347 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1013291 GCAAAAATTT
1013301 GTATCGATACCCGAGTCA
1 GTATCGATACCCGAGTCA
1013319 GTATCGATACCCGAGTCA
1 GTATCGATACCCGAGTCA
*
1013337 GTATTGATACC
1 GTATCGATACC
1013348 TAAGCCCGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (18 bp):
GTATCGATACCCGAGTCA
Found at i:1023022 original size:31 final size:31
Alignment explanation
Indices: 1022984--1023061 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
1022974 TAAAAAATAA
**
1022984 TAAGTTTTGGTCACTTACGTTATTATTTTAT
1 TAAGTTTTGGTCACTTACGTTACCATTTTAT
* *
1023015 TAAGTTTTGATCACTTACGTTACCATTTTGT
1 TAAGTTTTGGTCACTTACGTTACCATTTTAT
*
1023046 TAAGTTTTAGTCACTT
1 TAAGTTTTGGTCACTT
1023062 GGACGTTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGTTACCATTTTAT
Found at i:1024455 original size:31 final size:31
Alignment explanation
Indices: 1024420--1024528 Score: 123
Period size: 31 Copynumber: 3.5 Consensus size: 31
1024410 TTCAACGTCC
*
1024420 AAGTGACCAAAACTTAATAAAG-CGATAATAT
1 AAGTGACCAAAACTTAATAAAGTC-ATAACAT
*
1024451 AAGTGACCAAAACTTAATAAAGTCATAACGT
1 AAGTGACCAAAACTTAATAAAGTCATAACAT
* * * *
1024482 AAGTGACCAAAACTTTATAAAATGATAACGT
1 AAGTGACCAAAACTTAATAAAGTCATAACAT
*
1024513 ACA-TGAACAAAACTTA
1 A-AGTGACCAAAACTTA
1024529 TGTTTTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
31 67 0.97
32 2 0.03
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.23
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAGTCATAACAT
Found at i:1032372 original size:13 final size:13
Alignment explanation
Indices: 1032354--1032379 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1032344 GTCCAGGTTG
1032354 AAAAATATTATTA
1 AAAAATATTATTA
1032367 AAAAATATTATTA
1 AAAAATATTATTA
1032380 TTATTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAAATATTATTA
Found at i:1032378 original size:3 final size:3
Alignment explanation
Indices: 1032372--1032431 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
1032362 TATTAAAAAA
*
1032372 TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAAT TAT T-T TCT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT T-AT TAT TAT TAT
* *
1032418 TAA TGT TAT TAT TA
1 TAT TAT TAT TAT TA
1032432 CATTGCAGGC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1037657 original size:28 final size:27
Alignment explanation
Indices: 1037610--1037669 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
1037600 ATTGGGATCA
1037610 ACAT-TTTTGCATTTTCATCTACATTT
1 ACATCTTTTGCATTTTCATCTACATTT
*
1037636 ACATCTTTT-CATTTTACCATCTGCATTT
1 ACATCTTTTGCATTTT--CATCTACATTT
*
1037664 GCATCT
1 ACATCT
1037670 CCGCATTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 10 0.34
27 4 0.14
28 15 0.52
ACGTcount: A:0.22, C:0.23, G:0.05, T:0.50
Consensus pattern (27 bp):
ACATCTTTTGCATTTTCATCTACATTT
Found at i:1037811 original size:64 final size:63
Alignment explanation
Indices: 1037653--1037875 Score: 311
Period size: 63 Copynumber: 3.5 Consensus size: 63
1037643 TTCATTTTAC
* *
1037653 CATCTGCATTTGCATCTCCGCATTCTGCATGATGCATTGCATTTCAGAGGATCATCAATTTTG
1 CATCTGCATTTGCATCTTCGCATTCTACATGATGCATTGCATTTCAGAGGATCATCAATTTTG
* * * * * *
1037716 CATCTGTATTTGTACCTTCGTATTCTACATGATGCATTGCATTTAAGAGGATCATCAGTTTTTG
1 CATCTGCATTTGCATCTTCGCATTCTACATGATGCATTGCATTTCAGAGGATCATCA-ATTTTG
* * * *
1037780 CATCTGTATTTGCATCTTCGCATTCTGCATGATGAATTGCATTTCATAGGATCATCAATTTTG
1 CATCTGCATTTGCATCTTCGCATTCTACATGATGCATTGCATTTCAGAGGATCATCAATTTTG
* *
1037843 CATCTGCATTTGCATATTTGCATTCTACATGAT
1 CATCTGCATTTGCATCTTCGCATTCTACATGAT
1037876 CATCATAAGT
Statistics
Matches: 139, Mismatches: 20, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
63 84 0.60
64 55 0.40
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.40
Consensus pattern (63 bp):
CATCTGCATTTGCATCTTCGCATTCTACATGATGCATTGCATTTCAGAGGATCATCAATTTTG
Found at i:1039756 original size:2 final size:2
Alignment explanation
Indices: 1039740--1039773 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1039730 TCATTTATCC
* *
1039740 AT AT AT GT AT GT 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
1039774 CCTTTGTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1040027 original size:12 final size:12
Alignment explanation
Indices: 1040012--1040091 Score: 65
Period size: 12 Copynumber: 6.4 Consensus size: 12
1040002 ATAAGAGCAA
1040012 AAAAAAGAAAAG
1 AAAAAAGAAAAG
* *
1040024 AAAAAATAAAAT
1 AAAAAAGAAAAG
*
1040036 AAAAAATAAAAG
1 AAAAAAGAAAAG
1040048 AAAAAAGAACAA-
1 AAAAAAGAA-AAG
*
1040060 AAGAACAAAAAAAG
1 AA-AA-AAGAAAAG
1040074 -AAAAAGCAAAAAG
1 AAAAAAG--AAAAG
1040087 AAAAA
1 AAAAA
1040092 GGGACGATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
11 2 0.04
12 33 0.60
13 12 0.22
14 8 0.15
ACGTcount: A:0.82, C:0.04, G:0.10, T:0.04
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:1040062 original size:39 final size:37
Alignment explanation
Indices: 1040001--1040091 Score: 94
Period size: 39 Copynumber: 2.4 Consensus size: 37
1039991 AAATAAGAGC
* * *
1040001 AATAAGAGCAAAAAAAAGAAAAGAAAAAATAAAATAAAA
1 AATAAAAG-AAAAAAAACAAAAGAAAAAA-AAAAGAAAA
*
1040040 AATAAAAGAAAAAAGAACAAAAGAACAAAAAAAGAAAA
1 AATAAAAGAAAAAA-AACAAAAGAAAAAAAAAAGAAAA
1040078 AGCA-AAAAGAAAAA
1 A--ATAAAAGAAAAA
1040092 GGGACGATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
38 15 0.33
39 29 0.64
40 1 0.02
ACGTcount: A:0.80, C:0.04, G:0.11, T:0.04
Consensus pattern (37 bp):
AATAAAAGAAAAAAAACAAAAGAAAAAAAAAAGAAAA
Found at i:1040092 original size:13 final size:13
Alignment explanation
Indices: 1040068--1040092 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1040058 AAAAGAACAA
1040068 AAAAAGAAAAAGC
1 AAAAAGAAAAAGC
1040081 AAAAAGAAAAAG
1 AAAAAGAAAAAG
1040093 GGACGATAAT
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:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGC
Found at i:1041109 original size:18 final size:18
Alignment explanation
Indices: 1041082--1041124 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1041072 GCTCATGCTT
* *
1041082 AGAAATAGTGGTGAAACG
1 AGAAACAGTGGTGAAACA
*
1041100 AGAAACAGTGGTGAAGCA
1 AGAAACAGTGGTGAAACA
1041118 AGAAACA
1 AGAAACA
1041125 ATGAGGCACA
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:0.49, C:0.09, G:0.30, T:0.12
Consensus pattern (18 bp):
AGAAACAGTGGTGAAACA
Found at i:1041187 original size:32 final size:32
Alignment explanation
Indices: 1041151--1041226 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
1041141 GCATATTTAA
*
1041151 AGATTCAACAGT-AAATGTTGGGGCATCTTTGG
1 AGATTCAACA-TCAAATATTGGGGCATCTTTGG
*
1041183 AGATTCAACATCGAATATTGGGGCATCTTTGG
1 AGATTCAACATCAAATATTGGGGCATCTTTGG
* *
1041215 GGATTTAACATC
1 AGATTCAACATC
1041227 TTGATACGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 1 0.03
32 38 0.97
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATCTTTGG
Found at i:1041751 original size:128 final size:127
Alignment explanation
Indices: 1041487--1042428 Score: 538
Period size: 129 Copynumber: 7.3 Consensus size: 127
1041477 TGTAGGGACT
* *
1041487 GTGTCATCACCTGACCAGATTTCCTCATTATGTAGGAGATGTGTCAACCCCAGATAACCAGTCGT
1 GTGTCATCACCTGACCAGATTTCCTCATTATGTAGGAGCTGTGTCAA-CCCAGATAACAAGTCGT
** *** * * *
1041552 CCTCATCAAGTAGGAA-CAGTGTTATCACCTAAAGATGG-CATGTCGTCCTT-ATCGCGTAGGAA
65 CCTCATCAA-TAGGAACCA-TGTTATCACCTTTAGATGGCCAAAAC-T-CTTCATCACGTATGAG
1041614 CC
126 CC
* ** * * * *
1041616 GTTTCATCACCCAACCATATTTCCTCATTATGTAGGAGCTGTGTCAAACCAGATAACGAGTGGTC
1 GTGTCATCACCTGACCAGATTTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACAAGTCGTC
*
1041681 CTCATCATATAGAAACCATGTTATCACCTTTAGATGGCCAAAACTCTTCATCACGTATGAGCC
66 CTCATCA-ATAGGAACCATGTTATCACCTTTAGATGGCCAAAACTCTTCATCACGTATGAGCC
* * * * *
1041744 GTGTCATCACTTGACCAGATCTCCTCATTCTGTAGGAGCTGTGTCAACCCAAATAACAAGCCGTC
1 GTGTCATCACCTGACCAGATTTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACAAGTCGTC
* * * * *
1041809 CTCATCACGTAGGAACCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCT
66 CTCATCA-ATAGGAACCATGTTATCACCTTTAGATGGCCAAAACTCTTCATCACGTATGAGCC
* ** * * * ** * ** * *
1041872 GTGTCATCA-TTCGACTTGATCTCCTAATCACATAAGAGCCATGTCAA-CCAGATAACTAGCCGT
1 GTGTCATCACCT-GACCAGATTTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACAAGTCGT
* * ** * * * * *
1041935 CCTCGTCACGTAGGAACTGTGTTATTATCTTTAGATGGCCAAAAGTCTTTATCACGTATGAGCT
65 CCTCATCA-ATAGGAACCATGTTATCACCTTTAGATGGCCAAAACTCTTCATCACGTATGAGCC
* * * * * * * ** ** *
1041999 GTGTCATCA-TTCAACCTGATCTACTCATCATATAGGAAATGTGTCAACCTTTGATAAACAA-CC
1 GTGTCATCACCT-GACCAGATTTCCTCATTATGTAGGAGCTGTGTCAACC-CAGAT-AACAAGTC
* * ** * * *
1042062 ATCCTCATCACGTAGGAACTGTGTTATCATCTTTAGATGGCTAGAACTCTTCATCACGTATGAGC
63 GTCCTCATCA-ATAGGAACCATGTTATCACCTTTAGATGGCCAAAACTCTTCATCACGTATGAGC
1042127 C
127 C
* * * * * * * * * * ** ** * *
1042128 ATATCATCA-TTCGACCTGATCTCTTAATCACGTAGAAGCCATGTCAACCTTTGATAACCAGCCG
1 GTGTCATCACCT-GACCAGATTTCCTCATTATGTAGGAGCTGTGTCAACC-CAGATAACAAGTCG
* * * * ****** * * * *
1042192 TCCTCACCACGTAGGAACCGTGTTATCATCTTTAGATGGCTTGCTGTCCTCATCGCGTAGGAACC
64 TCCTCATCA-ATAGGAACCATGTTATCACCTTTAGATGGCCAAAACTCTTCATCACGTATGAGCC
* * * * * * *
1042257 GTGTCATCA-CTCAACTAGATTTCCTCATTATGTAGGAGCTATGTCAACCTAGATAGCCAGCCGT
1 GTGTCATCACCT-GACCAGATTTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACAAGTCGT
** * * *
1042321 CCTTTTCACGTAGGAACCGA-GTTATCACATTTCCTAAAGATGGCCAAGAACTCTTCATCACGCA
65 CCTCATCA-ATAGGAACC-ATGTTATCAC-CTT--T--AGATGGCCAA-AACTCTTCATCACGTA
**
1042385 TGAGAA
122 TGAGCC
* *
1042391 GTGTCATCCCCTGACTAGATCTT-CTCATTATGTAGGAG
1 GTGTCATCACCTGACCAGAT-TTCCTCATTATGTAGGAG
1042429 TCTTATCACT
Statistics
Matches: 659, Mismatches: 136, Indels: 31
0.80 0.16 0.04
Matches are distributed among these distances:
127 114 0.17
128 239 0.36
129 248 0.38
130 4 0.01
131 1 0.00
133 7 0.01
134 42 0.06
135 4 0.01
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (127 bp):
GTGTCATCACCTGACCAGATTTCCTCATTATGTAGGAGCTGTGTCAACCCAGATAACAAGTCGTC
CTCATCAATAGGAACCATGTTATCACCTTTAGATGGCCAAAACTCTTCATCACGTATGAGCC
Found at i:1042123 original size:256 final size:256
Alignment explanation
Indices: 1041694--1042231 Score: 726
Period size: 256 Copynumber: 2.1 Consensus size: 256
1041684 ATCATATAGA
* * *
1041694 AACCATGTTATCACCTTTAGATGGCCAAAACTCTTCATCACGTATGAGCCGTGTCATCACTTGAC
1 AACCGTGTTATCATCTTTAGATGGCCAAAACTCTTCATCACGTATGAGCCGTGTCATCACTTAAC
* * ** *
1041759 CAGATCTCCTCATTCTGTAGGAGCTGTGTCAACCCAAATAACAAGCCGTCCTCATCACGTAGGAA
66 CAGATCTACTCATTCTATAGGAAATGTGTCAACCCAAATAACAAGCCATCCTCATCACGTAGGAA
** * *
1041824 CCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCTGTGTCATCATTCGACTT
131 CCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCATATCATCATTCGACCT
* **
1041889 GATCTCCTAATCACATA-AGAGCCATGTCAACC-AGATAACTAGCCGTCCTCGTCACGTAGG
196 GATCTCCTAATCACATAGA-AGCCATGTCAACCTAGATAACCAGCCGTCCTCACCACGTAGG
* * * * *
1041949 AACTGTGTTATTATCTTTAGATGGCCAAAAGTCTTTATCACGTATGAGCTGTGTCATCA-TTCAA
1 AACCGTGTTATCATCTTTAGATGGCCAAAACTCTTCATCACGTATGAGCCGTGTCATCACTT-AA
* ***
1042013 CCTGATCTACTCA-TCATATAGGAAATGTGTCAACCTTTGATAAACAA-CCATCCTCATCACGTA
65 CCAGATCTACTCATTC-TATAGGAAATGTGTCAACC-CAAAT-AACAAGCCATCCTCATCACGTA
* *
1042076 GGAACTGTGTTATCATCTTTAGATGGCTAGAACTCTTCATCACGTATGAGCCATATCATCATTCG
127 GGAACCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCATATCATCATTCG
* * *
1042141 ACCTGATCTCTTAATCACGTAGAAGCCATGTCAACCTTTGATAACCAGCCGTCCTCACCACGTAG
192 ACCTGATCTCCTAATCACATAGAAGCCATGTCAACC-TAGATAACCAGCCGTCCTCACCACGTAG
1042206 G
256 G
1042207 AACCGTGTTATCATCTTTAGATGGC
1 AACCGTGTTATCATCTTTAGATGGC
1042232 TTGCTGTCCT
Statistics
Matches: 245, Mismatches: 31, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
254 4 0.02
255 80 0.33
256 108 0.44
257 6 0.02
258 47 0.19
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (256 bp):
AACCGTGTTATCATCTTTAGATGGCCAAAACTCTTCATCACGTATGAGCCGTGTCATCACTTAAC
CAGATCTACTCATTCTATAGGAAATGTGTCAACCCAAATAACAAGCCATCCTCATCACGTAGGAA
CCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCATATCATCATTCGACCT
GATCTCCTAATCACATAGAAGCCATGTCAACCTAGATAACCAGCCGTCCTCACCACGTAGG
Found at i:1042245 original size:129 final size:128
Alignment explanation
Indices: 1041678--1042398 Score: 637
Period size: 129 Copynumber: 5.6 Consensus size: 128
1041668 ATAACGAGTG
** * * * *
1041678 GTCCTCATCATATAGAAACCATGTTATCACCTTTAGATGGCCAAAACTCTTCATCACGTATGAGC
1 GTCCTCATCACGTAGGAACCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
* * ** * ** * * *
1041743 CGTGTCATCACTT-GACCAGATCTCCTCATTC-TGTAGGAGCTGTGTCAACCCAAATAACAAGCC
66 CGTGTCATCA-TTCGACCTGATCTCCT-AATCACATAGAAGCCATGTCAACCTAGATAACCAGCC
1041806 GTCCTCATCACGTAGGAACCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
1 GTCCTCATCACGTAGGAACCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
* * *
1041871 TGTGTCATCATTCGACTTGATCTCCTAATCACATA-AGAGCCATGTCAACC-AGATAACTAGCC
66 CGTGTCATCATTCGACCTGATCTCCTAATCACATAGA-AGCCATGTCAACCTAGATAACCAGCC
* * * * * *
1041933 GTCCTCGTCACGTAGGAACTGTGTTATTATCTTTAGATGGCCAAAAGTCTTTATCACGTATGAGC
1 GTCCTCATCACGTAGGAACCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
* * * * * *** * * *
1041998 TGTGTCATCATTCAACCTGATCTACTCATCATATAGGAA-ATGTGTCAACCTTTGATAAACAACC
66 CGTGTCATCATTCGACCTGATCTCCTAATCACATA-GAAGCCATGTCAACC-TAGATAACCAGCC
* * *
1042062 ATCCTCATCACGTAGGAACTGTGTTATCATCTTTAGATGGCTAGAACTCTTCATCACGTATGAGC
1 GTCCTCATCACGTAGGAACCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
* * * * *
1042127 CATATCATCATTCGACCTGATCTCTTAATCACGTAGAAGCCATGTCAACCTTTGATAACCAGCC
66 CGTGTCATCATTCGACCTGATCTCCTAATCACATAGAAGCCATGTCAACC-TAGATAACCAGCC
* ** *** * * * *
1042191 GTCCTCACCACGTAGGAACCGTGTTATCATCTTTAGATGGCTTGCTGTCCTCATCGCGTAGGAAC
1 GTCCTCATCACGTAGGAACCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
* * * * * ** * * *
1042256 CGTGTCATCACTC-AACTAGATTTCCTCATTATGTAGGAGCTATGTCAACCTAGATAGCCAGCC
66 CGTGTCATCATTCGACCT-GATCTCCTAATCACATAGAAGCCATGTCAACCTAGATAACCAGCC
** *
1042319 GTCCTTTTCACGTAGGAACCGAGTTATCA-CATTTCCTAAAGATGGCCAAGAACTCTTCATCACG
1 GTCCTCATCACGTAGGAACCGTGTTATCATC--TT--T--AGATGGCC-AGAACTCTTCATCACG
* **
1042383 CATGAGAAGTGTCATC
59 TATGAGCCGTGTCATC
1042399 CCCTGACTAG
Statistics
Matches: 481, Mismatches: 96, Indels: 26
0.80 0.16 0.04
Matches are distributed among these distances:
127 113 0.23
128 135 0.28
129 204 0.42
131 1 0.00
133 7 0.01
134 21 0.04
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (128 bp):
GTCCTCATCACGTAGGAACCGTGTTATCATCTTTAGATGGCCAGAACTCTTCATCACGTATGAGC
CGTGTCATCATTCGACCTGATCTCCTAATCACATAGAAGCCATGTCAACCTAGATAACCAGCC
Found at i:1042616 original size:13 final size:13
Alignment explanation
Indices: 1042598--1042624 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1042588 TGTCTGGGTC
1042598 AAAAAATATTATT
1 AAAAAATATTATT
1042611 AAAAAATATTATT
1 AAAAAATATTATT
1042624 A
1 A
1042625 TTATTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAAAATATTATT
Found at i:1042623 original size:3 final size:3
Alignment explanation
Indices: 1042617--1042662 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
1042607 TATTAAAAAA
* *
1042617 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TGT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1042663 CAGGCCACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1047458 original size:2 final size:2
Alignment explanation
Indices: 1047451--1047476 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1047441 TACATATTTA
1047451 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
1047477 TAATAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1050084 original size:23 final size:23
Alignment explanation
Indices: 1050058--1050106 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1050048 ATAAAGAACC
*
1050058 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
1050081 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
1050104 AAA
1 AAA
1050107 CTAACCACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:1050313 original size:25 final size:25
Alignment explanation
Indices: 1050278--1050341 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
1050268 CACCACGAAC
*
1050278 CACCTTAGCTCGCTAGCTCCTCTCGG
1 CACC-TAGCTCGCCAGCTCCTCTCGG
1050304 CACCTAGCTCGCCAGCTCCTCTCGG
1 CACCTAGCTCGCCAGCTCCTCTCGG
1050329 CACCTAGC-CGCCA
1 CACCTAGCTCGCCA
1050342 CCTAGCTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
24 5 0.14
25 28 0.76
26 4 0.11
ACGTcount: A:0.14, C:0.47, G:0.19, T:0.20
Consensus pattern (25 bp):
CACCTAGCTCGCCAGCTCCTCTCGG
Found at i:1050345 original size:11 final size:12
Alignment explanation
Indices: 1050299--1050354 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
1050289 GCTAGCTCCT
*
1050299 CTCGGCACCTAG
1 CTCGCCACCTAG
* **
1050311 CTCGCCAGCTCCT
1 CTCGCCACCT-AG
*
1050324 CTCGGCACCTAG
1 CTCGCCACCTAG
1050336 C-CGCCACCTAG
1 CTCGCCACCTAG
1050347 CTCGCCAC
1 CTCGCCAC
1050355 TTCTTGGAGC
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
11 10 0.30
12 15 0.45
13 8 0.24
ACGTcount: A:0.14, C:0.50, G:0.20, T:0.16
Consensus pattern (12 bp):
CTCGCCACCTAG
Found at i:1053442 original size:20 final size:20
Alignment explanation
Indices: 1053406--1053450 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1053396 GATAAAAAGT
*
1053406 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
*
1053426 AAAAGTTAAGGAA-GAAAGAG
1 AAAAGTTAA-AAATGAAAGAG
1053446 AAAAG
1 AAAAG
1053451 AAAAAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.13
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Found at i:1060333 original size:23 final size:23
Alignment explanation
Indices: 1060285--1060333 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1060275 ATAAAGAACC
* *
1060285 AAAATAAACTTAAATATACCAGT
1 AAAATAAAATTAAACATACCAGT
*
1060308 AAAATAAAATCTAAACAT-CCATT
1 AAAATAAAAT-TAAACATACCAGT
1060331 AAA
1 AAA
1060334 CCAACCACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAATAAAATTAAACATACCAGT
Found at i:1075000 original size:17 final size:17
Alignment explanation
Indices: 1074960--1075001 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1074950 CTTGCAAATT
* *
1074960 TTTTAAATTTTATTGTA
1 TTTTAATTTTTATTATA
*
1074977 TTTTAATTTTTTTTATA
1 TTTTAATTTTTATTATA
1074994 TTTTAATT
1 TTTTAATT
1075002 AATAATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTAATTTTTATTATA
Found at i:1076503 original size:12 final size:12
Alignment explanation
Indices: 1076488--1076533 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1076478 CGGTTTTTTT
*
1076488 ACCGGATAAAAA
1 ACCGGTTAAAAA
1076500 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
1076515 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1076527 ACCGGTT
1 ACCGGTT
1076534 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1076515 original size:15 final size:13
Alignment explanation
Indices: 1076494--1076534 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
1076484 TTTTACCGGA
1076494 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1076507 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
1076521 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1076534 T
1 T
1076535 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:1078850 original size:21 final size:21
Alignment explanation
Indices: 1078826--1078865 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1078816 TTTATTTTAT
1078826 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1078847 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1078866 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1078913 original size:33 final size:33
Alignment explanation
Indices: 1078860--1078958 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1078850 TTTGTTTCAA
1078860 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1078892 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1078925 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1078958 T
1 T
1078959 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1078987 original size:13 final size:13
Alignment explanation
Indices: 1078944--1078998 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1078934 TTGGAAGTAT
1078944 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1078957 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1078971 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1078984 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1078997 TT
1 TT
1078999 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1079419 original size:15 final size:15
Alignment explanation
Indices: 1079394--1079449 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
1079384 ATCTGGAATA
*
1079394 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
1079409 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
1079424 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
1079441 TTAAAACCG
1 TTAAAACCG
1079450 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:1079458 original size:21 final size:18
Alignment explanation
Indices: 1079413--1079446 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1079403 GTTTTTTTAT
1079413 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
1079430 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
1079447 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:1081059 original size:19 final size:20
Alignment explanation
Indices: 1081028--1081072 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1081018 GGGGTACAGA
1081028 ATGCGGTCTGATGCGATCCG
1 ATGCGGTCTGATGCGATCCG
* *
1081048 ATGCGG-CTGATGCGGTCTG
1 ATGCGGTCTGATGCGATCCG
1081067 ATGCGG
1 ATGCGG
1081073 GCCGATGCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.24
Consensus pattern (20 bp):
ATGCGGTCTGATGCGATCCG
Found at i:1081067 original size:10 final size:10
Alignment explanation
Indices: 1081028--1081072 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
1081018 GGGGTACAGA
1081028 ATGCGGTCTG
1 ATGCGGTCTG
* *
1081038 ATGCGATCCG
1 ATGCGGTCTG
1081048 ATGCGG-CTG
1 ATGCGGTCTG
1081057 ATGCGGTCTG
1 ATGCGGTCTG
1081067 ATGCGG
1 ATGCGG
1081073 GCCGATGCGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.24
Consensus pattern (10 bp):
ATGCGGTCTG
Found at i:1082703 original size:147 final size:148
Alignment explanation
Indices: 1082415--1082712 Score: 553
Period size: 147 Copynumber: 2.0 Consensus size: 148
1082405 GTCACTAGAG
1082415 TATGATTTCAATAAAGCTTCAAATCTCTTCACCCATAACCTACAAACTTCAGCTCAAACAAGGCC
1 TATGATTTCAATAAAGCTTCAAATCTCTTCACCCATAACCTACAAACTTCAGCTCAAACAAGGCC
1082480 TAACTAATTTCCAATTTCTAATGTATGGCATAAGTAATATGTGGACAAATAAAATCCATGAATGA
66 TAAC--ATTTCCAATTTCTAATGTATGGCATAAGTAATATGTGGACAAATAAAATCCATGAATGA
1082545 GGCTTTATTTCCCAGTAACA
129 GGCTTTATTTCCCAGTAACA
*
1082565 TATGATTTCAATAAAGCTTCAAATCTCTTCACCCTTAACCTACAAACTTCAGCTCAAACAAGGCC
1 TATGATTTCAATAAAGCTTCAAATCTCTTCACCCATAACCTACAAACTTCAGCTCAAACAAGGCC
*
1082630 TAAC-TTTCCAATTTCTAATGTATGGCATAAGTAATATGTGGGCAAATAAAATCCATGAATGAGG
66 TAACATTTCCAATTTCTAATGTATGGCATAAGTAATATGTGGACAAATAAAATCCATGAATGAGG
1082694 CTTTATTTCCCAGTAACA
131 CTTTATTTCCCAGTAACA
1082712 T
1 T
1082713 GTTTCACAAT
Statistics
Matches: 146, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
147 78 0.53
150 68 0.47
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (148 bp):
TATGATTTCAATAAAGCTTCAAATCTCTTCACCCATAACCTACAAACTTCAGCTCAAACAAGGCC
TAACATTTCCAATTTCTAATGTATGGCATAAGTAATATGTGGACAAATAAAATCCATGAATGAGG
CTTTATTTCCCAGTAACA
Found at i:1087216 original size:22 final size:22
Alignment explanation
Indices: 1087189--1087230 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1087179 TTAATCTTTA
*
1087189 GGATTTAGGATTTGAGATTTTT
1 GGATTTAGGATTTAAGATTTTT
* *
1087211 GGATTTCGGGTTTAAGATTT
1 GGATTTAGGATTTAAGATTT
1087231 GAGATTGAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.02, G:0.29, T:0.48
Consensus pattern (22 bp):
GGATTTAGGATTTAAGATTTTT
Found at i:1090538 original size:26 final size:26
Alignment explanation
Indices: 1090473--1090541 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
1090463 TAATGAATAG
*
1090473 TTAATTCATAATAATTAAATAAGATT
1 TTAATTAATAATAATTAAATAAGATT
* * *
1090499 TTTATTCATAATAATTAAATATG-TT
1 TTAATTAATAATAATTAAATAAGATT
*
1090524 TTAATTAATTTATAATTA
1 TTAATTAA-TAATAATTA
1090542 CAAACCCTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 8 0.22
26 29 0.78
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (26 bp):
TTAATTAATAATAATTAAATAAGATT
Found at i:1102276 original size:223 final size:223
Alignment explanation
Indices: 1101887--1102329 Score: 751
Period size: 223 Copynumber: 2.0 Consensus size: 223
1101877 TATGTCTTAC
1101887 AAAATATAAAAACATATAACAAACTGAATAATTATTTCTTTCATCAAAAACCTAAAAATGCATTC
1 AAAATATAAAAACATATAACAAACTGAATAATTATTTCTTTCATCAAAAACCTAAAAATGCATTC
* * * *
1101952 AGAAAATAATCCCCTATTCACGTATCAAATATCAAATTAAGATATATTTTCAATGAATTAATTAA
66 AGAAAATAATCACATATTCACGTATCAAATATCAAATTAAGATATACTTTCAATGAATTAATAAA
* * *
1102017 TCCTTCATATTTTAGAACATTTTAACAAATAGCCCAATGTACACAAGTAAGAATATTAGGTACAC
131 TCCTGCATATTTTAGAACATTTTAACAAACAGCCCAATGTACACAACTAAGAATATTAGGTACAC
1102082 GAGTCAGAATGAGTGTGTGCACAATTAT
196 GAGTCAGAATGAGTGTGTGCACAATTAT
* * * *
1102110 AAAATATAAGAACATATAACAGACTGAGTAATTCTTTCTTTCATCAAAAACCTAAAAATGCATTC
1 AAAATATAAAAACATATAACAAACTGAATAATTATTTCTTTCATCAAAAACCTAAAAATGCATTC
*
1102175 AGAAAATAATCACATATTCACGTATCAAATATCAAATTAAGATTTACTTTCAATGAATTAATAAA
66 AGAAAATAATCACATATTCACGTATCAAATATCAAATTAAGATATACTTTCAATGAATTAATAAA
* * *
1102240 TCCTGCATATTTTAGAGCATTTTAACAAGCAGCCCAATGTACACAACTAAGAATATTAGGTACAT
131 TCCTGCATATTTTAGAACATTTTAACAAACAGCCCAATGTACACAACTAAGAATATTAGGTACAC
1102305 GAGTCAGAATGAGTGTGTGCACAAT
196 GAGTCAGAATGAGTGTGTGCACAAT
1102330 ATGCAGTCGT
Statistics
Matches: 205, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
223 205 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.30
Consensus pattern (223 bp):
AAAATATAAAAACATATAACAAACTGAATAATTATTTCTTTCATCAAAAACCTAAAAATGCATTC
AGAAAATAATCACATATTCACGTATCAAATATCAAATTAAGATATACTTTCAATGAATTAATAAA
TCCTGCATATTTTAGAACATTTTAACAAACAGCCCAATGTACACAACTAAGAATATTAGGTACAC
GAGTCAGAATGAGTGTGTGCACAATTAT
Found at i:1112347 original size:20 final size:20
Alignment explanation
Indices: 1112324--1112371 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1112314 TCCTACCCTA
* *
1112324 AGGTTTTATAGATGACCCGG
1 AGGTTTTACAAATGACCCGG
*
1112344 AGGTTTTACAAATTACCCGG
1 AGGTTTTACAAATGACCCGG
1112364 AGGTTTTA
1 AGGTTTTA
1112372 ATTTTATAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (20 bp):
AGGTTTTACAAATGACCCGG
Found at i:1112467 original size:20 final size:20
Alignment explanation
Indices: 1112442--1112490 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1112432 ATCCTACTAT
*
1112442 GAGGTTTTACAGATGACCCA
1 GAGGTTTTACAAATGACCCA
* *
1112462 GAGGTTTTACAAATTACCCG
1 GAGGTTTTACAAATGACCCA
1112482 GAGGTTTTA
1 GAGGTTTTA
1112491 ATTTTCTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (20 bp):
GAGGTTTTACAAATGACCCA
Found at i:1112521 original size:119 final size:118
Alignment explanation
Indices: 1112310--1112588 Score: 486
Period size: 119 Copynumber: 2.3 Consensus size: 118
1112300 TTAAAGTAAG
* *
1112310 AACATCCTACCCTAAGGTTTTATAGATGACCCGGAGGTTTTACAAATTACCCGGAGGTTTTAATT
1 AACATCCTA-CCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATTACCCGGAGGTTTTAATT
1112375 TTATAGAACATTAAATGAGAAACTTTGTTTATTACTTTCTCATTTTCATGCGAA
65 TTATAGAACATTAAATGAGAAACTTTGTTTATTACTTTCTCATTTTCATGCGAA
* *
1112429 AACATCCTACTATGAGGTTTTACAGATGACCCAGAGGTTTTACAAATTACCCGGAGGTTTTAATT
1 AACATCCTAC-CTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATTACCCGGAGGTTTTAATT
* *
1112494 TTCTAGAACATTAAATGAGAAACTTTGTTTATTACTTTCTCATTTTCATGTGAA
65 TTATAGAACATTAAATGAGAAACTTTGTTTATTACTTTCTCATTTTCATGCGAA
1112548 AACATCCTACCTGAGGTTTTACAGATGACCCGGAGGTTTTA
1 AACATCCTACCTGAGGTTTTACAGATGACCCGGAGGTTTTA
1112589 ATTTTCTAGA
Statistics
Matches: 151, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
118 30 0.20
119 121 0.80
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.36
Consensus pattern (118 bp):
AACATCCTACCTGAGGTTTTACAGATGACCCGGAGGTTTTACAAATTACCCGGAGGTTTTAATTT
TATAGAACATTAAATGAGAAACTTTGTTTATTACTTTCTCATTTTCATGCGAA
Found at i:1112647 original size:98 final size:98
Alignment explanation
Indices: 1112462--1112640 Score: 322
Period size: 98 Copynumber: 1.8 Consensus size: 98
1112452 AGATGACCCA
* *
1112462 GAGGTTTTACAAATTACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGTTTATT
1 GAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGTTTAAT
*
1112527 ACTTTCTCATTTTCATGTGAAAACATCCTACCT
66 AATTTCTCATTTTCATGTGAAAACATCCTACCT
*
1112560 GAGGTTTTACAGATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGTTTAAT
1 GAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGTTTAAT
1112625 AATTTCTCATTTTCAT
66 AATTTCTCATTTTCAT
1112641 TCGAAAATCA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 77 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (98 bp):
GAGGTTTTACAAATGACCCGGAGGTTTTAATTTTCTAGAACATTAAATGAGAAACTTTGTTTAAT
AATTTCTCATTTTCATGTGAAAACATCCTACCT
Found at i:1112921 original size:249 final size:249
Alignment explanation
Indices: 1112584--1113242 Score: 1151
Period size: 249 Copynumber: 2.6 Consensus size: 249
1112574 GACCCGGAGG
** *** * *
1112584 TTTTAATTTTCTAGAACATTAAATGAGAAACTTTGTTTAA-TAATTTCTCATTTTCATTCGAAAA
1 TTTT-ATTTTCTAGAACATTAAATGAGAAACTTTG-AAAACCGCTATCTCATTTTCATGCGAAAA
* * *
1112648 TCATATGTGAACATCTTACCCAAAGGCTTTACGGATGGCCTTAAGGACTTATCATCTTGCTCGAA
64 TCATATGTGAACATCCTACCCAAAGGCTTTACGGGTGGCCCTAAGGACTTATCATCTTGCTCGAA
*
1112713 AGACTGACAGATGACCTGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAATGA
129 AGACTAACAGATGACCTGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAATGA
1112778 TTTATAAATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAA
194 TTTATAAATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAA
1112834 TTTTATTTTCTAGAACATTAAATGAGAAACTTTGAAAACCGCTATCTCATTTTCATGCGAAAATC
1 TTTTATTTTCTAGAACATTAAATGAGAAACTTTGAAAACCGCTATCTCATTTTCATGCGAAAATC
1112899 ATATGTGAACATCCTACCCAAAGGCTTTACGGGTGGCCCTAAGGACTTATCATCTTGCTCGAAAG
66 ATATGTGAACATCCTACCCAAAGGCTTTACGGGTGGCCCTAAGGACTTATCATCTTGCTCGAAAG
1112964 ACTAACAGATGACCTGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAATGATT
131 ACTAACAGATGACCTGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAATGATT
1113029 TATAAATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAA
196 TATAAATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAA
*
1113083 TTTGATTTTCTAGAACATTAAATGAGAAACTTTGAAAACCGCTATCTCATTTTCATGCGAAAATC
1 TTTTATTTTCTAGAACATTAAATGAGAAACTTTGAAAACCGCTATCTCATTTTCATGCGAAAATC
1113148 ATATGTGAACATCCTA-CCAAAGGCTTTACGGGTGGCCCTAAGGACTTATCATCTTGCTCGAAAG
66 ATATGTGAACATCCTACCCAAAGGCTTTACGGGTGGCCCTAAGGACTTATCATCTTGCTCGAAAG
* * *
1113212 ACTAACAGATGACCCGAAGGATTTAAACATC
131 ACTAACAGATGACCTGAAGGTTTTAAGCATC
1113243 CTACCCAAAC
Statistics
Matches: 393, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
248 78 0.20
249 311 0.79
250 4 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (249 bp):
TTTTATTTTCTAGAACATTAAATGAGAAACTTTGAAAACCGCTATCTCATTTTCATGCGAAAATC
ATATGTGAACATCCTACCCAAAGGCTTTACGGGTGGCCCTAAGGACTTATCATCTTGCTCGAAAG
ACTAACAGATGACCTGAAGGTTTTAAGCATCATGCTCGAAAGACTAACAGATGACCCGAATGATT
TATAAATTTGTGGGAAATACTTTACTAGGTAAGAAACTTCTTACTTTTCAAGAA
Found at i:1113575 original size:9 final size:9
Alignment explanation
Indices: 1113552--1113614 Score: 67
Period size: 9 Copynumber: 6.9 Consensus size: 9
1113542 CAATTTCTTT
1113552 TTTTTTCCTC
1 TTTTTT-CTC
*
1113562 ATTTTTCTC
1 TTTTTTCTC
1113571 -TTTTTCTC
1 TTTTTTCTC
1113579 TTTTTTCCCTC
1 TTTTTT--CTC
*
1113590 ATTTTTCTC
1 TTTTTTCTC
1113599 -TTTTTCTC
1 TTTTTTCTC
1113607 TTTTTTCT
1 TTTTTTCT
1113615 TTATGATGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
8 16 0.34
9 18 0.38
10 5 0.11
11 8 0.17
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:1113577 original size:28 final size:28
Alignment explanation
Indices: 1113545--1113613 Score: 120
Period size: 28 Copynumber: 2.5 Consensus size: 28
1113535 CTTGTTTCAA
* *
1113545 TTTCTTTTTTTTTCCTCATTTTTCTCTT
1 TTTCTCTTTTTTCCCTCATTTTTCTCTT
1113573 TTTCTCTTTTTTCCCTCATTTTTCTCTT
1 TTTCTCTTTTTTCCCTCATTTTTCTCTT
1113601 TTTCTCTTTTTTC
1 TTTCTCTTTTTTC
1113614 TTTATGATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (28 bp):
TTTCTCTTTTTTCCCTCATTTTTCTCTT
Found at i:1113582 original size:7 final size:8
Alignment explanation
Indices: 1113553--1113616 Score: 67
Period size: 8 Copynumber: 7.4 Consensus size: 8
1113543 AATTTCTTTT
1113553 TTTTTCCTC
1 TTTTT-CTC
1113562 ATTTTTCTC
1 -TTTTTCTC
1113571 TTTTTCTC
1 TTTTTCTC
1113579 TTTTTTCCCTC
1 -TTTTT--CTC
1113590 ATTTTTCTC
1 -TTTTTCTC
1113599 TTTTTCTC
1 TTTTTCTC
1113607 TTTTT-TC
1 TTTTTCTC
1113614 TTT
1 TTT
1113617 ATGATGGATT
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
7 5 0.10
8 21 0.42
9 11 0.22
10 5 0.10
11 8 0.16
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTTCTC
Found at i:1121045 original size:3 final size:3
Alignment explanation
Indices: 1121039--1121109 Score: 88
Period size: 3 Copynumber: 22.7 Consensus size: 3
1121029 GTATTATTTG
1121039 TAA TAA TAAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
1121086 TTTC TTA TAA TAA TAA TAA TAA TA
1 -TAA TAA TAA TAA TAA TAA TAA TA
1121110 TATAGTCTCG
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
3 54 0.89
4 7 0.11
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1123470 original size:17 final size:18
Alignment explanation
Indices: 1123448--1123481 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1123438 AGGTTGTTTT
*
1123448 AAAAAACGCAA-AAAAAA
1 AAAAAAAGCAATAAAAAA
1123465 AAAAAAAGCAATAAAAA
1 AAAAAAAGCAATAAAAA
1123482 TTAGAAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.82, C:0.09, G:0.06, T:0.03
Consensus pattern (18 bp):
AAAAAAAGCAATAAAAAA
Found at i:1125329 original size:22 final size:22
Alignment explanation
Indices: 1125294--1125339 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1125284 GACAAAAATT
1125294 CTCAGAGGGAACCGATTCCCCC
1 CTCAGAGGGAACCGATTCCCCC
* *
1125316 CTCAGGGGGTACCGATTCCCCC
1 CTCAGAGGGAACCGATTCCCCC
1125338 CT
1 CT
1125340 GAATGGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (22 bp):
CTCAGAGGGAACCGATTCCCCC
Found at i:1131118 original size:23 final size:20
Alignment explanation
Indices: 1131067--1131126 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
1131057 TTTTGCTGCA
*
1131067 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
1131086 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
1131107 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
1131127 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:1131135 original size:21 final size:21
Alignment explanation
Indices: 1131109--1131148 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1131099 CCCCCTTTGA
*
1131109 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1131130 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1131149 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1134519 original size:16 final size:15
Alignment explanation
Indices: 1134492--1134523 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1134482 ATTACATATC
1134492 TCTATTTTATCTTTA
1 TCTATTTTATCTTTA
1134507 TCTATTCTTATCTTTA
1 TCTATT-TTATCTTTA
1134523 T
1 T
1134524 TTTATCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.66
Consensus pattern (15 bp):
TCTATTTTATCTTTA
Found at i:1134542 original size:18 final size:18
Alignment explanation
Indices: 1134519--1134560 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
1134509 TATTCTTATC
1134519 TTTATTTTATCCATATTT
1 TTTATTTTATCCATATTT
*
1134537 TTTA--TTATCCTTATTT
1 TTTATTTTATCCATATTT
*
1134553 TTCATTTT
1 TTTATTTT
1134561 CTTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 14 0.70
18 6 0.30
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTTATCCATATTT
Found at i:1138777 original size:16 final size:15
Alignment explanation
Indices: 1138743--1138839 Score: 88
Period size: 16 Copynumber: 6.3 Consensus size: 15
1138733 TAGTTCTATT
1138743 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
*
1138758 TTTTATTTTATTTTCG
1 TTTTATTTTATTTT-A
1138774 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
**** *
1138789 TTTTTAGCAAACTTTA
1 -TTTTATTTTATTTTA
*
1138805 TTTTCATTCTA-TTTA
1 TTTT-ATTTTATTTTA
1138820 TTTTATTTTTATTTTA
1 TTTTA-TTTTATTTTA
1138836 TTTT
1 TTTT
1138840 TCTCTGAATA
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
14 1 0.02
15 30 0.46
16 34 0.52
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:1138777 original size:21 final size:20
Alignment explanation
Indices: 1138743--1138839 Score: 88
Period size: 21 Copynumber: 4.7 Consensus size: 20
1138733 TAGTTCTATT
1138743 TTTTATTTTATTTTATTTTA
1 TTTTATTTTATTTTATTTTA
*
1138763 TTTTATTTTCGTTTTATTTTA
1 TTTTATTTT-ATTTTATTTTA
**** *
1138784 TTTTATTTTTAGCAAACTTTA
1 TTTTA-TTTTATTTTATTTTA
*
1138805 TTTTCATTCTA-TTTATTTTA
1 TTTT-ATTTTATTTTATTTTA
1138825 TTTTTATTTTATTTT
1 -TTTTATTTTATTTT
1138840 TCTCTGAATA
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
20 19 0.32
21 35 0.59
22 5 0.08
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTATTTTATTTTATTTTA
Found at i:1138840 original size:6 final size:5
Alignment explanation
Indices: 1138743--1138839 Score: 88
Period size: 5 Copynumber: 18.8 Consensus size: 5
1138733 TAGTTCTATT
*
1138743 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTCG TTTTA TTTTA TTTTA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA -TTTTA
**** * *
1138795 GCAAA CTTTA TTTTCA TTCTA -TTTA TTTTA TTTTTA TTTTA TTTT
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA -TTTTA TTTTA TTTT
1138840 TCTCTGAATA
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
4 3 0.04
5 53 0.72
6 18 0.24
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:1145154 original size:2 final size:2
Alignment explanation
Indices: 1145147--1145171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1145137 GTCAATCTAC
1145147 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1145172 TTACGAAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1145985 original size:5 final size:5
Alignment explanation
Indices: 1145975--1146021 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
1145965 CCCAATTTAG
*
1145975 TTATT TTATT TTATT TTA-T TTATT TTCTTT CCTTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT TT-ATT --TTATT TTATT TTATT
1146022 CTATATTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
4 4 0.11
5 26 0.72
6 2 0.06
7 2 0.06
8 2 0.06
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:1146264 original size:13 final size:13
Alignment explanation
Indices: 1146246--1146270 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1146236 AAGATCATCA
1146246 TTTTTCAATTTTG
1 TTTTTCAATTTTG
1146259 TTTTTCAATTTT
1 TTTTTCAATTTT
1146271 TCCAGTTTAG
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:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTTCAATTTTG
Found at i:1146337 original size:11 final size:11
Alignment explanation
Indices: 1146317--1146358 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
1146307 ATTTTTATTC
1146317 AAAAATAAAAGG
1 AAAAA-AAAAGG
1146329 AAAAAAAAA-G
1 AAAAAAAAAGG
1146339 AAAAGAAAAAGG
1 AAAA-AAAAAGG
1146351 AAAAAAAA
1 AAAAAAAA
1146359 TATTAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 10 0.36
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAGG
Found at i:1146369 original size:22 final size:21
Alignment explanation
Indices: 1146317--1146358 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 21
1146307 ATTTTTATTC
1146317 AAAAATAAAAGGAAAAAAAAAG
1 AAAAA-AAAAGGAAAAAAAAAG
1146339 AAAAGAAAAAGGAAAAAAAA
1 AAAA-AAAAAGGAAAAAAAA
1146359 TATTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAGGAAAAAAAAAG
Found at i:1149614 original size:16 final size:15
Alignment explanation
Indices: 1149589--1149618 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1149579 TACATATCTC
1149589 TATTTTATCTTTATG
1 TATTTTATCTTTATG
1149604 TATTCTTATCTTTAT
1 TATT-TTATCTTTAT
1149619 TTTATTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (15 bp):
TATTTTATCTTTATG
Found at i:1157535 original size:21 final size:21
Alignment explanation
Indices: 1157509--1157548 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1157499 CCTAGCTCAT
1157509 CTTCTTATAAATAACATAACG
1 CTTCTTATAAATAACATAACG
*
1157530 CTTCTTATAAGTAACATAA
1 CTTCTTATAAATAACATAA
1157549 ATAACCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (21 bp):
CTTCTTATAAATAACATAACG
Found at i:1174727 original size:94 final size:94
Alignment explanation
Indices: 1174566--1174753 Score: 376
Period size: 94 Copynumber: 2.0 Consensus size: 94
1174556 TATTCGTAAA
1174566 TCAAAAACAAAGAAAAATAAATCAATACTTACCGTTAGTCCCTGGAAACTGTGCCAATTTGATAA
1 TCAAAAACAAAGAAAAATAAATCAATACTTACCGTTAGTCCCTGGAAACTGTGCCAATTTGATAA
1174631 CTGACATTTTGTTATCAAAATAATTTCGG
66 CTGACATTTTGTTATCAAAATAATTTCGG
1174660 TCAAAAACAAAGAAAAATAAATCAATACTTACCGTTAGTCCCTGGAAACTGTGCCAATTTGATAA
1 TCAAAAACAAAGAAAAATAAATCAATACTTACCGTTAGTCCCTGGAAACTGTGCCAATTTGATAA
1174725 CTGACATTTTGTTATCAAAATAATTTCGG
66 CTGACATTTTGTTATCAAAATAATTTCGG
1174754 CTTCTTAATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (94 bp):
TCAAAAACAAAGAAAAATAAATCAATACTTACCGTTAGTCCCTGGAAACTGTGCCAATTTGATAA
CTGACATTTTGTTATCAAAATAATTTCGG
Found at i:1177165 original size:14 final size:14
Alignment explanation
Indices: 1177107--1177159 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
1177097 ACCCAAACTA
* *
1177107 AGTAAACTCATTTG
1 AGTAAACTCGTCTG
*
1177121 AGTCAACTCGTCTG
1 AGTAAACTCGTCTG
1177135 AGTAAACTCGTCTG
1 AGTAAACTCGTCTG
1177149 AGTAAACTCGT
1 AGTAAACTCGT
1177160 TCGAGTCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (14 bp):
AGTAAACTCGTCTG
Found at i:1182815 original size:258 final size:255
Alignment explanation
Indices: 1182325--1182838 Score: 1001
Period size: 258 Copynumber: 2.0 Consensus size: 255
1182315 ATCAAGAAGT
1182325 TTATATTGGAATTAGGGGTGGTTCTCAGCATATCAGATGTTGTAGAACTCCGTTGTGACAATAAT
1 TTATATTGGAATTAGGGGTGGTTCTCAGCATATCAGATGTTGTAGAACTCCGTTGTGACAATAAT
1182390 AGAGTCATTGCACAAGCAAAGGAACCATGATCTCATCAACGATCTAACTATTCTTAGCACTTTCA
66 AGAGTCATTGCACAAGCAAAGGAACCATGATCTCATCAACGATCTAACTATTCTTAGCACTTTCA
1182455 TCTCATTCGAGAGATCATAGATCAAGGAGATATGGAAATATGCAGAGTACACACGGATGACAACA
131 TCTCATTCGAGAGATCATAGATCAAGGAGATATGGAAATATGCAGAGTACACACGGATGACAACA
1182520 TTGATGATCCCTTGACGAAGCCTATTACACAGCAGAGGCATGATCTTCACACTAAGTCAC
196 TTGATGATCCCTTGACGAAGCCTATTACACAGCAGAGGCATGATCTTCACACTAAGTCAC
1182580 TTATATTGGAATTAGGGGTGGTTCTCAGCATATCAGATGTTGTAGAACTCCGTTGTGACAATAAT
1 TTATATTGGAATTAGGGGTGGTTCTCAGCATATCAGATGTTGTAGAACTCCGTTGTGACAATAAT
1182645 AGAGTCATTGCACAAGCAAAGGAACCATGATCTCATCAACGATCTAAACATATTCTTAGGCACTT
66 AGAGTCATTGCACAAGCAAAGGAACCATGATCTCATCAACGATCT-AAC-TATTCTTA-GCACTT
1182710 TCATCTCATTCGAGAGATCATAGATCAAGGAGATATGGAAATATGCAGAGTACACACGGATGACA
128 TCATCTCATTCGAGAGATCATAGATCAAGGAGATATGGAAATATGCAGAGTACACACGGATGACA
1182775 ACATTGATGATCCCTTGACGAAGCCTATTACACAGCAGAGGCATGATCTTCACACTAAGTCAC
193 ACATTGATGATCCCTTGACGAAGCCTATTACACAGCAGAGGCATGATCTTCACACTAAGTCAC
1182838 T
1 T
1182839 CGGTATTAGA
Statistics
Matches: 256, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
255 110 0.43
256 3 0.01
257 8 0.03
258 135 0.53
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (255 bp):
TTATATTGGAATTAGGGGTGGTTCTCAGCATATCAGATGTTGTAGAACTCCGTTGTGACAATAAT
AGAGTCATTGCACAAGCAAAGGAACCATGATCTCATCAACGATCTAACTATTCTTAGCACTTTCA
TCTCATTCGAGAGATCATAGATCAAGGAGATATGGAAATATGCAGAGTACACACGGATGACAACA
TTGATGATCCCTTGACGAAGCCTATTACACAGCAGAGGCATGATCTTCACACTAAGTCAC
Found at i:1190614 original size:2 final size:2
Alignment explanation
Indices: 1190603--1190633 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1190593 TTTGTCAATC
1190603 TA TA -A 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
1190634 ATTTACGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1190814 original size:13 final size:13
Alignment explanation
Indices: 1190790--1190844 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
1190780 AATGACGCTC
*
1190790 AATGAGCGTCATA
1 AATGTGCGTCATA
*
1190803 AATGTGCATCATA
1 AATGTGCGTCATA
*
1190816 AATGTTCGTCATA
1 AATGTGCGTCATA
*
1190829 AATGTGTGTCATA
1 AATGTGCGTCATA
1190842 AAT
1 AAT
1190845 TTATGACGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
AATGTGCGTCATA
Found at i:1190815 original size:85 final size:85
Alignment explanation
Indices: 1190653--1190818 Score: 194
Period size: 85 Copynumber: 2.0 Consensus size: 85
1190643 ATAGAATCAC
* *
1190653 GACACACAAATGTGTGTCATCTTTTCTAATAACGTGTGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTTTCTAATAACGGGGGCTTCAATGACACGCAATGTAAGTCATA
**
1190718 AATGCGTGTCATAAATTTAT
66 AATGCGCATCATAAATTTAT
* * * * *
1190738 GACACACAAATGTGTGTCGTCTTCATT-T-ATGACGGGGGCTTCAATGACGCTCAATG-AGCGTC
1 GACACACAAATGTGTGTCATCTT--TTCTAATAACGGGGGCTTCAATGACACGCAATGTA-AGTC
*
1190800 ATAAATGTGCATCATAAAT
63 ATAAATGCGCATCATAAAT
1190819 GTTCGTCATA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
84 1 0.01
85 64 0.94
86 1 0.01
87 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTTTCTAATAACGGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCGCATCATAAATTTAT
Found at i:1193786 original size:19 final size:19
Alignment explanation
Indices: 1193758--1193795 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1193748 CTTAAATTTA
1193758 ATTATAAAA-TATTTCTATT
1 ATTATAAAATTATTT-TATT
*
1193777 ATTATGAAATTATTTTATT
1 ATTATAAAATTATTTTATT
1193796 TTAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTATAAAATTATTTTATT
Found at i:1197205 original size:39 final size:37
Alignment explanation
Indices: 1197143--1197330 Score: 170
Period size: 39 Copynumber: 4.9 Consensus size: 37
1197133 ATATTAAATT
1197143 TTTTGAAAATATATAT-A-ATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
1197178 TTTTGAATATATATATATAATATATAGTTTTTAAAAACA
1 TTTTGAA-A-ATATATATAATATATAGTTTTTGAAAACA
*
1197217 TTTTGAATATATATATATATATAATATAG-TTTT-AAAACGT
1 TTTTGAA-A-ATATATATA-AT-ATATAGTTTTTGAAAAC-A
* *
1197257 TTTTAGAAAATATATATAATTTATA-TTTTAGAAAACA
1 TTTT-GAAAATATATATAATATATAGTTTTTGAAAACA
* * * * *
1197294 TGTTGGAAGACTATATATAATATTTGGGTTTTGAAAA
1 T-TTTGAA-AATATATATAATATATAGTTTTTGAAAA
1197331 TGATAGTTTT
Statistics
Matches: 128, Mismatches: 12, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
35 7 0.05
36 1 0.01
37 19 0.15
38 23 0.18
39 58 0.45
40 11 0.09
41 9 0.07
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:1197274 original size:41 final size:41
Alignment explanation
Indices: 1197151--1197253 Score: 176
Period size: 39 Copynumber: 2.6 Consensus size: 41
1197141 TTTTTTGAAA
*
1197151 ATATATATAATATAGTTTTTGAAAACATTTTGAATATATAT
1 ATATATATAATATAGTTTTTAAAAACATTTTGAATATATAT
1197192 ATATA-AT-ATATAGTTTTTAAAAACATTTTGAATATATAT
1 ATATATATAATATAGTTTTTAAAAACATTTTGAATATATAT
1197231 ATATATATAATATAG-TTTTAAAA
1 ATATATATAATATAGTTTTTAAAA
1197254 CGTTTTTAGA
Statistics
Matches: 59, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
39 36 0.61
40 12 0.20
41 11 0.19
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.46
Consensus pattern (41 bp):
ATATATATAATATAGTTTTTAAAAACATTTTGAATATATAT
Found at i:1199448 original size:13 final size:13
Alignment explanation
Indices: 1199430--1199454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1199420 TACATACGCG
1199430 CATATGAAGACTA
1 CATATGAAGACTA
1199443 CATATGAAGACT
1 CATATGAAGACT
1199455 GTTCAACGAT
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
CATATGAAGACTA
Found at i:1199694 original size:21 final size:21
Alignment explanation
Indices: 1199640--1199696 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 21
1199630 GTTGTTAATT
*
1199640 TTTTATTATTATTTATTTTTA
1 TTTTATTTTTATTTATTTTTA
*
1199661 TTCCCTTATTTTTTATTTATTTTTG
1 TT---TTA-TTTTTATTTATTTTTA
1199686 TTTTATTTTTA
1 TTTTATTTTTA
1199697 GGGTCTAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 8 0.27
22 3 0.10
24 3 0.10
25 16 0.53
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTATTTTTATTTATTTTTA
Found at i:1202056 original size:19 final size:18
Alignment explanation
Indices: 1202025--1202062 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1202015 ACTTTTTTCC
1202025 TTTCATTTTTTTCATTTTT
1 TTTCATTTTTTTC-TTTTT
1202044 TTTC-TTTTCTTTCTTTTT
1 TTTCATTTT-TTTCTTTTT
1202062 T
1 T
1202063 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTCATTTTTTTCTTTTT
Found at i:1205213 original size:99 final size:99
Alignment explanation
Indices: 1205080--1205264 Score: 298
Period size: 99 Copynumber: 1.9 Consensus size: 99
1205070 ATATTATGTG
*
1205080 TATACAATAAAGCATGAGATGTCCCTCTAGAGCAATTGATTAAACACCCCGACTTTATGGATAAG
1 TATACAATAAAGCATGAGATGTCACTCTAGAGCAATTGATTAAACACCCCGACTTTATGGATAAG
* * *
1205145 ATTTAGCTAGCCTAATAAAGGTGATTATAATATA
66 AATCAACTAGCCTAATAAAGGTGATTATAATATA
* * *
1205179 TATACAATAAAGCTTGAGCTGTCACTCTAGAGCAATTGGTTAAACACCCCGACTTTATGGATAAG
1 TATACAATAAAGCATGAGATGTCACTCTAGAGCAATTGATTAAACACCCCGACTTTATGGATAAG
*
1205244 AATCAACTAGCCTGATAAAGG
66 AATCAACTAGCCTAATAAAGG
1205265 CAAATTACAA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 78 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (99 bp):
TATACAATAAAGCATGAGATGTCACTCTAGAGCAATTGATTAAACACCCCGACTTTATGGATAAG
AATCAACTAGCCTAATAAAGGTGATTATAATATA
Found at i:1206120 original size:31 final size:31
Alignment explanation
Indices: 1206079--1206139 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1206069 CCATTTATCA
* *
1206079 AAATGGTGTTGTGTTTGCATGCATATATATG
1 AAATGATGTTGTGTTCGCATGCATATATATG
1206110 AAATGATGTTGTGTTCGCATGCATATATAT
1 AAATGATGTTGTGTTCGCATGCATATATAT
1206140 ATATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (31 bp):
AAATGATGTTGTGTTCGCATGCATATATATG
Found at i:1213571 original size:6 final size:6
Alignment explanation
Indices: 1213547--1213585 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
1213537 CATTTGTTGT
1213547 ATTTCTC ATCTTT- ATTTTC ATTTTC ATTTTC ATTTTC AT
1 ATTT-TC AT-TTTC ATTTTC ATTTTC ATTTTC ATTTTC AT
1213586 CTTCTTGTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 3 0.10
6 22 0.73
7 3 0.10
8 2 0.07
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTTC
Found at i:1213581 original size:18 final size:19
Alignment explanation
Indices: 1213547--1213590 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
1213537 CATTTGTTGT
1213547 ATTTCTCATCTTTATTTTC
1 ATTTCTCATCTTTATTTTC
1213566 ATTT-TCAT-TTTCATTTTC
1 ATTTCTCATCTTT-ATTTTC
1213584 ATCTTCT
1 AT-TTCT
1213591 TGTCTTAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.14
18 12 0.55
19 6 0.27
20 1 0.05
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTCTCATCTTTATTTTC
Found at i:1214138 original size:7 final size:7
Alignment explanation
Indices: 1214126--1214159 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
1214116 AGCATGTATT
1214126 TACAATA
1 TACAATA
1214133 TACAATA
1 TACAATA
1214140 TACAATA
1 TACAATA
1214147 TACAATA
1 TACAATA
1214154 TACAAT
1 TACAAT
1214160 GCAGACATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (7 bp):
TACAATA
Found at i:1218795 original size:22 final size:22
Alignment explanation
Indices: 1218770--1218815 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1218760 TTCATTTTAA
1218770 TTGA-GTTTGACTTGATTGTGGT
1 TTGATGTTTGACTTGATT-TGGT
* *
1218792 TTGATTTTTGAGTTGATTTGGT
1 TTGATGTTTGACTTGATTTGGT
1218814 TT
1 TT
1218816 TTTTAGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.13, C:0.02, G:0.28, T:0.57
Consensus pattern (22 bp):
TTGATGTTTGACTTGATTTGGT
Found at i:1221781 original size:18 final size:18
Alignment explanation
Indices: 1221746--1221781 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1221736 TAATTTATAA
*
1221746 ATTTTTTTTAGAACTTAT
1 ATTTTTTTTAGAAATTAT
*
1221764 ATTTTTTTTATAAATTAT
1 ATTTTTTTTAGAAATTAT
1221782 TTTACGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTTTTTTAGAAATTAT
Found at i:1226668 original size:32 final size:32
Alignment explanation
Indices: 1226626--1226710 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 32
1226616 AGAAAGTTCG
* *
1226626 GGGCCACAGGGCCTACCTAAGAACAT-ATCTTA
1 GGGCCGCAGGGCCTACCTAAGAA-ATGATCTCA
**
1226658 GGGCCGCAGGGCCTACCCGAG-AATGATCTCA
1 GGGCCGCAGGGCCTACCTAAGAAATGATCTCA
* *
1226689 GGGCCGTAGAGCCTACCTAAGA
1 GGGCCGCAGGGCCTACCTAAGA
1226711 GTTACATTAG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
30 2 0.05
31 23 0.53
32 18 0.42
ACGTcount: A:0.27, C:0.29, G:0.28, T:0.15
Consensus pattern (32 bp):
GGGCCGCAGGGCCTACCTAAGAAATGATCTCA
Found at i:1240903 original size:20 final size:20
Alignment explanation
Indices: 1240878--1241114 Score: 168
Period size: 20 Copynumber: 10.7 Consensus size: 20
1240868 TAATTAAAAT
1240878 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1240898 GCATGAAATGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
* *
1240924 GCATGGAAGGATCCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1240944 GCATGAAAGGATGTCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
1240970 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1240990 GCATGAAAGAATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
* *
1241016 GCATGAAATGATTCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1241036 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
1241062 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
1241082 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
1241102 GCATGAAAGGATG
1 GCATGAAAGGATG
1241115 TCATAATTAA
Statistics
Matches: 173, Mismatches: 20, Indels: 48
0.72 0.08 0.20
Matches are distributed among these distances:
20 87 0.50
21 4 0.02
22 12 0.07
24 12 0.07
25 4 0.02
26 54 0.31
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.23
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1240934 original size:46 final size:46
Alignment explanation
Indices: 1240866--1241095 Score: 397
Period size: 46 Copynumber: 5.0 Consensus size: 46
1240856 AAATCAAATT
*
1240866 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
1240912 CATAATTAAAATGCATGGAAGGATCCATTAAGGCATGAAAGGATGT
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
1240958 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGAATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
1241004 CATAATTAAAATGCATGAAATGATTCATTAAGGCATGAAAGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1241050 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1241096 ATTAAGGCAT
Statistics
Matches: 171, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 171 1.00
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.23
Consensus pattern (46 bp):
CATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:1241147 original size:47 final size:47
Alignment explanation
Indices: 1241082--1241182 Score: 141
Period size: 47 Copynumber: 2.1 Consensus size: 47
1241072 ATGCATTAAG
**
1241082 GCATGAAAGGATGCATTAAGGCATG-AAAGGATGTCATAATTAAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAAAAATGTCATAATT-AAAAT
* *
1241129 GCATGAAATGATGTATTAAGGCATGAAAAAAATGTCATAATTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAAAAATGTCATAATTAAAAT
*
1241176 GTATGAA
1 GCATGAA
1241183 TAGATGATCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 34 0.71
48 14 0.29
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (47 bp):
GCATGAAAGGATGCATTAAGGCATGAAAAAAATGTCATAATTAAAAT
Found at i:1241154 original size:20 final size:21
Alignment explanation
Indices: 1240878--1241156 Score: 122
Period size: 20 Copynumber: 12.4 Consensus size: 21
1240868 TAATTAAAAT
*
1240878 GCATGAAAGGATG-CATTAAG
1 GCATGAAAGGATGTAATTAAG
* *
1240898 GCATGAAATGATGCCATAATTAAAAT
1 GCATGAAAGGATG---TAATT--AAG
* **
1240924 GCATGGAAGGAT-CCATTAAG
1 GCATGAAAGGATGTAATTAAG
*
1240944 GCATGAAAGGATGTCATAATTAAAAT
1 GCATGAAAGGATG---TAATT--AAG
*
1240970 GCATGAAAGGATG-CATTAAG
1 GCATGAAAGGATGTAATTAAG
* *
1240990 GCATGAAAGAATGCCATAATTAAAAT
1 GCATGAAAGGATG---TAATT--AAG
* *
1241016 GCATGAAATGAT-TCATTAAG
1 GCATGAAAGGATGTAATTAAG
*
1241036 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG---TAATT--AAG
*
1241062 GCATGAAAGGATG-CATTAAG
1 GCATGAAAGGATGTAATTAAG
*
1241082 GCATGAAAGGATG-CATTAAG
1 GCATGAAAGGATGTAATTAAG
*
1241102 GCATGAAAGGATGTCATAATTAAAAAT
1 GCATGAAAGGATG---TAATT---AAG
*
1241129 GCATGAAATGATGT-ATTAAG
1 GCATGAAAGGATGTAATTAAG
1241149 GCATGAAA
1 GCATGAAA
1241157 AAAATGTCAT
Statistics
Matches: 198, Mismatches: 30, Indels: 62
0.68 0.10 0.21
Matches are distributed among these distances:
20 97 0.49
22 13 0.07
23 3 0.02
24 17 0.09
26 54 0.27
27 14 0.07
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (21 bp):
GCATGAAAGGATGTAATTAAG
Found at i:1254189 original size:21 final size:19
Alignment explanation
Indices: 1254161--1254206 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1254151 TAATTGAATC
1254161 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
1254181 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
1254200 ACTTAGT
1 A-TTAGT
1254207 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:1263336 original size:31 final size:31
Alignment explanation
Indices: 1263298--1263373 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
1263288 TTTCATTTAA
*
1263298 GTCCCCCAATATTTATTCCATTTGCAATATG
1 GTCCCCCAACATTTATTCCATTTGCAATATG
*
1263329 GTCCCCCAACATTTATTCCGTTTGCAATATG
1 GTCCCCCAACATTTATTCCATTTGCAATATG
*
1263360 GTCCCCAAACATTT
1 GTCCCCCAACATTT
1263374 GGGGGACTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.36
Consensus pattern (31 bp):
GTCCCCCAACATTTATTCCATTTGCAATATG
Found at i:1264069 original size:24 final size:27
Alignment explanation
Indices: 1264018--1264069 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 27
1264008 ATAAATTCGA
*
1264018 TAAATTGTTTATAGGAAATTTTTTTAT
1 TAAATTGTTTATAGGAAATTTTTATAT
*
1264045 TAAATT-TTTAT-GGATA-TTTTATAT
1 TAAATTGTTTATAGGAAATTTTTATAT
1264069 T
1 T
1264070 TTATAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.35
25 4 0.17
26 5 0.22
27 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.58
Consensus pattern (27 bp):
TAAATTGTTTATAGGAAATTTTTATAT
Found at i:1264127 original size:5 final size:5
Alignment explanation
Indices: 1264117--1264142 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1264107 CTAATCAAAC
1264117 AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT A
1264143 CCAAACATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:1271283 original size:23 final size:23
Alignment explanation
Indices: 1271257--1271338 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
1271247 TGTGCATATA
1271257 GTATCGATACCCCCTTTGAATAG
1 GTATCGATACCCCCTTTGAATAG
* *
1271280 GTATCGGTA-CCCC--TGCAATAA
1 GTATCGATACCCCCTTTG-AATAG
** *
1271301 GTATCGATACCATCTTTGAATGG
1 GTATCGATACCCCCTTTGAATAG
*
1271324 GTATTGATACCCCCT
1 GTATCGATACCCCCT
1271339 GATGGTACCG
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
20 2 0.04
21 12 0.27
22 6 0.13
23 23 0.51
24 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (23 bp):
GTATCGATACCCCCTTTGAATAG
Found at i:1276116 original size:2 final size:2
Alignment explanation
Indices: 1276109--1276149 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1276099 ATAAAAGTAT
1276109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1276150 TATCTTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1284924 original size:14 final size:15
Alignment explanation
Indices: 1284905--1284933 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1284895 TGCAAAGAGA
1284905 GAAATAAAA-AAAAG
1 GAAATAAAATAAAAG
1284919 GAAATAAAATAAAAG
1 GAAATAAAATAAAAG
1284934 AAGGAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (15 bp):
GAAATAAAATAAAAG
Found at i:1288015 original size:21 final size:20
Alignment explanation
Indices: 1287991--1288039 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
1287981 CTCTATTCTC
*
1287991 TTATTTTTATTTAAATTGCTT
1 TTATTTTTATTT-AATCGCTT
1288012 TTA--TTTATTTAATCGCTT
1 TTATTTTTATTTAATCGCTT
1288030 TTATTATTTA
1 TTATT-TTTA
1288040 AATATCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
21 7 0.29
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (20 bp):
TTATTTTTATTTAATCGCTT
Found at i:1288031 original size:18 final size:18
Alignment explanation
Indices: 1287996--1288040 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1287986 TTCTCTTATT
*
1287996 TTTATTTAAATTGCTTTTA
1 TTTATTT-AATCGCTTTTA
1288015 TTTATTTAATCGCTTTTA
1 TTTATTTAATCGCTTTTA
1288033 -TTATTTAA
1 TTTATTTAA
1288041 ATATCTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.32
18 10 0.40
19 7 0.28
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Found at i:1291626 original size:40 final size:40
Alignment explanation
Indices: 1291563--1291679 Score: 207
Period size: 40 Copynumber: 2.9 Consensus size: 40
1291553 GTTTATAGTG
*
1291563 CACTTCGGTGTATATGGTTGGCACGACCTTATGTGTAATA
1 CACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAATA
*
1291603 CACTTCGGTGTATATAGTGGGCACGACCTTATGTGTAATA
1 CACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAATA
*
1291643 CACTTCGGTGTATATGGTGGGCACGACCTTATCTGTA
1 CACTTCGGTGTATATGGTGGGCACGACCTTATGTGTA
1291680 GCACTACGGT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (40 bp):
CACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAATA
Found at i:1291834 original size:45 final size:45
Alignment explanation
Indices: 1291784--1292051 Score: 367
Period size: 45 Copynumber: 6.0 Consensus size: 45
1291774 GTAAGCATGC
* *
1291784 AAATAAACTTACGAGCTTATTGAATAAATGGTAAATATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
* * *
1291829 AAATAAGCTTACGAGCTTATGGATTAAATGTTAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
* *
1291874 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAATGTATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
* * * *
1291919 AAATAAGCTTACGATCTTATGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
* * *
1291964 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTCTGTT-AGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGA-TA
* * *
1292009 AAATAAGCTTGCGAGCTTATGGGATAAATGGTAAATATTTTGA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGA
1292052 AAATAAATTT
Statistics
Matches: 199, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
45 198 0.99
46 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAATATATTGATA
Found at i:1297592 original size:18 final size:18
Alignment explanation
Indices: 1297561--1297605 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
1297551 TTCTCTTATT
1297561 TTTATTTAAATTGCTTTTA
1 TTTATTT-AATTGCTTTTA
1297580 TTTATTTAATTGCTTTTA
1 TTTATTTAATTGCTTTTA
1297598 -TTATTTAA
1 TTTATTTAA
1297606 ATATCTCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 8 0.31
18 11 0.42
19 7 0.27
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTATTTAATTGCTTTTA
Found at i:1316790 original size:20 final size:21
Alignment explanation
Indices: 1316752--1316795 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1316742 TAACTTTTTA
*
1316752 TTTTCTCTTTCATCCTTAACT
1 TTTTCTATTTCATCCTTAACT
*
1316773 TTTTCTATTTCAT-TTTAACT
1 TTTTCTATTTCATCCTTAACT
1316793 TTT
1 TTT
1316796 ACTTTTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTCTATTTCATCCTTAACT
Found at i:1317880 original size:24 final size:24
Alignment explanation
Indices: 1317853--1317903 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1317843 ACCTGACTCT
1317853 TGATCAGCACCATTCTGAGACACC
1 TGATCAGCACCATTCTGAGACACC
* * *
1317877 TGATCCGCATCATTCTGAGACCCC
1 TGATCAGCACCATTCTGAGACACC
1317901 TGA
1 TGA
1317904 ATATCCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (24 bp):
TGATCAGCACCATTCTGAGACACC
Found at i:1333570 original size:53 final size:53
Alignment explanation
Indices: 1333467--1333571 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 53
1333457 CAAGTCATCA
* *
1333467 CCATGCCCTGCCATCTCCAATACCCCACGTGAAGCACCACCAATTAAGCAGAG
1 CCATGCCCTGCCATCTCCAATACCCCACGTGAAGCACCACAAACTAAGCAGAG
* *
1333520 CCATGCCCTGCCATCTCCAGTACCCCACGTGAAGCACCACAAACTGAGCAGA
1 CCATGCCCTGCCATCTCCAATACCCCACGTGAAGCACCACAAACTAAGCAGA
1333572 CCCTTGCACT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.30, C:0.40, G:0.16, T:0.14
Consensus pattern (53 bp):
CCATGCCCTGCCATCTCCAATACCCCACGTGAAGCACCACAAACTAAGCAGAG
Found at i:1333738 original size:16 final size:17
Alignment explanation
Indices: 1333708--1333741 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1333698 GAGGGGGAAC
1333708 AACCAAAATCAAAGGGG
1 AACCAAAATCAAAGGGG
1333725 AACCAAAA-CAAAGGGG
1 AACCAAAATCAAAGGGG
1333741 A
1 A
1333742 GAATGGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.56, C:0.18, G:0.24, T:0.03
Consensus pattern (17 bp):
AACCAAAATCAAAGGGG
Found at i:1337565 original size:20 final size:20
Alignment explanation
Indices: 1337540--1337582 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1337530 TGCATCTTGG
1337540 CATGTGTATATTTTTATTTT
1 CATGTGTATATTTTTATTTT
*
1337560 CATGTGTATCTTTTTATTTT
1 CATGTGTATATTTTTATTTT
1337580 CAT
1 CAT
1337583 ATGCATCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.63
Consensus pattern (20 bp):
CATGTGTATATTTTTATTTT
Found at i:1338992 original size:12 final size:11
Alignment explanation
Indices: 1338977--1339061 Score: 61
Period size: 12 Copynumber: 7.5 Consensus size: 11
1338967 AAAAGATATA
1338977 AAAAAGAGAAAG
1 AAAAA-AGAAAG
1338989 -AAAAAGAAAG
1 AAAAAAGAAAG
1338999 AAAAAAGTGAAA-
1 AAAAAA--GAAAG
*
1339011 AAGAAA-AAAG
1 AAAAAAGAAAG
*
1339021 AAAAAAGAGAGG
1 AAAAAAGA-AAG
*
1339033 AAAAAATAAA-
1 AAAAAAGAAAG
1339043 AAAATAAGAAAG
1 AAAA-AAGAAAG
1339055 AAGAAAA
1 AA-AAAA
1339062 TATACAGATC
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
9 3 0.05
10 15 0.26
11 16 0.28
12 18 0.31
13 6 0.10
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:1338993 original size:23 final size:22
Alignment explanation
Indices: 1338966--1339063 Score: 76
Period size: 23 Copynumber: 4.4 Consensus size: 22
1338956 GATATAGCAA
*
1338966 AAAAAGATATAAAAAAGAGAAAG
1 AAAAA-ATAGAAAAAAGAGAAAG
* *
1338989 AAAAAGAAAGAAAAAAGTGAAA-
1 AAAAA-ATAGAAAAAAGAGAAAG
* *
1339011 AAGAAAAAAGAAAAAAGAG-AGG
1 AA-AAAATAGAAAAAAGAGAAAG
*
1339033 AAAAAATA-AAAAAATAAGAAAG
1 AAAAAATAGAAAAAA-GAGAAAG
1339055 AAGAAAATA
1 AA-AAAATA
1339064 TACAGATCCA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
20 6 0.10
21 8 0.13
22 20 0.32
23 28 0.45
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (22 bp):
AAAAAATAGAAAAAAGAGAAAG
Found at i:1339002 original size:22 final size:22
Alignment explanation
Indices: 1338976--1339030 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1338966 AAAAAGATAT
1338976 AAAAAAGAGAAAGAA-AAAGAAAG
1 AAAAAAGAGAAA-AAGAAA-AAAG
*
1338999 AAAAAAGTGAAAAAGAAAAAAG
1 AAAAAAGAGAAAAAGAAAAAAG
1339021 AAAAAAGAGA
1 AAAAAAGAGA
1339031 GGAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (22 bp):
AAAAAAGAGAAAAAGAAAAAAG
Found at i:1339018 original size:7 final size:7
Alignment explanation
Indices: 1338976--1339028 Score: 54
Period size: 7 Copynumber: 7.1 Consensus size: 7
1338966 AAAAAGATAT
1338976 AAAAAAG
1 AAAAAAG
1338983 AGAAAGAA-
1 A-AAA-AAG
1338991 AAAGAAAG
1 AAA-AAAG
1338999 AAAAAAG
1 AAAAAAG
*
1339006 TGAAAAAG
1 -AAAAAAG
1339014 AAAAAAG
1 AAAAAAG
1339021 AAAAAAG
1 AAAAAAG
1339028 A
1 A
1339029 GAGGAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 23 0.59
8 14 0.36
9 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:1339026 original size:14 final size:14
Alignment explanation
Indices: 1338976--1339028 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
1338966 AAAAAGATAT
1338976 AAAAAAGAGAAAGAA-
1 AAAAAAGA-AAA-AAG
1338991 AAAGAAAGAAAAAAG
1 AAA-AAAGAAAAAAG
*
1339006 TGAAAAAGAAAAAAG
1 -AAAAAAGAAAAAAG
1339021 AAAAAAGA
1 AAAAAAGA
1339029 GAGGAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 9 0.27
15 17 0.52
16 7 0.21
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAAAAAG
Done.