Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 23
Found at i:1034900 original size:19 final size:18
Alignment explanation
Indices: 1034858--1034903 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
1034848 AGTCATGCAT
* * *
1034858 ACATACAATTAATGTAAT
1 ACATATAATTAATATAAC
1034876 ACATATAATTACATATAAC
1 ACATATAATTA-ATATAAC
1034895 ACATATAAT
1 ACATATAAT
1034904 CATAACAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (18 bp):
ACATATAATTAATATAAC
Found at i:1041093 original size:24 final size:26
Alignment explanation
Indices: 1041057--1041109 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
1041047 TATATATTCA
1041057 ATATTTTTATAA-TAATTTTAAT-TT
1 ATATTTTTATAATTAATTTTAATCTT
1041081 ATATTTATT-TAATTAATTTTAATCTT
1 ATATTT-TTATAATTAATTTTAATCTT
1041107 ATA
1 ATA
1041110 AATGGTTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 9 0.35
25 12 0.46
26 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
ATATTTTTATAATTAATTTTAATCTT
Found at i:1045739 original size:6 final size:6
Alignment explanation
Indices: 1045728--1045754 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1045718 GGAGGCGAGT
1045728 CTGGAA CTGGAA CTGGAA CTGGAA CTG
1 CTGGAA CTGGAA CTGGAA CTGGAA CTG
1045755 AGATATGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.19
Consensus pattern (6 bp):
CTGGAA
Found at i:1054040 original size:82 final size:83
Alignment explanation
Indices: 1053861--1054027 Score: 266
Period size: 82 Copynumber: 2.0 Consensus size: 83
1053851 CAAGGAAGTA
* *
1053861 AACTCAAAAACCTTAATTACAAGAAGCAAAAGTAAAACAAATAAGAAAACAAAAGTAGGAATTGG
1 AACTCCAAAACCTTAAATACAAGAAG-AAAAGTAAAACAAATAAGAAAACAAAAGTAGGAATTGG
1053926 AGATGAACATCTTGAAAAC
65 AGATGAACATCTTGAAAAC
* *
1053945 AACTCCAAAACCTTAAATATAAGAAG-AAAGTAAAACAAATAAGAAAACAGAAGTAGGAATAT-G
1 AACTCCAAAACCTTAAATACAAGAAGAAAAGTAAAACAAATAAGAAAACAAAAGTAGGAAT-TGG
1054008 AGATGAACATCTTGAAAAC
65 AGATGAACATCTTGAAAAC
1054027 A
1 A
1054028 TTCTTCACAC
Statistics
Matches: 78, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
82 54 0.69
83 1 0.01
84 23 0.29
ACGTcount: A:0.56, C:0.13, G:0.14, T:0.17
Consensus pattern (83 bp):
AACTCCAAAACCTTAAATACAAGAAGAAAAGTAAAACAAATAAGAAAACAAAAGTAGGAATTGGA
GATGAACATCTTGAAAAC
Found at i:1055836 original size:3 final size:3
Alignment explanation
Indices: 1055828--1055863 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1055818 AGCTGACATT
1055828 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1055864 GGGACAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1063668 original size:49 final size:49
Alignment explanation
Indices: 1063595--1063698 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
1063585 GATGGCACGC
* * *
1063595 TGATAAACTAATGTTAACGAAACTTTTATCCCAACATTGGAGAAGATGA
1 TGATATACTAATGTTAACGAAACTTTTATCCCAACATCGGAGAAGAGGA
*
1063644 TGATATACTAATGTTAACGGAACTTTTATCCCAACATCGGAGAAGAGGA
1 TGATATACTAATGTTAACGAAACTTTTATCCCAACATCGGAGAAGAGGA
1063693 TGATAT
1 TGATAT
1063699 CTCCATCGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (49 bp):
TGATATACTAATGTTAACGAAACTTTTATCCCAACATCGGAGAAGAGGA
Found at i:1065076 original size:32 final size:33
Alignment explanation
Indices: 1065035--1065103 Score: 113
Period size: 35 Copynumber: 2.1 Consensus size: 33
1065025 GATCAGAGGA
1065035 ATAAAAATTGAACA-TATTATATCTACTTTCCT
1 ATAAAAATTGAACATTATTATATCTACTTTCCT
1065067 ATAAAAATTGAACATGTTATTATATCTACTTTCCT
1 ATAAAAATTGAACA--TTATTATATCTACTTTCCT
1065102 AT
1 AT
1065104 CATGGGATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
35 20 0.59
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.42
Consensus pattern (33 bp):
ATAAAAATTGAACATTATTATATCTACTTTCCT
Found at i:1068323 original size:107 final size:107
Alignment explanation
Indices: 1068134--1068349 Score: 342
Period size: 107 Copynumber: 2.0 Consensus size: 107
1068124 TATTTATTTA
* * * *
1068134 AATTCAAACTATGAATTATTCTTTTATAAATACAAAGAACGACAATCCTAATCTTAAATGATGAA
1 AATTCAAACTAAGAATTATTCTATTATAAATACAAAGAACGACAATCCAAATCTTAAACGATGAA
**
1068199 ATGTAAACACAGTATTTACAAAATTGCACATACCACTAAACG
66 ATGTAAACACAAAATTTACAAAATTGCACATACCACTAAACG
* *
1068241 AATTCAAACTAAGAATTATTCTATTATAAATATAAAGAACGACAATCCAAATCTTACACGATGAA
1 AATTCAAACTAAGAATTATTCTATTATAAATACAAAGAACGACAATCCAAATCTTAAACGATGAA
**
1068306 ATGTAAACACAAAATTTACAAAATTGCACATACTGCTAAACG
66 ATGTAAACACAAAATTTACAAAATTGCACATACCACTAAACG
1068348 AA
1 AA
1068350 CCAATCTTTT
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 99 1.00
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (107 bp):
AATTCAAACTAAGAATTATTCTATTATAAATACAAAGAACGACAATCCAAATCTTAAACGATGAA
ATGTAAACACAAAATTTACAAAATTGCACATACCACTAAACG
Found at i:1071882 original size:65 final size:64
Alignment explanation
Indices: 1071813--1071963 Score: 198
Period size: 65 Copynumber: 2.3 Consensus size: 64
1071803 AATTAAATTG
* * *
1071813 AACATCGAATGCATTTCATGCATCGATGCACTTA-CCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCACCGATGCACTCAGGATATTT-TG
1071876 AA
64 -A
* * *
1071878 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTGA
*
1071942 AACATCGAATGCACTTGATGCA
1 AACATCGAATGCATTTGATGCA
1071964 CTCTTAGTGC
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
64 23 0.30
65 51 0.66
66 3 0.04
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTGA
Found at i:1074859 original size:22 final size:22
Alignment explanation
Indices: 1074831--1074881 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1074821 TGGTAGATGA
1074831 CTATTCTAGATATACTTGGGTT
1 CTATTCTAGATATACTTGGGTT
1074853 CTATTCTAGATATACTTGGGTT
1 CTATTCTAGATATACTTGGGTT
1074875 CTATTCT
1 CTATTCT
1074882 TAAGTACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (22 bp):
CTATTCTAGATATACTTGGGTT
Found at i:1075543 original size:238 final size:239
Alignment explanation
Indices: 1075125--1075595 Score: 903
Period size: 238 Copynumber: 2.0 Consensus size: 239
1075115 GAACCATGCT
1075125 TGAAAATAATTTGCCAAAATATTTTTGGGCTGAAGCCACAAATACACTTGTTATGTTGTAAATCG
1 TGAAAATAATTTGCCAAAATATTTTTGGGCTGAAGCCACAAATACACTTGTTATGTTGTAAATCG
1075190 AGTAATGATTAGGCCAATTTTAAAAAAAACTCCATATGAATTTTTAAAAATAAAAAGCCTAACAT
66 AGTAATGATTAGGCCAATTTTAAAAAAAACTCCATATGAATTTTTAAAAATAAAAAGCCTAACAT
1075255 TCGCTATTTTTATCCTTTTGGATGTAAATGTTTTGTTTTAAACAACGGT-AAGAAAACCTTGGCA
131 TCGCTATTTTTATCCTTTTGGATGTAAATGTTTTGTTTTAAACAACGGTAAAGAAAACCTTGGCA
1075319 AATTTGATGCT-AAAGTGATGAAGGAATTTTTCTGGGTTGCTTTG
196 AATTTGATGCTAAAAGTGATGAAGGAA-TTTTCTGGGTTGCTTTG
1075363 TGAAAATAATTTGCCAAAATATTTTTGGGCTGAAGCCACAAATAACACTTGTTATGTTGTAAATC
1 TGAAAATAATTTGCCAAAATATTTTTGGGCTGAAGCCACAAAT-ACACTTGTTATGTTGTAAATC
1075428 GAGTAATGATTAGGCCAATTTT-AAAAAAACTCCATATGAATTTTTAAAAATAAAAAGCCTAACA
65 GAGTAATGATTAGGCCAATTTTAAAAAAAACTCCATATGAATTTTTAAAAATAAAAAGCCTAACA
1075492 TTCGCTATTTTTATCCTTTTGGATGTAAATGTTTTGTTTTAAACAACGGTAAAGAAAACCTTGGC
130 TTCGCTATTTTTATCCTTTTGGATGTAAATGTTTTGTTTTAAACAACGGTAAAGAAAACCTTGGC
1075557 AAATTTGATGCTAAAAGTGATGAAGGAATTTTCTGGGTT
195 AAATTTGATGCTAAAAGTGATGAAGGAATTTTCTGGGTT
1075596 ATTCCTTAAA
Statistics
Matches: 230, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
238 135 0.59
239 80 0.35
240 15 0.07
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (239 bp):
TGAAAATAATTTGCCAAAATATTTTTGGGCTGAAGCCACAAATACACTTGTTATGTTGTAAATCG
AGTAATGATTAGGCCAATTTTAAAAAAAACTCCATATGAATTTTTAAAAATAAAAAGCCTAACAT
TCGCTATTTTTATCCTTTTGGATGTAAATGTTTTGTTTTAAACAACGGTAAAGAAAACCTTGGCA
AATTTGATGCTAAAAGTGATGAAGGAATTTTCTGGGTTGCTTTG
Found at i:1079685 original size:15 final size:15
Alignment explanation
Indices: 1079621--1079687 Score: 55
Period size: 15 Copynumber: 4.5 Consensus size: 15
1079611 GTTGGAGGTC
*
1079621 TGTTTGATTGTTGGA
1 TGTTTGATTGATGGA
* *
1079636 TGTCTGTTTGATGGA
1 TGTTTGATTGATGGA
* * **
1079651 TGATTG-TGGATGTT
1 TGTTTGATTGATGGA
*
1079665 TGTTTGATTGTTGGA
1 TGTTTGATTGATGGA
1079680 TGTTTGAT
1 TGTTTGAT
1079688 GGATATTTCA
Statistics
Matches: 38, Mismatches: 13, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
14 10 0.26
15 28 0.74
ACGTcount: A:0.13, C:0.01, G:0.33, T:0.52
Consensus pattern (15 bp):
TGTTTGATTGATGGA
Found at i:1079685 original size:19 final size:19
Alignment explanation
Indices: 1079608--1079682 Score: 78
Period size: 19 Copynumber: 3.6 Consensus size: 19
1079598 ATTTCATATA
*
1079608 ATTGTTGGAGGTCTGTTTG
1 ATTGTTGGATGTCTGTTTG
1079627 ATTGTTGGATGTCTGTTTG
1 ATTGTTGGATGTCTGTTTG
*
1079646 ATGGATGATTGTGGATGTTTGTTTG
1 AT---TG--T-TGGATGTCTGTTTG
1079671 ATTGTTGGATGT
1 ATTGTTGGATGT
1079683 TTGATGGATA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
19 27 0.56
20 1 0.02
22 4 0.08
24 1 0.02
25 15 0.31
ACGTcount: A:0.13, C:0.03, G:0.35, T:0.49
Consensus pattern (19 bp):
ATTGTTGGATGTCTGTTTG
Found at i:1080402 original size:56 final size:56
Alignment explanation
Indices: 1080342--1080449 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 56
1080332 GATGCACTTA
* *
1080342 CCATGCACCGATGCACTGAGGAT-TTTATGAAACATCGAATGCATTTGATGCACCAG
1 CCATGCACCGATGCACTCAGGATATTT-TGAAACATCGAATGCACTTGATGCACCAG
* * *
1080398 CCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCA
1 CCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCA
1080450 TCGAAACGGC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
56 43 0.93
57 3 0.07
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (56 bp):
CCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCACCAG
Found at i:1080718 original size:24 final size:25
Alignment explanation
Indices: 1080691--1080745 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
1080681 GTGTTCTTTC
1080691 TTTGCTCTA-AATTGTGCAAACATA
1 TTTGCTCTAGAATTGTGCAAACATA
*
1080715 TTTGCCCTAGAATTGTGCAAACATA
1 TTTGCTCTAGAATTGTGCAAACATA
1080740 TTTGCT
1 TTTGCT
1080746 TGTGAGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (25 bp):
TTTGCTCTAGAATTGTGCAAACATA
Found at i:1083262 original size:3 final size:3
Alignment explanation
Indices: 1083254--1083342 Score: 133
Period size: 3 Copynumber: 29.3 Consensus size: 3
1083244 TTTGTAAATA
* * *
1083254 AAT AAT AAT AAT AAT AAT AATT TAT AAT AAT AAT AAC AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
*
1083300 AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1083343 TGTTAAAATA
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
3 75 0.97
4 2 0.03
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1083847 original size:44 final size:44
Alignment explanation
Indices: 1083784--1083893 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
1083774 GGTGATGCTG
*** *
1083784 ATCCAACTCCTTATGTGATGGAATCGAGCGTGGTGTTGGTGTTA
1 ATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGTTA
* * * * *
1083828 ATCCAACTCCTTGTGTGATGAAATTGAGTGAAATGTTGATGTTG
1 ATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGTTA
*
1083872 ATCCAAATCCTTATGTGATGGA
1 ATCCAACTCCTTATGTGATGGA
1083894 CAAGCCCAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (44 bp):
ATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGTTA
Found at i:1084798 original size:19 final size:18
Alignment explanation
Indices: 1084767--1084806 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1084757 CTCATTTTCA
1084767 TTTTTTTTCTTTCTTATT
1 TTTTTTTTCTTTCTTATT
* *
1084785 TTTTTTATTTTTTCTTCTT
1 TTTTTT-TTCTTTCTTATT
1084804 TTT
1 TTT
1084807 CAACTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTTTCTTTCTTATT
Found at i:1088332 original size:29 final size:29
Alignment explanation
Indices: 1088257--1088332 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 29
1088247 AGTCGGCGAT
* * *
1088257 TTTCTCGATATATCACCGTTGAACAGTATA
1 TTTCTCGATCTAACACCGTTCAACA-TATA
* *
1088287 TTTTTCGATC-AGGCACCGTTCAGAC-TATA
1 TTTCTCGATCTA-ACACCGTTCA-ACATATA
1088316 TTTCTCGATCTAACACC
1 TTTCTCGATCTAACACC
1088333 CTTTGCAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
29 18 0.49
30 17 0.46
31 2 0.05
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (29 bp):
TTTCTCGATCTAACACCGTTCAACATATA
Found at i:1092055 original size:22 final size:22
Alignment explanation
Indices: 1092027--1092077 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1092017 TGGTAGATGA
1092027 CTATTCTAGATATACTTGGGTT
1 CTATTCTAGATATACTTGGGTT
1092049 CTATTCTAGATATACTTGGGTT
1 CTATTCTAGATATACTTGGGTT
1092071 CTATTCT
1 CTATTCT
1092078 TAAGTACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47
Consensus pattern (22 bp):
CTATTCTAGATATACTTGGGTT
Found at i:1094770 original size:24 final size:24
Alignment explanation
Indices: 1094743--1094823 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
1094733 GCACTTAACA
1094743 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
1094767 GTGCATCGATTCAT-CGTGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
1094789 -TGCACCGATGCA-CTCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
1094811 GTGCATCGATGCA
1 GTGCATCGATGCA
1094824 CAGGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:1096407 original size:21 final size:21
Alignment explanation
Indices: 1096365--1096408 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1096355 ACTCCGGGAG
*
1096365 CTAGTTCCTCACGAGCTGCTC
1 CTAGTTCCTCACGAGCTCCTC
* *
1096386 CTAGTTCCTCTCGTGCTCCTC
1 CTAGTTCCTCACGAGCTCCTC
1096407 CT
1 CT
1096409 CCTCCTCTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGTTCCTCACGAGCTCCTC
Found at i:1096875 original size:19 final size:19
Alignment explanation
Indices: 1096851--1096890 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1096841 TTTCATGTAA
1096851 ATTGTTGGAGGTCTGTTTG
1 ATTGTTGGAGGTCTGTTTG
*
1096870 ATTGTTGGATGTCTGTTTG
1 ATTGTTGGAGGTCTGTTTG
1096889 AT
1 AT
1096891 GGATGATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.05, G:0.33, T:0.50
Consensus pattern (19 bp):
ATTGTTGGAGGTCTGTTTG
Found at i:1096904 original size:11 final size:11
Alignment explanation
Indices: 1096883--1096946 Score: 71
Period size: 11 Copynumber: 6.1 Consensus size: 11
1096873 GTTGGATGTC
*
1096883 TGTTTGATGGA
1 TGTTTGTTGGA
*
1096894 TGATTGTTGGA
1 TGTTTGTTGGA
1096905 TGTTTGTT---
1 TGTTTGTTGGA
*
1096913 TGATTGTTGGA
1 TGTTTGTTGGA
1096924 TGTTTGTTGGA
1 TGTTTGTTGGA
*
1096935 TGTTTGATGGA
1 TGTTTGTTGGA
1096946 T
1 T
1096947 ATTTCAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
8 7 0.16
11 37 0.84
ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52
Consensus pattern (11 bp):
TGTTTGTTGGA
Found at i:1096913 original size:45 final size:45
Alignment explanation
Indices: 1096851--1096936 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
1096841 TTTCATGTAA
*
1096851 ATTGTTGGAGGTCTGTTTGATTGTTGGATGTCTGTTTGATGGATG
1 ATTGTTGGAGGTCTGTTTGATTGTTGGATGTCTGTTGGATGGATG
* * *
1096896 ATTGTTGGATGTTTGTTTGATTGTTGGATGTTTGTTGGATG
1 ATTGTTGGAGGTCTGTTTGATTGTTGGATGTCTGTTGGATG
1096937 TTTGATGGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.13, C:0.02, G:0.35, T:0.50
Consensus pattern (45 bp):
ATTGTTGGAGGTCTGTTTGATTGTTGGATGTCTGTTGGATGGATG
Found at i:1096918 original size:19 final size:19
Alignment explanation
Indices: 1096894--1096931 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1096884 GTTTGATGGA
1096894 TGATTGTTGGATGTTTGTT
1 TGATTGTTGGATGTTTGTT
1096913 TGATTGTTGGATGTTTGTT
1 TGATTGTTGGATGTTTGTT
1096932 GGATGTTTGA
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:0.11, C:0.00, G:0.32, T:0.58
Consensus pattern (19 bp):
TGATTGTTGGATGTTTGTT
Found at i:1096938 original size:26 final size:26
Alignment explanation
Indices: 1096868--1096942 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 26
1096858 GAGGTCTGTT
* *
1096868 TGATTGTTGGATGTCTGTTTGATGGA
1 TGATTGTTGGATGTTTGATTGATGGA
*
1096894 TGATTGTTGGATGTTTGTTTGATTGTTGGA
1 TGATTGTTGGA----TGTTTGATTGATGGA
*
1096924 TGTTTGTTGGATGTTTGAT
1 TGATTGTTGGATGTTTGAT
1096943 GGATATTTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
26 19 0.46
30 22 0.54
ACGTcount: A:0.13, C:0.01, G:0.33, T:0.52
Consensus pattern (26 bp):
TGATTGTTGGATGTTTGATTGATGGA
Found at i:1097749 original size:64 final size:64
Alignment explanation
Indices: 1097591--1097770 Score: 215
Period size: 65 Copynumber: 2.8 Consensus size: 64
1097581 AATTAAATTG
* * *
1097591 AACATCGAATGCATTTCATGCATCGATGCACTTACCATGCACCGATGCACTGAGGATTTTAGGAA
1 AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCGATGCACTCAGGATTTTA-GAA
* *
1097656 AACATCGAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTTT-G
1 AACATCGAATGCATTTGATGCATCGATGCACTCA-CCATGCACCGATGCACTCAGG--ATTTTAG
1097719 -A
63 AA
* **
1097720 AACATCGAATGCACTTGATGCATCGATGCACTC-TTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTCACCA-TGCACCGATGCACT
1097771 AAGGGTCCAA
Statistics
Matches: 101, Mismatches: 9, Indels: 11
0.83 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 45 0.45
65 50 0.50
67 5 0.05
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCACCATGCACCGATGCACTCAGGATTTTAGAA
Found at i:1097750 original size:17 final size:19
Alignment explanation
Indices: 1097722--1097770 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1097712 TATTTTGAAA
1097722 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1097740 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1097759 CACCGATGCACT
1 CATCGATGCACT
1097771 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1097838 original size:21 final size:21
Alignment explanation
Indices: 1097808--1097863 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1097798 TTTTACACTG
*
1097808 ATGCACCGATGCACCATGGGT
1 ATGCATCGATGCACCATGGGT
*
1097829 ATGCATCGATGCATCATGGGT
1 ATGCATCGATGCACCATGGGT
1097850 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1097864 TGACGCTCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (21 bp):
ATGCATCGATGCACCATGGGT
Found at i:1098176 original size:25 final size:25
Alignment explanation
Indices: 1098148--1098203 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
1098138 GTGTTCTTTC
*
1098148 TTTGCTCTAAAATTGTGCAAACATA
1 TTTGCCCTAAAATTGTGCAAACATA
*
1098173 TTTGCCCTAGAATTGTGCAAACATA
1 TTTGCCCTAAAATTGTGCAAACATA
1098198 TTTGCC
1 TTTGCC
1098204 TTGTGAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (25 bp):
TTTGCCCTAAAATTGTGCAAACATA
Found at i:1100786 original size:3 final size:3
Alignment explanation
Indices: 1100778--1100872 Score: 136
Period size: 3 Copynumber: 31.3 Consensus size: 3
1100768 AAAGTTTGTA
* * *
1100778 AAT AAT AAT AAT AAT AAT AAT AATT TAT AAT AAT AAT AAC AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
* *
1100824 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1100872 A
1 A
1100873 TGTTAAAATA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
3 79 0.98
4 2 0.02
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1101377 original size:44 final size:44
Alignment explanation
Indices: 1101314--1101423 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
1101304 GGTGATGCTG
*** *
1101314 ATCCAACTCCTTATGTGATGGAATCGAGCGTGGTGTTGGTGTTA
1 ATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGTTA
* * * * *
1101358 ATCCAACTCCTTGTGTGATGAAATTGAGTGAAATGTTGATGTTG
1 ATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGTTA
*
1101402 ATCCAAATCCTTATGTGATGGA
1 ATCCAACTCCTTATGTGATGGA
1101424 CAAGCCCAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (44 bp):
ATCCAACTCCTTATGTGATGGAATCGAGCGAAATGTTGATGTTA
Found at i:1102345 original size:16 final size:16
Alignment explanation
Indices: 1102292--1102337 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
1102282 TGAACCCTCA
*
1102292 TTTTCATTTTTTTTCT
1 TTTTTATTTTTTTTCT
* *
1102308 TTCTTATTTTTTTTATT
1 TTTTTATTTTTTTT-CT
1102325 TTTTTATTTTTTT
1 TTTTTATTTTTTT
1102338 CTTCTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTATTTTTTTTCT
Found at i:1102345 original size:17 final size:16
Alignment explanation
Indices: 1102298--1102346 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
1102288 CTCATTTTCA
1102298 TTTTTTTTCTTTCTTAT
1 TTTTTTTTCTTT-TTAT
*
1102315 TTTTTTTATTTTTTTAT
1 TTTTTTT-TCTTTTTAT
1102332 TTTTTTCTTCTTTTT
1 TTTTTT-TTCTTTTT
1102347 CAACTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.06, C:0.08, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTTTCTTTTTAT
Found at i:1105878 original size:29 final size:29
Alignment explanation
Indices: 1105803--1105878 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 29
1105793 AGTCGGCGAT
* * *
1105803 TTTCTCGATATATCACCGTTGAACAGTATA
1 TTTCTCGATCTAACACCGTTCAACA-TATA
* *
1105833 TTTTTCGATC-AGGCACCGTTCAGAC-TATA
1 TTTCTCGATCTA-ACACCGTTCA-ACATATA
1105862 TTTCTCGATCTAACACC
1 TTTCTCGATCTAACACC
1105879 CTTTGCAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
29 18 0.49
30 17 0.46
31 2 0.05
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (29 bp):
TTTCTCGATCTAACACCGTTCAACATATA
Found at i:1110351 original size:13 final size:13
Alignment explanation
Indices: 1110333--1110377 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1110323 TAAATAATAA
*
1110333 AAAAAATTACAAT
1 AAAAAACTACAAT
* *
1110346 AAAAAAGTCCAAT
1 AAAAAACTACAAT
*
1110359 AAACAACTACAAT
1 AAAAAACTACAAT
1110372 AAAAAA
1 AAAAAA
1110378 GTACTAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.69, C:0.13, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAACTACAAT
Found at i:1110390 original size:26 final size:26
Alignment explanation
Indices: 1110340--1110403 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
1110330 TAAAAAAAAT
*
1110340 TACAATAAAAAAGTCCAATAAACAAC
1 TACAATAAAAAAGTCCAATAAACAAA
* *
1110366 TACAATAAAAAAGTACTAA-ATACAAA
1 TACAATAAAAAAGT-CCAATAAACAAA
*
1110392 TATAATAAAAAA
1 TACAATAAAAAA
1110404 ACAAAATCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 30 0.91
27 3 0.09
ACGTcount: A:0.66, C:0.12, G:0.03, T:0.19
Consensus pattern (26 bp):
TACAATAAAAAAGTCCAATAAACAAA
Found at i:1112627 original size:21 final size:22
Alignment explanation
Indices: 1112603--1112665 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 22
1112593 AATAAACATT
1112603 TAAATAAAATAAATACTT-AAA
1 TAAATAAAATAAATACTTAAAA
1112624 TAAATTAAATATAAAATA-TTAAAAA
1 TAAA-TAAA-AT-AAATACTT-AAAA
*
1112649 TATAATAAAATATATAC
1 TA-AATAAAATAAATAC
1112666 CTTAGACAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
21 4 0.12
22 4 0.12
23 8 0.24
24 7 0.21
25 9 0.26
26 2 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAATAAAATAAATACTTAAAA
Found at i:1112633 original size:17 final size:17
Alignment explanation
Indices: 1112592--1112634 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1112582 AAAATTAATT
* *
1112592 AAATAAACATTTAAATA
1 AAATAAATACTTAAATA
1112609 AAATAAATACTTAAATA
1 AAATAAATACTTAAATA
*
1112626 AATTAAATA
1 AAATAAATA
1112635 TAAAATATTA
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:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAAATACTTAAATA
Found at i:1122450 original size:14 final size:14
Alignment explanation
Indices: 1122407--1122450 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1122397 AATACAAATA
*
1122407 AAAAT-AAACGAAT
1 AAAATAAAAAGAAT
* *
1122420 AAAATAAAGAGAGT
1 AAAATAAAAAGAAT
1122434 AAAATAAAAAGAAT
1 AAAATAAAAAGAAT
1122448 AAA
1 AAA
1122451 GAAAGGAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (14 bp):
AAAATAAAAAGAAT
Found at i:1122480 original size:25 final size:26
Alignment explanation
Indices: 1122402--1122489 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 26
1122392 AAGAAAATAC
*
1122402 AAATAAAAATAAACGAATAAAATAAA-G
1 AAATAAAAGTAAA-GAATAAAA-AAAGG
* *
1122429 AGAGTAAAA-TAAAAAGAATAAAGAAAGG
1 A-AATAAAAGT--AAAGAATAAAAAAAGG
*
1122457 AAATAAAAGTAAAG-ATAAAAAAAGT
1 AAATAAAAGTAAAGAATAAAAAAAGG
1122482 AAATAAAA
1 AAATAAAA
1122490 TAAGCAACAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
25 17 0.33
26 4 0.08
27 11 0.22
28 16 0.31
29 3 0.06
ACGTcount: A:0.73, C:0.01, G:0.12, T:0.14
Consensus pattern (26 bp):
AAATAAAAGTAAAGAATAAAAAAAGG
Found at i:1122527 original size:4 final size:4
Alignment explanation
Indices: 1122520--1122667 Score: 52
Period size: 4 Copynumber: 34.8 Consensus size: 4
1122510 AAACAGATTA
* * * * *
1122520 AAAT AAAT AAAT AAAAT AAAAA AAAC AAAA AAAT AAAG AGAT AAAT AAAT
1 AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
1122570 AATGT AAAT AAAAT ATAAT AAA- AATT ATA- AAAT GAAAT AAATT AAAT
1 AA-AT AAAT -AAAT A-AAT AAAT AAAT AAAT AAAT -AAAT AAA-T AAAT
* * *
1122617 ATAT GAAA- ATAAT -AAT AAGAAT AACAT ATAC ACAAT AAAT AAAT AAAT
1 AAAT -AAAT A-AAT AAAT -A-AAT AA-AT AAAT A-AAT AAAT AAAT AAAT
1122665 AAA
1 AAA
1122668 AGCGAGGAGA
Statistics
Matches: 108, Mismatches: 20, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
3 8 0.07
4 62 0.57
5 35 0.32
6 3 0.03
ACGTcount: A:0.70, C:0.03, G:0.04, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1122536 original size:9 final size:9
Alignment explanation
Indices: 1122520--1122617 Score: 58
Period size: 9 Copynumber: 10.6 Consensus size: 9
1122510 AAACAGATTA
1122520 AAAT-AAAT
1 AAATAAAAT
1122528 AAATAAAAT
1 AAATAAAAT
* *
1122537 AAAAAAAAC
1 AAATAAAAT
1122546 AAA-AAAAT
1 AAATAAAAT
*
1122554 AAAGAGATAAAT
1 -AA-ATA-AAAT
**
1122566 AAATAATGT
1 AAATAAAAT
1122575 AAATAAAAT
1 AAATAAAAT
1122584 ATAATAAAA-
1 A-AATAAAAT
*
1122593 ATTATAAAAT
1 A-AATAAAAT
*
1122603 GAAATAAATT
1 -AAATAAAAT
1122613 AAATA
1 AAATA
1122618 TATGAAAATA
Statistics
Matches: 71, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
8 8 0.11
9 39 0.55
10 16 0.23
11 4 0.06
12 4 0.06
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1122801 original size:2 final size:2
Alignment explanation
Indices: 1122794--1122846 Score: 58
Period size: 2 Copynumber: 27.5 Consensus size: 2
1122784 TGGAAAAGAA
* *
1122794 AT AT AT AT AT AT AT AT AT A- AT A- AT GAT A- AT AA AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
1122834 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1122847 ATTAAATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
1 3 0.07
2 38 0.88
3 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1123276 original size:2 final size:2
Alignment explanation
Indices: 1123269--1123330 Score: 62
Period size: 2 Copynumber: 33.5 Consensus size: 2
1123259 GTAATAAATA
* *
1123269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T A- AA AC A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1123307 AA AT A- AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1123331 ATAATAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
1 5 0.09
2 48 0.91
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1123453 original size:3 final size:3
Alignment explanation
Indices: 1123447--1123733 Score: 122
Period size: 3 Copynumber: 95.3 Consensus size: 3
1123437 TGTAGATAGT
* *
1123447 ATA ATA ATA ATA A-A ATA AT- ATA TTT ATA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
1123492 GACA A-A AGA TCTA A-A AAA ATAA ATA A-A AAA CATA ATA AT- ATA ATA
1 -ATA ATA ATA -ATA ATA ATA AT-A ATA ATA ATA -ATA ATA ATA ATA ATA
* * * **
1123537 GTA ATAA ATAA ATA A-A ATA ACCGA A-A ATA ATA AAA ATA ATA ACG ATA
1 ATA AT-A AT-A ATA ATA ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1123584 ATA ATA ATA AAA AGTG A-A ATA TATA TATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA A-TA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA ATA
* * ** *
1123630 TATA ATA GTA A-A AAA ATA ATA ACG ATA ATA ATA A-A A-A ATG A-A
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1123672 ATA TATA TATA TATA AT- ATA ATA ATA ATA A-A ATA TATA ATA ATA ATA
1 ATA -ATA -ATA -ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
1123719 ATA ATTA ATA CATA A
1 ATA A-TA ATA -ATA A
1123734 ATGTAAGGTA
Statistics
Matches: 223, Mismatches: 31, Indels: 60
0.71 0.10 0.19
Matches are distributed among these distances:
2 31 0.14
3 145 0.65
4 45 0.20
5 2 0.01
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1123593 original size:76 final size:72
Alignment explanation
Indices: 1123513--1123716 Score: 200
Period size: 76 Copynumber: 2.7 Consensus size: 72
1123503 TAAAAAAATA
1123513 AATAAAAAACATAATAATATAATAGTAATAAATAAATAAAATA-ACCGAA-AATAATAAAAATAA
1 AATAAAAAACATAATAATATAATA-TAAT-AAT-AATAAAATATA--GAATAATAA-AAAAATAA
1123576 TAACGATAATAAT
60 TAACGATAATAAT
** * *
1123589 AATAAAAAGTGA-AAT-ATATATATAATAATAATAATAAAATATATAATAGTAAAAAAATAATAA
1 AATAAAAA-ACATAATAATATA-AT-ATAATAATAATAAAATATAGAATAATAAAAAAATAATAA
1123652 CGATAATAAT
63 CGATAATAAT
* * *
1123662 AAAAAATGAAATATATATATATATAATATAATAATAATAAAATATATAATAATAA
1 AATAAA--AAACATA-ATA-ATATAATATAATAATAATAAAATATAGAATAATAA
1123717 TAATAATTAA
Statistics
Matches: 109, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
73 28 0.26
74 14 0.13
75 12 0.11
76 46 0.42
77 4 0.04
78 5 0.05
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (72 bp):
AATAAAAAACATAATAATATAATATAATAATAATAAAATATAGAATAATAAAAAAATAATAACGA
TAATAAT
Found at i:1123613 original size:23 final size:23
Alignment explanation
Indices: 1123587--1123687 Score: 84
Period size: 23 Copynumber: 4.3 Consensus size: 23
1123577 AACGATAATA
*
1123587 ATAATAAAAAGTGAAATATATAT
1 ATAATAAAAAATGAAATATATAT
*
1123610 ATAATAATAATAATAAAATATATA-
1 ATAATAA-AA-AATGAAATATATAT
* *
1123634 ATAGTAAAAAA--ATAATA-ACGAT
1 ATAATAAAAAATGA-AATATA-TAT
1123656 AATAATAAAAAATGAAATATATAT
1 -ATAATAAAAAATGAAATATATAT
1123680 ATATATAA
1 ATA-ATAA
1123688 TATAATAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
20 2 0.03
21 5 0.08
22 2 0.03
23 22 0.35
24 18 0.29
25 13 0.21
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (23 bp):
ATAATAAAAAATGAAATATATAT
Found at i:1124726 original size:19 final size:19
Alignment explanation
Indices: 1124698--1124734 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1124688 CCTGTACAAC
*
1124698 AAATAAATAATGAATATAT
1 AAATAAATAATCAATATAT
*
1124717 AAATATATAATCAATATA
1 AAATAAATAATCAATATA
1124735 ATATATGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AAATAAATAATCAATATAT
Found at i:1128472 original size:29 final size:29
Alignment explanation
Indices: 1128344--1128552 Score: 215
Period size: 29 Copynumber: 7.2 Consensus size: 29
1128334 TTTACACAAT
* * *
1128344 TATCACCTTTTTAAGAAATATTTACAAAAA
1 TATCACCATTTTAA-AAATAATTACGAAAA
*** * *
1128374 TATCAATTTTTTTTAAAATAATTACGAAAC
1 TATC-ACCATTTTAAAAATAATTACGAAAA
*
1128404 TGTCA-CATTTTAAAAATAATTACGAAAA
1 TATCACCATTTTAAAAATAATTACGAAAA
*
1128432 TATCA-CTTTTTAAAAATAATTACGAAAA
1 TATCACCATTTTAAAAATAATTACGAAAA
* **
1128460 TATCACCCTTTTAAAAATAATTATAAAAA
1 TATCACCATTTTAAAAATAATTACGAAAA
* * *
1128489 TAACACCATTTTTAAAATAATTACCAAAA
1 TATCACCATTTTAAAAATAATTACGAAAA
* * *
1128518 TATAACTATTTTAAAAATAATTACTAAAA
1 TATCACCATTTTAAAAATAATTACGAAAA
1128547 TATCAC
1 TATCAC
1128553 TCGGTCAATG
Statistics
Matches: 150, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
28 50 0.33
29 74 0.49
30 19 0.13
31 7 0.05
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.36
Consensus pattern (29 bp):
TATCACCATTTTAAAAATAATTACGAAAA
Found at i:1129988 original size:22 final size:22
Alignment explanation
Indices: 1129966--1130006 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1129956 TTATAATTAT
1129966 TTAAAAA-ATTAAATAAAAATA
1 TTAAAAATATTAAATAAAAATA
*
1129987 TTAAAAATATTTAATAAAAA
1 TTAAAAATATTAAATAAAAA
1130007 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TTAAAAATATTAAATAAAAATA
Found at i:1130426 original size:18 final size:16
Alignment explanation
Indices: 1130405--1130435 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1130395 CTTCTAAATT
1130405 TTTTTTGAGTTCAAGC
1 TTTTTTGAGTTCAAGC
1130421 TTTTTTGAGTTCAAG
1 TTTTTTGAGTTCAAG
1130436 TTTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Found at i:1133484 original size:44 final size:44
Alignment explanation
Indices: 1133436--1133521 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
1133426 TATTCAGTGT
*
1133436 ATTTAAACACTTCGGTCAGAAGCAAC-AGCCAAACATGATACAAC
1 ATTTAAACACTTCGGTCAGAAGCAACAACCCAAA-ATGATACAAC
* *
1133480 ATTTAAACACTTTGGTCAGGAGCAACAACCCAAAATGATACA
1 ATTTAAACACTTCGGTCAGAAGCAACAACCCAAAATGATACA
1133522 TCAACATAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 32 0.84
45 6 0.16
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (44 bp):
ATTTAAACACTTCGGTCAGAAGCAACAACCCAAAATGATACAAC
Found at i:1143006 original size:63 final size:63
Alignment explanation
Indices: 1142906--1143025 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 63
1142896 TATAGCGGCT
* * * *
1142906 ACCTCATCACGTAAAGTAGATATCTCACCACGTAGCGCACCATTTTCATCGCGAAAAACATCC
1 ACCTCACCACGTAAAGTACATACCTCACCACGTAGCGCACCATTTTCATCACGAAAAACATCC
* * * *
1142969 ACCTCACCACGTAAAG-ATCATACCTCATCACTTAGCGCATCATTTTCTTCACGAAAA
1 ACCTCACCACGTAAAGTA-CATACCTCACCACGTAGCGCACCATTTTCATCACGAAAA
1143026 GTACTGACCT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 1 0.02
63 47 0.98
ACGTcount: A:0.33, C:0.32, G:0.11, T:0.24
Consensus pattern (63 bp):
ACCTCACCACGTAAAGTACATACCTCACCACGTAGCGCACCATTTTCATCACGAAAAACATCC
Found at i:1144760 original size:20 final size:20
Alignment explanation
Indices: 1144693--1144753 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
1144683 AATTCGTAAT
1144693 GCGAAAATGAAAATCGCAAC
1 GCGAAAATGAAAATCGCAAC
* *
1144713 GCGAACATGAAAATCGCAAT
1 GCGAAAATGAAAATCGCAAC
1144733 GCGAAAATGAAAATCGCAAC
1 GCGAAAATGAAAATCGCAAC
1144753 G
1 G
1144754 ACAAAATCGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (20 bp):
GCGAAAATGAAAATCGCAAC
Found at i:1144808 original size:20 final size:20
Alignment explanation
Indices: 1144783--1144829 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1144773 CTAAATTTGC
1144783 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1144803 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
1144823 GTTGCGA
1 GTTGCGA
1144830 ATTTAAGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.11, C:0.15, G:0.23, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:1145360 original size:20 final size:20
Alignment explanation
Indices: 1145335--1145393 Score: 118
Period size: 20 Copynumber: 3.0 Consensus size: 20
1145325 ATAAACGCGC
1145335 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
1145355 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
1145375 TTTGACTTCTGTGTTGCGA
1 TTTGACTTCTGTGTTGCGA
1145394 TTTACAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.14, C:0.15, G:0.25, T:0.46
Consensus pattern (20 bp):
TTTGACTTCTGTGTTGCGAA
Found at i:1145511 original size:20 final size:20
Alignment explanation
Indices: 1145488--1145534 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1145478 TGGAAACTGG
*
1145488 GTTGCGAAATTAGAGTTCGC
1 GTTGCGAAATTAGAGATCGC
* *
1145508 GTTGC-AAATTTGAGATCGT
1 GTTGCGAAATTAGAGATCGC
1145527 GTTGCGAA
1 GTTGCGAA
1145535 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.32
Consensus pattern (20 bp):
GTTGCGAAATTAGAGATCGC
Found at i:1154761 original size:21 final size:21
Alignment explanation
Indices: 1154679--1154758 Score: 124
Period size: 21 Copynumber: 3.8 Consensus size: 21
1154669 CCATGATTAG
1154679 TGCTACAGTGTACCGATACAC
1 TGCTACAGTGTACCGATACAC
1154700 TGCTACAGTGTACCGATACAC
1 TGCTACAGTGTACCGATACAC
* * *
1154721 TGCTACAGTGTACTGTTGCAC
1 TGCTACAGTGTACCGATACAC
*
1154742 TGCTACAATGTACCGAT
1 TGCTACAGTGTACCGAT
1154759 GCATAAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (21 bp):
TGCTACAGTGTACCGATACAC
Found at i:1158418 original size:15 final size:13
Alignment explanation
Indices: 1158398--1158435 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
1158388 CTTTCTTAGC
1158398 ATTATCATATATATT
1 ATTATCAT-TAT-TT
1158413 ATTATCATTATTT
1 ATTATCATTATTT
1158426 A-TATCATTAT
1 ATTATCATTAT
1158436 CATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 3 0.13
15 8 0.35
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATCATTATTT
Found at i:1158579 original size:2 final size:2
Alignment explanation
Indices: 1158572--1158624 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1158562 CATATCCATC
1158572 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
1158614 AT AT AT A- AT AT
1 AT AT AT AT AT AT
1158625 TTGTTATGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1158745 original size:23 final size:23
Alignment explanation
Indices: 1158727--1158810 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
1158717 CTCGTATAAA
* *
1158727 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
1158750 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
* *
1158773 TACACCGTAGTGCCAAGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
1158796 TACACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1158811 TTTAATAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:1162695 original size:21 final size:21
Alignment explanation
Indices: 1162671--1162715 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1162661 GAATAAATAT
1162671 GTTGTAGCAATATATTTATGA
1 GTTGTAGCAATATATTTATGA
*
1162692 GTTGTAGTAATATATTTATGA
1 GTTGTAGCAATATATTTATGA
1162713 GTT
1 GTT
1162716 ATGCAACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (21 bp):
GTTGTAGCAATATATTTATGA
Found at i:1167353 original size:15 final size:15
Alignment explanation
Indices: 1167335--1167399 Score: 130
Period size: 15 Copynumber: 4.3 Consensus size: 15
1167325 CGAGGGTTCT
1167335 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1167350 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1167365 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1167380 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
1167395 GTAGT
1 GTAGT
1167400 GGTCCTACGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.14, C:0.25, G:0.34, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:1174794 original size:24 final size:24
Alignment explanation
Indices: 1174767--1174815 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1174757 GATAGCCCAA
1174767 TCTTTTCAGAGGATGAATAAGCTG
1 TCTTTTCAGAGGATGAATAAGCTG
1174791 TCTTTTCAGAGGATGAATAAGCTG
1 TCTTTTCAGAGGATGAATAAGCTG
1174815 T
1 T
1174816 GTAAATAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (24 bp):
TCTTTTCAGAGGATGAATAAGCTG
Found at i:1175827 original size:1 final size:1
Alignment explanation
Indices: 1175823--1175851 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1175813 GCTATCCTAT
1175823 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1175852 ACACATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1176794 original size:19 final size:20
Alignment explanation
Indices: 1176770--1176838 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
1176760 CATACTGAAG
1176770 GTATCGATACT-A-GCCAAAA
1 GTATCGATACTCATG-CAAAA
*
1176789 GTATCGATATTCATGCAAAA
1 GTATCGATACTCATGCAAAA
* * *
1176809 GTTTCGATACTTAT-AAAAA
1 GTATCGATACTCATGCAAAA
*
1176828 GTTTCGATACT
1 GTATCGATACT
1176839 TTTTTATAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
19 25 0.58
20 17 0.40
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (20 bp):
GTATCGATACTCATGCAAAA
Found at i:1179116 original size:25 final size:24
Alignment explanation
Indices: 1179080--1179128 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1179070 AACATCTAAT
1179080 TTTTAACTAATTAAATGGATTAAA
1 TTTTAACTAATTAAATGGATTAAA
* * *
1179104 TTTTAATTAAATTAATTTGATTAAA
1 TTTTAACT-AATTAAATGGATTAAA
1179129 ATCAAACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (24 bp):
TTTTAACTAATTAAATGGATTAAA
Found at i:1182638 original size:36 final size:36
Alignment explanation
Indices: 1182531--1182653 Score: 151
Period size: 36 Copynumber: 3.4 Consensus size: 36
1182521 TATACTATAA
* *
1182531 TATATAATATATAATTTT-AAAATGTTTTCAAAAAC
1 TATATATTATATATTTTTCAAAATGTTTTCAAAAAC
*
1182566 TATATATTATATATATTTTCAAAACAT-TTTTAAAAAAC
1 TATATATTATATAT-TTTTC-AAA-ATGTTTTCAAAAAC
* *
1182604 TATATATTATATATTTTTCAAAATGCTTTCAAAAAT
1 TATATATTATATATTTTTCAAAATGTTTTCAAAAAC
*
1182640 TGTATATTATATAT
1 TATATATTATATAT
1182654 ATGTTTTCGA
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
35 14 0.18
36 28 0.37
37 5 0.07
38 27 0.36
39 2 0.03
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (36 bp):
TATATATTATATATTTTTCAAAATGTTTTCAAAAAC
Found at i:1182666 original size:28 final size:28
Alignment explanation
Indices: 1182630--1182683 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1182620 TTCAAAATGC
* *
1182630 TTTCAAAAATTGTATATTATATATATGT
1 TTTCAAAAACTATATATTATATATATGT
*
1182658 TTTCGAAAACTATATATTATATATAT
1 TTTCAAAAACTATATATTATATATAT
1182684 ATTAAATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (28 bp):
TTTCAAAAACTATATATTATATATATGT
Found at i:1194221 original size:18 final size:19
Alignment explanation
Indices: 1194194--1194230 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1194184 TTAATTAAGT
*
1194194 TAAAACAAGAA-TAAAAAA
1 TAAAAAAAGAATTAAAAAA
1194212 TAAAAAAAGAATTAAAAAA
1 TAAAAAAAGAATTAAAAAA
1194231 GAATTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (19 bp):
TAAAAAAAGAATTAAAAAA
Found at i:1194228 original size:11 final size:11
Alignment explanation
Indices: 1194214--1194239 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1194204 ATAAAAAATA
1194214 AAAAAAGAATT
1 AAAAAAGAATT
1194225 AAAAAAGAATT
1 AAAAAAGAATT
1194236 AAAA
1 AAAA
1194240 CGTGAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAAAGAATT
Found at i:1195483 original size:7 final size:7
Alignment explanation
Indices: 1195463--1195511 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
1195453 TTACAATAAC
*
1195463 ATAATAA
1 ATAATAT
1195470 ATAATAT
1 ATAATAT
1195477 ATAATAT
1 ATAATAT
*
1195484 -T-GTACT
1 ATAATA-T
1195490 ATAATAT
1 ATAATAT
1195497 ATAATAT
1 ATAATAT
1195504 ATAA-AT
1 ATAATAT
1195510 AT
1 AT
1195512 TTTAAAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
5 2 0.06
6 6 0.17
7 26 0.72
8 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:1195541 original size:43 final size:43
Alignment explanation
Indices: 1195480--1195802 Score: 145
Period size: 37 Copynumber: 8.4 Consensus size: 43
1195470 ATAATATATA
*
1195480 ATATTGTACTATA-ATATATAATAT-ATAAATATTTTAAAAAACT
1 ATATTATA-TATATATATATAATATCA-AAATATTTTAAAAAACT
* * * *
1195523 ATATTATATATATATATATATTTTCAAAATGTTTTCAAAAAC-
1 ATATTATATATATATATATAATATCAAAATATTTTAAAAAACT
*
1195565 --------TATATATATAT-AT-TCAAAATATTTTCAAAAACT
1 ATATTATATATATATATATAATATCAAAATATTTTAAAAAACT
*
1195598 ATA-TATAATATAT--AT-T--T-TCAAAATATTTTCAAAAACT
1 ATATTAT-ATATATATATATAATATCAAAATATTTTAAAAAACT
* * * *
1195635 ATA-TAT-TATATATATGT--TTTCAAAATGTTTTTCAAAAACT
1 ATATTATATATATATATATAATATCAAAAT-ATTTTAAAAAACT
* * * *
1195675 ATA-TAT-CATATATATAT-AT-TCAAAATGTTTTCAAAAGCT
1 ATATTATATATATATATATAATATCAAAATATTTTAAAAAACT
*
1195714 ATA-TAT-TAT-T-TATAT--TTTCAAAATATTTTAAAAAACT
1 ATATTATATATATATATATAATATCAAAATATTTTAAAAAACT
** *
1195751 ATA-TAT-TATATATAT-T--T-TCAAAATGCTTTCAAAAACT
1 ATATTATATATATATATATAATATCAAAATATTTTAAAAAACT
1195788 ATA-TAT-TATATATAT
1 ATATTATATATATATAT
1195803 GTTTTCGAAA
Statistics
Matches: 241, Mismatches: 19, Indels: 46
0.79 0.06 0.15
Matches are distributed among these distances:
32 18 0.07
33 1 0.00
34 11 0.05
35 5 0.02
36 1 0.00
37 92 0.38
38 7 0.03
39 31 0.13
40 34 0.14
41 6 0.02
42 4 0.02
43 30 0.12
44 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (43 bp):
ATATTATATATATATATATAATATCAAAATATTTTAAAAAACT
Found at i:1195544 original size:32 final size:33
Alignment explanation
Indices: 1195487--1195551 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1195477 ATAATATTGT
1195487 ACTATAATATATAATATATAAATATTTTAAAAA
1 ACTATAATATATAATATATAAATATTTTAAAAA
* * *
1195520 ACTATATTATAT-ATATATATATATTTTCAAAA
1 ACTATAATATATAATATATAAATATTTTAAAAA
1195552 TGTTTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (33 bp):
ACTATAATATATAATATATAAATATTTTAAAAA
Found at i:1195569 original size:32 final size:32
Alignment explanation
Indices: 1195533--1195645 Score: 154
Period size: 32 Copynumber: 3.3 Consensus size: 32
1195523 ATATTATATA
*
1195533 TATATATATATTTTCAAAATGTTTTCAAAAAC
1 TATATATATATTTTCAAAATATTTTCAAAAAC
*
1195565 TATATATATATATTCAAAATATTTTCAAAAAC
1 TATATATATATTTTCAAAATATTTTCAAAAAC
1195597 TATATATAATATATATTTTCAAAATATTTTCAAAAAC
1 ----TAT-ATATATATTTTCAAAATATTTTCAAAAAC
1195634 TATATATTATAT
1 TATATA-TATAT
1195646 ATATGTTTTC
Statistics
Matches: 72, Mismatches: 3, Indels: 11
0.84 0.03 0.13
Matches are distributed among these distances:
32 33 0.46
33 8 0.11
36 3 0.04
37 28 0.39
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (32 bp):
TATATATATATTTTCAAAATATTTTCAAAAAC
Found at i:1195591 original size:11 final size:11
Alignment explanation
Indices: 1195572--1195631 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
1195562 AACTATATAT
*
1195572 ATATATTCAAA
1 ATATTTTCAAA
1195583 ATATTTTCAAAA
1 ATATTTTC-AAA
*
1195595 ACTATATAT-AATA
1 A-TAT-TTTCAA-A
1195608 TATATTTTCAAA
1 -ATATTTTCAAA
1195620 ATATTTTCAAA
1 ATATTTTCAAA
1195631 A
1 A
1195632 ACTATATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
11 19 0.47
12 9 0.22
13 9 0.22
14 3 0.08
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATTTTCAAA
Found at i:1195618 original size:37 final size:37
Alignment explanation
Indices: 1195527--1195802 Score: 346
Period size: 37 Copynumber: 7.4 Consensus size: 37
1195517 AAAACTATAT
*
1195527 TATATATATATATATATTTTCAAAATGTTTTCAAAAAC
1 TATATATA-ATATATATTTTCAAAATATTTTCAAAAAC
1195565 --TATAT-ATATATA--TTCAAAATATTTTCAAAAAC
1 TATATATAATATATATTTTCAAAATATTTTCAAAAAC
1195597 TATATATAATATATATTTTCAAAATATTTTCAAAAAC
1 TATATATAATATATATTTTCAAAATATTTTCAAAAAC
* *
1195634 TATATATTATATATATGTTTTCAAAATGTTTTTCAAAAAC
1 TATATA-TA-ATATATATTTTCAAAAT-ATTTTCAAAAAC
* * *
1195674 TATATATCATATATATATATTCAAAATGTTTTCAAAAGC
1 TATATAT-A-ATATATATTTTCAAAATATTTTCAAAAAC
* * *
1195713 TATATATTATTTATATTTTCAAAATATTTTAAAAAAC
1 TATATATAATATATATTTTCAAAATATTTTCAAAAAC
* **
1195750 TATATATTATATATATTTTCAAAATGCTTTCAAAAAC
1 TATATATAATATATATTTTCAAAATATTTTCAAAAAC
*
1195787 TATATATTATATATAT
1 TATATATAATATATAT
1195803 GTTTTCGAAA
Statistics
Matches: 212, Mismatches: 17, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
32 19 0.09
34 12 0.06
35 7 0.03
36 5 0.02
37 99 0.47
38 2 0.01
39 34 0.16
40 34 0.16
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (37 bp):
TATATATAATATATATTTTCAAAATATTTTCAAAAAC
Found at i:1195728 original size:116 final size:113
Alignment explanation
Indices: 1195527--1195802 Score: 395
Period size: 116 Copynumber: 2.5 Consensus size: 113
1195517 AAAACTATAT
*
1195527 TATATATATATATATATTTTCAAAATGTTTTCAAAAAC------T-ATATATATATATTCAAAAT
1 TATATAT-TATATATATTTTCAAAATGCTTTCAAAAACTATATATCATATATATATATTCAAAAT
*
1195585 ATTTTCAAAAACTATATATAATATATATTTTCAAAATATTTTCAAAAAC
65 ATTTTCAAAAACTATATATAATATATATTTTCAAAATATTTTAAAAAAC
*
1195634 TATATATTATATATATGTTTTCAAAATGTTTTTCAAAAACTATATATCATATATATATATTCAAA
1 TATATATTATATATA--TTTTCAAAATG-CTTTCAAAAACTATATATCATATATATATATTCAAA
* * * *
1195699 ATGTTTTCAAAAGCTATATATTATTTATATTTTCAAAATATTTTAAAAAAC
63 ATATTTTCAAAAACTATATATAATATATATTTTCAAAATATTTTAAAAAAC
*
1195750 TATATATTATATATATTTTCAAAATGCTTTCAAAAACTATATATTATATATAT
1 TATATATTATATATATTTTCAAAATGCTTTCAAAAACTATATATCATATATAT
1195803 GTTTTCGAAA
Statistics
Matches: 152, Mismatches: 7, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
106 8 0.05
107 7 0.05
108 11 0.07
109 11 0.07
113 25 0.16
114 11 0.07
115 1 0.01
116 78 0.51
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (113 bp):
TATATATTATATATATTTTCAAAATGCTTTCAAAAACTATATATCATATATATATATTCAAAATA
TTTTCAAAAACTATATATAATATATATTTTCAAAATATTTTAAAAAAC
Found at i:1195825 original size:26 final size:28
Alignment explanation
Indices: 1195777--1195830 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1195767 TTCAAAATGC
1195777 TTTCAAAAACTATATATTATATATATGT
1 TTTCAAAAACTATATATTATATATATGT
*
1195805 TTTCGAAAACTATATATTATATATAT
1 TTTCAAAAACTATATATTATATATAT
1195831 TAAATAGAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (28 bp):
TTTCAAAAACTATATATTATATATATGT
Found at i:1199001 original size:23 final size:23
Alignment explanation
Indices: 1198975--1199029 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1198965 ATGGCATTTC
*
1198975 GGTGCATTTCTACGCGTCACTTA
1 GGTGCATTTCTACGCGCCACTTA
* * *
1198998 GGTGCAATTCTACGTGCCACTTC
1 GGTGCATTTCTACGCGCCACTTA
1199021 GGTGCATTT
1 GGTGCATTT
1199030 ATATGAGCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (23 bp):
GGTGCATTTCTACGCGCCACTTA
Found at i:1201382 original size:45 final size:45
Alignment explanation
Indices: 1201326--1201417 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
1201316 AATTTTAAGA
1201326 TTTTTTGAAATCAAGTTTTGAAATTACTCCCCCTTACTTTAACAC
1 TTTTTTGAAATCAAGTTTTGAAATTACTCCCCCTTACTTTAACAC
1201371 TTTTTTGAAATCAAGTTTTGAAATTACTCCCCCTTACTTTAACAC
1 TTTTTTGAAATCAAGTTTTGAAATTACTCCCCCTTACTTTAACAC
1201416 TT
1 TT
1201418 CTTCAATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (45 bp):
TTTTTTGAAATCAAGTTTTGAAATTACTCCCCCTTACTTTAACAC
Found at i:1201446 original size:26 final size:26
Alignment explanation
Indices: 1201416--1201468 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1201406 ACTTTAACAC
1201416 TTCTTCAATTTATCATGTAAAACATT
1 TTCTTCAATTTATCATGTAAAACATT
1201442 TTCTTCAATTTATCATGTAAAACATT
1 TTCTTCAATTTATCATGTAAAACATT
1201468 T
1 T
1201469 AACTTAACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.47
Consensus pattern (26 bp):
TTCTTCAATTTATCATGTAAAACATT
Found at i:1212529 original size:21 final size:21
Alignment explanation
Indices: 1212505--1212556 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1212495 ATTTTGAAGG
1212505 TGCATCGATGCATTAAGGGGA
1 TGCATCGATGCATTAAGGGGA
1212526 TGCATCGATGCATTAAGGGGA
1 TGCATCGATGCATTAAGGGGA
1212547 TGCATCGATG
1 TGCATCGATG
1212557 TATGAGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (21 bp):
TGCATCGATGCATTAAGGGGA
Found at i:1214001 original size:20 final size:20
Alignment explanation
Indices: 1213976--1214013 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1213966 GTCTACGTGG
*
1213976 TCCTTTGGGACATATATGTA
1 TCCTTTGGAACATATATGTA
*
1213996 TCCTTTGGAACATCTATG
1 TCCTTTGGAACATATATG
1214014 AGGTCTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (20 bp):
TCCTTTGGAACATATATGTA
Found at i:1214135 original size:23 final size:23
Alignment explanation
Indices: 1214104--1214163 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1214094 CTTATATGGA
*
1214104 ACTTCGGTGCATTTCTACGCGGC
1 ACTTCGGTGCATTTCTACGCGCC
* * *
1214127 ACTTAGGTGCAATTCTACGTGCC
1 ACTTCGGTGCATTTCTACGCGCC
1214150 ACTTCGGTGCATTT
1 ACTTCGGTGCATTT
1214164 ATATGAGCTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGCC
Found at i:1217863 original size:15 final size:15
Alignment explanation
Indices: 1217843--1217876 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1217833 TCCCCATCTT
*
1217843 TTAACATGTGAAGAA
1 TTAACAAGTGAAGAA
*
1217858 TTAACAAGTGGAGAA
1 TTAACAAGTGAAGAA
1217873 TTAA
1 TTAA
1217877 AATTTCATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (15 bp):
TTAACAAGTGAAGAA
Found at i:1218297 original size:18 final size:18
Alignment explanation
Indices: 1218274--1218308 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1218264 GGTGTCATTT
*
1218274 GACACCTCTCATCATAGG
1 GACACCACTCATCATAGG
*
1218292 GACACCAGTCATCATAG
1 GACACCACTCATCATAG
1218309 AATGACTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (18 bp):
GACACCACTCATCATAGG
Found at i:1235327 original size:656 final size:656
Alignment explanation
Indices: 1234074--1235386 Score: 2608
Period size: 656 Copynumber: 2.0 Consensus size: 656
1234064 CATCATCATA
1234074 TGGCTGCGAGCAAGGCCCTGATGAGCCGCTGAATCTTCAAGCCAAGCACTATCTCTGAACTCTGA
1 TGGCTGCGAGCAAGGCCCTGATGAGCCGCTGAATCTTCAAGCCAAGCACTATCTCTGAACTCTGA
1234139 GAAACAAACTTTAGTTTCTTACAGTTAGATTCAGTTCTTGAGTAGTTTTCTTCTTCTTTTCTTTT
66 GAAACAAACTTTAGTTTCTTACAGTTAGATTCAGTTCTTGAGTAGTTTTCTTCTTCTTTTCTTTT
1234204 TTCTTTTTTTGTTCAGCAGTTCTTCTGTAGGTAAAGCACTGTGTTTTTTACTACCAAGTGAAATG
131 TTCTTTTTTTGTTCAGCAGTTCTTCTGTAGGTAAAGCACTGTGTTTTTTACTACCAAGTGAAATG
1234269 AGGAAAAGAAAGACCTATACAACAAACCTTCTAGCATCGAAGTGGTCGACCCCAAGGTCTTCATC
196 AGGAAAAGAAAGACCTATACAACAAACCTTCTAGCATCGAAGTGGTCGACCCCAAGGTCTTCATC
1234334 CCAAAGGAAGATGTAGGAATACTCCGAAACAATATTTGGATGTAAAAAGCGCTTTGCAAACCACC
261 CCAAAGGAAGATGTAGGAATACTCCGAAACAATATTTGGATGTAAAAAGCGCTTTGCAAACCACC
1234399 TGATTTGTGAGAGTGCATTATACAAAGCCAAGTTACTTCGAACTGAATCAACATATATAAAAGTT
326 TGATTTGTGAGAGTGCATTATACAAAGCCAAGTTACTTCGAACTGAATCAACATATATAAAAGTT
1234464 TTTTTTACCCCAAATTAAGAGCTAATGACCATTTACCACTTGGTTTGATTGGCAGCAGAGACATG
391 TTTTTTACCCCAAATTAAGAGCTAATGACCATTTACCACTTGGTTTGATTGGCAGCAGAGACATG
1234529 TATAGCATGGTCATTCCACTCTAAGTTCTTCCACTGGTCCACAATGCCGTCGTAATGGAAAAGCA
456 TATAGCATGGTCATTCCACTCTAAGTTCTTCCACTGGTCCACAATGCCGTCGTAATGGAAAAGCA
*
1234594 TCACAGCAAAATCACTCTCTGGAAACTGTGAAATGGAACAAAATGAGCGAAAAAATGATATATAT
521 TCACAGCAAAATCACTCTCTGGAAACTGTGAAATGGAACAAAATGAGCGAAAAAAGGATATATAT
*
1234659 AATAAATTAACATAAACAATGCAATAAAAAATTGGCATTTAACAATAATCTAAATAATAACATAA
586 AATAAATTAACATAAACAATGCAATAAAAAATTGGCATCTAACAATAATCTAAATAATAACATAA
1234724 ATAAAG
651 ATAAAG
1234730 TGGCTGCGAGCAAGGCCCTGATGAGCCGCTGAATCTTCAAGCCAAGCACTATCTCTGAACTCTGA
1 TGGCTGCGAGCAAGGCCCTGATGAGCCGCTGAATCTTCAAGCCAAGCACTATCTCTGAACTCTGA
1234795 GAAACAAACTTTAGTTTCTTACAGTTAGATTCAGTTCTTGAGTAGTTTTCTTCTTCTTTTCTTTT
66 GAAACAAACTTTAGTTTCTTACAGTTAGATTCAGTTCTTGAGTAGTTTTCTTCTTCTTTTCTTTT
1234860 TTCTTTTTTTGTTCAGCAGTTCTTCTGTAGGTAAAGCACTGTGTTTTTTACTACCAAGTGAAATG
131 TTCTTTTTTTGTTCAGCAGTTCTTCTGTAGGTAAAGCACTGTGTTTTTTACTACCAAGTGAAATG
1234925 AGGAAAAGAAAGACCTATACAACAAACCTTCTAGCATCGAAGTGGTCGACCCCAAGGTCTTCATC
196 AGGAAAAGAAAGACCTATACAACAAACCTTCTAGCATCGAAGTGGTCGACCCCAAGGTCTTCATC
1234990 CCAAAGGAAGATGTAGGAATACTCCGAAACAATATTTGGATGTAAAAAGCGCTTTGCAAACCACC
261 CCAAAGGAAGATGTAGGAATACTCCGAAACAATATTTGGATGTAAAAAGCGCTTTGCAAACCACC
1235055 TGATTTGTGAGAGTGCATTATACAAAGCCAAGTTACTTCGAACTGAATCAACATATATAAAAGTT
326 TGATTTGTGAGAGTGCATTATACAAAGCCAAGTTACTTCGAACTGAATCAACATATATAAAAGTT
1235120 TTTTTTACCCCAAATTAAGAGCTAATGACCATTTACCACTTGGTTTGATTGGCAGCAGAGACATG
391 TTTTTTACCCCAAATTAAGAGCTAATGACCATTTACCACTTGGTTTGATTGGCAGCAGAGACATG
1235185 TATAGCATGGTCATTCCACTCTAAGTTCTTCCACTGGTCCACAATGCCGTCGTAATGGAAAAGCA
456 TATAGCATGGTCATTCCACTCTAAGTTCTTCCACTGGTCCACAATGCCGTCGTAATGGAAAAGCA
1235250 TCACAGCAAAATCACTCTCTGGAAACTGTGAAATGGAACAAAATGAGCGAAAAAAGGATATATAT
521 TCACAGCAAAATCACTCTCTGGAAACTGTGAAATGGAACAAAATGAGCGAAAAAAGGATATATAT
1235315 AATAAATTAACATAAACAATGCAATAAAAAATTGGCATCTAACAATAATCTAAATAATAACATAA
586 AATAAATTAACATAAACAATGCAATAAAAAATTGGCATCTAACAATAATCTAAATAATAACATAA
1235380 ATAAAG
651 ATAAAG
1235386 T
1 T
1235387 CAATCCTTTC
Statistics
Matches: 655, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
656 655 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (656 bp):
TGGCTGCGAGCAAGGCCCTGATGAGCCGCTGAATCTTCAAGCCAAGCACTATCTCTGAACTCTGA
GAAACAAACTTTAGTTTCTTACAGTTAGATTCAGTTCTTGAGTAGTTTTCTTCTTCTTTTCTTTT
TTCTTTTTTTGTTCAGCAGTTCTTCTGTAGGTAAAGCACTGTGTTTTTTACTACCAAGTGAAATG
AGGAAAAGAAAGACCTATACAACAAACCTTCTAGCATCGAAGTGGTCGACCCCAAGGTCTTCATC
CCAAAGGAAGATGTAGGAATACTCCGAAACAATATTTGGATGTAAAAAGCGCTTTGCAAACCACC
TGATTTGTGAGAGTGCATTATACAAAGCCAAGTTACTTCGAACTGAATCAACATATATAAAAGTT
TTTTTTACCCCAAATTAAGAGCTAATGACCATTTACCACTTGGTTTGATTGGCAGCAGAGACATG
TATAGCATGGTCATTCCACTCTAAGTTCTTCCACTGGTCCACAATGCCGTCGTAATGGAAAAGCA
TCACAGCAAAATCACTCTCTGGAAACTGTGAAATGGAACAAAATGAGCGAAAAAAGGATATATAT
AATAAATTAACATAAACAATGCAATAAAAAATTGGCATCTAACAATAATCTAAATAATAACATAA
ATAAAG
Found at i:1240620 original size:23 final size:23
Alignment explanation
Indices: 1240594--1240684 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
1240584 CACCACAGCT
* *
1240594 CGTATAAATGCATCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1240617 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCG
*
1240640 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
*
1240663 CGTAGAAATGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1240685 ATATAATGTC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.29, C:0.25, G:0.27, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1248599 original size:12 final size:11
Alignment explanation
Indices: 1248584--1248637 Score: 56
Period size: 12 Copynumber: 4.7 Consensus size: 11
1248574 AAATTTTGGC
1248584 TTTTTTTGCTCT
1 TTTTTTTG-TCT
*
1248596 TTTTTTGTGCCT
1 TTTTTT-TGTCT
*
1248608 TTTTTTTGTGCC
1 TTTTTTTGT-CT
1248620 TTTTTTTGT-T
1 TTTTTTTGTCT
1248630 TTTTTTTG
1 TTTTTTTG
1248638 AAAAAAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 8 0.22
11 2 0.06
12 24 0.67
13 2 0.06
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.76
Consensus pattern (11 bp):
TTTTTTTGTCT
Found at i:1248611 original size:13 final size:13
Alignment explanation
Indices: 1248595--1248626 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1248585 TTTTTTGCTC
1248595 TTTTTTTGTGCCT
1 TTTTTTTGTGCCT
1248608 TTTTTTTGTGCCT
1 TTTTTTTGTGCCT
1248621 TTTTTT
1 TTTTTT
1248627 GTTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.75
Consensus pattern (13 bp):
TTTTTTTGTGCCT
Found at i:1250106 original size:19 final size:19
Alignment explanation
Indices: 1250082--1250118 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1250072 TTTTAAGGGG
1250082 TGCATCGATGCACTACTTA
1 TGCATCGATGCACTACTTA
1250101 TGCATCGATGCACTACTT
1 TGCATCGATGCACTACTT
1250119 GCATTCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (19 bp):
TGCATCGATGCACTACTTA
Found at i:1251206 original size:26 final size:26
Alignment explanation
Indices: 1251177--1251254 Score: 147
Period size: 26 Copynumber: 3.0 Consensus size: 26
1251167 TTAAGACATC
1251177 TAATAATAACAACAATTCCTTTAATT
1 TAATAATAACAACAATTCCTTTAATT
1251203 TAATAATAACAACAATTCCTTTAATT
1 TAATAATAACAACAATTCCTTTAATT
*
1251229 TAATAATAACAACAATTCATTTAATT
1 TAATAATAACAACAATTCCTTTAATT
1251255 ATTAAAGTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATAATAACAACAATTCCTTTAATT
Found at i:1251916 original size:28 final size:28
Alignment explanation
Indices: 1251884--1251949 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 28
1251874 AGGAATAGAT
1251884 ATAAAATTTTATGTTAGAGAGTGAATTA
1 ATAAAATTTTATGTTAGAGAGTGAATTA
1251912 ATAAAAATTTTATGTTAGAGAGTGAATTA
1 AT-AAAATTTTATGTTAGAGAGTGAATTA
1251941 ATAAAATTT
1 ATAAAATTT
1251950 AAGATAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 9 0.24
29 28 0.76
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (28 bp):
ATAAAATTTTATGTTAGAGAGTGAATTA
Found at i:1251958 original size:12 final size:12
Alignment explanation
Indices: 1251941--1251965 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1251931 GAGTGAATTA
1251941 ATAAAATTTAAG
1 ATAAAATTTAAG
1251953 ATAAAATTTAAG
1 ATAAAATTTAAG
1251965 A
1 A
1251966 GAGTGAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAAAATTTAAG
Found at i:1252379 original size:24 final size:24
Alignment explanation
Indices: 1252335--1252381 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1252325 TAATGTGATC
* *
1252335 TTTTTATTATTCTTATTTTTCATA
1 TTTTTATTATTCTAATATTTCATA
1252359 TTTTTATTTATT-TAATATTTCAT
1 TTTTTA-TTATTCTAATATTTCAT
1252382 TGTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTATTATTCTAATATTTCATA
Found at i:1253506 original size:2 final size:2
Alignment explanation
Indices: 1253499--1253553 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
1253489 ACAGTATAAC
*
1253499 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1253540 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1253554 ATTGTTTGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1254895 original size:172 final size:174
Alignment explanation
Indices: 1254609--1254956 Score: 673
Period size: 172 Copynumber: 2.0 Consensus size: 174
1254599 AATTTGAATA
1254609 TTTAATATTTAATTTTTTTTAAAATATATAATTTTAAAATTTCAAGATAATATTTTCTAAAAATT
1 TTTAATATTTAATTTTTTTTAAAATATATAATTTTAAAATTTCAAGATAATATTTTCTAAAAATT
1254674 TATAAACCGTCCAATTTTAAATGATTGATATATTTTTTTCTCG-AA-AATAACATTAAAATTGTT
66 TATAAACCGTCCAATTTTAAATGATTGATATATTTTTTTCTCGAAATAATAACATTAAAATTGTT
1254737 AGACAGATAATTTAAACGACACTTATTTTTTAGTTAATATGTAT
131 AGACAGATAATTTAAACGACACTTATTTTTTAGTTAATATGTAT
1254781 TTTAATATTTAATTTTTTTTAAAATATATAATTTTAAAATTTCAAGATAATATTTTCTAAAAATT
1 TTTAATATTTAATTTTTTTTAAAATATATAATTTTAAAATTTCAAGATAATATTTTCTAAAAATT
1254846 TATAAACCGTCCAATTTTAAATGATTGATATATTTTTTTCTCGAAAATAATAACATTAAAATTGT
66 TATAAACCGTCCAATTTTAAATGATTGATATATTTTTTTCTCG-AAATAATAACATTAAAATTGT
1254911 TAGACAGATAATTTAAACGACACTTATTTTTTAGTTAATATGTAT
130 TAGACAGATAATTTAAACGACACTTATTTTTTAGTTAATATGTAT
1254956 T
1 T
1254957 ATAAATAGAG
Statistics
Matches: 173, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
172 108 0.62
174 2 0.01
175 63 0.36
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.46
Consensus pattern (174 bp):
TTTAATATTTAATTTTTTTTAAAATATATAATTTTAAAATTTCAAGATAATATTTTCTAAAAATT
TATAAACCGTCCAATTTTAAATGATTGATATATTTTTTTCTCGAAATAATAACATTAAAATTGTT
AGACAGATAATTTAAACGACACTTATTTTTTAGTTAATATGTAT
Found at i:1255075 original size:20 final size:19
Alignment explanation
Indices: 1255048--1255382 Score: 90
Period size: 20 Copynumber: 16.9 Consensus size: 19
1255038 ATAATCAAAA
* *
1255048 AATTCGCAACACGAACTCT
1 AATTCGCAACACGAATTCC
*
1255067 AATTTCGCAACAC-AGTTTCC
1 AA-TTCGCAACACGA-ATTCC
*
1255087 AAATTCGCAACACGGAATTTCG
1 -AATTCGCAACAC-GAA-TTCC
* * *
1255109 AATTCGCAACTCGATTTCTG
1 AATTCGCAACACGAATTC-C
*
1255129 AATTCGCAACACGAACTCC
1 AATTCGCAACACGAATTCC
* *
1255148 AATTTCGCAACGC-AGTTTCC
1 AA-TTCGCAACACGA-ATTCC
* * *
1255168 AAATTCGCAATATGGAATTTCA
1 -AATTCGCAACA-CGAA-TTCC
*
1255190 AATTCGCAACACGAAATTTCA
1 AATTCGCAACACG-AA-TTCC
* * * * *
1255211 AAATCGTAACTCGATTTCTG
1 AATTCGCAACACGAATTC-C
*
1255231 AATTCGCAACACGAATTTCT
1 AATTCGCAACACGAA-TTCC
** *
1255251 TTTTCGCAACGCG-ATT--
1 AATTCGCAACACGAATTCC
* *
1255267 -TTTTGCAACAC-AAGTTTCC
1 AATTCGCAACACGAA--TTCC
** * * *
1255286 TTTTCGCAACAAGATTTTCT
1 AATTCGCAACACGA-ATTCC
* * *
1255306 AATTCGCAACAAGATTTTCT
1 AATTCGCAACACGA-ATTCC
* *
1255326 AATTCGCAACACGATTTTCT
1 AATTCGCAACACGA-ATTCC
* *
1255346 AATTCGCAACACGATTTTCT
1 AATTCGCAACACGA-ATTCC
*
1255366 AATTCGCAACATGAATT
1 AATTCGCAACACGAATT
1255383 TTCGCAACAC
Statistics
Matches: 247, Mismatches: 45, Indels: 48
0.73 0.13 0.14
Matches are distributed among these distances:
15 10 0.04
17 2 0.01
18 2 0.01
19 15 0.06
20 164 0.66
21 46 0.19
22 8 0.03
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.31
Consensus pattern (19 bp):
AATTCGCAACACGAATTCC
Found at i:1255185 original size:81 final size:81
Alignment explanation
Indices: 1255048--1255199 Score: 259
Period size: 81 Copynumber: 1.9 Consensus size: 81
1255038 ATAATCAAAA
* *
1255048 AATTCGCAACACGAACTCTAATTTCGCAACACAGTTTCCAAATTCGCAACACGGAATTTCGAATT
1 AATTCGCAACACGAACTCCAATTTCGCAACACAGTTTCCAAATTCGCAACACGGAATTTCAAATT
1255113 CGCAACTCGATTTCTG
66 CGCAACTCGATTTCTG
* * *
1255129 AATTCGCAACACGAACTCCAATTTCGCAACGCAGTTTCCAAATTCGCAATATGGAATTTCAAATT
1 AATTCGCAACACGAACTCCAATTTCGCAACACAGTTTCCAAATTCGCAACACGGAATTTCAAATT
1255194 CGCAAC
66 CGCAAC
1255200 ACGAAATTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (81 bp):
AATTCGCAACACGAACTCCAATTTCGCAACACAGTTTCCAAATTCGCAACACGGAATTTCAAATT
CGCAACTCGATTTCTG
Found at i:1255266 original size:40 final size:40
Alignment explanation
Indices: 1255048--1255385 Score: 207
Period size: 40 Copynumber: 8.5 Consensus size: 40
1255038 ATAATCAAAA
** * *
1255048 AATTCGCAACACGA-ACTCTAATTTCGCAACAC-AGTTTCCA
1 AATTCGCAACACGATTTTCTAA-TTCGCAACACGAATTT-CT
* * *
1255088 AATTCGCAACACGGAATTTCGAATTCGCAACTCG-ATTTCT
1 AATTCGCAACAC-GATTTTCTAATTCGCAACACGAATTTCT
** * * * *
1255128 GAATTCGCAACACGA-ACTCCAATTTCGCAACGC-AGTTTCCA
1 -AATTCGCAACACGATTTTCTAA-TTCGCAACACGAATTT-CT
* * * * *
1255169 AATTCGCAATATGGAATTTCAAATTCGCAACACGAAATTTCA
1 AATTCGCAACA-CGATTTTCTAATTCGCAACACG-AATTTCT
* * *
1255211 AAATCGTAACTCGA-TTTCTGAATTCGCAACACGAATTTCT
1 AATTCGCAACACGATTTTCT-AATTCGCAACACGAATTTCT
** *
1255251 TTTTCGCAACGCGA-TTT-T--TT-GCAACAC-AAGTTTCCT
1 AATTCGCAACACGATTTTCTAATTCGCAACACGAA-TTT-CT
* * * *
1255287 -TTTCGCAACAAGATTTTCTAATTCGCAACAAGATTTTCT
1 AATTCGCAACACGATTTTCTAATTCGCAACACGAATTTCT
*
1255326 AATTCGCAACACGATTTTCTAATTCGCAACACGATTTTCT
1 AATTCGCAACACGATTTTCTAATTCGCAACACGAATTTCT
*
1255366 AATTCGCAACATGAATTTTC
1 AATTCGCAACACG-ATTTTC
1255386 GCAACACAAA
Statistics
Matches: 237, Mismatches: 39, Indels: 43
0.74 0.12 0.13
Matches are distributed among these distances:
34 2 0.01
35 21 0.09
36 7 0.03
37 1 0.00
39 9 0.04
40 116 0.49
41 60 0.25
42 17 0.07
43 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (40 bp):
AATTCGCAACACGATTTTCTAATTCGCAACACGAATTTCT
Found at i:1255302 original size:35 final size:35
Alignment explanation
Indices: 1255236--1255303 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
1255226 TTCTGAATTC
* **
1255236 GCAACACGAATTTCTTTTTCGCAACGCGATTTTTT
1 GCAACACGAATTTCCTTTTCGCAACAAGATTTTTT
1255271 GCAACAC-AAGTTTCCTTTTCGCAACAAGATTTT
1 GCAACACGAA-TTTCCTTTTCGCAACAAGATTTT
1255304 CTAATTCGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 2 0.07
35 27 0.93
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (35 bp):
GCAACACGAATTTCCTTTTCGCAACAAGATTTTTT
Found at i:1256286 original size:24 final size:24
Alignment explanation
Indices: 1256259--1256312 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1256249 GTATTCAAAA
1256259 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1256283 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1256307 TTTGAT
1 TTTGAT
1256313 GATGTTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1258493 original size:18 final size:18
Alignment explanation
Indices: 1258470--1258505 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1258460 AAGAAAAAGG
1258470 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
1258488 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
1258506 CAACCGCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:1260367 original size:21 final size:21
Alignment explanation
Indices: 1260343--1260457 Score: 53
Period size: 21 Copynumber: 5.5 Consensus size: 21
1260333 TAAACGGTGG
1260343 GAGGTGGATCTTGAAAGATGA
1 GAGGTGGATCTTGAAAGATGA
* *
1260364 GAGG-GGCCTCTT-AAACGATGG
1 GAGGTGG-ATCTTGAAA-GATGA
** *
1260385 GATGG-GCCTCTTGAACGATGA
1 GA-GGTGGATCTTGAAAGATGA
* * *
1260406 CAGGTGAATCCTGAACA-ATGA
1 GAGGTGGATCTTGAA-AGATGA
*
1260427 GAGGTGGATCCTGAACA-ATG-
1 GAGGTGGATCTTGAA-AGATGA
1260447 GTAGGTGGATC
1 G-AGGTGGATC
1260458 GAGCTTCTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
20 8 0.11
21 62 0.83
22 5 0.07
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.22
Consensus pattern (21 bp):
GAGGTGGATCTTGAAAGATGA
Found at i:1261439 original size:45 final size:45
Alignment explanation
Indices: 1261338--1261441 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
1261328 ATGCACAGGA
**
1261338 AGTGCATCGATGCACCCATTAAAAATGAAAACATCGAATGCTATT
1 AGTGCATCGATGCACCCATTAAAAATGAAAACATCGAATGAGATT
*
1261383 AGTGCATCGATGCACCCGCTT-AAAAT-ACAAACATCGAATGAGATTT
1 AGTGCATCGATGCACCC-ATTAAAAATGA-AAACATCGAATGAGA-TT
*
1261429 A-TGCACCGATGCA
1 AGTGCATCGATGCA
1261442 TAGAAAGTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
44 1 0.02
45 46 0.88
46 5 0.10
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (45 bp):
AGTGCATCGATGCACCCATTAAAAATGAAAACATCGAATGAGATT
Found at i:1262049 original size:2 final size:2
Alignment explanation
Indices: 1262042--1262097 Score: 55
Period size: 2 Copynumber: 28.5 Consensus size: 2
1262032 ACATATTACA
* *
1262042 AT AT AT AT AT AT AT AT -T AT AT GAGT -T GT A- AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT AT AT AT
1262083 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1262098 AATTGGATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 1 0.02
4 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1262473 original size:31 final size:31
Alignment explanation
Indices: 1262389--1262512 Score: 97
Period size: 31 Copynumber: 4.0 Consensus size: 31
1262379 GTCTAGGGTT
* *
1262389 TACCTATGTTCTACGGAACATATGGACAGAA
1 TACCTATGTTCTAAGGAACATATGGACAGTA
* *** * *
1262420 TTAACTATG-TCTTTCGAGACATATAGATAGTA
1 -TACCTATGTTCTAAGGA-ACATATGGACAGTA
*
1262452 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAAGGAACATATGGACAGTA
* ** * *
1262483 TACCTAGGTTCTTCGGGACCTATGGACAGT
1 TACCTATGTTCTAAGGAACATATGGACAGT
1262513 TGTAAAAGAT
Statistics
Matches: 71, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
31 48 0.68
32 23 0.32
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTA
Found at i:1269930 original size:13 final size:13
Alignment explanation
Indices: 1269914--1269961 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
1269904 CGCAATGTAA
*
1269914 GTCATAAATGCAC
1 GTCATAAATGCGC
*
1269927 GTCATAAATGCGT
1 GTCATAAATGCGC
1269940 GTCATAAATGCGC
1 GTCATAAATGCGC
1269953 GTCATAAAT
1 GTCATAAAT
1269962 TTATGACGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:1269931 original size:85 final size:85
Alignment explanation
Indices: 1269770--1269935 Score: 269
Period size: 85 Copynumber: 2.0 Consensus size: 85
1269760 ATACAATCAC
* * *
1269770 GACACACGAATGTGTGTCATTTTCATTTATGACGGGGGCTTCAATGACATGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
***
1269835 AATGTGTGTCATAAATTTAT
66 AATGCACGTCATAAATTTAT
*
1269855 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
1269920 AATGCACGTCATAAAT
66 AATGCACGTCATAAAT
1269936 GCGTGTCATA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 74 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCACGTCATAAATTTAT
Found at i:1269936 original size:26 final size:26
Alignment explanation
Indices: 1269907--1269961 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1269897 AATGACGCGC
*
1269907 AATGTAAGTCATAAATGCACGTCATA
1 AATGCAAGTCATAAATGCACGTCATA
** *
1269933 AATGCGTGTCATAAATGCGCGTCATA
1 AATGCAAGTCATAAATGCACGTCATA
1269959 AAT
1 AAT
1269962 TTATGACGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (26 bp):
AATGCAAGTCATAAATGCACGTCATA
Found at i:1271401 original size:2 final size:2
Alignment explanation
Indices: 1271394--1271469 Score: 86
Period size: 2 Copynumber: 38.5 Consensus size: 2
1271384 ACATGTTACA
* * *
1271394 AT AT AT AT AT AT AT AT AT -T AT GAGT -T GT GT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT AT AT AT
1271436 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1271470 AATTGGATAA
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
1 3 0.05
2 61 0.92
3 1 0.02
4 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1272746 original size:21 final size:20
Alignment explanation
Indices: 1272686--1272758 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1272676 AAATGACCAA
**
1272686 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGATTTC
*
1272706 CAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACACGA-TTTC
1272726 CAAATTCGCAACACGATTTTC
1 CAAATTCGCAACACGA-TTTC
1272747 CAAATTCGCAAC
1 CAAATTCGCAAC
1272759 GCGAATATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.02
20 28 0.61
21 17 0.37
ACGTcount: A:0.36, C:0.32, G:0.10, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACACGATTTC
Found at i:1272777 original size:20 final size:20
Alignment explanation
Indices: 1272752--1272800 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1272742 TTTTCCAAAT
*
1272752 TCGCAACGCGAATATGTAAA
1 TCGCAACACGAATATGTAAA
* *
1272772 TCGCAACACGAATTTGTAAT
1 TCGCAACACGAATATGTAAA
1272792 TCGCAACAC
1 TCGCAACAC
1272801 AGAAGTCAAA
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:0.37, C:0.24, G:0.16, T:0.22
Consensus pattern (20 bp):
TCGCAACACGAATATGTAAA
Found at i:1273148 original size:12 final size:12
Alignment explanation
Indices: 1273131--1273157 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1273121 TTTCACTTAG
1273131 ATTACTTAGTAA
1 ATTACTTAGTAA
1273143 ATTACTTAGTAA
1 ATTACTTAGTAA
1273155 ATT
1 ATT
1273158 TTCGCATTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (12 bp):
ATTACTTAGTAA
Found at i:1273200 original size:20 final size:20
Alignment explanation
Indices: 1273157--1273200 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1273147 CTTAGTAAAT
* * *
1273157 TTTCGCATTGCGATTTTCAT
1 TTTCGCATTGCGAATTTAAG
*
1273177 TTTCGCGTTGCGAATTTAAG
1 TTTCGCATTGCGAATTTAAG
1273197 TTTC
1 TTTC
1273201 AGAAACTACT
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:0.16, C:0.18, G:0.18, T:0.48
Consensus pattern (20 bp):
TTTCGCATTGCGAATTTAAG
Found at i:1273342 original size:20 final size:19
Alignment explanation
Indices: 1273308--1273360 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1273298 AATCGCAACA
1273308 CGATTTTAATTTCGCATTG
1 CGATTTTAATTTCGCATTG
* *
1273327 CGATTTTCATTTTCGCGTTG
1 CGATTTT-AATTTCGCATTG
*
1273347 CGAATTTAAGTTTC
1 CGATTTTAA-TTTC
1273361 AGAAACTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 8 0.29
20 20 0.71
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (19 bp):
CGATTTTAATTTCGCATTG
Found at i:1274985 original size:63 final size:62
Alignment explanation
Indices: 1274877--1274998 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 62
1274867 AGGTCGGTAC
* * *
1274877 TTTACGTGACGACAATGGTGCATGACATGATGAGGTACGGTCTTTACGTGGTGAGGTAGATGT
1 TTTACGCGACGACAATGGTGCATGACATGATGAGGTAC-GTCTTTACGTGATAAGGTAGATGT
* * * *
1274940 TTTACGCGATGACAATGGTGCTTTACATGGTGAGGTATC-TACTTTACGTGATAAGGTAG
1 TTTACGCGACGACAATGGTGCATGACATGATGAGGTA-CGT-CTTTACGTGATAAGGTAG
1274999 CCGCTCTACG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 48 0.96
64 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (62 bp):
TTTACGCGACGACAATGGTGCATGACATGATGAGGTACGTCTTTACGTGATAAGGTAGATGT
Done.