Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 28
Found at i:1089192 original size:21 final size:21
Alignment explanation
Indices: 1089132--1089198 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1089122 CGGTACACTG
*
1089132 CATAGTGTAACGATGCACATT
1 CATAGTGTATCGATGCACATT
* * * *
1089153 CAAAGAATGCATCGGTGCACCTT
1 CATAG--TGTATCGATGCACATT
*
1089176 CATAGTGTATCGATGCATATT
1 CATAGTGTATCGATGCACATT
1089197 CA
1 CA
1089199 AGGAATGCAT
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
21 18 0.53
23 16 0.47
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (21 bp):
CATAGTGTATCGATGCACATT
Found at i:1089238 original size:21 final size:21
Alignment explanation
Indices: 1089132--1089239 Score: 58
Period size: 21 Copynumber: 5.0 Consensus size: 21
1089122 CGGTACACTG
* *
1089132 CATAGTGTAACGATGCACATT
1 CATAGTGTATCGATGCACTTT
* * * *
1089153 CAAAGAATGCATCGGTGCACCTT
1 CATAG--TGTATCGATGCACTTT
1089176 CATAGTGTATCGATGCA-TATT
1 CATAGTGTATCGATGCACT-TT
* * * *
1089197 CA-AGGAATGCATTGGTACACTTT
1 CATA-G--TGTATCGATGCACTTT
1089220 CATAGTGTATCGATGCACTT
1 CATAGTGTATCGATGCACTT
1089240 AGCATAAAAA
Statistics
Matches: 62, Mismatches: 17, Indels: 16
0.65 0.18 0.17
Matches are distributed among these distances:
20 1 0.02
21 30 0.48
23 29 0.47
24 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (21 bp):
CATAGTGTATCGATGCACTTT
Found at i:1101895 original size:14 final size:14
Alignment explanation
Indices: 1101872--1101916 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1101862 CAAGTTTTAC
*
1101872 ATACATACATACAT
1 ATACATACATATAT
* *
1101886 ATATATACATATAC
1 ATACATACATATAT
*
1101900 ATACACACATATAT
1 ATACATACATATAT
1101914 ATA
1 ATA
1101917 TATATATTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (14 bp):
ATACATACATATAT
Found at i:1101901 original size:20 final size:20
Alignment explanation
Indices: 1101876--1101918 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1101866 TTTTACATAC
* *
1101876 ATACATACATATATATACAT
1 ATACATACACACATATACAT
*
1101896 ATACATACACACATATATAT
1 ATACATACACACATATACAT
1101916 ATA
1 ATA
1101919 TATATTCCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (20 bp):
ATACATACACACATATACAT
Found at i:1101901 original size:24 final size:24
Alignment explanation
Indices: 1101872--1101922 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1101862 CAAGTTTTAC
*
1101872 ATACATACATACATATATATACAT
1 ATACATACACACATATATATACAT
*
1101896 ATACATACACACATATATATATAT
1 ATACATACACACATATATATACAT
1101920 ATA
1 ATA
1101923 TTCCTTATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (24 bp):
ATACATACACACATATATATACAT
Found at i:1103269 original size:20 final size:20
Alignment explanation
Indices: 1103244--1103295 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 20
1103234 ATGCATGTAA
1103244 GTATTGAAGTTAATCGAATT
1 GTATTGAAGTTAATCGAATT
*
1103264 GTATTGAA-TTAAT-AAATT
1 GTATTGAAGTTAATCGAATT
1103282 -T-TTG-AGTTAATCGA
1 GTATTGAAGTTAATCGA
1103296 GAAGATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 1 0.04
16 8 0.29
17 2 0.07
18 4 0.14
19 5 0.18
20 8 0.29
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (20 bp):
GTATTGAAGTTAATCGAATT
Found at i:1103616 original size:21 final size:20
Alignment explanation
Indices: 1103591--1103651 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
1103581 TATTAATATC
*
1103591 AAAAATATTTATTTTAAATA
1 AAAAATATATATTTTAAATA
*
1103611 ATAAAAT-TAATATTTTTAATA
1 A-AAAATAT-ATATTTTAAATA
1103632 AAAAATA-ATATTTTAAATA
1 AAAAATATATATTTTAAATA
1103651 A
1 A
1103652 CGTCCTACCA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 12 0.34
20 7 0.20
21 16 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAAATATATATTTTAAATA
Found at i:1103640 original size:19 final size:21
Alignment explanation
Indices: 1103600--1103651 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1103590 CAAAAATATT
1103600 TATTTTAAATAATAAAATTAA
1 TATTTTAAATAATAAAATTAA
*
1103621 TATTTTTAATAA-AAAA-TAA
1 TATTTTAAATAATAAAATTAA
1103640 TATTTTAAATAA
1 TATTTTAAATAA
1103652 CGTCCTACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 14 0.48
20 4 0.14
21 11 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTTTAAATAATAAAATTAA
Found at i:1107251 original size:6 final size:6
Alignment explanation
Indices: 1107240--1107277 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
1107230 ACAGATTGAT
1107240 CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA CC
1 CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA CC
1107278 CGAGACAGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
CCACGA
Found at i:1107855 original size:121 final size:120
Alignment explanation
Indices: 1107632--1107864 Score: 396
Period size: 121 Copynumber: 1.9 Consensus size: 120
1107622 TGGAAACAAG
* *
1107632 TGTTGGTAATGCTCAATCCCACATAGTATTAGAAACACTATTGTGAATGGTATTTAAGGCTTGGC
1 TGTTGGTAATGCTCAATCCCACATAGTATTAGAAACACTATTGGGAATGGTATTTAAGGCTTGAC
*
1107697 TTTCCCACTTCCTTGTTGAGTGATAGAGAACAAGGGGGACTCTCGCGCGTCGCCGC
66 ATTCCCACTTCCTTGTTGAGTGATAGAGAACAAGGGGG-CTCTCGCGCGTCGCCGC
* *
1107753 TGTTGGTAATGCTCAATCCCACATAGTGTTGGAAACACTATTGGGAATGGTATTTAAGGCTTGAC
1 TGTTGGTAATGCTCAATCCCACATAGTATTAGAAACACTATTGGGAATGGTATTTAAGGCTTGAC
1107818 ATT-CCACTTCCTTGTTGAGTGATAGAGAACAAGGGGGGCTCTCGCGC
66 ATTCCCACTTCCTTGTTGAGTGATAGAGAACAA-GGGGGCTCTCGCGC
1107865 ACCGCCGCCG
Statistics
Matches: 106, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
120 38 0.36
121 68 0.64
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (120 bp):
TGTTGGTAATGCTCAATCCCACATAGTATTAGAAACACTATTGGGAATGGTATTTAAGGCTTGAC
ATTCCCACTTCCTTGTTGAGTGATAGAGAACAAGGGGGCTCTCGCGCGTCGCCGC
Found at i:1107894 original size:5 final size:5
Alignment explanation
Indices: 1107876--1107930 Score: 60
Period size: 5 Copynumber: 11.4 Consensus size: 5
1107866 CCGCCGCCGC
* * *
1107876 CGTC- CGTC- CGTCT CGTCT CGACT CGGCT CGTCT CGTCT CGTCT CGACT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
*
1107924 CGGCT CG
1 CGTCT CG
1107931 GCACGGCACG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
4 8 0.18
5 37 0.82
ACGTcount: A:0.04, C:0.42, G:0.25, T:0.29
Consensus pattern (5 bp):
CGTCT
Found at i:1107913 original size:25 final size:24
Alignment explanation
Indices: 1107880--1107930 Score: 93
Period size: 25 Copynumber: 2.1 Consensus size: 24
1107870 CGCCGCCGTC
1107880 CGTCCGTCTCGTCTCGACTCGGCT
1 CGTCCGTCTCGTCTCGACTCGGCT
1107904 CGTCTCGTCTCGTCTCGACTCGGCT
1 CGTC-CGTCTCGTCTCGACTCGGCT
1107929 CG
1 CG
1107931 GCACGGCACG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.04, C:0.41, G:0.25, T:0.29
Consensus pattern (24 bp):
CGTCCGTCTCGTCTCGACTCGGCT
Found at i:1108025 original size:5 final size:5
Alignment explanation
Indices: 1107924--1108022 Score: 153
Period size: 5 Copynumber: 19.8 Consensus size: 5
1107914 CGTCTCGACT
*
1107924 CGGCT CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA
1 CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA
* * * *
1107974 CGGCA CGGCA CGGCA CGGCA CGGCA CGGCT CGGCT CGGCT CGGCT CGGC
1 CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGC
1108023 TCGTGGTCGT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 92 1.00
ACGTcount: A:0.14, C:0.40, G:0.40, T:0.05
Consensus pattern (5 bp):
CGGCA
Found at i:1108034 original size:6 final size:6
Alignment explanation
Indices: 1108023--1108047 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1108013 TCGGCTCGGC
1108023 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
1108048 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:1113890 original size:5 final size:5
Alignment explanation
Indices: 1113870--1113913 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
1113860 CTCGTCTCAT
* * *
1113870 CTCGG CTAGG CTCGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1113914 TGGTCGTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.07, C:0.39, G:0.39, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:1113922 original size:6 final size:6
Alignment explanation
Indices: 1113911--1113977 Score: 98
Period size: 6 Copynumber: 11.2 Consensus size: 6
1113901 TCGGCTCGGC
* * * *
1113911 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1113959 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
1113978 AATACGTGTC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.06, C:0.16, G:0.49, T:0.28
Consensus pattern (6 bp):
TCGTGG
Found at i:1114277 original size:22 final size:22
Alignment explanation
Indices: 1114252--1114306 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1114242 TCAGGAGTTA
* *
1114252 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1114274 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1114296 CGGGAGTTATA
1 CAGGAGTTATA
1114307 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1114802 original size:5 final size:5
Alignment explanation
Indices: 1114788--1114828 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
1114778 CAGCCGCCGC
*
1114788 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT TGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
1114829 GGTCGGGTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
4 4 0.12
5 30 0.88
ACGTcount: A:0.00, C:0.39, G:0.22, T:0.39
Consensus pattern (5 bp):
CGTCT
Found at i:1114844 original size:20 final size:23
Alignment explanation
Indices: 1114821--1114867 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 23
1114811 TCGTCTTGTC
*
1114821 TCGTCTCG-GGTCG-GGTCG-GG
1 TCGTCTCGTAGTCGTGGTCGTGG
1114841 TCGTCTCGTAGTCGTGGTCGTGG
1 TCGTCTCGTAGTCGTGGTCGTGG
1114864 TCGT
1 TCGT
1114868 GGTAAAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 4 0.17
22 5 0.22
23 6 0.26
ACGTcount: A:0.02, C:0.23, G:0.43, T:0.32
Consensus pattern (23 bp):
TCGTCTCGTAGTCGTGGTCGTGG
Found at i:1118050 original size:33 final size:34
Alignment explanation
Indices: 1117991--1118073 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 34
1117981 ATTATATATA
1117991 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
1118025 TATATATATAATATTTTATAT-TTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
1118058 TATATATATAATATTT
1 TATATATATAATATTT
1118074 AATGAAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 28 0.57
34 21 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:1123506 original size:29 final size:29
Alignment explanation
Indices: 1123429--1123509 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
1123419 GCTTGATTCA
1123429 AGAACTCTTTTACGACTATCTTTACTTATT
1 AGAACTCTTTTACGAC-ATCTTTACTTATT
* * *
1123459 AGAACTCTTTCATGGCATCTTTACTTATT
1 AGAACTCTTTTACGACATCTTTACTTATT
*
1123488 AGAACTCTTTTACAACATCTTT
1 AGAACTCTTTTACGACATCTTT
1123510 GTCCAGCGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 31 0.70
30 13 0.30
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.44
Consensus pattern (29 bp):
AGAACTCTTTTACGACATCTTTACTTATT
Found at i:1128003 original size:20 final size:20
Alignment explanation
Indices: 1127974--1128026 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1127964 TATCCATTTG
1127974 AATT-TAAAAAAATCAGATAA
1 AATTATAAAAAAATCAGA-AA
1127994 AA-TATAAAAAAATCAGAAA
1 AATTATAAAAAAATCAGAAA
*
1128013 AATTACAAAAAAAT
1 AATTATAAAAAAAT
1128027 AGTAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.21
Consensus pattern (20 bp):
AATTATAAAAAAATCAGAAA
Found at i:1128125 original size:102 final size:102
Alignment explanation
Indices: 1127992--1128209 Score: 305
Period size: 102 Copynumber: 2.1 Consensus size: 102
1127982 AAAATCAGAT
* * *
1127992 AAAATATAAAAAAATCAGAAAAATTACAAAAAAATAGTAAATTTATTTATTTATTTTTAATATAT
1 AAAAAATAAAAAAATCAGAAAAATTACAAAAAAATAGTAAATTTATATATTTAATTTTAATATAT
* *
1128057 TTTTATCTATCTTGCAAATTAATCT-ATTTGAATTTAA
66 TTTTATCTATATTACAAATTAATCTAATTT-AATTTAA
* ** *
1128094 AAAAAATAGAAAAATCAGAAAAATTACAAAAAAATAGTATGTTTATATATTTAATTTTAATGTAT
1 AAAAAATAAAAAAATCAGAAAAATTACAAAAAAATAGTAAATTTATATATTTAATTTTAATATAT
* *
1128159 TTTTATCTATATTATAATTTAATCTAATTTAATTT-A
66 TTTTATCTATATTACAAATTAATCTAATTTAATTTAA
1128195 AAAAAATCAAAAAAA
1 AAAAAAT-AAAAAAA
1128210 ATGTAGCGTT
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
101 8 0.08
102 90 0.88
103 4 0.04
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (102 bp):
AAAAAATAAAAAAATCAGAAAAATTACAAAAAAATAGTAAATTTATATATTTAATTTTAATATAT
TTTTATCTATATTACAAATTAATCTAATTTAATTTAA
Found at i:1128193 original size:15 final size:17
Alignment explanation
Indices: 1128163--1128195 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1128153 ATGTATTTTT
1128163 ATCTATATTATAATTTA
1 ATCTATATTATAATTTA
1128180 ATCTA-ATT-TAATTTA
1 ATCTATATTATAATTTA
1128195 A
1 A
1128196 AAAAATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
ATCTATATTATAATTTA
Found at i:1129432 original size:29 final size:29
Alignment explanation
Indices: 1129390--1129503 Score: 194
Period size: 29 Copynumber: 3.9 Consensus size: 29
1129380 CAGTGGCAAC
*
1129390 ATAGGTCGCCATGCACGCCCGACGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1129419 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1129448 ATAGGTCGCCATGCACGCCCGGCGTCC-T
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
*
1129476 ATAAGGTCTCCATGCACGCCCGGCGTCC
1 AT-AGGTCGCCATGCACGCCCGGCGTCC
1129504 ATCATTATTT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 3 0.04
29 79 0.96
ACGTcount: A:0.16, C:0.39, G:0.26, T:0.19
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCTT
Found at i:1129561 original size:31 final size:31
Alignment explanation
Indices: 1129526--1129590 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
1129516 CCTGGTTCTT
*
1129526 TGCCCGTTGTTGCTCGCTGATGCTGCTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1129557 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1 TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
1129588 TGC
1 TGC
1129591 TATGCATGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.03, C:0.28, G:0.32, T:0.37
Consensus pattern (31 bp):
TGCCCGCTGTTGCTCGCTGATGCTGCTTTGG
Found at i:1129792 original size:29 final size:29
Alignment explanation
Indices: 1129753--1129823 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
1129743 AGGTTGCCGG
1129753 CGACATGGTAGGTCGCCATGGAGTCCCGA
1 CGACATGGTAGGTCGCCATGGAGTCCCGA
*
1129782 CGACATGGTAGGCCGCCATGGAGTCCCGA
1 CGACATGGTAGGTCGCCATGGAGTCCCGA
1129811 CGACATGGTAGGT
1 CGACATGGTAGGT
1129824 GGTAGGGTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.21, C:0.27, G:0.35, T:0.17
Consensus pattern (29 bp):
CGACATGGTAGGTCGCCATGGAGTCCCGA
Found at i:1129834 original size:12 final size:12
Alignment explanation
Indices: 1129817--1129841 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1129807 CCGACGACAT
1129817 GGTAGGTGGTAG
1 GGTAGGTGGTAG
1129829 GGTAGGTGGTAG
1 GGTAGGTGGTAG
1129841 G
1 G
1129842 TCGCCATGGA
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:0.16, C:0.00, G:0.60, T:0.24
Consensus pattern (12 bp):
GGTAGGTGGTAG
Found at i:1129920 original size:35 final size:35
Alignment explanation
Indices: 1129881--1129948 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
1129871 TCCTGCATCG
1129881 CGACCAAGCTTTAACTGTATCACTCATGCATGCAA
1 CGACCAAGCTTTAACTGTATCACTCATGCATGCAA
1129916 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1129949 GTTGCATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (35 bp):
CGACCAAGCTTTAACTGTATCACTCATGCATGCAA
Found at i:1130411 original size:21 final size:21
Alignment explanation
Indices: 1130386--1130429 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1130376 AATCTAGTTA
*
1130386 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTGGTTAGTATAAATT
* *
1130407 ATTAGTTGGTTAGTTTAAGTT
1 ATTAGTTGGTTAGTATAAATT
1130428 AT
1 AT
1130430 ATATTATATT
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:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (21 bp):
ATTAGTTGGTTAGTATAAATT
Found at i:1130851 original size:14 final size:14
Alignment explanation
Indices: 1130832--1130858 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1130822 AGTAATTTAT
1130832 TATTTTTTGTTGTC
1 TATTTTTTGTTGTC
1130846 TATTTTTTGTTGT
1 TATTTTTTGTTGT
1130859 TGTGTATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
TATTTTTTGTTGTC
Found at i:1130858 original size:17 final size:17
Alignment explanation
Indices: 1130829--1130861 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1130819 GTGAGTAATT
1130829 TATTATTTTTTGTTGTC
1 TATTATTTTTTGTTGTC
1130846 TATT-TTTTGTTGTTGT
1 TATTATTTT-TTGTTGT
1130862 GTATGTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.73
Consensus pattern (17 bp):
TATTATTTTTTGTTGTC
Found at i:1134191 original size:26 final size:26
Alignment explanation
Indices: 1134165--1134580 Score: 352
Period size: 26 Copynumber: 16.7 Consensus size: 26
1134155 GATGATTTAG
*
1134165 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
1134191 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
1134217 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
1134243 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
1134266 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
1134289 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
1134315 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
1134341 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
1134367 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
1134390 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
1134413 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
1134439 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
1134465 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
1134491 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
1134514 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
1134537 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
*
1134563 TAATGATTTTATAATAAT
1 TAATGATTTGATAATAAT
1134581 TAGTTATTAT
Statistics
Matches: 316, Mismatches: 50, Indels: 48
0.76 0.12 0.12
Matches are distributed among these distances:
21 12 0.04
22 9 0.03
23 36 0.11
24 21 0.07
25 21 0.07
26 214 0.68
27 3 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:1134327 original size:124 final size:124
Alignment explanation
Indices: 1134107--1134580 Score: 930
Period size: 124 Copynumber: 3.8 Consensus size: 124
1134097 ATGTATTTAT
1134107 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1134172 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1134231 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1134296 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1134355 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1134420 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1134479 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* *
1134544 TTGATAATAATCATTATAATAATGATTTTATAATAAT
66 TTGATAATAATCATTATAGTAATGATTTGATAATAAT
1134581 TAGTTATTAT
Statistics
Matches: 348, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 348 1.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:1134345 original size:150 final size:145
Alignment explanation
Indices: 1134162--1134505 Score: 412
Period size: 150 Copynumber: 2.3 Consensus size: 145
1134152 TTTGATGATT
* *
1134162 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATAATAATCATTATAAAAATGA-TT-
* * *
1134227 GTAATAATCATTATAAAAATGATTTAAT-A-ATGATTTA-AAT-ATTTAATGATTTGATGATT-T
63 -TAATAATCATT-T--AAAT-ATTTAATGATATGATTTAGAATGATTTAAT-A-ATAATCATTAT
1134287 AGTAATGATTTGATAATAATCATTA
121 AGTAATGATTTGATAATAATCATTA
1134312 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTA-TAATAATCATTATAAAAATGATTTA
* *
1134377 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
65 ATAATCATTTAAATATTTAATGA--T-ATGATTTAG-AATGATTTAATAATAATCATTATAGTAA
1134442 TGATTTGATAATAATCATTA
126 TGATTTGATAATAATCATTA
* *
1134462 TAATAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAAT
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTT-ATAAT
1134506 GATTTAAATA
Statistics
Matches: 173, Mismatches: 9, Indels: 24
0.84 0.04 0.12
Matches are distributed among these distances:
143 7 0.04
144 5 0.03
146 1 0.01
147 10 0.06
148 8 0.05
149 10 0.06
150 125 0.72
151 7 0.04
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (145 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTATAATAATCATTATAAAAATGATTTAA
TAATCATTTAAATATTTAATGATATGATTTAGAATGATTTAATAATAATCATTATAGTAATGATT
TGATAATAATCATTA
Found at i:1134659 original size:38 final size:38
Alignment explanation
Indices: 1134589--1134662 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1134579 ATTAGTTATT
* **
1134589 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
1134627 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
1134663 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:1137051 original size:15 final size:14
Alignment explanation
Indices: 1137028--1137058 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1137018 TACAACACTA
1137028 AACTTTAATATAAT
1 AACTTTAATATAAT
1137042 AACTTATAATATAAT
1 AACTT-TAATATAAT
1137057 AA
1 AA
1137059 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:1137066 original size:16 final size:16
Alignment explanation
Indices: 1137033--1137079 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1137023 CACTAAACTT
*
1137033 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
1137048 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
1137064 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
1137080 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:1137569 original size:21 final size:21
Alignment explanation
Indices: 1137539--1137591 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1137529 CCCTTTCTTC
* *
1137539 TTCTTACTTTCCTTTCTCCCT
1 TTCTTTCTTTCCTTTCTCACT
1137560 TTCTTTCTTTCCTTTCTCACT
1 TTCTTTCTTTCCTTTCTCACT
1137581 TTCTTTCTTTC
1 TTCTTTCTTTC
1137592 TCGGCTGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.04, C:0.34, G:0.00, T:0.62
Consensus pattern (21 bp):
TTCTTTCTTTCCTTTCTCACT
Found at i:1137582 original size:17 final size:16
Alignment explanation
Indices: 1137562--1137593 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1137552 TTCTCCCTTT
1137562 CTTTCTTTCCTTTCTCA
1 CTTTCTTT-CTTTCTCA
1137579 CTTTCTTTCTTTCTC
1 CTTTCTTTCTTTCTC
1137594 GGCTGCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTCTTTCTTTCTCA
Found at i:1137682 original size:25 final size:25
Alignment explanation
Indices: 1137654--1137705 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1137644 TTTCTTTTAT
1137654 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
1137679 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
1137704 AA
1 AA
1137706 TAATTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (25 bp):
AACCGGCTGCCTCAATTATTTCACC
Found at i:1137917 original size:29 final size:29
Alignment explanation
Indices: 1137884--1137992 Score: 157
Period size: 29 Copynumber: 3.8 Consensus size: 29
1137874 ATGGGAATGG
1137884 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
***
1137913 CGCCGGGACTACATGGCGACCTTGTAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
1137942 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
1137971 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
1137993 CTCTATTCCT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 69 0.97
30 2 0.03
ACGTcount: A:0.20, C:0.31, G:0.32, T:0.17
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:1138032 original size:13 final size:13
Alignment explanation
Indices: 1138014--1138039 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1138004 GTATAGGACT
1138014 GCATGGCGACCTC
1 GCATGGCGACCTC
1138027 GCATGGCGACCTC
1 GCATGGCGACCTC
1138040 TCCCCATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GCATGGCGACCTC
Found at i:1138762 original size:93 final size:93
Alignment explanation
Indices: 1138606--1138849 Score: 314
Period size: 93 Copynumber: 2.6 Consensus size: 93
1138596 AAACGTGGAC
** ** * * **
1138606 TCTTCTTCTTCTTCACCACCACCACCATAATCCAAAAAGAGCTTATTTTTCATTACTGTTCTTCT
1 TCTTCTTCTTCTTCTTCTTCACCACCATAATCCAAAAAGAGTTTACTTTTCATTACCATTCTTCT
* *
1138671 TATTTTCACCATAGTCACTCACGGGTCT
66 TATTTTCACCATAATCACTCACGGGCCT
1138699 TCTTCTTCTTCTTCTTCTTCACCACCATAATCCAAAAAGAGTTTACTTTTCATTACCATTCTTCT
1 TCTTCTTCTTCTTCTTCTTCACCACCATAATCCAAAAAGAGTTTACTTTTCATTACCATTCTTCT
* *
1138764 TCTTTTCACCATAATCACTCATGGGCCT
66 TATTTTCACCATAATCACTCACGGGCCT
* * *
1138792 TAATTTTTCTTCTTCTTCTT---CACCATTATCCAAAAAGAGTTTACTTTTCATTCACCAT
1 T-CTTCTTCTTCTTCTTCTTCACCACCATAATCCAAAAAGAGTTTACTTTTCATT-ACCAT
1138850 AATCACTCAC
Statistics
Matches: 134, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
91 31 0.23
92 5 0.04
93 82 0.61
94 16 0.12
ACGTcount: A:0.24, C:0.29, G:0.06, T:0.42
Consensus pattern (93 bp):
TCTTCTTCTTCTTCTTCTTCACCACCATAATCCAAAAAGAGTTTACTTTTCATTACCATTCTTCT
TATTTTCACCATAATCACTCACGGGCCT
Found at i:1143969 original size:57 final size:57
Alignment explanation
Indices: 1143899--1144014 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
1143889 ACTAACCCAC
* * *
1143899 AAGTATCGATACTTGTCCTTGGGTATCGATATTATACGATTATTATAAACTGAGGAG
1 AAGTATCAATACTTATCCTTGGGTATCGATATTATACGATTATTACAAACTGAGGAG
* *
1143956 AAGTATCAATACTTATCCTTGGGTATCGATATTATGCGGTTATTACAAACTGAGGAG
1 AAGTATCAATACTTATCCTTGGGTATCGATATTATACGATTATTACAAACTGAGGAG
1144013 AA
1 AA
1144015 ATGGTAGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.34
Consensus pattern (57 bp):
AAGTATCAATACTTATCCTTGGGTATCGATATTATACGATTATTACAAACTGAGGAG
Found at i:1146247 original size:21 final size:21
Alignment explanation
Indices: 1146221--1146294 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
1146211 AATTTGTCCT
1146221 GAAGGACCACTGTATTATCCC
1 GAAGGACCACTGTATTATCCC
*
1146242 GAAGGACCATTGTATTATCCC
1 GAAGGACCACTGTATTATCCC
*
1146263 GAAGGACCACTGTATTGTCCC
1 GAAGGACCACTGTATTATCCC
*
1146284 TAAGGACCACT
1 GAAGGACCACT
1146295 ATATCCCTCG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
GAAGGACCACTGTATTATCCC
Found at i:1147570 original size:16 final size:16
Alignment explanation
Indices: 1147566--1147605 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1147556 GAAGAAAAAG
1147566 GAAGAAGAAGAAGGAA
1 GAAGAAGAAGAAGGAA
1147582 GAAGAAGAAGAAGGAA
1 GAAGAAGAAGAAGGAA
1147598 GAAGAAGA
1 GAAGAAGA
1147606 CTGAAGAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAAGAAGAAGAAGGAA
Found at i:1147574 original size:3 final size:3
Alignment explanation
Indices: 1147550--1147605 Score: 67
Period size: 3 Copynumber: 17.7 Consensus size: 3
1147540 CTTCCACGGG
* *
1147550 GAA GAG GAA GAA AAA GGAA GAA GAA GAA GGAA GAA GAA GAA GAA GGAA
1 GAA GAA GAA GAA GAA -GAA GAA GAA GAA -GAA GAA GAA GAA GAA -GAA
1147598 GAA GAA GA
1 GAA GAA GA
1147606 CTGAAGAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 38 0.83
4 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1147605 original size:13 final size:13
Alignment explanation
Indices: 1147556--1147604 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
1147546 CGGGGAAGAG
*
1147556 GAAGAAAAAGGAA
1 GAAGAAGAAGGAA
1147569 GAAGAAGAAGGAA
1 GAAGAAGAAGGAA
1147582 GAAGAAGAA-GAA
1 GAAGAAGAAGGAA
1147594 GGAAGAAGAAG
1 -GAAGAAGAAG
1147605 ACTGAAGAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 3 0.09
13 30 0.91
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAGGAA
Found at i:1147612 original size:13 final size:12
Alignment explanation
Indices: 1147550--1147605 Score: 67
Period size: 13 Copynumber: 4.4 Consensus size: 12
1147540 CTTCCACGGG
*
1147550 GAAGAGGAAGAA
1 GAAGAAGAAGAA
*
1147562 AAAGGAAGAAGAA
1 GAA-GAAGAAGAA
1147575 GAAGGAAGAAGAA
1 GAA-GAAGAAGAA
1147588 GAAGAAGGAAGAA
1 GAAGAA-GAAGAA
1147601 GAAGA
1 GAAGA
1147606 CTGAAGAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
12 5 0.13
13 34 0.87
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAGAA
Found at i:1149843 original size:18 final size:16
Alignment explanation
Indices: 1149815--1149856 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
1149805 CGGTTTGACC
*
1149815 CGTTGATTTTGACTAG
1 CGTTGACTTTGACTAG
1149831 ACTGTTGACTTTGACTAG
1 -C-GTTGACTTTGACTAG
1149849 CGTTGACT
1 CGTTGACT
1149857 GTTGTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 2 0.09
18 14 0.61
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (16 bp):
CGTTGACTTTGACTAG
Found at i:1154668 original size:21 final size:21
Alignment explanation
Indices: 1154608--1154668 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
1154598 CAGAACCCTC
* **
1154608 AGGGGGTATCGATTCCCCTGT
1 AGGGGGTATCGATTCCCTTCA
* * *
1154629 TGGGGGAATCGGTTCCCCTTCA
1 AGGGGGTATCGATT-CCCTTCA
1154651 AGGGGGTATCGATTCCCT
1 AGGGGGTATCGATTCCCT
1154669 CTGCACCAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.28
Consensus pattern (21 bp):
AGGGGGTATCGATTCCCTTCA
Found at i:1163599 original size:60 final size:59
Alignment explanation
Indices: 1163530--1163711 Score: 217
Period size: 59 Copynumber: 3.1 Consensus size: 59
1163520 TTTGGAGGAA
*
1163530 TTTGAGGATGAAATTGGAA-GATCTAAAAGTTT-AGTGATTAATTTAGAATGAGATTCATAG
1 TTTGAGGATGAAATTGGAACG-T-TAAAAGTTTAAG-GATTAATTTAGAATGAGAGTCATAG
* * * * *
1163590 TTTGAGGATGAAATTAGAACGTTCAAAGTTTAAGAACTAATTAAGAATGAGAGTCATAG
1 TTTGAGGATGAAATTGGAACGTTAAAAGTTTAAGGATTAATTTAGAATGAGAGTCATAG
* * * *
1163649 TTTGAGGATGAAA-TGTAATGTTTAAAAGTTTAAGGATTAATTTAAAATGAGGGTCATAG
1 TTTGAGGATGAAATTGGAACG-TTAAAAGTTTAAGGATTAATTTAGAATGAGAGTCATAG
1163708 TTTG
1 TTTG
1163712 GGGACATATG
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
58 4 0.04
59 78 0.75
60 21 0.20
61 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (59 bp):
TTTGAGGATGAAATTGGAACGTTAAAAGTTTAAGGATTAATTTAGAATGAGAGTCATAG
Found at i:1163607 original size:31 final size:31
Alignment explanation
Indices: 1163572--1163662 Score: 84
Period size: 31 Copynumber: 3.0 Consensus size: 31
1163562 AGTGATTAAT
1163572 TTAGAATGAGATTCATAGTTTGAGGATGAAA
1 TTAGAATGAGATTCATAGTTTGAGGATGAAA
* * * *
1163603 TTAGAA--CG-TTCAAAGTTTAAGAACT--AA
1 TTAGAATGAGATTCATAGTTTGAGGA-TGAAA
*
1163630 TTAAGAATGAGAGTCATAGTTTGAGGATGAAA
1 TT-AGAATGAGATTCATAGTTTGAGGATGAAA
1163662 T
1 T
1163663 GTAATGTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 13
0.67 0.14 0.20
Matches are distributed among these distances:
27 4 0.09
28 16 0.36
29 2 0.05
30 2 0.05
31 17 0.39
32 3 0.07
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (31 bp):
TTAGAATGAGATTCATAGTTTGAGGATGAAA
Found at i:1170055 original size:147 final size:147
Alignment explanation
Indices: 1169786--1170065 Score: 386
Period size: 147 Copynumber: 1.9 Consensus size: 147
1169776 ATGGCAAGGA
* *
1169786 AATTCCAAGCAACCATGGAAAGCTTGATTTGTCGAGAATGGGACATAAGGAAGGAGACACTAAGT
1 AATTCCAAGCAACCATGGAAAGCTTGATTTGTCAAGAATGGAACATAAGGAAGGAGACACTAAGT
* * *
1169851 TTAAGGGAGGACTTCCGTCTTTTACTTGTCCATGAATTTGCATGAGTGTTAAGAAATTTGCATAA
66 TTAAGGGAGGACATCCATCTTTTACTTGTCCATGAATTTACATGAGTGTTAAGAAATTTGCATAA
1169916 CATTATAAATTTGCATG
131 CATTATAAATTTGCATG
* * *
1169933 AATTCCAAG-AAGCCATGGAAAGCTTGATTTGTCAAGATTGGAACGTGAGGAAAGG-GACACTAT
1 AATTCCAAGCAA-CCATGGAAAGCTTGATTTGTCAAGAATGGAACATAAGG-AAGGAGACACTA-
* * * * *
1169996 A-TTTGAGGGATGACATCCATCTTTTACTTGTGCATTAATTTACATGAGTGTTAATAAATTTGCA
63 AGTTTAAGGGAGGACATCCATCTTTTACTTGTCCATGAATTTACATGAGTGTTAAGAAATTTGCA
*
1170060 TGACAT
128 TAACAT
1170066 AAAGTTGCAT
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
146 2 0.02
147 109 0.94
148 5 0.04
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (147 bp):
AATTCCAAGCAACCATGGAAAGCTTGATTTGTCAAGAATGGAACATAAGGAAGGAGACACTAAGT
TTAAGGGAGGACATCCATCTTTTACTTGTCCATGAATTTACATGAGTGTTAAGAAATTTGCATAA
CATTATAAATTTGCATG
Found at i:1170981 original size:2 final size:2
Alignment explanation
Indices: 1170974--1171006 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1170964 ACACAATTCG
1170974 AT 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 AT A
1171007 ATTCTTTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1171488 original size:28 final size:28
Alignment explanation
Indices: 1171440--1171494 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
1171430 CAACACAACT
* * *
1171440 TTTTATAAATCACATTTAAGGACAAAAC
1 TTTTATAAATTACAATAAAGGACAAAAC
* *
1171468 TTTTATAAATTACACTAAAGGATAAAA
1 TTTTATAAATTACAATAAAGGACAAAA
1171495 TATTTTAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (28 bp):
TTTTATAAATTACAATAAAGGACAAAAC
Found at i:1171514 original size:49 final size:49
Alignment explanation
Indices: 1171457--1171555 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 49
1171447 AATCACATTT
* * * *
1171457 AAGGACAAAACTTT-TATAAATTACACTAAAGGATAAAATATTTTAGTAA
1 AAGGACAAAACTTTACATAAATTAAAATAAAGGACAAAATATTTTA-TAA
*
1171506 AAGGACAAAACTTTACATAAATTAAAATTAAGGACAAAATATTTTATAA
1 AAGGACAAAACTTTACATAAATTAAAATAAAGGACAAAATATTTTATAA
1171555 A
1 A
1171556 TTAAAATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 18 0.41
50 26 0.59
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (49 bp):
AAGGACAAAACTTTACATAAATTAAAATAAAGGACAAAATATTTTATAA
Found at i:1171554 original size:29 final size:29
Alignment explanation
Indices: 1171506--1171616 Score: 109
Period size: 29 Copynumber: 3.8 Consensus size: 29
1171496 ATTTTAGTAA
*
1171506 AAGGACAAAAC-TTTACATAAATTAAAATT
1 AAGGACAAAACATTT-TATAAATTAAAATT
*
1171535 AAGGACAAAATATTTTATAAATTAAAATT
1 AAGGACAAAACATTTTATAAATTAAAATT
** * *
1171564 AAGGTTAAAACCTTTTATAAATTATAA-T
1 AAGGACAAAACATTTTATAAATTAAAATT
* * *
1171592 AGAGGCCACAACTTTTTATAAATTA
1 A-AGGACAAAACATTTTATAAATTA
1171617 CATTAAAGGA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 64 0.93
30 3 0.04
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (29 bp):
AAGGACAAAACATTTTATAAATTAAAATT
Found at i:1175376 original size:2 final size:2
Alignment explanation
Indices: 1175369--1175395 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1175359 GGTAGTTTTG
1175369 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 T
1175396 GATGTAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1180100 original size:31 final size:32
Alignment explanation
Indices: 1180064--1180125 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
1180054 TCAATAACAC
*
1180064 TCATCATCTCCAATGATAAA-TTAAGTAAAAA
1 TCATCATCTCCAATGACAAATTTAAGTAAAAA
1180095 TCATCATCTCCAATGACAAATTTAAGTAAAA
1 TCATCATCTCCAATGACAAATTTAAGTAAAA
1180126 TCTTATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (32 bp):
TCATCATCTCCAATGACAAATTTAAGTAAAAA
Found at i:1181390 original size:24 final size:24
Alignment explanation
Indices: 1181363--1181424 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
1181353 CGTTCGTGAA
*
1181363 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
* *
1181387 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
1181411 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
1181425 TAACCTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.13, C:0.11, G:0.23, T:0.53
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:1182949 original size:10 final size:10
Alignment explanation
Indices: 1182934--1183008 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
1182924 GGGTCTCCAA
1182934 CGTTTATGTT
1 CGTTTATGTT
1182944 CGTTTATGTT
1 CGTTTATGTT
1182954 CG----TGTT
1 CGTTTATGTT
*
1182960 CATTTATGTT
1 CGTTTATGTT
*
1182970 CGTGTT-CGTTT
1 CGT-TTATG-TT
* *
1182981 ATGTTTGTGTT
1 -CGTTTATGTT
1182992 CGTTTATGTT
1 CGTTTATGTT
1183002 CGTTTAT
1 CGTTTAT
1183009 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 8 0.16
12 3 0.06
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1182965 original size:16 final size:16
Alignment explanation
Indices: 1182940--1183004 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1182930 CCAACGTTTA
1182940 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1182956 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1182972 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
1182988 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1183004 T
1 T
1183005 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1183095 original size:16 final size:16
Alignment explanation
Indices: 1183074--1183105 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1183064 AAAAAAATTT
1183074 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1183090 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1183106 CTTATTTATT
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:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1184959 original size:31 final size:31
Alignment explanation
Indices: 1184893--1184952 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1184883 CAATTTAAGG
*
1184893 CAAAATAGTTTTTGGACTTGAATTGAATTTA
1 CAAAATAGTATTTGGACTTGAATTGAATTTA
1184924 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATAGTATTTGGACTTGAATTGAATTTA
1184953 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATAGTATTTGGACTTGAATTGAATTTA
Found at i:1200572 original size:10 final size:10
Alignment explanation
Indices: 1200557--1200583 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1200547 CCCCACTTTG
1200557 AAAAAAAAGA
1 AAAAAAAAGA
1200567 AAAAAAAAGA
1 AAAAAAAAGA
1200577 AAAAAAA
1 AAAAAAA
1200584 TGAAGTTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:1209219 original size:28 final size:28
Alignment explanation
Indices: 1209188--1209266 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
1209178 GGCTAGTAAC
* *
1209188 CAAAATATAAGTTTTAAAAGTTTAGTG-G
1 CAAAATATAAATTTTAAAAGTTTA-TGAA
* *
1209216 CAAAGTATAAATTTGGAAAAGTTTATGAA
1 CAAAATATAAATTT-TAAAAGTTTATGAA
* *
1209245 AAAAATATAATTTTTAAAAGTT
1 CAAAATATAAATTTTAAAAGTT
1209267 ATATATTTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 21 0.51
29 20 0.49
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.35
Consensus pattern (28 bp):
CAAAATATAAATTTTAAAAGTTTATGAA
Found at i:1220157 original size:16 final size:16
Alignment explanation
Indices: 1220136--1220168 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1220126 ACTTCTATGA
1220136 AAAACAACTCCTTTCT
1 AAAACAACTCCTTTCT
1220152 AAAACAACTCCTTTCT
1 AAAACAACTCCTTTCT
1220168 A
1 A
1220169 CCACTAAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAACAACTCCTTTCT
Found at i:1222288 original size:28 final size:28
Alignment explanation
Indices: 1222256--1222320 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
1222246 TCATATCTTT
1222256 TAAAATTTTATAAATTTGTTTCTTAATA
1 TAAAATTTTATAAATTTGTTTCTTAATA
*
1222284 TAAAATTTTATAAATTTGTTTTTTAATA
1 TAAAATTTTATAAATTTGTTTCTTAATA
1222312 TAAAATTTT
1 TAAAATTTT
1222321 GTTTCCGTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (28 bp):
TAAAATTTTATAAATTTGTTTCTTAATA
Found at i:1224205 original size:3 final size:3
Alignment explanation
Indices: 1224197--1224271 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
1224187 AAGCATTGGG
1224197 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1224245 A-A ATA ATA AT- ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1224272 GGTTTGGAGT
Statistics
Matches: 70, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.06
3 66 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1224534 original size:16 final size:16
Alignment explanation
Indices: 1224513--1224543 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1224503 ATAAATAAAT
1224513 GAACATAAACGAACAC
1 GAACATAAACGAACAC
*
1224529 GAACATAAGCGAACA
1 GAACATAAACGAACA
1224544 ATTTTTTTTT
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:0.55, C:0.23, G:0.16, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:1224645 original size:16 final size:16
Alignment explanation
Indices: 1224605--1224651 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
1224595 TGTTCATTTA
1224605 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
1224619 ATAAA-GAACACGAAC
1 ATAAATGAACACGAAC
1224634 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
1224650 AT
1 AT
1224652 TAACGTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.23
15 11 0.37
16 12 0.40
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.13
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:1228828 original size:3 final size:3
Alignment explanation
Indices: 1228816--1228856 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1228806 CACTCAAATC
1228816 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1228857 GAACAAACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1240378 original size:21 final size:23
Alignment explanation
Indices: 1240331--1240379 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1240321 GTACTGTGTT
* *
1240331 TATTTTTAAAAATTAAATTAACT
1 TATTTGTAAAAATTAAATTAACG
*
1240354 TATTTGTAAATATTAAA-TAA-G
1 TATTTGTAAAAATTAAATTAACG
1240375 TATTT
1 TATTT
1240380 TTATAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.22
22 3 0.13
23 15 0.65
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TATTTGTAAAAATTAAATTAACG
Found at i:1240403 original size:22 final size:23
Alignment explanation
Indices: 1240331--1240406 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 23
1240321 GTACTGTGTT
*
1240331 TATTTTTA-AAA-ATTAAATTAAC
1 TATTTTTATAAATATTAAA-TAAA
* * *
1240353 T-TATTTGTAAATATTAAATAAG
1 TATTTTTATAAATATTAAATAAA
*
1240375 TATTTTTATAAATA-TAATTAAA
1 TATTTTTATAAATATTAAATAAA
1240397 TATTTTTATA
1 TATTTTTATA
1240407 TAAAAGTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 4 0.09
22 24 0.55
23 16 0.36
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (23 bp):
TATTTTTATAAATATTAAATAAA
Found at i:1242504 original size:18 final size:19
Alignment explanation
Indices: 1242481--1242523 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1242471 CAACAATCTT
1242481 ATTCC-CTAGTAATCTTAC
1 ATTCCACTAGTAATCTTAC
* *
1242499 ATTCCCACTAGTAATTTTAT
1 ATT-CCACTAGTAATCTTAC
1242519 ATTCC
1 ATTCC
1242524 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.19
20 14 0.67
ACGTcount: A:0.28, C:0.26, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTCCACTAGTAATCTTAC
Found at i:1242511 original size:20 final size:20
Alignment explanation
Indices: 1242486--1242523 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1242476 ATCTTATTCC
1242486 CTAGTAATCTTACATTCCCA
1 CTAGTAATCTTACATTCCCA
* *
1242506 CTAGTAATTTTATATTCC
1 CTAGTAATCTTACATTCC
1242524 GTGAACCAAA
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:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (20 bp):
CTAGTAATCTTACATTCCCA
Found at i:1251149 original size:20 final size:20
Alignment explanation
Indices: 1251124--1251175 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1251114 TAGTTGAAAA
*
1251124 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
*
1251144 TCGCGTTGTGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1251164 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1251176 AGTCTATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1251220 original size:41 final size:41
Alignment explanation
Indices: 1251167--1251256 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
1251157 TTCCATTTCG
* *
1251167 CGTTGCGATAGTCTATAGTTGTCGTTGCTATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
*
1251208 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCTAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1251249 CGTTGCGA
1 CGTTGCGA
1251257 AAATTCGTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:1251244 original size:22 final size:22
Alignment explanation
Indices: 1251167--1251238 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
1251157 TTCCATTTCG
*
1251167 CGTTGCGATAGTCTATAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * **
1251189 CGTTGC--TATTTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
1251208 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1251230 CGTTGCGAT
1 CGTTGCGAT
1251239 TTTCTAAATT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 7 0.19
20 6 0.17
21 7 0.19
22 16 0.44
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1251253 original size:19 final size:19
Alignment explanation
Indices: 1251188--1251256 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
1251178 TCTATAGTTG
* *
1251188 TCGTTGCTATTTTCCAAAT
1 TCGTTGCGATTTTCTAAAT
** *
1251207 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGATTTTCTA-A-AT
1251228 GTCGTTGCGATTTTCTAAAT
1 -TCGTTGCGATTTTCTAAAT
1251248 TCGTTGCGA
1 TCGTTGCGA
1251257 AAATTCGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 21 0.54
20 2 0.05
21 2 0.05
22 14 0.36
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCTAAAT
Found at i:1252078 original size:21 final size:21
Alignment explanation
Indices: 1252017--1252078 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
1252007 AACTGTAGAT
*
1252017 TATCGCAACGCGAAATGGAA-
1 TATCGCAACGCGAAATGCAAC
* ** *
1252037 AATCGCAACGCGATTTTCAAC
1 TATCGCAACGCGAAATGCAAC
1252058 TATCGCAACGCGAAATGCAAC
1 TATCGCAACGCGAAATGCAAC
1252079 GCGAATTTGC
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (21 bp):
TATCGCAACGCGAAATGCAAC
Found at i:1253709 original size:18 final size:18
Alignment explanation
Indices: 1253686--1253738 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
1253676 GAAAGGCTTA
1253686 TAAAATTTGATTTTTTTG
1 TAAAATTTGATTTTTTTG
1253704 TAAAATTTGATTTTTTTG
1 TAAAATTTGATTTTTTTG
1253722 TAAAATTTGATTTTTTT
1 TAAAATTTGATTTTTTT
1253739 TGGAAACTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (18 bp):
TAAAATTTGATTTTTTTG
Found at i:1254564 original size:14 final size:14
Alignment explanation
Indices: 1254540--1254582 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1254530 TTTCTTTTAA
*
1254540 ATTATATTTTAAAT
1 ATTAAATTTTAAAT
*
1254554 TTTAAATTTTAAAT
1 ATTAAATTTTAAAT
*
1254568 ATTATATATTTAAAT
1 ATTAAAT-TTTAAAT
1254583 CAAATAAGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTAAATTTTAAAT
Found at i:1255440 original size:18 final size:18
Alignment explanation
Indices: 1255413--1255451 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1255403 AATCATATAT
1255413 TTAATGACATATG-TTTAA
1 TTAATGACATA-GCTTTAA
*
1255431 TTAATTACATAGCTTTAA
1 TTAATGACATAGCTTTAA
1255449 TTA
1 TTA
1255452 GGTCACCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (18 bp):
TTAATGACATAGCTTTAA
Found at i:1256407 original size:41 final size:41
Alignment explanation
Indices: 1256350--1256445 Score: 176
Period size: 41 Copynumber: 2.4 Consensus size: 41
1256340 TTTTCACCTA
1256350 ACCCGAACCAGAACCAGAACCGATATATAACTTAAAAACCG
1 ACCCGAACCAGAACCAGAACCGATATATAACTTAAAAACCG
1256391 ACCCGAACCAGAACCAGAACCGATATATAACTTAAAAACCG
1 ACCCGAACCAGAACCAGAACCGATATATAACTTAAAAACCG
*
1256432 ACCCG-ACCCGAACC
1 ACCCGAACCAGAACC
1256446 CGAATATTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 8 0.15
41 46 0.85
ACGTcount: A:0.44, C:0.33, G:0.12, T:0.10
Consensus pattern (41 bp):
ACCCGAACCAGAACCAGAACCGATATATAACTTAAAAACCG
Found at i:1257588 original size:35 final size:35
Alignment explanation
Indices: 1257548--1257626 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
1257538 CATACGGGAA
1257548 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1257583 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1 CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
1257618 CATACGAGC
1 CATACGAGC
1257627 GTTCTCCCCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.27, C:0.34, G:0.20, T:0.19
Consensus pattern (35 bp):
CATACGAGCCAATGGTTCTCCCCATGCATACGAGC
Found at i:1257642 original size:26 final size:26
Alignment explanation
Indices: 1257613--1257670 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
1257603 CCCATGCATA
1257613 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
1257639 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
1257665 CGAGCC
1 CGAGCC
1257671 CCATGCATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.19, C:0.40, G:0.24, T:0.17
Consensus pattern (26 bp):
CGAGCCATACGAGCGTTCTCCCCATG
Found at i:1257686 original size:67 final size:67
Alignment explanation
Indices: 1257602--1257819 Score: 276
Period size: 67 Copynumber: 3.0 Consensus size: 67
1257592 CAATGGTTCT
1257602 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
1257667 AG
66 AG
*
1257669 CCCCATGCATACGAGCCATACGAGTGTTCTCCCCATGCGAGCCATACGAGCGTTCT-CCCATGCG
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
1257733 AGGTGG
66 A----G
1257739 TTCCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCGT
1 ---CCCCATGCATACGAGCCATACGAG-C----GTTCTCCCCATG----CGAGCCATACGAGCGT
1257804 TCTCCCCATGCGAG
54 TCTCCCCATGCGAG
1257818 CC
1 CC
1257820 ATACGAGCGT
Statistics
Matches: 132, Mismatches: 2, Indels: 25
0.83 0.01 0.16
Matches are distributed among these distances:
66 9 0.07
67 55 0.42
70 1 0.01
73 24 0.18
76 2 0.02
78 12 0.09
79 1 0.01
82 19 0.14
83 9 0.07
ACGTcount: A:0.21, C:0.37, G:0.22, T:0.19
Consensus pattern (67 bp):
CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
AG
Found at i:1257711 original size:26 final size:26
Alignment explanation
Indices: 1257680--1257845 Score: 134
Period size: 26 Copynumber: 6.2 Consensus size: 26
1257670 CCCATGCATA
*
1257680 CGAGCCATACGAGTGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
1257706 CGAGCCATACGAGCGTTCT-CCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
*
1257731 CGAG------GTG-GTTC-CCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
1257749 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 ----CGAGCCATACGAG-C----GTTCTCCCCATG
1257784 CATACGAGCCATACGAGCGTTCTCCCCATG
1 ----CGAGCCATACGAGCGTTCTCCCCATG
1257814 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
1257840 CGAGCC
1 CGAGCC
1257846 CCATGCATAC
Statistics
Matches: 119, Mismatches: 3, Indels: 36
0.75 0.02 0.23
Matches are distributed among these distances:
18 10 0.08
19 2 0.02
22 4 0.03
25 10 0.08
26 50 0.42
28 2 0.02
30 12 0.10
34 5 0.04
35 24 0.20
ACGTcount: A:0.20, C:0.36, G:0.23, T:0.20
Consensus pattern (26 bp):
CGAGCCATACGAGCGTTCTCCCCATG
Found at i:1257794 original size:108 final size:97
Alignment explanation
Indices: 1257597--1257909 Score: 388
Period size: 92 Copynumber: 3.5 Consensus size: 97
1257587 CGAGCCAATG
1257597 GTTCTCCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCC
1 GTTCTCCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCC
*
1257662 ATGCGAGCCCCATGCATACGAGCCATACGAGT
66 ATGCGAGCCCCATGCATACGAGCCATACGAGC
*
1257694 GTTCTCCCCATG----CGAGCCATACGAGCGTTCT-CCCATGCGAG------GTG-GTTC-CCCC
1 GTTCTCCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCC
** * *
1257746 ATGC-A-TACGA-GCCATACGAGCCA-A--TG-
66 ATGCGAGCCCCATG-CATACGAGCCATACGAGC
1257772 GTTCTCCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCC
1 GTTCTCCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCC
1257837 ATGCGAGCCCCATGCATACGAGCCATACGAGC
66 ATGCGAGCCCCATGCATACGAGCCATACGAGC
1257869 GTTCT-CCCATG----CGAGCCATACGAGCGTTCTCCCCATGCGAG
1 GTTCTCCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAG
1257910 GTGGCCATGC
Statistics
Matches: 185, Mismatches: 10, Indels: 47
0.76 0.04 0.19
Matches are distributed among these distances:
78 12 0.06
79 1 0.01
81 2 0.01
82 32 0.17
83 11 0.06
84 8 0.04
85 4 0.02
86 2 0.01
89 2 0.01
90 4 0.02
91 8 0.04
92 41 0.22
93 32 0.17
94 2 0.01
96 7 0.04
97 17 0.09
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.20
Consensus pattern (97 bp):
GTTCTCCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCC
ATGCGAGCCCCATGCATACGAGCCATACGAGC
Found at i:1257858 original size:175 final size:176
Alignment explanation
Indices: 1257560--1257913 Score: 676
Period size: 175 Copynumber: 2.0 Consensus size: 176
1257550 TACGAGCCAA
1257560 TGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGA
1 TGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGA
1257625 GCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAGCCATAC
66 GCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAGCCATAC
*
1257690 GAGTGTTCTCCCCATGCGAGCCATACGAGCGTTCT-CCCATGCGAGG
131 GAGCGTTCT-CCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGG
1257736 TGGTTC-CCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGA
1 TGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGA
1257800 GCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAGCCATAC
66 GCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAGCCATAC
1257865 GAGCGTTCTCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGG
131 GAGCGTTCTCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGG
1257911 TGG
1 TGG
1257914 CCATGCAGTG
Statistics
Matches: 176, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
174 25 0.14
175 145 0.82
176 6 0.03
ACGTcount: A:0.21, C:0.36, G:0.23, T:0.20
Consensus pattern (176 bp):
TGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGA
GCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGCCCCATGCATACGAGCCATAC
GAGCGTTCTCCCATGCGAGCCATACGAGCGTTCTCCCCATGCGAGG
Found at i:1257886 original size:25 final size:26
Alignment explanation
Indices: 1257855--1257909 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 26
1257845 CCCATGCATA
1257855 CGAGCCATACGAGCGTTCT-CCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
1257880 CGAGCCATACGAGCGTTCTCCCCATG
1 CGAGCCATACGAGCGTTCTCCCCATG
1257906 CGAG
1 CGAG
1257910 GTGGCCATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.18
Consensus pattern (26 bp):
CGAGCCATACGAGCGTTCTCCCCATG
Found at i:1257906 original size:66 final size:67
Alignment explanation
Indices: 1257777--1257909 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 67
1257767 CAATGGTTCT
1257777 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
1257842 AG
66 AG
1257844 CCCCATGCATACGAGCCATACGAGCGTTCT-CCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
1 CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
1257908 AG
66 AG
1257910 GTGGCCATGC
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
66 36 0.55
67 30 0.45
ACGTcount: A:0.21, C:0.38, G:0.23, T:0.18
Consensus pattern (67 bp):
CCCCATGCATACGAGCCATACGAGCGTTCTCCCCATGCGAGCCATACGAGCGTTCTCCCCATGCG
AG
Found at i:1258017 original size:28 final size:29
Alignment explanation
Indices: 1257932--1258039 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
1257922 TGGAATAGAG
* *
1257932 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
1257961 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1257990 AGGTCGCCATGTAGT-CCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1258018 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
1258040 CCATTCCCAT
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
28 28 0.37
29 45 0.60
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:1258058 original size:13 final size:13
Alignment explanation
Indices: 1258040--1258071 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1258030 AGTCCCGGCG
*
1258040 CCATTCCCATCGT
1 CCATTCCCATCAT
1258053 CCATTCCCATCAT
1 CCATTCCCATCAT
1258066 CCATTC
1 CCATTC
1258072 ACATGCAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.47, G:0.03, T:0.31
Consensus pattern (13 bp):
CCATTCCCATCAT
Found at i:1258279 original size:25 final size:25
Alignment explanation
Indices: 1258251--1258302 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1258241 TGTACAATTA
*
1258251 TTGGTGAAATAATTAAGGCAGTCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
*
1258276 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
1258301 TT
1 TT
1258303 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (25 bp):
TTGGTGAAATAATTAAGGCAGCCGG
Found at i:1258398 original size:21 final size:20
Alignment explanation
Indices: 1258365--1258415 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
1258355 TTGCAGCCGA
1258365 GAAAGAA-AAAGGGAGAAAG
1 GAAAGAAGAAAGGGAGAAAG
1258384 GAAAGAAAGAAAGGGAGAAAG
1 GAAAG-AAGAAAGGGAGAAAG
1258405 GAAAGTAAGAA
1 GAAAG-AAGAA
1258416 GAAGAAAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 5 0.17
20 2 0.07
21 22 0.76
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (20 bp):
GAAAGAAGAAAGGGAGAAAG
Found at i:1258688 original size:41 final size:40
Alignment explanation
Indices: 1258578--1258688 Score: 100
Period size: 44 Copynumber: 2.6 Consensus size: 40
1258568 TACATAAATT
* *
1258578 AAAAATTATTTAATTAGTATATGT-TTGATAGTTATATAGTTA
1 AAAAATTA-TTAATTAGT-T-TGTGTTAATAGTTATATAGTAA
* *
1258620 AAAAATAATTAATTAGTTTTTATTGTTAATAGTTAGTTATA-TAA
1 AAAAATTATTAATTAG--TTT-GTGTTAATAGTTA--TATAGTAA
1258664 AAAAATTATTAATTAGTTTGTGTTA
1 AAAAATTATTAATTAGTTTGTGTTA
1258689 GATAAATAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
41 14 0.25
42 12 0.21
43 10 0.18
44 17 0.30
45 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (40 bp):
AAAAATTATTAATTAGTTTGTGTTAATAGTTATATAGTAA
Found at i:1261112 original size:26 final size:24
Alignment explanation
Indices: 1261054--1261112 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
1261044 CTAATAAACC
*
1261054 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
1261078 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
1261106 TAATAAT
1 TAATAAT
1261113 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:1261954 original size:27 final size:28
Alignment explanation
Indices: 1261916--1261994 Score: 101
Period size: 27 Copynumber: 2.9 Consensus size: 28
1261906 ATATAATATA
1261916 ATATATAACTTAAACTAATAAACTAA-T
1 ATATATAACTTAAACTAATAAACTAATT
*
1261943 ATATATAACTTAAACTAACAAACTAATT
1 ATATATAACTTAAACTAATAAACTAATT
* *
1261971 TTATACTAAC--AAACTAATTAACTA
1 ATATA-TAACTTAAACTAATAAACTA
1261995 GATTTTAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
27 37 0.80
28 5 0.11
29 4 0.09
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (28 bp):
ATATATAACTTAAACTAATAAACTAATT
Found at i:1262477 original size:33 final size:34
Alignment explanation
Indices: 1262417--1262564 Score: 191
Period size: 33 Copynumber: 4.4 Consensus size: 34
1262407 CCATGCACAG
*
1262417 TTCCCACGTCCAATGCACCATCCCCTCCCCCATGCA
1 TTCCCACGTCCCATG--CCATCCCCTCCCCCATGCA
1262453 TTCCCACGTCCCATG-CATCCCCTCCCCCATGCA
1 TTCCCACGTCCCATGCCATCCCCTCCCCCATGCA
* **
1262486 TTCCCACATCCCATGTTGAT-CCCTCCCCCATGCA
1 TTCCCACGTCCCATG-CCATCCCCTCCCCCATGCA
1262520 TTCCCAC--CCCATG-CATCCCC-CCCCCATGCA
1 TTCCCACGTCCCATGCCATCCCCTCCCCCATGCA
1262550 TTCCCACGTCCCATG
1 TTCCCACGTCCCATG
1262565 TTGATTGCAT
Statistics
Matches: 103, Mismatches: 4, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
30 19 0.18
31 3 0.03
32 12 0.12
33 32 0.31
34 21 0.20
35 2 0.02
36 14 0.14
ACGTcount: A:0.17, C:0.53, G:0.09, T:0.22
Consensus pattern (34 bp):
TTCCCACGTCCCATGCCATCCCCTCCCCCATGCA
Found at i:1262529 original size:15 final size:15
Alignment explanation
Indices: 1262444--1262556 Score: 93
Period size: 15 Copynumber: 7.1 Consensus size: 15
1262434 CCATCCCCTC
1262444 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
1262459 CGTCCCATGCATCCCCTC
1 C--CCCATGCATTCCC-A
1262477 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
1262492 CATCCCATG-TTGATCCCTC
1 C--CCCATGCAT--TCCC-A
1262511 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
1262526 CCCCATGCATCCCCC
1 CCCCATGCATTCCCA
1262541 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
1262556 C
1 C
1262557 GTCCCATGTT
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
15 29 0.38
16 17 0.22
17 24 0.31
18 6 0.08
19 1 0.01
ACGTcount: A:0.17, C:0.54, G:0.08, T:0.21
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:1262562 original size:64 final size:66
Alignment explanation
Indices: 1262439--1262569 Score: 230
Period size: 64 Copynumber: 2.0 Consensus size: 66
1262429 ATGCACCATC
1262439 CCCTCCCCCATGCATTCCCACGTCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTG
1 CCCTCCCCCATGCATTCCCACG-CCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTG
1262504 AT
65 AT
*
1262506 CCCTCCCCCATGCATTCCCAC-CCCATGCATCCCC-CCCCCATGCATTCCCACGTCCCATGTTGA
1 CCCTCCCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGA
1262569 T
66 T
1262570 TGCATGGCGA
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
64 29 0.46
65 13 0.21
67 21 0.33
ACGTcount: A:0.16, C:0.52, G:0.09, T:0.23
Consensus pattern (66 bp):
CCCTCCCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGA
T
Found at i:1262564 original size:17 final size:16
Alignment explanation
Indices: 1262443--1262556 Score: 108
Period size: 17 Copynumber: 7.1 Consensus size: 16
1262433 ACCATCCCCT
1262443 CCCCCATGCATTCCCA
1 CCCCCATGCATTCCCA
* * *
1262459 CGTCCCATGCATCCCCT
1 C-CCCCATGCATTCCCA
1262476 CCCCCATGCATTCCCA
1 CCCCCATGCATTCCCA
* * *
1262492 CATCCCATG-TTGATCCCT
1 C-CCCCATGCAT--TCCCA
1262510 CCCCCATGCATTCCCA
1 CCCCCATGCATTCCCA
*
1262526 -CCCCATGCA-TCCCC
1 CCCCCATGCATTCCCA
1262540 CCCCCATGCATTCCCA
1 CCCCCATGCATTCCCA
1262556 C
1 C
1262557 GTCCCATGTT
Statistics
Matches: 77, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
14 4 0.05
15 18 0.23
16 24 0.31
17 25 0.32
18 6 0.08
ACGTcount: A:0.17, C:0.54, G:0.08, T:0.21
Consensus pattern (16 bp):
CCCCCATGCATTCCCA
Found at i:1262644 original size:29 final size:29
Alignment explanation
Indices: 1262602--1262690 Score: 169
Period size: 29 Copynumber: 3.1 Consensus size: 29
1262592 TAATACACAC
*
1262602 AGGTCGCCCGGATGCCATGGCGACCTTCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
1262631 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
1262660 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
1262689 AG
1 AG
1262691 ACCACTGTAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:1267018 original size:12 final size:12
Alignment explanation
Indices: 1267003--1267040 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
1266993 CTATATCTAT
1267003 ATCTTACTCAAA
1 ATCTTACTCAAA
*
1267015 ATCTTACTCCAAT
1 ATCTTACT-CAAA
1267028 ATCTTACTCAAA
1 ATCTTACTCAAA
1267040 A
1 A
1267041 CAATATCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.34
Consensus pattern (12 bp):
ATCTTACTCAAA
Found at i:1267033 original size:13 final size:13
Alignment explanation
Indices: 1267001--1267036 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1266991 ATCTATATCT
1267001 ATATCTTACT-CA
1 ATATCTTACTCCA
*
1267013 AAATCTTACTCCA
1 ATATCTTACTCCA
1267026 ATATCTTACTC
1 ATATCTTACTC
1267037 AAAACAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATCTTACTCCA
Found at i:1270664 original size:26 final size:26
Alignment explanation
Indices: 1270643--1270706 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 26
1270633 TTTTATTTTC
1270643 TAAAATTTTATAAATTTATTATCTTA
1 TAAAATTTTATAAATTTATTATCTTA
*
1270669 TAGAATTTTATAAATTTATTCATCTAATA
1 TAAAATTTTATAAATTTATT-ATCT--TA
1270698 TAAAATTTT
1 TAAAATTTT
1270707 GTGTTAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 19 0.58
27 4 0.12
29 10 0.30
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (26 bp):
TAAAATTTTATAAATTTATTATCTTA
Found at i:1272754 original size:13 final size:13
Alignment explanation
Indices: 1272736--1272762 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1272726 TGGACCAACT
1272736 TTTATAAAACTCA
1 TTTATAAAACTCA
1272749 TTTATAAAACTCA
1 TTTATAAAACTCA
1272762 T
1 T
1272763 AAAAATTTAA
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:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTATAAAACTCA
Found at i:1273478 original size:16 final size:18
Alignment explanation
Indices: 1273459--1273495 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1273449 TTCTATCACA
1273459 TATCA-TAT-GAATCATG
1 TATCATTATCGAATCATG
1273475 TATCATTTATCGAATCATG
1 TATCA-TTATCGAATCATG
1273494 TA
1 TA
1273496 AACACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
18 3 0.17
19 10 0.56
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (18 bp):
TATCATTATCGAATCATG
Found at i:1280744 original size:23 final size:23
Alignment explanation
Indices: 1280712--1280772 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
1280702 CTCGTATAAA
*
1280712 TACACTGAAGTGCCACATAGAAT
1 TACACCGAAGTGCCACATAGAAT
** *
1280735 TACACCGAAGTGCTGCGTAGAAT
1 TACACCGAAGTGCCACATAGAAT
*
1280758 TGCACCGAAGTGCCA
1 TACACCGAAGTGCCA
1280773 TATAAAATGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.20
Consensus pattern (23 bp):
TACACCGAAGTGCCACATAGAAT
Found at i:1282472 original size:64 final size:63
Alignment explanation
Indices: 1282359--1282495 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 63
1282349 CCTTTAACAT
* * *
1282359 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCAT-TTTAAGAGG
1 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCAATG-TTTCATCTTTAA-AGA
* * * ** *
1282423 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCAATGTTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCGATACACCAATCACATTCAATGTTTCATCTTTAAAGA
1282486 GTGCATCGAT
1 GTGCATCGAT
1282496 ACGCATTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
63 19 0.31
64 43 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCAATGTTTCATCTTTAAAGA
Found at i:1282644 original size:20 final size:22
Alignment explanation
Indices: 1282621--1282663 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1282611 TACCATTACT
1282621 TAAACCAAC-TTATA-TCCATA
1 TAAACCAACTTTATATTCCATA
*
1282641 TAAACCATCTTTATATTCCATA
1 TAAACCAACTTTATATTCCATA
1282663 T
1 T
1282664 TTCATCATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 5 0.25
22 7 0.35
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAACCAACTTTATATTCCATA
Found at i:1288185 original size:32 final size:32
Alignment explanation
Indices: 1288134--1288206 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
1288124 TCTTTTAGCA
* *
1288134 TTAG-TTTATAGTTCATTTATACAATTAATTT
1 TTAGTTTTGTAGTTCATTTATACAATCAATTT
* *
1288165 TTAGTTTTGTAGTTCGTTTATATAATCAATTT
1 TTAGTTTTGTAGTTCATTTATACAATCAATTT
1288197 TTAGTTTTGT
1 TTAGTTTTGT
1288207 TCTTTCATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 4 0.11
32 33 0.89
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (32 bp):
TTAGTTTTGTAGTTCATTTATACAATCAATTT
Found at i:1289067 original size:20 final size:20
Alignment explanation
Indices: 1289039--1289081 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1289029 CCAATTTCGT
*
1289039 AACGTGAATCTGTAAATCGC
1 AACGCGAATCTGTAAATCGC
*
1289059 AACGCGAATTTGTAAATCGC
1 AACGCGAATCTGTAAATCGC
1289079 AAC
1 AAC
1289082 ACAGAAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
AACGCGAATCTGTAAATCGC
Found at i:1289098 original size:20 final size:20
Alignment explanation
Indices: 1289075--1289121 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1289065 AATTTGTAAA
1289075 TCGCAACACAGA-AGTCAAAT
1 TCGCAACAC-GATAGTCAAAT
*
1289095 TCGCAACGCGATAGTCAAAT
1 TCGCAACACGATAGTCAAAT
1289115 TCGCAAC
1 TCGCAAC
1289122 GCGAACTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (20 bp):
TCGCAACACGATAGTCAAAT
Found at i:1289122 original size:20 final size:20
Alignment explanation
Indices: 1289087--1289125 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1289077 GCAACACAGA
1289087 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
1289107 AGTCAAATTCGCAACGCGA
1 AGTCAAATTCGCAACGCGA
1289126 ACTCTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:1289137 original size:20 final size:20
Alignment explanation
Indices: 1289089--1289142 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1289079 AACACAGAAG
*
1289089 TCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACGCGATAC
1289109 TCAAATTCGCAACGCGA-AC
1 TCAAATTCGCAACGCGATAC
*
1289128 TCTAATTTCGCAACG
1 TC-AAATTCGCAACG
1289143 TGAATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (20 bp):
TCAAATTCGCAACGCGATAC
Done.