Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_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: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 20
Found at i:927087 original size:18 final size:18
Alignment explanation
Indices: 927064--927099 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
927054 ACATATCACT
927064 TATGTCCCAAAGGACCAC
1 TATGTCCCAAAGGACCAC
*
927082 TATGTCCCGAAGGACCAC
1 TATGTCCCAAAGGACCAC
927100 ATAGAACCCT
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:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
TATGTCCCAAAGGACCAC
Found at i:928208 original size:101 final size:102
Alignment explanation
Indices: 928033--928238 Score: 405
Period size: 101 Copynumber: 2.0 Consensus size: 102
928023 CACAAATTAC
928033 ATTCGAAAGTTTTCACTGTTCAAGGGGGTATCGATACATTCCTTAATGTATCGGTACACTTTGAA
1 ATTCGAAAGTTTTCACTGTTCAAGGGGGTATCGATACATTCCTTAATGTATCGGTACACTTTGAA
928098 CGTCTTCCCAGATTTTACTCTTGATGTATCAATA-CT
66 CGTCTTCCCAGATTTTACTCTTGATGTATCAATACCT
928134 ATTCGAAAGTTTTCACTGTTCAAGGGGGTATCGATACATTCCTTAATGTATCGGTACACTTTGAA
1 ATTCGAAAGTTTTCACTGTTCAAGGGGGTATCGATACATTCCTTAATGTATCGGTACACTTTGAA
928199 CGTCTTCCCAGATTTTACTCTTGATGTATCAATACCT
66 CGTCTTCCCAGATTTTACTCTTGATGTATCAATACCT
928236 ATT
1 ATT
928239 GAATGTGTAC
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 99 0.95
102 5 0.05
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (102 bp):
ATTCGAAAGTTTTCACTGTTCAAGGGGGTATCGATACATTCCTTAATGTATCGGTACACTTTGAA
CGTCTTCCCAGATTTTACTCTTGATGTATCAATACCT
Found at i:928604 original size:10 final size:10
Alignment explanation
Indices: 928589--928643 Score: 60
Period size: 10 Copynumber: 5.3 Consensus size: 10
928579 CTTGGTGTTT
928589 TAAGCTTATA
1 TAAGCTTATA
928599 TAAGCTT-TA
1 TAAGCTTATA
928608 CTTAAGCTTATA
1 --TAAGCTTATA
928620 TAAGCTT-TA
1 TAAGCTTATA
928629 CTTAAGCTTATA
1 --TAAGCTTATA
928641 TAA
1 TAA
928644 CACCCATAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
9 4 0.10
10 17 0.44
11 14 0.36
12 4 0.10
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (10 bp):
TAAGCTTATA
Found at i:928614 original size:21 final size:21
Alignment explanation
Indices: 928588--928643 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
928578 TCTTGGTGTT
928588 TTAAGCTTATATAAGCTTTAC
1 TTAAGCTTATATAAGCTTTAC
928609 TTAAGCTTATATAAGCTTTAC
1 TTAAGCTTATATAAGCTTTAC
928630 TTAAGCTTATATAA
1 TTAAGCTTATATAA
928644 CACCCATAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (21 bp):
TTAAGCTTATATAAGCTTTAC
Found at i:928615 original size:11 final size:11
Alignment explanation
Indices: 928599--928637 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
928589 TAAGCTTATA
928599 TAAGCTTTACT
1 TAAGCTTTACT
928610 TAAGC-TTA-T
1 TAAGCTTTACT
928619 ATAAGCTTTACT
1 -TAAGCTTTACT
928631 TAAGCTT
1 TAAGCTT
928638 ATATAACACC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 1 0.04
10 8 0.32
11 15 0.60
12 1 0.04
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (11 bp):
TAAGCTTTACT
Found at i:928847 original size:7 final size:7
Alignment explanation
Indices: 928835--928861 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
928825 TTACCATAAT
928835 TCCCTTC
1 TCCCTTC
928842 TCCCTTC
1 TCCCTTC
928849 TCCCTTC
1 TCCCTTC
928856 TCCCTT
1 TCCCTT
928862 TCCATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (7 bp):
TCCCTTC
Found at i:929145 original size:21 final size:24
Alignment explanation
Indices: 929101--929153 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
929091 CCATTAACCT
*
929101 TATACTCATATACAGTCCTCTTTC
1 TATACTCATATACAGTCATCTTTC
929125 TATACTCA-ATACA-T-ATCTTTC
1 TATACTCATATACAGTCATCTTTC
*
929146 -CTACTCAT
1 TATACTCAT
929154 TCTATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 6 0.23
21 6 0.23
22 1 0.04
23 5 0.19
24 8 0.31
ACGTcount: A:0.28, C:0.28, G:0.02, T:0.42
Consensus pattern (24 bp):
TATACTCATATACAGTCATCTTTC
Found at i:931618 original size:18 final size:18
Alignment explanation
Indices: 931595--931630 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
931585 ACATATCACT
931595 TATGTCCCAAATGACCAC
1 TATGTCCCAAATGACCAC
*
931613 TATGTCCCGAATGACCAC
1 TATGTCCCAAATGACCAC
931631 ATAGAACCCT
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:0.31, C:0.33, G:0.14, T:0.22
Consensus pattern (18 bp):
TATGTCCCAAATGACCAC
Found at i:932835 original size:20 final size:20
Alignment explanation
Indices: 932761--932831 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
932751 TGGAGCGTGG
*
932761 GGGGAATCAGTACCCCTTAA
1 GGGGAATCGGTACCCCTTAA
*
932781 CGGGAATCGGTACCCCTTAA
1 GGGGAATCGGTACCCCTTAA
*
932801 GGGGAATCGGTTCCCCTTAA
1 GGGGAATCGGTACCCCTTAA
932821 GGGGAATCGGT
1 GGGGAATCGGT
932832 TCCCTAAGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (20 bp):
GGGGAATCGGTACCCCTTAA
Found at i:935579 original size:21 final size:23
Alignment explanation
Indices: 935549--935609 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
935539 CAGAACCACA
* *
935549 GGGGGTATCGATTCCCC-T-AAG
1 GGGGGAATCGGTTCCCCTTAAAG
935570 GGGGGAATCGGTTCCCCTTCAAAG
1 GGGGGAATCGGTTCCCCTT-AAAG
935594 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
935610 TCATGAAGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 15 0.43
22 1 0.03
24 19 0.54
ACGTcount: A:0.18, C:0.25, G:0.36, T:0.21
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTAAAG
Found at i:942541 original size:3 final size:3
Alignment explanation
Indices: 942523--942596 Score: 94
Period size: 3 Copynumber: 24.3 Consensus size: 3
942513 GGTTGAAAAA
*
942523 ATT ACT ATT AATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
942569 ATT ACT ACT ACT AAT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
942597 CATTATGCAG
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:943514 original size:2 final size:2
Alignment explanation
Indices: 943507--943537 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
943497 TATGTTTTGG
943507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
943538 AACCTAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:944081 original size:30 final size:30
Alignment explanation
Indices: 944047--944139 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
944037 GTCCCTAGAC
*
944047 TTTTTGTTATTGCTATTTTGATCTTTTAAT
1 TTTTTGTTTTTGCTATTTTGATCTTTTAAT
* * * * *
944077 TTTTTGTTTTTGTTATCTT-AGTCATTTGAG
1 TTTTTGTTTTTGCTATTTTGA-TCTTTTAAT
* *
944107 TTTATGTTTTTGCTATTTTGGTCTTTGTAAT
1 TTTTTGTTTTTGCTATTTTGATCTTT-TAAT
944138 TT
1 TT
944140 CAAGTACTTA
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
29 1 0.02
30 42 0.89
31 4 0.09
ACGTcount: A:0.14, C:0.06, G:0.14, T:0.66
Consensus pattern (30 bp):
TTTTTGTTTTTGCTATTTTGATCTTTTAAT
Found at i:944087 original size:60 final size:61
Alignment explanation
Indices: 944022--944139 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 61
944012 GTCCTTTAAG
* * * *
944022 GTTTTTTTTATTTTAGTCCCTAGACTTTTTGTTATTGCTATTTTGATCTTT-TAATTTTTT
1 GTTTTTGTTATCTTAGTCACTAGACTTTATGTTATTGCTATTTTGATCTTTGTAATTTTTT
* * * * *
944082 GTTTTTGTTATCTTAGTCATTTGAGTTTATGTTTTTGCTATTTTGGTCTTTGTAATTT
1 GTTTTTGTTATCTTAGTCACTAGACTTTATGTTATTGCTATTTTGATCTTTGTAATTT
944140 CAAGTACTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
60 42 0.88
61 6 0.12
ACGTcount: A:0.14, C:0.08, G:0.14, T:0.64
Consensus pattern (61 bp):
GTTTTTGTTATCTTAGTCACTAGACTTTATGTTATTGCTATTTTGATCTTTGTAATTTTTT
Found at i:948279 original size:27 final size:25
Alignment explanation
Indices: 948249--948298 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
948239 GGATCAATAT
*
948249 TTTTGTATATGCATTTGCATCTTTTCA
1 TTTTGCATATGCATTT-CAT-TTTTCA
*
948276 TTTTGCATCTGCATTTCATTTTT
1 TTTTGCATATGCATTTCATTTTT
948299 AAGCATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 3 0.14
27 14 0.67
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.58
Consensus pattern (25 bp):
TTTTGCATATGCATTTCATTTTTCA
Found at i:949266 original size:15 final size:15
Alignment explanation
Indices: 949243--949276 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
949233 ATCTATCCCC
*
949243 CCTGTGAATACCTCT
1 CCTGCGAATACCTCT
949258 CCTGCGAATACCTCT
1 CCTGCGAATACCTCT
949273 CCTG
1 CCTG
949277 TGAAGACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.15, T:0.29
Consensus pattern (15 bp):
CCTGCGAATACCTCT
Found at i:953713 original size:18 final size:18
Alignment explanation
Indices: 953692--953730 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
953682 GTTAAAATTT
953692 TTTG-GAATACTATGATTG
1 TTTGAGAATAC-ATGATTG
953710 TTTGAGAATACATGATTG
1 TTTGAGAATACATGATTG
953728 TTT
1 TTT
953731 AGGTTATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.46
Consensus pattern (18 bp):
TTTGAGAATACATGATTG
Found at i:956162 original size:21 final size:21
Alignment explanation
Indices: 956118--956162 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
956108 AAGCAGAAAG
* *
956118 AAAAGCAAAGAACAAAGATTA
1 AAAAGAAAAGAACAAAGATGA
956139 AAAAGAAAAGAAGCAAAGA-GA
1 AAAAGAAAAGAA-CAAAGATGA
956160 AAA
1 AAA
956163 TAAACAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.71, C:0.07, G:0.18, T:0.04
Consensus pattern (21 bp):
AAAAGAAAAGAACAAAGATGA
Found at i:957680 original size:126 final size:127
Alignment explanation
Indices: 957455--957764 Score: 525
Period size: 126 Copynumber: 2.5 Consensus size: 127
957445 TGAAACCAAA
* * * * *
957455 ACCCTTAGATAGCCAAGACTCATGAATAGATGATCGGTGTCATCACCTGACCAGATC-TCATCAT
1 ACCCTTAGATGGCCAAGACTCATGAACATATGAGCAGTGTCATCACCTGACCAGATCTTCATCAT
957519 TATGTAGGAGCTGTGTCAACTCAGATAACCAGCCGTCCCAAGCAGAGTGGAACCGTGTTATC
66 TATGTAGGAGCTGTGTCAACTCAGATAACCAGCCGTCCCAAGCAGAGTGGAACCGTGTTATC
957581 ACCCTTAGATGGCCAAGACTCATGAACATATGAGCAGTGTCATCACCTGACCAGATCTTC-TCAT
1 ACCCTTAGATGGCCAAGACTCATGAACATATGAGCAGTGTCATCACCTGACCAGATCTTCATCAT
* *
957645 TATGTAGGAGGTGTGTCAACTCAGATAACCAGCCGTCCCCAGCAGAGTGGAACCGTGTTATC
66 TATGTAGGAGCTGTGTCAACTCAGATAACCAGCCGTCCCAAGCAGAGTGGAACCGTGTTATC
* *
957707 ACCTTTACATGGCCAAGACTCATGAACATATGAGCAGTGTCATCACCTGACCAGATCT
1 ACCCTTAGATGGCCAAGACTCATGAACATATGAGCAGTGTCATCACCTGACCAGATCT
957765 CCTTATCGCG
Statistics
Matches: 174, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
126 172 0.99
127 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (127 bp):
ACCCTTAGATGGCCAAGACTCATGAACATATGAGCAGTGTCATCACCTGACCAGATCTTCATCAT
TATGTAGGAGCTGTGTCAACTCAGATAACCAGCCGTCCCAAGCAGAGTGGAACCGTGTTATC
Found at i:957854 original size:47 final size:47
Alignment explanation
Indices: 957791--957926 Score: 200
Period size: 47 Copynumber: 2.9 Consensus size: 47
957781 CCATGTCAAC
* *
957791 CCTAGATAACCAAGACTTATCATAATATAAGCAGTGTTATCACCCTT
1 CCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTT
* * *
957838 CCTAGATAACCAAGACTTATCATAGCATGAGCAGTGTTAGCACCTTT
1 CCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTT
** *
957885 CCTAGATGGCCAAGACTTATCATAGTATGAGCAGTGTCATCA
1 CCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCA
957927 ACCGACCTGA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 79 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (47 bp):
CCTAGATAACCAAGACTTATCATAGTATGAGCAGTGTTATCACCCTT
Found at i:958222 original size:3 final size:3
Alignment explanation
Indices: 958209--958289 Score: 126
Period size: 3 Copynumber: 26.7 Consensus size: 3
958199 AAAATTATAC
958209 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
958255 TAT TAT TAT TAT TAT TAT TAC TAA TAT TAT AAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
958290 CATTATGCAG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:961783 original size:21 final size:21
Alignment explanation
Indices: 961757--961796 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
961747 AAACAATTGG
961757 TAACAATTAATATCATTTTGT
1 TAACAATTAATATCATTTTGT
* *
961778 TAACAATTGATATCTTTTT
1 TAACAATTAATATCATTTT
961797 CATTAAACAT
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:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (21 bp):
TAACAATTAATATCATTTTGT
Found at i:962044 original size:21 final size:21
Alignment explanation
Indices: 962018--962096 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
962008 AGGGTGTCAA
962018 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTAC
962039 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTAC
* * **
962061 TAGTGCATCGATGCA-CCATGT
1 -AGTGCATCCATGCACCCCTAC
962082 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
962097 TCCATTTCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 14 0.29
21 16 0.33
22 3 0.06
23 15 0.31
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:967362 original size:58 final size:58
Alignment explanation
Indices: 967292--967402 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 58
967282 AAATTTATAC
* * * * *
967292 AATAACATATTTGATCCTCATTATTTTTATATTCTATTAATTTAGCCATAATTAGTAT
1 AATAACACATTTGATCCTCATTATTTATACATCCTATCAATTTAGCCATAATTAGTAT
** * *
967350 AATAACACATTTGATTGTTATTATTTATACATCCTATCAATTTAGTCATAATT
1 AATAACACATTTGATCCTCATTATTTATACATCCTATCAATTTAGCCATAATT
967403 TTAATTAGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (58 bp):
AATAACACATTTGATCCTCATTATTTATACATCCTATCAATTTAGCCATAATTAGTAT
Found at i:969070 original size:24 final size:26
Alignment explanation
Indices: 969043--969105 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
969033 ATCTCGACAC
969043 AAAAATAT-TGTTTT-ACTATAAATT
1 AAAAATATATGTTTTAACTATAAATT
*
969067 AAAAATATAT-TATTTAATTATAAATT
1 AAAAATATATGT-TTTAACTATAAATT
*
969093 AAAAATATGTGTT
1 AAAAATATATGTT
969106 CATGTATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 9 0.27
25 4 0.12
26 19 0.58
27 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (26 bp):
AAAAATATATGTTTTAACTATAAATT
Found at i:971165 original size:16 final size:16
Alignment explanation
Indices: 971141--971171 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
971131 AAAGTTAAAT
*
971141 AATAGAAATAAAATGC
1 AATAAAAATAAAATGC
971157 AATAAAAATAAAATG
1 AATAAAAATAAAATG
971172 TTAGTATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.03, G:0.10, T:0.19
Consensus pattern (16 bp):
AATAAAAATAAAATGC
Found at i:971638 original size:104 final size:103
Alignment explanation
Indices: 971347--971658 Score: 412
Period size: 103 Copynumber: 3.0 Consensus size: 103
971337 AGTTAGCGGC
*
971347 TAGTGGTTAACAGAGTCCGAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGT
1 TAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATA-CCCGGATCGGGTCACCACAAGGT
* *
971412 CGAATCGAATAATTCAAACAAATATATATATATATAAA-
65 CGAATCGAATAATTCAAACAAATATATATAAATAAAAAT
* * *
971450 TAGTGGTTAGCAGGGTCCGAACCATAATAATGTGTATCATACCTCGGATCTGGTCACCACAAGGT
1 TAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACC-CGGATCGGGTCACCACAAGGT
* *
971515 CGAATTGAATAATTCAAACAAATATATATAAAAAAAAAT
65 CGAATCGAATAATTCAAACAAATATATATAAATAAAAAT
* ** * **
971554 TAGTGGTTAGTAGAGTCTAAACCATAGTAACATGGATCATACCCGAGATCGGGTCACCACAAGGT
1 TAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCG-GATCGGGTCACCACAAGGT
* * *
971619 CGAATCGAAT-ATTAGAAACAATAAATAAATAAATAAAAAT
65 CGAATCGAATAATT-CAAACAA-ATATATATAAATAAAAAT
971659 GGTTAAAGTG
Statistics
Matches: 182, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
102 2 0.01
103 97 0.53
104 68 0.37
105 15 0.08
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (103 bp):
TAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCATACCCGGATCGGGTCACCACAAGGTC
GAATCGAATAATTCAAACAAATATATATAAATAAAAAT
Found at i:973232 original size:139 final size:139
Alignment explanation
Indices: 972972--973427 Score: 538
Period size: 139 Copynumber: 3.3 Consensus size: 139
972962 TTGGATATAA
* * * * * *
972972 TTTGTAGACAACACGGCTCCTTCGTGATGAGGAAGTTTGGTTATATAAGGATGACGTTGCTCCTA
1 TTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATATGAGGATGACGCTGCTCCTA
* * * * * *
973037 CGCGTTGAGGAGATCTGGTTGGTGGATGACGTTGTTCCTACGTGATGAGGATGTCTAGCCATCAT
66 CGCGTTGAGGAGATCTGATCGGTGGAAGACATTGTTCCTACGTGATGAGGACGTCTAACCATCAT
*
973102 TAAGGATAC
131 TAGGGATAC
* * *
973111 TTTGGAGACAACACGGTTCCTACGTGATAAGGAAGTCTGGTTATTTGAGGATGACGGTGCTCCTA
1 TTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATATGAGGATGACGCTGCTCCTA
* * * * * *
973176 CACGTT-ACGGAGATCTGATCGATGGAAGACATTGTTCCTTCGTGATAAGGACGTCTAATCATCT
66 CGCGTTGA-GGAGATCTGATCGGTGGAAGACATTGTTCCTACGTGATGAGGACGTCTAACCATCA
973240 TTAGGGATAC
130 TTAGGGATAC
* * * *
973250 TTTGGAGACAACACGGTTCCTATGTGATGAGGAAGTCTAGTTATCTGAGGATGACACTGCTCCTA
1 TTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATATGAGGATGACGCTGCTCCTA
* * ** * ***
973315 TGCATTGAGGAGATCT-AGTCGGTGGTCGACATTGTTCCTACGTGATGAGGACGTCTATCTGCCA
66 CGCGTTGAGGAGATCTGA-TCGGTGGAAGACATTGTTCCTACGTGATGAGGACGTCTAACCATCA
973379 TTAGGGATAC
130 TTAGGGATAC
* * * *
973389 TTTGAAAACAATACAGTTCCTACGTGATGAGGAAGTCTG
1 TTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTG
973428 ATTGTCTGGA
Statistics
Matches: 267, Mismatches: 47, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
138 2 0.01
139 264 0.99
140 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (139 bp):
TTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATATGAGGATGACGCTGCTCCTA
CGCGTTGAGGAGATCTGATCGGTGGAAGACATTGTTCCTACGTGATGAGGACGTCTAACCATCAT
TAGGGATAC
Found at i:973791 original size:104 final size:104
Alignment explanation
Indices: 973674--973974 Score: 365
Period size: 104 Copynumber: 2.9 Consensus size: 104
973664 CATTTCAAAA
* * * *
973674 GAAAATTGTCTCAAGCGAGATGAAATTTGTTTTTAAGAAAAACAATCTAAAATGTTATCAATTTT
1 GAAAACTGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAACAATCTCAAATGATATCAATTTT
973739 GTTTCAAGTGAAACAATTTCTAAATTTTGTGTTTTGAGG
66 GTTTCAAGTGAAACAATTTCTAAATTTTGTGTTTTGAGG
* * *
973778 GAAAACTGTCTCAAGCGAGACAAAATTTATTTTTAAGAAAAACAATCTCAAATGCTATCAATTTT
1 GAAAACTGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAACAATCTCAAATGATATCAATTTT
*** * *
973843 GTTTCAAGTGAAATTTTTTTTCAGAA-TTTGTGTTTTGAAG
66 GTTTCAAGTGAAACAATTTCT-A-AATTTTGTGTTTTGAGG
** * * ** *
973883 GACGACTGTCTCAAGCGAGACGAAATTTG-TTTTGAGAGAAAC-ATGCTCAAATGAGGTAAATTT
1 GAAAACTGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAACAAT-CTCAAATGATATCAATTT
* *
973946 TATTTCAAGTGAAACAATTTCAAAATTTT
65 TGTTTCAAGTGAAACAATTTCTAAATTTT
973975 TATTTCTAGG
Statistics
Matches: 166, Mismatches: 27, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
102 2 0.01
103 6 0.04
104 117 0.70
105 39 0.23
106 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (104 bp):
GAAAACTGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAACAATCTCAAATGATATCAATTTT
GTTTCAAGTGAAACAATTTCTAAATTTTGTGTTTTGAGG
Found at i:976280 original size:25 final size:23
Alignment explanation
Indices: 976220--976287 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 23
976210 TTTTATTTTC
* *
976220 AAAATTTTGAAAATATCAATTAAA
1 AAAATTTTGAAAAAAT-ATTTAAA
*
976244 AGAATTTT-AAAAAATATTTAATCA
1 AAAATTTTGAAAAAATATTTAA--A
976268 AAAATTTTGAAAAAAATATT
1 AAAATTTTG-AAAAAATATT
976288 ACGCCTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 5 0.14
23 6 0.17
24 15 0.42
26 10 0.28
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (23 bp):
AAAATTTTGAAAAAATATTTAAA
Found at i:977184 original size:13 final size:12
Alignment explanation
Indices: 977154--977221 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 12
977144 TCTTTCTTCT
*
977154 TTTTTCTCTTTT
1 TTTTTCTCTTTC
*
977166 TTTTTCTTATTTC
1 TTTTTC-TCTTTC
*
977179 TCTTTCCTCTTTC
1 T-TTTTCTCTTTC
*
977192 TTTTTCTTTTTC
1 TTTTTCTCTTTC
* *
977204 -TTTGCTCTTTT
1 TTTTTCTCTTTC
977215 TTTTTCT
1 TTTTTCT
977222 TTTTTTCTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
11 8 0.19
12 20 0.47
13 11 0.26
14 4 0.09
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.76
Consensus pattern (12 bp):
TTTTTCTCTTTC
Found at i:977221 original size:42 final size:43
Alignment explanation
Indices: 977140--977250 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 43
977130 TAATTTGTTT
* *
977140 TCTTTCTTTCTTCTTTTTTCTCTT-TTTTTTTCTTATTTCTCTTTCC
1 TCTTTCTTT-TTC-TTTTTCT-TTGCTCTTTTCTTATTTCT-TTTCC
**
977186 TCTTTCTTTTTCTTTTTCTTTGCTCTTTT-TT-TTTCTTTTTT
1 TCTTTCTTTTTCTTTTTCTTTGCTCTTTTCTTATTTCTTTTCC
*
977227 TCTTTGTTTTTTCTTTTTCCTTTG
1 TCTTT-CTTTTTCTTTTT-CTTTG
977251 ATTTGATCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
41 8 0.14
42 16 0.28
43 9 0.16
44 12 0.21
45 3 0.05
46 9 0.16
ACGTcount: A:0.01, C:0.20, G:0.03, T:0.77
Consensus pattern (43 bp):
TCTTTCTTTTTCTTTTTCTTTGCTCTTTTCTTATTTCTTTTCC
Found at i:977224 original size:7 final size:7
Alignment explanation
Indices: 977142--977249 Score: 57
Period size: 7 Copynumber: 16.0 Consensus size: 7
977132 ATTTGTTTTC
977142 TTTCTTT
1 TTTCTTT
*
977149 CTTCTTT
1 TTTCTTT
*
977156 TTTC-TC
1 TTTCTTT
977162 TTT-TTT
1 TTTCTTT
*
977168 TTTCTTA
1 TTTCTTT
*
977175 TTTC-TC
1 TTTCTTT
* *
977181 TTTCCTC
1 TTTCTTT
977188 TTTC-TT
1 TTTCTTT
977194 TTTC-TT
1 TTTCTTT
977200 TTTCTTT
1 TTTCTTT
**
977207 GCTCTTT
1 TTTCTTT
977214 TTT-TTT
1 TTTCTTT
*
977220 CTTTTTTT
1 -TTTCTTT
*
977228 CTTTGTTT
1 -TTTCTTT
977236 TTTCTTT
1 TTTCTTT
*
977243 TTCCTTT
1 TTTCTTT
977250 GATTTGATCT
Statistics
Matches: 81, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
6 27 0.33
7 44 0.54
8 10 0.12
ACGTcount: A:0.01, C:0.19, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTCTTT
Found at i:977236 original size:11 final size:12
Alignment explanation
Indices: 977188--977242 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
977178 CTCTTTCCTC
*
977188 TTTCTTTTTCTT
1 TTTCTTTGTCTT
977200 TTTCTTTGCTCTT
1 TTTCTTTG-TCTT
* * *
977213 TTTTTTTCTTTT
1 TTTCTTTGTCTT
977225 TTTCTTTGT-TT
1 TTTCTTTGTCTT
977236 TTTCTTT
1 TTTCTTT
977243 TTCCTTTGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.25
12 17 0.47
13 10 0.28
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.82
Consensus pattern (12 bp):
TTTCTTTGTCTT
Found at i:977238 original size:19 final size:19
Alignment explanation
Indices: 977137--977244 Score: 87
Period size: 19 Copynumber: 5.5 Consensus size: 19
977127 AATTAATTTG
*
977137 TTTTCTTTCTTTC-TTCTT
1 TTTTCTTTTTTTCTTTCTT
977155 TTTTCTCTTTTTT-TTTCTT
1 TTTTCT-TTTTTTCTTTCTT
* **
977174 ATTTCTCTTTCCTCTTTC-T
1 TTTTCT-TTTTTTCTTTCTT
*
977193 TTTTCTTTTTCTTTGCTCTTTTT
1 TTTTC-TTTT-TTT-CT-TTCTT
*
977216 TTTTCTTTTTTTCTTTGTT
1 TTTTCTTTTTTTCTTTCTT
977235 TTTTCTTTTT
1 TTTTCTTTTT
977245 CCTTTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 15
0.75 0.09 0.15
Matches are distributed among these distances:
18 6 0.08
19 42 0.58
20 8 0.11
21 5 0.07
22 6 0.08
23 6 0.08
ACGTcount: A:0.01, C:0.19, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTCTTTTTTTCTTTCTT
Found at i:977250 original size:18 final size:19
Alignment explanation
Indices: 977210--977250 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
977200 TTTCTTTGCT
*
977210 CTTT-TTTTTTCTTTTTTT
1 CTTTGTTTTTTCTTTTTTC
977228 CTTTGTTTTTTC-TTTTTC
1 CTTTGTTTTTTCTTTTTTC
977246 CTTTG
1 CTTTG
977251 ATTTGATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (19 bp):
CTTTGTTTTTTCTTTTTTC
Found at i:977261 original size:48 final size:49
Alignment explanation
Indices: 977160--977261 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 49
977150 TTCTTTTTTC
* ** *
977160 TCTTTTTTTTTCTTATTTCTCTTTCCTCTTTCTTTTTCTTTTTCTTTGC
1 TCTTTTTTTTTCTTATTTCTCTTTCCTCTTTCTTTTTCCTTTGATTTGA
* ** *
977209 TCTTTTTTTTTCTT-TTTTTCTTTGTTTTTTCTTTTTCCTTTGATTTGA
1 TCTTTTTTTTTCTTATTTCTCTTTCCTCTTTCTTTTTCCTTTGATTTGA
977257 TCTTT
1 TCTTT
977262 GCACTTTGCA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 31 0.69
49 14 0.31
ACGTcount: A:0.03, C:0.18, G:0.04, T:0.75
Consensus pattern (49 bp):
TCTTTTTTTTTCTTATTTCTCTTTCCTCTTTCTTTTTCCTTTGATTTGA
Found at i:982027 original size:114 final size:116
Alignment explanation
Indices: 981837--982047 Score: 272
Period size: 114 Copynumber: 1.8 Consensus size: 116
981827 AATAAAATAT
* * *
981837 AATAAAATAAATAAAAAAAGTTAGTGGTTAACAGAGTCTGAACCATAATAAAGTGAATCATACCT
1 AATAAAAAAAATAAAAAAAGTTAGTAGTTAACAGAGTCTGAACCATAATAAAGTGAATCATACCC
* *
981902 CGGATATGGTCACTACAA-ATCGAATCAAATAATTCAAACAAATATATAAA
66 CGAATATGGTCACCACAATATCGAATCAAATAATTCAAACAAATATATAAA
*
981952 AATAAAAAAAAT-AAAAAAGTTAGTAGTTAGCAGAGT-TCGAACCATAATAATA-T-AGATCATA
1 AATAAAAAAAATAAAAAAAGTTAGTAGTTAACAGAGTCT-GAACCATAATAA-AGTGA-ATCATA
* *
982013 CCCCGAATCA-GGTCACCACAATGTCGAATCGAATA
63 CCCCGAAT-ATGGTCACCACAATATCGAATCAAATA
982048 TTAGAAACAA
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
113 2 0.02
114 57 0.69
115 24 0.29
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (116 bp):
AATAAAAAAAATAAAAAAAGTTAGTAGTTAACAGAGTCTGAACCATAATAAAGTGAATCATACCC
CGAATATGGTCACCACAATATCGAATCAAATAATTCAAACAAATATATAAA
Found at i:982079 original size:114 final size:114
Alignment explanation
Indices: 981824--982079 Score: 258
Period size: 114 Copynumber: 2.2 Consensus size: 114
981814 ACAAATATAT
*
981824 ATAAATAAAATATAATAAAATAAATAAAAAAAGTTAGTGGTTAACAGAGTCTGAACCATAATAAA
1 ATAAAT-AAATA-AAT-AAAT-AAT-AAAAAAGTTAGTAGTTAACAGAGTCTGAACCATAATAAA
* * *
981889 GTGAATCATACCTCGGATATGGTCACTACAAATCGAATCAAATAATTCAAACAA
61 GTGAATCATACCCCGAATATGGTCACCACAAATCGAATCAAATAATTCAAACAA
* *
981943 ATATATAAAAATAAA-AAA-AATAAAAAAGTTAGTAGTTAGCAGAGT-TCGAACCATAATAATA-
1 ATA-A-ATAAATAAATAAATAATAAAAAAGTTAGTAGTTAACAGAGTCT-GAACCATAATAA-AG
* * *
982004 T-AGATCATACCCCGAATCA-GGTCACCACAATGTCGAATCGAAT-ATTAGAAAC-A
62 TGA-ATCATACCCCGAAT-ATGGTCACCACAA-ATCGAATCAAATAATT-CAAACAA
982057 ATAAATAAATAAATAAATAATAA
1 ATAAATAAATAAATAAATAATAA
982080 TGGTTAAAGT
Statistics
Matches: 117, Mismatches: 10, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
112 8 0.07
113 6 0.05
114 69 0.59
115 19 0.16
117 3 0.03
119 5 0.04
120 6 0.05
121 1 0.01
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.24
Consensus pattern (114 bp):
ATAAATAAATAAATAAATAATAAAAAAGTTAGTAGTTAACAGAGTCTGAACCATAATAAAGTGAA
TCATACCCCGAATATGGTCACCACAAATCGAATCAAATAATTCAAACAA
Found at i:987936 original size:14 final size:13
Alignment explanation
Indices: 987907--987933 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
987897 AAATTTTAAG
987907 ATTTTCTTTGAAA
1 ATTTTCTTTGAAA
987920 ATTTTCTTTGAAA
1 ATTTTCTTTGAAA
987933 A
1 A
987934 ATTACTCCCC
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:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTTTCTTTGAAA
Found at i:991415 original size:21 final size:22
Alignment explanation
Indices: 991376--991418 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
991366 GATTCAAAGA
*
991376 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTACCCTGCTAC
991398 AGGGAACCGA-TACCCTGCTAC
1 AGGGAACCGATTACCCTGCTAC
991419 GGTACTGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.26, C:0.35, G:0.23, T:0.16
Consensus pattern (22 bp):
AGGGAACCGATTACCCTGCTAC
Found at i:992198 original size:24 final size:24
Alignment explanation
Indices: 992171--992256 Score: 86
Period size: 24 Copynumber: 3.7 Consensus size: 24
992161 CACCACAGCT
*
992171 CGTATAAATTGCACCGAAGTACCA
1 CGTAGAAATTGCACCGAAGTACCA
* * * **
992195 CGTAGAATTTGTACCGAAGGACTG
1 CGTAGAAATTGCACCGAAGTACCA
* *
992219 CATAG-AATTGCACCGAAGTGCCA
1 CGTAGAAATTGCACCGAAGTACCA
992242 CGTAGAAA-TGCACCG
1 CGTAGAAATTGCACCG
992257 TAGTGCCATA
Statistics
Matches: 47, Mismatches: 14, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
23 23 0.49
24 24 0.51
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (24 bp):
CGTAGAAATTGCACCGAAGTACCA
Found at i:992203 original size:23 final size:23
Alignment explanation
Indices: 992177--992256 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
992167 AGCTCGTATA
992177 AATTGCACCGAAGTACCACGTAG
1 AATTGCACCGAAGTACCACGTAG
* * ** *
992200 AATTTGTACCGAAGGACTGCATAG
1 AA-TTGCACCGAAGTACCACGTAG
*
992224 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTACCACGTAG
*
992247 AAATGCACCG
1 AATTGCACCG
992257 TAGTGCCATA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
23 26 0.59
24 18 0.41
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTACCACGTAG
Found at i:992261 original size:23 final size:23
Alignment explanation
Indices: 992171--992264 Score: 73
Period size: 23 Copynumber: 4.0 Consensus size: 23
992161 CACCACAGCT
* *
992171 CGTATAAATTGCACCGAAGTACCA
1 CGTAGAAA-TGCACCGAAGTGCCA
* * **
992195 CGTAGAATTTGTACCGAAG-GACTG
1 CGTAGAA-ATGCACCGAAGTG-CCA
* *
992219 CATAGAATTGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
992242 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
992265 TATAAGATTT
Statistics
Matches: 54, Mismatches: 13, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
23 31 0.57
24 23 0.43
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:992408 original size:23 final size:23
Alignment explanation
Indices: 992378--992421 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
992368 AATACATATA
992378 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
992401 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCGAAGGACCACGTAGA
992422 CCCTAAGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:997500 original size:81 final size:81
Alignment explanation
Indices: 997360--997517 Score: 280
Period size: 81 Copynumber: 2.0 Consensus size: 81
997350 CATCTTCATT
* *
997360 ATTTGAGTCACTCTCATCTTTAGTGGATTTTAGAGAAACCCTAATATTTTTCTTCTTTTCCATTT
1 ATTTGAGTCACTCTCATCTTTAGTGGATTTTAGAGAAACCCTAATATTTTTCCTATTTTCCATTT
*
997425 CCTTCTTTTCTTTATC
66 CCTTATTTTCTTTATC
*
997441 ATTTGAGTCACTCTCATCTTTAGTGGATTTTAGAGCAACCCTAATATTTTTCCTATTTTCCATTT
1 ATTTGAGTCACTCTCATCTTTAGTGGATTTTAGAGAAACCCTAATATTTTTCCTATTTTCCATTT
997506 CCTTATTTTCTT
66 CCTTATTTTCTT
997518 CATCTTTCTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.20, C:0.21, G:0.09, T:0.50
Consensus pattern (81 bp):
ATTTGAGTCACTCTCATCTTTAGTGGATTTTAGAGAAACCCTAATATTTTTCCTATTTTCCATTT
CCTTATTTTCTTTATC
Found at i:997547 original size:15 final size:15
Alignment explanation
Indices: 997511--997543 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
997501 CATTTCCTTA
997511 TTTTCTTCATCTTTC
1 TTTTCTTCATCTTTC
*
997526 TTTTCTTGATC-TTC
1 TTTTCTTCATCTTTC
997540 TTTT
1 TTTT
997544 TCTTTTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.06, C:0.21, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTCTTCATCTTTC
Found at i:1001884 original size:2 final size:2
Alignment explanation
Indices: 1001877--1001918 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1001867 TAAGAGCTCA
1001877 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1001918 A
1 A
1001919 AAAAAATAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1001949 original size:6 final size:6
Alignment explanation
Indices: 1001940--1002003 Score: 60
Period size: 6 Copynumber: 10.2 Consensus size: 6
1001930 ATGAATAAAC
1001940 AGAAAA AGAAAGA AGAAAA AGAAAAAA AGGAAAA TAG-AAA A-AAAA AGAAAA
1 AGAAAA AGAAA-A AGAAAA AG--AAAA A-GAAAA -AGAAAA AGAAAA AGAAAA
*
1001991 AGAAAA TGAAAA A
1 AGAAAA AGAAAA A
1002004 AATGTGATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
5 5 0.10
6 26 0.53
7 11 0.22
8 6 0.12
9 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:1001962 original size:9 final size:9
Alignment explanation
Indices: 1001948--1001994 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 9
1001938 ACAGAAAAAG
1001948 AAAGAAGAA
1 AAAGAAGAA
1001957 AAAGAA-AA
1 AAAGAAGAA
1001965 AAAG--GAA
1 AAAGAAGAA
1001972 AATAGAA-AA
1 AA-AGAAGAA
1001981 AAA-AAGAA
1 AAAGAAGAA
1001989 AAAGAA
1 AAAGAA
1001995 AATGAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
7 6 0.19
8 14 0.44
9 12 0.38
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:1001967 original size:22 final size:22
Alignment explanation
Indices: 1001940--1002005 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
1001930 ATGAATAAAC
*
1001940 AGAAAAAGAAAGAAGAAAAAGAA
1 AGAAAAAGAAA-AAGAAAAAAAA
*
1001963 A-AAAAGGAAAATAGAAAAAAAA
1 AGAAAAAGAAAA-AGAAAAAAAA
*
1001985 AGAAAAAGAAAATGAAAAAAA
1 AGAAAAAGAAAAAGAAAAAAA
1002006 TGTGATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.03
22 26 0.70
23 10 0.27
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (22 bp):
AGAAAAAGAAAAAGAAAAAAAA
Found at i:1001980 original size:16 final size:15
Alignment explanation
Indices: 1001918--1001996 Score: 65
Period size: 15 Copynumber: 5.3 Consensus size: 15
1001908 TATATATTAT
*
1001918 AAAAAAATAG-AAATG
1 AAAAAAA-AGAAAAAG
* *
1001933 AATAAACAGAAAAAG
1 AAAAAAAAGAAAAAG
*
1001948 --AAAGAAGAAAAAG
1 AAAAAAAAGAAAAAG
*
1001961 AAAAAAAGGAAAATAG
1 AAAAAAAAGAAAA-AG
1001977 AAAAAAAAAGAAAAAG
1 -AAAAAAAAGAAAAAG
1001993 AAAA
1 AAAA
1001997 TGAAAAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
13 10 0.20
14 2 0.04
15 22 0.44
16 4 0.08
17 12 0.24
ACGTcount: A:0.78, C:0.01, G:0.15, T:0.05
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:1002599 original size:47 final size:47
Alignment explanation
Indices: 1002441--1002599 Score: 218
Period size: 47 Copynumber: 3.5 Consensus size: 47
1002431 GTAAGTATGC
* **
1002441 AAATAAGTTTACGAGCTTATG-AA--T-AATGACAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGAAATTTAAATGGTAAGTATATTGATA
* * *
1002484 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATGTTGCTA
1 AAATAAGCTTACGAGCTTATGAAATTTAAATGGTAAGTATATTGATA
* *
1002531 AAATAAGCTTACGAGCTTATGAAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGAAATTTAAATGGTAAGTATATTGATA
1002578 AAATAAGCTTACGAGCTTATGA
1 AAATAAGCTTACGAGCTTATGA
1002600 GATAAATGAT
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
43 20 0.19
44 2 0.02
46 1 0.01
47 81 0.78
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTATGAAATTTAAATGGTAAGTATATTGATA
Found at i:1003618 original size:6 final size:6
Alignment explanation
Indices: 1003602--1003661 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
1003592 AACAGAAATG
* *
1003602 AAGAAA CAGAAA AAG-AA AAG-AA AAGAAA ATAGAAA AA-AAA ATGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA
* *
1003648 ATGAAA ATGAAA AA
1 AAGAAA AAGAAA AA
1003662 AAATGAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
5 14 0.30
6 27 0.57
7 6 0.13
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.07
Consensus pattern (6 bp):
AAGAAA
Found at i:1003624 original size:17 final size:16
Alignment explanation
Indices: 1003602--1003674 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 16
1003592 AACAGAAATG
1003602 AAGAAACAGAAAAAGAA
1 AAGAAA-AGAAAAAGAA
1003619 AAGAAAAGAAAATAGAA
1 AAGAAAAGAAAA-AGAA
* *
1003636 AAAAAAATGAAAATGAA
1 AAGAAAA-GAAAAAGAA
*
1003653 AATGAAAA-AAAATGAA
1 AA-GAAAAGAAAAAGAA
1003669 AA-AAAA
1 AAGAAAA
1003675 TGAGAGATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
14 4 0.08
16 16 0.32
17 21 0.42
18 9 0.18
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.07
Consensus pattern (16 bp):
AAGAAAAGAAAAAGAA
Found at i:1003635 original size:12 final size:11
Alignment explanation
Indices: 1003612--1003677 Score: 84
Period size: 10 Copynumber: 6.1 Consensus size: 11
1003602 AAGAAACAGA
1003612 AAAAGAAAA-G
1 AAAAGAAAATG
1003622 AAAAGAAAATAG
1 AAAAGAAAAT-G
*
1003634 AAAAAAAAATG
1 AAAAGAAAATG
1003645 AAAATGAAAATG
1 AAAA-GAAAATG
1003657 AAAA-AAAATG
1 AAAAGAAAATG
1003667 AAAA-AAAATG
1 AAAAGAAAATG
1003677 A
1 A
1003678 GAGATGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
10 26 0.51
11 5 0.10
12 20 0.39
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (11 bp):
AAAAGAAAATG
Found at i:1003635 original size:23 final size:22
Alignment explanation
Indices: 1003609--1003675 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 22
1003599 ATGAAGAAAC
1003609 AGAAAAAGAAAAGAAAAGAAAAT
1 AGAAAAA-AAAAGAAAAGAAAAT
1003632 AGAAAAAAAAATGAAAATGAAAAT
1 AGAAAAAAAAA-GAAAA-GAAAAT
*
1003656 -GAAAAAAAATGAAAA-AAAAT
1 AGAAAAAAAAAGAAAAGAAAAT
1003676 GAGAGATGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
20 5 0.12
22 9 0.22
23 21 0.51
24 6 0.15
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (22 bp):
AGAAAAAAAAAGAAAAGAAAAT
Found at i:1003675 original size:10 final size:10
Alignment explanation
Indices: 1003597--1003677 Score: 74
Period size: 10 Copynumber: 7.6 Consensus size: 10
1003587 AAAAAAACAG
*
1003597 AAATGAAGAA
1 AAATGAAAAA
*
1003607 ACA-GAAAAA
1 AAATGAAAAA
*
1003616 GAAAAGAAAAGA
1 -AAATGAAAA-A
1003628 AAATAGAAAAAA
1 AAAT-G-AAAAA
1003640 AAATGAAAATGA
1 AAATGAAAA--A
1003652 AAATGAAAAA
1 AAATGAAAAA
1003662 AAATGAAAAA
1 AAATGAAAAA
1003672 AAATGA
1 AAATGA
1003678 GAGATGAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
9 5 0.08
10 25 0.42
11 9 0.15
12 17 0.28
13 4 0.07
ACGTcount: A:0.75, C:0.01, G:0.15, T:0.09
Consensus pattern (10 bp):
AAATGAAAAA
Found at i:1007590 original size:15 final size:15
Alignment explanation
Indices: 1007570--1007607 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1007560 AATCTACAAA
1007570 AATATTATTATTATT
1 AATATTATTATTATT
1007585 AATATTATTATTATT
1 AATATTATTATTATT
1007600 ACATATTA
1 A-ATATTA
1007608 CATTTTACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATTATTATTATT
Found at i:1008917 original size:20 final size:21
Alignment explanation
Indices: 1008894--1008933 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1008884 ATATCTTTGT
1008894 ATTTAATAGTA-ATTTTCAAC
1 ATTTAATAGTATATTTTCAAC
* *
1008914 ATTTACTCGTATATTTTCAA
1 ATTTAATAGTATATTTTCAA
1008934 GTTTCTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTTAATAGTATATTTTCAAC
Found at i:1015067 original size:236 final size:231
Alignment explanation
Indices: 1014655--1015186 Score: 736
Period size: 236 Copynumber: 2.3 Consensus size: 231
1014645 CTTATTCATA
* *
1014655 TATTGAATAAAAATA-TTTTTTACTATTTCGGGTC-G-GGTCGGGTTTCTAATTCATACATTCGG
1 TATTGAATAAAAATATTTTTTTATTATTTC-GGTCGGTGGTCGGGTTTCTAATTCATATATTCGG
* *
1014717 GTCGGGTCGGGTCGAGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGA
65 GTCGGGTCGGGTCGAGGTTTTTTAAGTGTGATATTCAGGTC-GG-CGAGTTCGGGTTTAGGGTGA
* *
1014782 AAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAC
128 AAAAAACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAC
* * *
1014847 CCCTCTATATATAATTTTTTTCAATTAAATCACTTTTTT
193 CCCTCTATATATAATTTTTTTCAATTAAATAAATGTTTT
*
1014886 TATTGAATAAAAATAATTTTTTTATTATTTCTGGTCGGGTTTGGTCGGATTTCTAATTCATATAT
1 TATTGAATAAAAAT-ATTTTTTTATTATTTC-GGTC-GG--TGGTCGGGTTTCTAATTCATATAT
*
1014951 TCGGTTCGGGTCGGGTC-AGGTTTTTTAAGTGTGATATTCAGGTC-G-G-GTTCGGGTTTAGGGT
61 TCGGGTCGGGTCGGGTCGAGGTTTTTTAAGTGTGATATTCAGGTCGGCGAGTTCGGGTTTAGGGT
1015012 GAAAAAAACGGATCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAA
126 GAAAAAAAC----CCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAA
*
1015077 TAATACCCCTCTATATATAATTTTTTTCAATTAAGTAAATGTTTT
187 TAATACCCCTCTATATATAATTTTTTTCAATTAAATAAATGTTTT
* * *
1015122 TATTGAATAAAATTTTTTTTTTATTATTTCGTGTCGTGTCGGGTCGGGTTTCTAATTTATATATT
1 TATTGAATAAAAATATTTTTTTATTATTTCG-GTCG-GT--GGTCGGGTTTCTAATTCATATATT
1015187 GAATAAAAAT
Statistics
Matches: 269, Mismatches: 17, Indels: 26
0.86 0.05 0.08
Matches are distributed among these distances:
231 14 0.05
232 24 0.09
233 19 0.07
234 2 0.01
235 43 0.16
236 105 0.39
237 25 0.09
238 37 0.14
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (231 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGTCGGTGGTCGGGTTTCTAATTCATATATTCGGG
TCGGGTCGGGTCGAGGTTTTTTAAGTGTGATATTCAGGTCGGCGAGTTCGGGTTTAGGGTGAAAA
AAACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCC
TCTATATATAATTTTTTTCAATTAAATAAATGTTTT
Found at i:1015557 original size:17 final size:18
Alignment explanation
Indices: 1015532--1015578 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1015522 TATGAAATTG
* *
1015532 GATTTTAATTCC-TGACA
1 GATTCTAATTCCTTCACA
1015549 GATTCTAATTCCTTCACA
1 GATTCTAATTCCTTCACA
*
1015567 GATTCCAATTCC
1 GATTCTAATTCC
1015579 CTCAGAAACG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.38
Consensus pattern (18 bp):
GATTCTAATTCCTTCACA
Found at i:1021512 original size:24 final size:24
Alignment explanation
Indices: 1021492--1021610 Score: 172
Period size: 23 Copynumber: 5.1 Consensus size: 24
1021482 CATCGAAGTG
* *
1021492 CCACATATAATTTTTCCCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
** *
1021516 CTGCATAGAATTTGTCCTGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
1021540 CCACATAGAA-TTGTCCCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
1021563 CCACATAGAA-TTGTCCCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
1021586 CCACATAG-ATTTGTCCCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
1021609 CC
1 CC
1021611 GCGTAGAACC
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
22 1 0.01
23 58 0.67
24 27 0.31
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (24 bp):
CCACATAGAATTTGTCCCGAAGGA
Found at i:1025436 original size:6 final size:6
Alignment explanation
Indices: 1025425--1025463 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1025415 GACATGTATT
*
1025425 ACCACG ACCACG ACCACA ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1025464 CGAGCCGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.36, C:0.51, G:0.13, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1032177 original size:29 final size:29
Alignment explanation
Indices: 1032145--1032205 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
1032135 GATTTTGGAT
* * *
1032145 AATTTACGGGTTTTAGATTTTTTTTAGAA
1 AATTTAAGGATTTTAGATTTTTTTAAGAA
* *
1032174 AA-TTAATGATTTTAGATTTTTTTAATAA
1 AATTTAAGGATTTTAGATTTTTTTAAGAA
1032202 AATT
1 AATT
1032206 GAAATAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (29 bp):
AATTTAAGGATTTTAGATTTTTTTAAGAA
Found at i:1035988 original size:2 final size:2
Alignment explanation
Indices: 1035981--1036021 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1035971 AATTTGCTTT
1035981 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
1036022 TCTAATAACC
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:1037916 original size:17 final size:16
Alignment explanation
Indices: 1037885--1037918 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1037875 CACGTGAGGA
1037885 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1037901 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1037918 T
1 T
1037919 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1044313 original size:20 final size:20
Alignment explanation
Indices: 1044271--1044314 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1044261 TAACTTTTTC
*
1044271 TTTTATCTTTCATTATTCAT
1 TTTTATCTTTCATTATTAAT
* *
1044291 TTTTCTCTTTCATT-TTAAC
1 TTTTATCTTTCATTATTAAT
1044310 TTTTA
1 TTTTA
1044315 CCCTTTTACC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATCTTTCATTATTAAT
Found at i:1048180 original size:17 final size:16
Alignment explanation
Indices: 1048149--1048182 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1048139 CACGTGAGGA
1048149 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1048165 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1048182 T
1 T
1048183 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1048770 original size:135 final size:135
Alignment explanation
Indices: 1048523--1048794 Score: 499
Period size: 135 Copynumber: 2.0 Consensus size: 135
1048513 ATTAGTATTC
1048523 AAATTTAATATTTCTATAACAATCAAATGTCAAATCTAAAGTATCTAATTGCACTATAATATCCG
1 AAATTTAATATTTCTATAACAATCAAATGTCAAATCTAAAGTATCTAATTGCACTATAATATCCG
*
1048588 AAATAACTCAAACTAAAGTACATAAATAGTGCTATCAAAAGTTGAAAACTCAAGTCATTGATAGT
66 AAATAACTCAAACTAAAGTACATAAATAGTGCTATCAAAAGTCGAAAACTCAAGTCATTGATAGT
1048653 TTCTG
131 TTCTG
* *
1048658 AAATTTAATATTTCTATAACAATCAAATGTCAAATCTAAAGTTTCTAATTGCACTATAATATCCT
1 AAATTTAATATTTCTATAACAATCAAATGTCAAATCTAAAGTATCTAATTGCACTATAATATCCG
* *
1048723 AAATAACTCAAACTAAAGTACATAAATAGTGCTATCAAAAGTCGAAAACTCAAGTCCTTGATTGT
66 AAATAACTCAAACTAAAGTACATAAATAGTGCTATCAAAAGTCGAAAACTCAAGTCATTGATAGT
1048788 TTCTG
131 TTCTG
1048793 AA
1 AA
1048795 GAATTCTTTA
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 132 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.32
Consensus pattern (135 bp):
AAATTTAATATTTCTATAACAATCAAATGTCAAATCTAAAGTATCTAATTGCACTATAATATCCG
AAATAACTCAAACTAAAGTACATAAATAGTGCTATCAAAAGTCGAAAACTCAAGTCATTGATAGT
TTCTG
Found at i:1052462 original size:14 final size:15
Alignment explanation
Indices: 1052443--1052483 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
1052433 TTAAATTATT
1052443 TTAAAA-AATAATA-A
1 TTAAAATAA-AATATA
1052457 TTAAAATAAAATATA
1 TTAAAATAAAATATA
1052472 TTAAAAGTAAAA
1 TTAAAA-TAAAA
1052484 GGACCATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 10 0.42
15 9 0.38
16 5 0.21
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
TTAAAATAAAATATA
Found at i:1059582 original size:20 final size:19
Alignment explanation
Indices: 1059553--1059592 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1059543 ATGACCATAA
* *
1059553 ATTATTAAAATTATTAATT
1 ATTATTAAAAATAATAATT
1059572 ATTATTTAAAAATAATAATT
1 ATTA-TTAAAAATAATAATT
1059592 A
1 A
1059593 ATGAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTATTAAAAATAATAATT
Found at i:1059694 original size:20 final size:20
Alignment explanation
Indices: 1059669--1059706 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1059659 AAACAATTAA
*
1059669 TTTTAAAATGTAAGAAATCT
1 TTTTAAAATATAAGAAATCT
1059689 TTTTAAAATATAAGAAAT
1 TTTTAAAATATAAGAAAT
1059707 TTATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (20 bp):
TTTTAAAATATAAGAAATCT
Found at i:1060666 original size:11 final size:10
Alignment explanation
Indices: 1060626--1060680 Score: 58
Period size: 11 Copynumber: 5.4 Consensus size: 10
1060616 ATACCATAAT
1060626 ATTTTTTAAA
1 ATTTTTTAAA
*
1060636 TTTTTTTAAAA
1 ATTTTTT-AAA
**
1060647 ATTACTTAAA
1 ATTTTTTAAA
1060657 GATTTTTTAAA
1 -ATTTTTTAAA
1060668 A-TTTTTAAA
1 ATTTTTTAAA
1060677 ATTT
1 ATTT
1060681 AACATATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 9 0.25
10 12 0.33
11 15 0.42
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:1065957 original size:82 final size:83
Alignment explanation
Indices: 1065863--1066017 Score: 224
Period size: 83 Copynumber: 1.9 Consensus size: 83
1065853 TTGCAGCTTT
* * * * *
1065863 TTAATTTAAAATGCCACTAATGTGCTG-AAAATTGTGGCGTTTGATAAAAATCCCATTATATATG
1 TTAATTTAAAATGCCACTAATGTGCTGAAAAATTGCGACGTTTAATAAAAATACCACTATATATG
1065927 AATCTTATTGTGATGTTC
66 AATCTTATTGTGATGTTC
* *
1065945 TTAA-TTACAAATGTCACTAATGTGCTGAAAAATTGCGACGTTTAATAAAAATATCACTATATAT
1 TTAATTTA-AAATGCCACTAATGTGCTGAAAAATTGCGACGTTTAATAAAAATACCACTATATAT
1066009 GAATCTTAT
65 GAATCTTAT
1066018 CGCGGCGTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
81 3 0.05
82 22 0.34
83 39 0.61
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (83 bp):
TTAATTTAAAATGCCACTAATGTGCTGAAAAATTGCGACGTTTAATAAAAATACCACTATATATG
AATCTTATTGTGATGTTC
Found at i:1067983 original size:24 final size:24
Alignment explanation
Indices: 1067956--1068005 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1067946 TATATCAAAA
*
1067956 ATCAAAACATAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
1067980 ATCAGATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
1068004 AT
1 AT
1068006 TCGTTCAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:1068001 original size:12 final size:13
Alignment explanation
Indices: 1067966--1068048 Score: 54
Period size: 12 Copynumber: 6.8 Consensus size: 13
1067956 ATCAAAACAT
1067966 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
1067979 TAT-CAGATCAA-
1 AATCCAGGTCAAG
1067990 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
1068003 TATTC-GTTC-AG
1 AATCCAGGTCAAG
1068014 AATCCAGGTCAAG
1 AATCCAGGTCAAG
*
1068027 TATCCTA--TC-AG
1 AATCC-AGGTCAAG
1068038 AATCCAGGTCA
1 AATCCAGGTCA
1068049 GGTATTATAA
Statistics
Matches: 50, Mismatches: 12, Indels: 16
0.64 0.15 0.21
Matches are distributed among these distances:
10 1 0.02
11 13 0.26
12 24 0.48
13 11 0.22
14 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:1068063 original size:24 final size:24
Alignment explanation
Indices: 1067966--1068053 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
1067956 ATCAAAACAT
* *
1067966 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCATATCAG
*
1067990 AATCCAGGTCAAGTATTCGT-TCAG
1 AATCCAGGTCAAGTA-TCATATCAG
*
1068014 AATCCAGGTCAAGTATCCTATCAG
1 AATCCAGGTCAAGTATCATATCAG
*
1068038 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
1068054 TATAATAGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
23 3 0.05
24 52 0.91
25 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCATATCAG
Found at i:1073080 original size:3 final size:3
Alignment explanation
Indices: 1073074--1073108 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1073064 AATTATTATT
* *
1073074 TAA TAA TAA TAA TAA TAA TTA TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1073109 GTAAGGACGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1073109 original size:12 final size:12
Alignment explanation
Indices: 1073074--1073112 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1073064 AATTATTATT
*
1073074 TAATAATAATAA
1 TAATAATAATAG
*
1073086 TAATAATTATAG
1 TAATAATAATAG
1073098 TAATAATAATAG
1 TAATAATAATAG
1073110 TAA
1 TAA
1073113 GGACGAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (12 bp):
TAATAATAATAG
Found at i:1073841 original size:250 final size:252
Alignment explanation
Indices: 1073388--1073998 Score: 881
Period size: 250 Copynumber: 2.4 Consensus size: 252
1073378 ATCAATTTTA
* * * *
1073388 GAAATAGTTTAGTGGGTAAGAAACTTTTGAAATCACTTTCTTACTTTTCAAAAATTTC-ATTTTA
1 GAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCAATTTCA
* * * *
1073452 TGAAAACATTTAAATGAGAAACTTTGAAAATCTTTTTCTAATTTT--TGTGAAAACATCCTACCC
66 -GAAAATATTTAAATGAGAAACTTTGGAAATCATTTTCTCATTTTCATGTGAAAACATCCTACCC
* * * * * *
1073515 GAAGGTTTTACTGATGGCTCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAG
130 GAAGGTCTTACGGATGGCCCGAAGGACATATCATCTTGCTCAAAAGACTTACAGATAACCCGAAG
* * * * **
1073580 GATTTAATCATCATTCTCGAAAGACTAACTGCTGGCTCAAATGACTTACCGA-TTTGG
195 GATTTAATCATCATGCTCGAAAGACTAACTGATGGCCCAAAGGACTTACAAATTTTGG
1073637 GAAATAGTTTACT-GGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCAATTTCA
1 GAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCAATTTCA
* * *
1073701 GAAAATATTTAATTGAGAAACTTTGGAAACCGTTTTCTCATTTTCATGTGAAAACATCCTACCCG
66 GAAAATATTTAAATGAGAAACTTTGGAAATCATTTTCTCATTTTCATGTGAAAACATCCTACCCG
* **
1073766 AAGGTCTTACGGATGGCCCGAATGACATATCATCTTGCTCAAAAGACTTACAGATAATTCGAAGG
131 AAGGTCTTACGGATGGCCCGAAGGACATATCATCTTGCTCAAAAGACTTACAGATAACCCGAAGG
* * *
1073831 ATTTAATCATCATGCTCGAAAGGCTTACTGATGGCCCGAAGGACTTACAAATTTTGG
196 ATTTAATCATCATGCTCGAAAGACTAACTGATGGCCCAAAGGACTTACAAATTTTGG
* * *
1073888 GAAATAGTTTACTGGGTAAGAAACTTTGGTAATCGTTTTCTTACTTTTCAAAAATTTCAATTTCT
1 GAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCAATTTCA
*
1073953 GAAAATATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTCA
66 GAAAATATTTAAATGAGAAACTTTGGAAATCATTTTCTCATTTTCA
1073999 AAACAACTTA
Statistics
Matches: 322, Mismatches: 35, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
248 80 0.25
249 17 0.05
250 117 0.36
251 18 0.06
252 90 0.28
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (252 bp):
GAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCAATTTCA
GAAAATATTTAAATGAGAAACTTTGGAAATCATTTTCTCATTTTCATGTGAAAACATCCTACCCG
AAGGTCTTACGGATGGCCCGAAGGACATATCATCTTGCTCAAAAGACTTACAGATAACCCGAAGG
ATTTAATCATCATGCTCGAAAGACTAACTGATGGCCCAAAGGACTTACAAATTTTGG
Found at i:1076290 original size:18 final size:18
Alignment explanation
Indices: 1076267--1076310 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1076257 ATGGGGTAAG
1076267 ATCAAGGGTCATTGTTTT
1 ATCAAGGGTCATTGTTTT
1076285 ATCAAGGGTCATTGTTTT
1 ATCAAGGGTCATTGTTTT
1076303 ATC-AGGGT
1 ATCAAGGGT
1076311 TCAATCTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (18 bp):
ATCAAGGGTCATTGTTTT
Found at i:1082636 original size:3 final size:3
Alignment explanation
Indices: 1082630--1082676 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
1082620 AATTATTATT
* *
1082630 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAG TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1082677 GGGACAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1084455 original size:24 final size:24
Alignment explanation
Indices: 1084387--1084454 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
1084377 AAAAATAATT
* *
1084387 AAATAAATGTTTATATATTTTATA
1 AAATTAATATTTATATATTTTATA
* *
1084411 AAATTAATATTAATTTATTTTA-A
1 AAATTAATATTTATATATTTTATA
1084434 AAATTAA-ATTTATGATATTTT
1 AAATTAATATTTAT-ATATTTT
1084455 TTATAATAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 5 0.14
23 14 0.38
24 18 0.49
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (24 bp):
AAATTAATATTTATATATTTTATA
Found at i:1086049 original size:22 final size:21
Alignment explanation
Indices: 1086006--1086049 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1085996 CGTTTTTAAT
* *
1086006 TAAAATTAATTCATGTTTATG
1 TAAAATTAATTCATATTGATG
*
1086027 TAAATATTAATTTATATTGATG
1 TAAA-ATTAATTCATATTGATG
1086049 T
1 T
1086050 CTTTTAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (21 bp):
TAAAATTAATTCATATTGATG
Found at i:1086410 original size:43 final size:43
Alignment explanation
Indices: 1086348--1086446 Score: 189
Period size: 43 Copynumber: 2.3 Consensus size: 43
1086338 TATATATATA
1086348 TAGGTAATTTAGTGAACGGAGGCTTAGATCTACCAAACATTTGT
1 TAGGT-ATTTAGTGAACGGAGGCTTAGATCTACCAAACATTTGT
1086392 TAGGTATTTAGTGAACGGAGGCTTAGATCTACCAAACATTTGT
1 TAGGTATTTAGTGAACGGAGGCTTAGATCTACCAAACATTTGT
1086435 TAGGTATTTAGT
1 TAGGTATTTAGT
1086447 TGTTTACTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 50 0.91
44 5 0.09
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.34
Consensus pattern (43 bp):
TAGGTATTTAGTGAACGGAGGCTTAGATCTACCAAACATTTGT
Found at i:1086548 original size:76 final size:75
Alignment explanation
Indices: 1086459--1086686 Score: 411
Period size: 76 Copynumber: 3.0 Consensus size: 75
1086449 TTTACTTTTC
*
1086459 TATAGTGTCAGCGATTAATATTTGAAATGGGTAAGAGTTTTAGATGAATTTGTTAAGGATAAGCG
1 TATAGTGTCAGCGATTAATATTTGAAATGGATAAGAGTTTTAGATGAATTTGTTAAGG-TAAGCG
1086524 ACGATTATAAA
65 ACGATTATAAA
1086535 TATAGTGTCAGCGATTAATATTTGAAATGGATAAGAGTTTTAGATGAATTTGTTAAGGGTAAGCG
1 TATAGTGTCAGCGATTAATATTTGAAATGGATAAGAGTTTTAGATGAATTTGTTAA-GGTAAGCG
1086600 ACGATTATAAA
65 ACGATTATAAA
*
1086611 TATAGTGTCAGGGATTAATATTTGAAATGGATAAGAGTTTTAGATGAATTTGTTAAAGGTAAGCG
1 TATAGTGTCAGCGATTAATATTTGAAATGGATAAGAGTTTTAGATGAATTTGTT-AAGGTAAGCG
1086676 ACGATTATAAA
65 ACGATTATAAA
1086687 AATGAAGTAG
Statistics
Matches: 148, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
76 144 0.97
77 4 0.03
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (75 bp):
TATAGTGTCAGCGATTAATATTTGAAATGGATAAGAGTTTTAGATGAATTTGTTAAGGTAAGCGA
CGATTATAAA
Found at i:1088282 original size:18 final size:18
Alignment explanation
Indices: 1088259--1088305 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1088249 TGTTTATGAG
1088259 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
*
1088277 GGAATTAGAATCTGTTAA
1 GGAATTAGAATCTGTGAA
*
1088295 -GAATTGGAATC
1 GGAATTAGAATC
1088306 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.38, C:0.06, G:0.26, T:0.30
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:1088922 original size:37 final size:38
Alignment explanation
Indices: 1088835--1088925 Score: 139
Period size: 38 Copynumber: 2.4 Consensus size: 38
1088825 TTTTCACCCT
*
1088835 AAACCCGAACCTGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTTAAAA
* *
1088874 AAACCCAACCCGACTCGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
1088911 AAACCCGACCCGACC
1 AAACCCGACCCGACC
1088926 TGAATATATG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 16 0.34
38 25 0.53
39 6 0.13
ACGTcount: A:0.40, C:0.40, G:0.10, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:1090223 original size:20 final size:20
Alignment explanation
Indices: 1090198--1090235 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1090188 ATCCTATTCT
1090198 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
1090218 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1090236 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1090603 original size:16 final size:16
Alignment explanation
Indices: 1090582--1090613 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1090572 CAGGGGTTCA
1090582 AATAAAATTTTACCCT
1 AATAAAATTTTACCCT
1090598 AATAAAATTTTACCCT
1 AATAAAATTTTACCCT
1090614 TTCATTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAAATTTTACCCT
Found at i:1091222 original size:21 final size:21
Alignment explanation
Indices: 1091197--1091239 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1091187 AGTGTTTAAG
*
1091197 TATTTGAACTATGCTTTCTTA
1 TATTTGAACCATGCTTTCTTA
*
1091218 TATTTGAACCATGTTTTCTTA
1 TATTTGAACCATGCTTTCTTA
1091239 T
1 T
1091240 GTTAATGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.53
Consensus pattern (21 bp):
TATTTGAACCATGCTTTCTTA
Found at i:1092788 original size:18 final size:18
Alignment explanation
Indices: 1092765--1092835 Score: 133
Period size: 18 Copynumber: 3.9 Consensus size: 18
1092755 TGTCATATTT
1092765 ATATTTTTTAAAAATAAA
1 ATATTTTTTAAAAATAAA
1092783 ATATTTTTTAAAAATAAA
1 ATATTTTTTAAAAATAAA
1092801 ATATTTTTTAAAAATAAA
1 ATATTTTTTAAAAATAAA
*
1092819 ATATTATTTAAAAATAA
1 ATATTTTTTAAAAATAA
1092836 TTTAAAAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTTTTTAAAAATAAA
Found at i:1098628 original size:32 final size:32
Alignment explanation
Indices: 1098592--1098668 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
1098582 CGTTCATGTG
* ** *
1098592 CATTATCTAAATGTAATGCTAACCCTATTGTA
1 CATTATCTGAATGTAACACTAACCCTATTATA
1098624 CATTATCTGAATGTAACACTAACCCTATTATA
1 CATTATCTGAATGTAACACTAACCCTATTATA
1098656 CATTATCTGAATG
1 CATTATCTGAATG
1098669 CCATATTGAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.36
Consensus pattern (32 bp):
CATTATCTGAATGTAACACTAACCCTATTATA
Found at i:1098692 original size:32 final size:31
Alignment explanation
Indices: 1098624--1098746 Score: 120
Period size: 32 Copynumber: 3.9 Consensus size: 31
1098614 CCCTATTGTA
** * * * *
1098624 CATTATCTGAATGTAACACTAACCCTATTATA
1 CATTATCTGAATGCCATACTGACTCT-TTATG
*
1098656 CATTATCTGAATGCCATATTGACTCTGTTATG
1 CATTATCTGAATGCCATACTGACTCT-TTATG
* * * *
1098688 CATTATCTAAATGTCATGCTGACTCTATATG
1 CATTATCTGAATGCCATACTGACTCTTTATG
*
1098719 CATTATCTGAATGCAATACTGACTCTTT
1 CATTATCTGAATGCCATACTGACTCTTT
1098747 TTTGCCTCAT
Statistics
Matches: 73, Mismatches: 18, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
31 27 0.37
32 46 0.63
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.38
Consensus pattern (31 bp):
CATTATCTGAATGCCATACTGACTCTTTATG
Found at i:1102707 original size:139 final size:136
Alignment explanation
Indices: 1102398--1102814 Score: 467
Period size: 139 Copynumber: 3.0 Consensus size: 136
1102388 TCAAATTATG
* *
1102398 TAATTTAAAGGACCTAGAG-G-ACTAAACCTATAAAT-ATAGGCTCTAATATTAACCCT-ATTGG
1 TAATTTAAAGGA-CTAGAGTGAAATAAACCTA-AAATGA-AGGCTCTAATATTAATCCTAATT-G
* * *
1102459 ATTTTAACGAATTATTGAATCGAATAATCGAAATAGA-TCCTCGGACATTAAGACGAGGGCCAAA
62 ATTTTAACCAATTATTGAATCGAATAATCGAAATGGACT-CTCGGA-ATTAAGGCGAGGGCCAAA
*
1102523 TCGAATATTCTC
125 TCGAATATTCCC
* * * *
1102535 TAAATTAAAGGACTAAAAGTAAAATTAAA-CTAAAATGAAGGTTCTAATTATTAATCCTAATTGA
1 TAATTTAAAGGACT-AGAGTGAAA-TAAACCTAAAATGAAGGCTCTAA-TATTAATCCTAATTGA
* * *
1102599 TTTTACCCAATTATTGAATTGAATAATCAAAATGGACTCTCGGGAATTAAGGCGAGGGCCAAATC
63 TTTTAACCAATTATTGAATCGAATAATCGAAATGGACTCTC-GGAATTAAGGCGAGGGCCAAATC
1102664 GAATATTCCC
127 GAATATTCCC
1102674 TAATTTAAAGGACTAGAGTGAAATAAAGCCTAAAATAGAA-GCTCTAATATT-ATCCCTAATT-A
1 TAATTTAAAGGACTAGAGTGAAATAAA-CCTAAAAT-GAAGGCTCTAATATTAAT-CCTAATTGA
* * **
1102736 TTTTTAATCAATTATTAAATCGAATAATCGAAATGGACAT-TCTGTCATTAAGGCGAGGGCCAAA
63 -TTTTAACCAATTATTGAATCGAATAATCGAAATGGAC-TCTC-GGAATTAAGGCGAGGGCCAAA
1102800 TCGAATATTCCC
125 TCGAATATTCCC
1102812 TAA
1 TAA
1102815 ATTTTAAAAA
Statistics
Matches: 240, Mismatches: 25, Indels: 29
0.82 0.09 0.10
Matches are distributed among these distances:
136 2 0.01
137 21 0.09
138 98 0.41
139 105 0.44
140 14 0.06
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (136 bp):
TAATTTAAAGGACTAGAGTGAAATAAACCTAAAATGAAGGCTCTAATATTAATCCTAATTGATTT
TAACCAATTATTGAATCGAATAATCGAAATGGACTCTCGGAATTAAGGCGAGGGCCAAATCGAAT
ATTCCC
Found at i:1107904 original size:144 final size:144
Alignment explanation
Indices: 1107644--1107931 Score: 576
Period size: 144 Copynumber: 2.0 Consensus size: 144
1107634 CACTCAACAA
1107644 CGCCTTCCCTATTCAATCAAAAAACCCATTTCATCACTGAGAAAAACGTTCACCATACCATAAAA
1 CGCCTTCCCTATTCAATCAAAAAACCCATTTCATCACTGAGAAAAACGTTCACCATACCATAAAA
1107709 TAACAATCGTAATAACAATACGAGTGAAAAGCTTACCATCTAATTCCCAGGGATGAAGCAGATGA
66 TAACAATCGTAATAACAATACGAGTGAAAAGCTTACCATCTAATTCCCAGGGATGAAGCAGATGA
1107774 AGATCAAGCTCGGG
131 AGATCAAGCTCGGG
1107788 CGCCTTCCCTATTCAATCAAAAAACCCATTTCATCACTGAGAAAAACGTTCACCATACCATAAAA
1 CGCCTTCCCTATTCAATCAAAAAACCCATTTCATCACTGAGAAAAACGTTCACCATACCATAAAA
1107853 TAACAATCGTAATAACAATACGAGTGAAAAGCTTACCATCTAATTCCCAGGGATGAAGCAGATGA
66 TAACAATCGTAATAACAATACGAGTGAAAAGCTTACCATCTAATTCCCAGGGATGAAGCAGATGA
1107918 AGATCAAGCTCGGG
131 AGATCAAGCTCGGG
1107932 AATGATGTTG
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 144 1.00
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.22
Consensus pattern (144 bp):
CGCCTTCCCTATTCAATCAAAAAACCCATTTCATCACTGAGAAAAACGTTCACCATACCATAAAA
TAACAATCGTAATAACAATACGAGTGAAAAGCTTACCATCTAATTCCCAGGGATGAAGCAGATGA
AGATCAAGCTCGGG
Found at i:1108237 original size:16 final size:16
Alignment explanation
Indices: 1108216--1108260 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1108206 AAAAAACGGT
*
1108216 GTGATCTATTAAATAA
1 GTGATCGATTAAATAA
1108232 GTGATCGATTAAATAA
1 GTGATCGATTAAATAA
* *
1108248 GTAATCGGTTAAA
1 GTGATCGATTAAA
1108261 ATTTAGACCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (16 bp):
GTGATCGATTAAATAA
Found at i:1108346 original size:23 final size:23
Alignment explanation
Indices: 1108311--1108358 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1108301 ATCAAGTACA
*
1108311 ATAATATATTAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
* *
1108334 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
1108357 AT
1 AT
1108359 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:1109290 original size:182 final size:181
Alignment explanation
Indices: 1108983--1109438 Score: 716
Period size: 182 Copynumber: 2.5 Consensus size: 181
1108973 ACTTTTTTAC
* *
1108983 TACCGGTTTTGTCATTTCGAGACTGATTTTGTCATATTTTTACCTGTTATATTATTATAGATCGA
1 TACCGGTTTTGTCATTTCGAGAC-GGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGA
* * * *
1109048 TACATTTTTATAAAGTATCGATACTTTATTGGCGCTATAATTTCTTTTCTTTTAAATTCCAAAAG
65 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
* *
1109113 TGTCGATACTTATAATAAAGTATCGACACT-TTCAACATATTTGGTAGCTCTT
130 TGTCGATACTTATAAAAAAGTATCGACACTATT-AACATATTTGGTAGCGCTT
1109165 TACCGGTTTTGTCATTTCGAGATCGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGA
1 TACCGGTTTTGTCATTTCGAGA-CGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGA
1109230 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
65 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
1109295 TGTCGATACTTATAAAAAAGTATCGACACTATTAACATATTTGGTAGCGCTT
130 TGTCGATACTTATAAAAAAGTATCGACACTATTAACATATTTGGTAGCGCTT
* * ** * * * * *
1109347 TATCTGTTTTGTCATTTATAGACCAGTTTTGTCATTTTTTTAACTATTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGA-CGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGA
1109412 TACATTTTTATAAAGTATCGACACTTT
65 TACATTTTTATAAAGTATCGACACTTT
1109439 CAATATATTC
Statistics
Matches: 254, Mismatches: 18, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
182 251 0.99
183 3 0.01
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (181 bp):
TACCGGTTTTGTCATTTCGAGACGGTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGAT
ACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
GTCGATACTTATAAAAAAGTATCGACACTATTAACATATTTGGTAGCGCTT
Found at i:1109557 original size:114 final size:112
Alignment explanation
Indices: 1109311--1109773 Score: 768
Period size: 112 Copynumber: 4.1 Consensus size: 112
1109301 TACTTATAAA
* * * *
1109311 AAAGTATCGACACTATT-AACATATTTGGTAGCGCTTTATCTGTTTTGTCATTTATAGACCAGTT
1 AAAGTATCGACACT-TTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTT
* *
1109375 TTGTCATTTTTTTAACTATTATATTGTTATGGATCGATACATTTTTAT
65 TTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
* *
1109423 AAAGTATCGACACTTTCAATATATTCGGTAGCGTTTTACATGTTTTGTCATTTATAGACCGGTTT
1 AAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTT
1109488 TGTCATTTTTTTACCTGTTATATATTGTTATGGATCGATACATTTTTAT
66 TGTCATTTTTTTACCTG-T-TATATTGTTATGGATCGATACATTTTTAT
*
1109537 AAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTT
1 AAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTT
1109602 TGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
66 TGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
*
1109649 AAAGTATCGACACTTTCAATATA-TCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGTT
1 AAAGTATCGACACTTTCAATATATTC-GGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTT
* *
1109713 TTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATATTTTTAT
65 TTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
1109761 AAAGTATCGACAC
1 AAAGTATCGACAC
1109774 AAACTTACAA
Statistics
Matches: 332, Mismatches: 15, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
111 3 0.01
112 219 0.66
113 2 0.01
114 108 0.33
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (112 bp):
AAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTT
TGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT
Found at i:1109705 original size:226 final size:224
Alignment explanation
Indices: 1109311--1109773 Score: 786
Period size: 226 Copynumber: 2.1 Consensus size: 224
1109301 TACTTATAAA
** *
1109311 AAAGTATCGACACTATTAACATATTTGGTAGCGCTTTATCTGTTTTGTCATTTATAGACCAGTTT
1 AAAGTATCGACACTATTAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTTT
1109376 TGTCATTTTTTTAACTATTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCA
66 TGTCATTTTTTTAACTATTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCA
1109441 ATATATTCGGTAGCGTTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGT
131 ATATATTCGGTAGCGTTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTG-
*
1109506 TATATATTGTTATGGATCGATACATTTTTAT
195 T-TATATTGTTATGGATCAATACATTTTTAT
* *
1109537 AAAGTATCGACACT-TTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTT
1 AAAGTATCGACACTATT-AACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTT
* *
1109601 TTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTC
65 TTGTCATTTTTTTAACTATTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTC
*
1109666 AATATA-TCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
130 AATATATTC-GGTAGCGTTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
*
1109730 GTTATATTGTTATGGATCAATATATTTTTAT
194 GTTATATTGTTATGGATCAATACATTTTTAT
1109761 AAAGTATCGACAC
1 AAAGTATCGACAC
1109774 AAACTTACAA
Statistics
Matches: 225, Mismatches: 10, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
224 40 0.18
225 5 0.02
226 180 0.80
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (224 bp):
AAAGTATCGACACTATTAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTTT
TGTCATTTTTTTAACTATTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCA
ATATATTCGGTAGCGTTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGT
TATATTGTTATGGATCAATACATTTTTAT
Found at i:1110102 original size:2 final size:2
Alignment explanation
Indices: 1110090--1110121 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1110080 AGAAAAAGGA
*
1110090 AT AT CT 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
1110122 TGTGCGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1110634 original size:105 final size:103
Alignment explanation
Indices: 1110430--1110638 Score: 400
Period size: 103 Copynumber: 2.0 Consensus size: 103
1110420 ATTAGAGATT
1110430 ATTATTTTCTAGTGTATGTTTTTTTAATATGATTCATTATATTATAAAATATGATCAACAATTTT
1 ATTATTTTCTAGTGTATGTTTTTTTAATATGATTCATTATATTATAAAATATGATCAACAATTTT
1110495 TTTTTTTTAAAGAAACCCCTTTTGAGATCTATAAATGC
66 TTTTTTTTAAAGAAACCCCTTTTGAGATCTATAAATGC
1110533 ATTATTTTCTAGTGTATGTTTTTTTAATATGATTCATTATATTATAAAATATGATCAACAATTTT
1 ATTATTTTCTAGTGTATGTTTTTTTAATATGATTCATTATATTATAAAATATGATCAACAA-TTT
1110598 GTTTTTTTTTAAAGAAACCCCTTTTGAGATCTATAAATGC
65 -TTTTTTTTTAAAGAAACCCCTTTTGAGATCTATAAATGC
1110638 A
1 A
1110639 AAAAAGTATC
Statistics
Matches: 104, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
103 61 0.59
104 3 0.03
105 40 0.38
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (103 bp):
ATTATTTTCTAGTGTATGTTTTTTTAATATGATTCATTATATTATAAAATATGATCAACAATTTT
TTTTTTTTAAAGAAACCCCTTTTGAGATCTATAAATGC
Found at i:1124187 original size:42 final size:42
Alignment explanation
Indices: 1124126--1124207 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
1124116 GTTTTAGCCC
* * *
1124126 AAACGTCACAATATAGTGGTAATTTAGCGGCGTTTATACCAT
1 AAACGCCACAATAGAGTGGTAAATTAGCGGCGTTTATACCAT
* * *
1124168 AAACGCCATAATAGAGTGGTAAATTAGTGGTGTTTATACC
1 AAACGCCACAATAGAGTGGTAAATTAGCGGCGTTTATACC
1124208 TCAAACACCG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (42 bp):
AAACGCCACAATAGAGTGGTAAATTAGCGGCGTTTATACCAT
Found at i:1124222 original size:42 final size:42
Alignment explanation
Indices: 1124135--1124222 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1124125 CAAACGTCAC
* * *
1124135 AATATAGTGGTAATTTAGCGGCGTTTATACCATAAACGCCAT
1 AATAGAGTGGTAAATTAGCGGCGTTTATACCATAAACACCAT
* * *
1124177 AATAGAGTGGTAAATTAGTGGTGTTTATACC-TCAAACACCGT
1 AATAGAGTGGTAAATTAGCGGCGTTTATACCAT-AAACACCAT
1124219 AATA
1 AATA
1124223 AGTTTTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (42 bp):
AATAGAGTGGTAAATTAGCGGCGTTTATACCATAAACACCAT
Found at i:1125979 original size:21 final size:22
Alignment explanation
Indices: 1125962--1126022 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
1125952 TGAAGCAAGG
1125962 GAAGCAGA-GAGAGCAGC-AGCA
1 GAAGCA-ACGAGAGCAGCAAGCA
*
1125983 GAAGCAACGAGAGCAGC-ATCA
1 GAAGCAACGAGAGCAGCAAGCA
*
1126004 GAAGC-ACAGAGAGAAGCAA
1 GAAGCAAC-GAGAGCAGCAA
1126023 CGGTAGCACA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 3 0.09
21 31 0.89
22 1 0.03
ACGTcount: A:0.46, C:0.20, G:0.33, T:0.02
Consensus pattern (22 bp):
GAAGCAACGAGAGCAGCAAGCA
Found at i:1126030 original size:21 final size:21
Alignment explanation
Indices: 1126006--1126063 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1125996 CAGCATCAGA
1126006 AGCACAGAGAGAAGCAACGGT
1 AGCACAGAGAGAAGCAACGGT
* *
1126027 AGCACACAGAGAAGCAGCGGT
1 AGCACAGAGAGAAGCAACGGT
1126048 AGCACAGAGAGAAGCA
1 AGCACAGAGAGAAGCA
1126064 CTGGCATCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.43, C:0.21, G:0.33, T:0.03
Consensus pattern (21 bp):
AGCACAGAGAGAAGCAACGGT
Found at i:1126074 original size:21 final size:20
Alignment explanation
Indices: 1126006--1126078 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 20
1125996 CAGCATCAGA
1126006 AGCACAGAGAGAAGCAACGGT
1 AGCACAGAGAGAAGC-ACGGT
*
1126027 AGCACACAGAGAAGCAGCGGT
1 AGCACAGAGAGAAGCA-CGGT
*
1126048 AGCACAGAGAGAAGCACTGGC
1 AGCACAGAGAGAAGCAC-GGT
*
1126069 ATCACAGAGA
1 AGCACAGAGA
1126079 AAATCAGCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.96
ACGTcount: A:0.41, C:0.22, G:0.32, T:0.05
Consensus pattern (20 bp):
AGCACAGAGAGAAGCACGGT
Found at i:1126483 original size:44 final size:44
Alignment explanation
Indices: 1126403--1126518 Score: 144
Period size: 44 Copynumber: 2.7 Consensus size: 44
1126393 ATTATGTGTT
* * * *
1126403 ATTTAGCGACGTTTGTA-ACAAAAAACACCGCAATATACCATAC
1 ATTTAGCGGCGTTTGTATCCAAAAAACGCCGCAATATACCAGAC
* * * *
1126446 ATTTTGCGGTGTTTGTATCCTAAAAACGCCGCTATATACCAGAC
1 ATTTAGCGGCGTTTGTATCCAAAAAACGCCGCAATATACCAGAC
*
1126490 CTTTAGCGGCGTTTGTATCCAAAAAACGC
1 ATTTAGCGGCGTTTGTATCCAAAAAACGC
1126519 TTCGAAATAT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
43 14 0.23
44 46 0.77
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (44 bp):
ATTTAGCGGCGTTTGTATCCAAAAAACGCCGCAATATACCAGAC
Found at i:1126643 original size:87 final size:87
Alignment explanation
Indices: 1126552--1126713 Score: 207
Period size: 87 Copynumber: 1.9 Consensus size: 87
1126542 GGCATTTTTG
* * * * * * *
1126552 GAAAAAACGCCACGAAATCTCAACAAGTATTGCGGCGTTTGTGAGAAAAATACCTCTAAATCTCA
1 GAAAAAACGCCACGAAACCTCAACAACTATTGCGACGTTTGTAAGAAAAACACCGCTAAATATCA
1126617 AAACCTATTGCATCGTTTGTGA
66 AAACCTATTGCATCGTTTGTGA
* * * *
1126639 GAAAAAACGCCGCTAAACCTCAACACCTATTGCGACGTTTGTAAGACAAACACCGCTAAATATCA
1 GAAAAAACGCCACGAAACCTCAACAACTATTGCGACGTTTGTAAGAAAAACACCGCTAAATATCA
* *
1126704 ACACTTATTG
66 AAACCTATTG
1126714 TGGCATTTGT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
87 62 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (87 bp):
GAAAAAACGCCACGAAACCTCAACAACTATTGCGACGTTTGTAAGAAAAACACCGCTAAATATCA
AAACCTATTGCATCGTTTGTGA
Found at i:1126713 original size:43 final size:43
Alignment explanation
Indices: 1126566--1126713 Score: 163
Period size: 43 Copynumber: 3.4 Consensus size: 43
1126556 AAACGCCACG
** * * *
1126566 AAATCTCAACAAGTATTGCGGCGTTTGTGAGAAAAATACCTCT
1 AAATCTCAACACCTATTGCGACGTTTGTGAGAAAAACACCGCT
* *
1126609 AAATCTCAAAACCTATTGC-ATCGTTTGTGAGAAAAAACGCCGCT
1 AAATCTCAACACCTATTGCGA-CGTTTGTGAG-AAAAACACCGCT
* * *
1126653 AAACCTCAACACCTATTGCGACGTTTGTAAGACAAACACCGCT
1 AAATCTCAACACCTATTGCGACGTTTGTGAGAAAAACACCGCT
* *
1126696 AAATATCAACACTTATTG
1 AAATCTCAACACCTATTG
1126714 TGGCATTTGT
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
43 51 0.59
44 35 0.40
45 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (43 bp):
AAATCTCAACACCTATTGCGACGTTTGTGAGAAAAACACCGCT
Found at i:1126723 original size:43 final size:43
Alignment explanation
Indices: 1126643--1126724 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 43
1126633 TTGTGAGAAA
* * *
1126643 AAACGCCGCTAAACCTCAACACCTATTGCGACGTTTGTAAGAC
1 AAACACCGCTAAACATCAACACCTATTGCGACATTTGTAAGAC
* * * *
1126686 AAACACCGCTAAATATCAACACTTATTGTGGCATTTGTA
1 AAACACCGCTAAACATCAACACCTATTGCGACATTTGTA
1126725 TATCGTCACC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 32 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (43 bp):
AAACACCGCTAAACATCAACACCTATTGCGACATTTGTAAGAC
Found at i:1126723 original size:87 final size:86
Alignment explanation
Indices: 1126523--1126723 Score: 195
Period size: 87 Copynumber: 2.3 Consensus size: 86
1126513 AAACGCTTCG
** * * * * * *
1126523 AAATATCTTAACCTTTTGAGGCATTTTTGGAAAAAACGCCACGAAATCTCAACAAGTATTGCGGC
1 AAATATCAAAACCTATTGCGGCATTTGTGGAAAAAACGCCACGAAACCTCAACAACTATTGCGAC
* * *
1126588 GTTTGTGAGAAAAATACCTCT
66 GTTTGTAAGAAAAACACCGCT
* ** * * * *
1126609 AAATCTCAAAACCTATTGCATCGTTTGTGAGAAAAAACGCCGCTAAACCTCAACACCTATTGCGA
1 AAATATCAAAACCTATTGCGGCATTTGTG-GAAAAAACGCCACGAAACCTCAACAACTATTGCGA
*
1126674 CGTTTGTAAGACAAACACCGCT
65 CGTTTGTAAGAAAAACACCGCT
* * *
1126696 AAATATCAACACTTATTGTGGCATTTGT
1 AAATATCAAAACCTATTGCGGCATTTGT
1126724 ATATCGTCAC
Statistics
Matches: 88, Mismatches: 26, Indels: 1
0.77 0.23 0.01
Matches are distributed among these distances:
86 20 0.23
87 68 0.77
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (86 bp):
AAATATCAAAACCTATTGCGGCATTTGTGGAAAAAACGCCACGAAACCTCAACAACTATTGCGAC
GTTTGTAAGAAAAACACCGCT
Found at i:1128476 original size:29 final size:28
Alignment explanation
Indices: 1128376--1128476 Score: 67
Period size: 29 Copynumber: 3.3 Consensus size: 28
1128366 AATTTCTGCA
** *
1128376 ATTTAAATTTTACACTTTTATTTTAATTAT
1 ATTT-AATTTTACTTTTTTATTTAAATT-T
* *
1128406 ATTTAATTTAGTCATTTTGTGTTCTTTAAATTT
1 ATTTAATTT--T-ACTTT-T-TTATTTAAATTT
*
1128439 ATTAAAATTTTACTTTTTTATTTAAATTGT
1 ATT-TAATTTTACTTTTTTATTTAAATT-T
1128469 ATTTAATT
1 ATTTAATT
1128477 ATGGCTTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
29 19 0.35
30 9 0.16
31 5 0.09
32 3 0.05
33 5 0.09
34 14 0.25
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (28 bp):
ATTTAATTTTACTTTTTTATTTAAATTT
Found at i:1128590 original size:133 final size:133
Alignment explanation
Indices: 1128448--1128717 Score: 531
Period size: 133 Copynumber: 2.0 Consensus size: 133
1128438 TATTAAAATT
1128448 TTACTTTTTTATTTAAATTGTATTTAATTATGGCTTAAAGAAAGTTGTGTGAAATTATTATGTTT
1 TTACTTTTTTATTT-AATTGTATTTAATTATGGCTTAAAGAAAGTTGTGTGAAATTATTATGTTT
1128513 TAGGATAAGTTATGTGAAATTTTAAAAAATTCACGACTGCGACACCCTCATTGACTGCGATGGCA
65 TAGGATAAGTTATGTGAAATTTTAAAAAATTCACGACTGCGACACCCTCATTGACTGCGATGGCA
1128578 TCTA
130 TCTA
1128582 TTACTTTTTTATTTAATTGTATTTAATTATGGCTTAAAGAAAGTTGTGTGAAATTATTATGTTTT
1 TTACTTTTTTATTTAATTGTATTTAATTATGGCTTAAAGAAAGTTGTGTGAAATTATTATGTTTT
1128647 AGGATAAGTTATGTGAAATTTTAAAAAATTCACGACTGCGACACCCTCATTGACTGCGATGGCAT
66 AGGATAAGTTATGTGAAATTTTAAAAAATTCACGACTGCGACACCCTCATTGACTGCGATGGCAT
1128712 CTA
131 CTA
1128715 TTA
1 TTA
1128718 TGTCTGCAAC
Statistics
Matches: 136, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
133 122 0.90
134 14 0.10
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (133 bp):
TTACTTTTTTATTTAATTGTATTTAATTATGGCTTAAAGAAAGTTGTGTGAAATTATTATGTTTT
AGGATAAGTTATGTGAAATTTTAAAAAATTCACGACTGCGACACCCTCATTGACTGCGATGGCAT
CTA
Found at i:1128950 original size:2 final size:2
Alignment explanation
Indices: 1128943--1129021 Score: 121
Period size: 2 Copynumber: 41.5 Consensus size: 2
1128933 TTCGTTTGGG
1128943 AT AT AT AT -T AT AT AT AT AT AT AT AT A- AT -T 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
*
1128982 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1129022 ATGGTCATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
1 4 0.06
2 67 0.94
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1130980 original size:2 final size:2
Alignment explanation
Indices: 1130973--1131012 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1130963 ATACAAAACA
1130973 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
1131013 TACATCTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1136886 original size:54 final size:54
Alignment explanation
Indices: 1136804--1137412 Score: 758
Period size: 54 Copynumber: 11.3 Consensus size: 54
1136794 TTACCAAATA
* *
1136804 GGCACTAAGGGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * *
1136858 GGCACTAAGTGTGCAATTCACGAAATTCATCATTTGTTGATGAATAACCATTTT
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* *
1136912 GGTACTAAGTGTGCAATTCAC-AGAATTCATCAAATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGA-AATTCATCATATGTTGATGAATAACCGTTTC
* * * * *
1136966 GACACTAAGTGTGCAATTCAAGGAATTCATCACATGTTGATGAATAACTGTTTC
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
*
1137020 GGCACTAAGTGTACAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * *** *
1137074 GACACTAAGTGTGTAATTCACGGTTTTCATCATATCTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * * *
1137128 GGTACTAAGTGTGTAATTCAC-ATAATTCATCATATGTTGTTGAATAATCGTTTC
1 GGCACTAAGTGTGCAATTCACGA-AATTCATCATATGTTGATGAATAACCGTTTC
*** * * *
1137182 TATATTAAGTGTGTAATTCACGAAATTCATCATATGTTGATGAATAACCATTTC
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
** * **
1137236 ACCACTAAGTGTGTAATTCAC-ATAATTCATCATATGTTGATGAATAACAATTTC
1 GGCACTAAGTGTGCAATTCACGA-AATTCATCATATGTTGATGAATAACCGTTTC
* *
1137290 GACAGTAAGTGTGCAATTCAC-ATAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACGA-AATTCATCATATGTTGATGAATAACCGTTTC
* * * * * * *
1137344 GGCACTAAGTGTGCAATTCACGGAATTAATAATATGTTTATGAATGACCGTATA
1 GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
*
1137398 GGCACTACGTGTGCA
1 GGCACTAAGTGTGCA
1137413 TCGTAACAAA
Statistics
Matches: 485, Mismatches: 64, Indels: 12
0.86 0.11 0.02
Matches are distributed among these distances:
53 2 0.00
54 482 0.99
55 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:1138680 original size:17 final size:17
Alignment explanation
Indices: 1138660--1138755 Score: 87
Period size: 17 Copynumber: 5.8 Consensus size: 17
1138650 TATCGCACTT
1138660 GAAAAAAGAAAAAGAAA
1 GAAAAAAGAAAAAGAAA
*
1138677 G-AAAAA-TAAAAGAAA
1 GAAAAAAGAAAAAGAAA
*
1138692 GAAGAAAAGAAAAA-AAG
1 GAA-AAAAGAAAAAGAAA
*
1138709 GAAGAAAA-ATAAAGAAA
1 GAA-AAAAGAAAAAGAAA
1138726 G-AAAAAGAATAAAGAATA
1 GAAAAAAGAA-AAAGAA-A
1138744 -AAAAAAGAAAAA
1 GAAAAAAGAAAAA
1138756 AGATAGATAG
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
15 13 0.20
16 12 0.18
17 27 0.42
18 13 0.20
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (17 bp):
GAAAAAAGAAAAAGAAA
Done.