Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 30
Found at i:3839620 original size:60 final size:60
Alignment explanation
Indices: 3839495--3839641 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
3839485 GAATATATGA
* * * **
3839495 ATAGTCGAGTGATCATTTTGTAACTTTTAATAGTCGAGGGACTGGATAAAGCAACACATT
1 ATAGTCGAGGGACCATTTTGTAACTTTTAATAGTCGAAGGACTCAATAAAGCAACACATT
* * *
3839555 TTAGTCGAGGGACCATTTTGTAACTTTTAATAGTTGAAGGACTCAATAAAGCAATATCA-T
1 ATAGTCGAGGGACCATTTTGTAACTTTTAATAGTCGAAGGACTCAATAAAGCAACA-CATT
*
3839615 ATAGTC-ATGGGACAATTTGTGT-ACTTT
1 ATAGTCGA-GGGACCATTT-TGTAACTTT
3839642 ACCCTTTAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.01
60 68 0.92
61 5 0.07
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (60 bp):
ATAGTCGAGGGACCATTTTGTAACTTTTAATAGTCGAAGGACTCAATAAAGCAACACATT
Found at i:3841944 original size:48 final size:46
Alignment explanation
Indices: 3841890--3842053 Score: 136
Period size: 48 Copynumber: 3.5 Consensus size: 46
3841880 TTGCTTATGG
* *
3841890 CCCTGCATCCACTGTTGGCGGCGGCATAGTCACCGTTGTTATTAATGA
1 CCCTGCAGCCACTGCTGGCGGCGGCATA--CACCGTTGTTATTAATGA
* * * * * * *
3841938 CCCTGCAGCCACTGCCGGTGGCGTACCTACAGCCGTTG---CTCATGG
1 CCCTGCAGCCACTGCTGGCGGCG-GCATACA-CCGTTGTTATTAATGA
* * *
3841983 CCCTGCATCCACTGTTGGCGGCGGCGTACACTCCGTTGTTATTAATGA
1 CCCTGCAGCCACTGCTGGCGGCGGCATACA--CCGTTGTTATTAATGA
*
3842031 CCCTGCAGCCACTGCTGGTGGCG
1 CCCTGCAGCCACTGCTGGCGGCG
3842054 TACCTGCATC
Statistics
Matches: 88, Mismatches: 22, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
44 5 0.06
45 29 0.33
47 2 0.02
48 49 0.56
49 3 0.03
ACGTcount: A:0.15, C:0.32, G:0.27, T:0.25
Consensus pattern (46 bp):
CCCTGCAGCCACTGCTGGCGGCGGCATACACCGTTGTTATTAATGA
Found at i:3842019 original size:45 final size:45
Alignment explanation
Indices: 3841877--3842020 Score: 110
Period size: 45 Copynumber: 3.1 Consensus size: 45
3841867 GTACCTACCC
* **
3841877 CCGTTGCTTATGGCCCTGCATCCACTGTTGGCGGCGGCATAGTCA
1 CCGTTGCTAATGGCCCTGCATCCACTGTTGGCGGCGGCATACACA
* * * ** * * * *
3841922 CCGTTGTTATTAATGACCCTGCAGCCACTGCCGGTGGCGTACCTACA-G
1 CCGTTG---CTAATGGCCCTGCATCCACTGTTGGCGGCG-GCATACACA
* * *
3841970 CCGTTGCTCATGGCCCTGCATCCACTGTTGGCGGCGGCGTACACT
1 CCGTTGCTAATGGCCCTGCATCCACTGTTGGCGGCGGCATACACA
3842015 CCGTTG
1 CCGTTG
3842021 TTATTAATGA
Statistics
Matches: 72, Mismatches: 22, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
44 5 0.07
45 35 0.49
48 29 0.40
49 3 0.04
ACGTcount: A:0.14, C:0.33, G:0.28, T:0.26
Consensus pattern (45 bp):
CCGTTGCTAATGGCCCTGCATCCACTGTTGGCGGCGGCATACACA
Found at i:3842026 original size:93 final size:93
Alignment explanation
Indices: 3841867--3842058 Score: 312
Period size: 93 Copynumber: 2.1 Consensus size: 93
3841857 CGGTCGCCGT
* * **
3841867 GTACCTACCCCCGTTGCTTATGGCCCTGCATCCACTGTTGGCGGCGGCATAGTCACCGTTGTTAT
1 GTACCTACACCCGTTGCTCATGGCCCTGCATCCACTGTTGGCGGCGGCATACACACCGTTGTTAT
3841932 TAATGACCCTGCAGCCACTGCCGGTGGC
66 TAATGACCCTGCAGCCACTGCCGGTGGC
* * *
3841960 GTACCTACAGCCGTTGCTCATGGCCCTGCATCCACTGTTGGCGGCGGCGTACACTCCGTTGTTAT
1 GTACCTACACCCGTTGCTCATGGCCCTGCATCCACTGTTGGCGGCGGCATACACACCGTTGTTAT
*
3842025 TAATGACCCTGCAGCCACTGCTGGTGGC
66 TAATGACCCTGCAGCCACTGCCGGTGGC
3842053 GTACCT
1 GTACCT
3842059 GCATCCACTG
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.15, C:0.33, G:0.26, T:0.26
Consensus pattern (93 bp):
GTACCTACACCCGTTGCTCATGGCCCTGCATCCACTGTTGGCGGCGGCATACACACCGTTGTTAT
TAATGACCCTGCAGCCACTGCCGGTGGC
Found at i:3842055 original size:45 final size:45
Alignment explanation
Indices: 3841921--3842058 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
3841911 CGGCATAGTC
*
3841921 ACCGTTGTTATTAATGACCCTGCAGCCACTGCCGGTGGCGTACCT
1 ACCGTTGTTATTAATGACCCTGCAGCCACTGCTGGTGGCGTACCT
* ** ** * * * * *
3841966 ACAGCCGTTGCTCATGGCCCTGCATCCACTGTTGGCGGCGGCGTACACT
1 ACCGTTGTTATTAATGACCCTGCAGCCACTGCT---GGTGGCGTAC-CT
3842015 -CCGTTGTTATTAATGACCCTGCAGCCACTGCTGGTGGCGTACCT
1 ACCGTTGTTATTAATGACCCTGCAGCCACTGCTGGTGGCGTACCT
3842059 GCATCCACTG
Statistics
Matches: 68, Mismatches: 21, Indels: 9
0.69 0.21 0.09
Matches are distributed among these distances:
44 2 0.03
45 32 0.47
48 32 0.47
49 2 0.03
ACGTcount: A:0.16, C:0.32, G:0.26, T:0.26
Consensus pattern (45 bp):
ACCGTTGTTATTAATGACCCTGCAGCCACTGCTGGTGGCGTACCT
Found at i:3842101 original size:72 final size:72
Alignment explanation
Indices: 3841984--3842130 Score: 231
Period size: 72 Copynumber: 2.0 Consensus size: 72
3841974 TGCTCATGGC
* * * * *
3841984 CCTGCATCCACTGTTGGCGGCGGCGTACACTCCGTTGTTATTAATGACCCTGCAGCCACTGCTGG
1 CCTGCATCCACTGTTGGCAGCGACGTACACACCGTTGTTACTAATGACCCTGCAGCCACTGCCGG
3842049 TGGCGTA
66 TGGCGTA
* *
3842056 CCTGCATCCACTGTTGGCAGCGACGTACACACCGTTGTTGCTAATGGCCCTGCAGCCACTGCCGG
1 CCTGCATCCACTGTTGGCAGCGACGTACACACCGTTGTTACTAATGACCCTGCAGCCACTGCCGG
3842121 TGGCGTA
66 TGGCGTA
3842128 CCT
1 CCT
3842131 ACCGTCGTTG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.16, C:0.33, G:0.27, T:0.24
Consensus pattern (72 bp):
CCTGCATCCACTGTTGGCAGCGACGTACACACCGTTGTTACTAATGACCCTGCAGCCACTGCCGG
TGGCGTA
Found at i:3843933 original size:22 final size:22
Alignment explanation
Indices: 3843907--3843979 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 22
3843897 ATATTATAAT
3843907 TAATTTTTAATTCATAAAATTA
1 TAATTTTTAATTCATAAAATTA
** *
3843929 TAATTATTT--TTTTTTAAATTA
1 TAATT-TTTAATTCATAAAATTA
*
3843950 TGAATTTATTAATTCAAAAAAATTA
1 T-AATTT-TTAATTC-ATAAAATTA
3843975 TAATT
1 TAATT
3843980 AATTTTTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
21 11 0.29
22 11 0.29
23 3 0.08
24 6 0.16
25 7 0.18
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (22 bp):
TAATTTTTAATTCATAAAATTA
Found at i:3844122 original size:20 final size:20
Alignment explanation
Indices: 3844097--3844137 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3844087 ATTTTTTTAA
*
3844097 TATAATTTAAAAAATATATT
1 TATAATTTAAAAAATAAATT
*
3844117 TATAATTTCAAAAATAAATT
1 TATAATTTAAAAAATAAATT
3844137 T
1 T
3844138 TTGAAAATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAATTTAAAAAATAAATT
Found at i:3844310 original size:30 final size:29
Alignment explanation
Indices: 3844276--3844336 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
3844266 TATATTAGTC
* * *
3844276 TTTAACGATAGTCAAATTTCAATACTTCTT
1 TTTAACGAAAGTAAAATTT-AATACTTATT
*
3844306 TTTAACGAAATTAAAATTTAATACTTATT
1 TTTAACGAAAGTAAAATTTAATACTTATT
3844335 TT
1 TT
3844337 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTAACGAAAGTAAAATTTAATACTTATT
Found at i:3850157 original size:14 final size:13
Alignment explanation
Indices: 3850123--3850148 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3850113 ACATAGTTGG
3850123 ACAGTCTTCATAT
1 ACAGTCTTCATAT
3850136 ACAGTCTTCATAT
1 ACAGTCTTCATAT
3850149 GCGAGTCTTT
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAGTCTTCATAT
Found at i:3850831 original size:16 final size:16
Alignment explanation
Indices: 3850810--3850871 Score: 97
Period size: 16 Copynumber: 3.9 Consensus size: 16
3850800 TAAATAAACA
*
3850810 AACATAAACGAACATG
1 AACATAAACGAACACG
*
3850826 AACATAATCGAACACG
1 AACATAAACGAACACG
*
3850842 AACATAAATGAACACG
1 AACATAAACGAACACG
3850858 AACATAAACGAACA
1 AACATAAACGAACA
3850872 TAAACGTTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.11
Consensus pattern (16 bp):
AACATAAACGAACACG
Found at i:3854565 original size:23 final size:23
Alignment explanation
Indices: 3854537--3854583 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3854527 GTTTCTCCCC
3854537 CTCCCCTAGGCCAACGTGTGGGA
1 CTCCCCTAGGCCAACGTGTGGGA
3854560 CTCCCCTAGGCCAACGTGTGGGA
1 CTCCCCTAGGCCAACGTGTGGGA
3854583 C
1 C
3854584 GTACACTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.36, G:0.30, T:0.17
Consensus pattern (23 bp):
CTCCCCTAGGCCAACGTGTGGGA
Found at i:3856934 original size:15 final size:15
Alignment explanation
Indices: 3856903--3856935 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3856893 TTATAAATTG
3856903 AAATATCAATTCTAA
1 AAATATCAATTCTAA
3856918 AAATA-CAATTCTAA
1 AAATATCAATTCTAA
3856932 AAAT
1 AAAT
3856936 GAATAAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATATCAATTCTAA
Found at i:3857092 original size:20 final size:21
Alignment explanation
Indices: 3857052--3857098 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3857042 ACAAAATTTT
3857052 ATAAAATATAATTATATAAAA
1 ATAAAATATAATTATATAAAA
3857073 ATAAAAT-TAACTTA-ATAAAA
1 ATAAAATATAA-TTATATAAAA
*
3857093 CTAAAA
1 ATAAAA
3857099 GGTAAAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAAATATAATTATATAAAA
Found at i:3857136 original size:19 final size:20
Alignment explanation
Indices: 3857097--3857134 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3857087 ATAAAACTAA
3857097 AAGGTAAAGAATAAAAAAAT
1 AAGGTAAAGAATAAAAAAAT
3857117 AAGGTAAAGAATAAAAAA
1 AAGGTAAAGAATAAAAAA
3857135 TATCGAATAT
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:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (20 bp):
AAGGTAAAGAATAAAAAAAT
Found at i:3859710 original size:18 final size:19
Alignment explanation
Indices: 3859682--3859719 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3859672 AAAGATTCAT
*
3859682 TTTGTTTTTCAAAATCAAA
1 TTTGTTTTTCAAAACCAAA
3859701 TTTG-TTTTCAAAACCAAA
1 TTTGTTTTTCAAAACCAAA
3859719 T
1 T
3859720 CATTTTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (19 bp):
TTTGTTTTTCAAAACCAAA
Found at i:3867238 original size:50 final size:50
Alignment explanation
Indices: 3867163--3867264 Score: 150
Period size: 50 Copynumber: 2.0 Consensus size: 50
3867153 ACTCAAAGTA
* * *
3867163 GGGGTTTCAAGACTGATTTTTCAGAGGTTGATTTCGGTACCGATAGTCAT
1 GGGGTTTCAAGACTGATTTTCCAGAGGTTGATTTCGGCACCGATACTCAT
* * *
3867213 GGGGTTTCGAGACTGGTTTTCCAGAGGTTGATTTTGGCACCGATACTCAT
1 GGGGTTTCAAGACTGATTTTCCAGAGGTTGATTTCGGCACCGATACTCAT
3867263 GG
1 GG
3867265 AAGTATCGGT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (50 bp):
GGGGTTTCAAGACTGATTTTCCAGAGGTTGATTTCGGCACCGATACTCAT
Found at i:3867444 original size:20 final size:20
Alignment explanation
Indices: 3867419--3867508 Score: 137
Period size: 20 Copynumber: 4.5 Consensus size: 20
3867409 AAATAGTTAT
*
3867419 GTATCGATACTCTAGGTGGA
1 GTATCGATACTCTAGGTTGA
3867439 GTATCGATACTCTAGGTTGA
1 GTATCGATACTCTAGGTTGA
3867459 GTATCGATACTCTAGGTTGA
1 GTATCGATACTCTAGGTTGA
*
3867479 GTATCGATACTCATGGGTT-A
1 GTATCGATACTC-TAGGTTGA
*
3867499 GTATTGATAC
1 GTATCGATAC
3867509 CGAGAGGGTC
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 61 0.92
21 5 0.08
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (20 bp):
GTATCGATACTCTAGGTTGA
Found at i:3868480 original size:25 final size:25
Alignment explanation
Indices: 3868452--3868506 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 25
3868442 TACTGAGTGC
* *
3868452 CATATAAAATTGTTCCGAATGACCA
1 CATATAAAATTGTCCCGAAGGACCA
*
3868477 C--ATAGAATTGTCCCGAAGGACCA
1 CATATAAAATTGTCCCGAAGGACCA
3868500 CATATAA
1 CATATAA
3868507 TTATCCCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
23 20 0.83
25 4 0.17
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.24
Consensus pattern (25 bp):
CATATAAAATTGTCCCGAAGGACCA
Found at i:3868485 original size:23 final size:23
Alignment explanation
Indices: 3868459--3868545 Score: 102
Period size: 23 Copynumber: 3.8 Consensus size: 23
3868449 TGCCATATAA
* *
3868459 AATTGTTCCGAATGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
*
3868482 AATTGTCCCGAAGGACCACATAT
1 AATTGTCCCGAAGGACCACATAG
* **
3868505 AATTATCCCTTAGGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
**
3868528 AATTGTCCCTTAGGACCA
1 AATTGTCCCGAAGGACCA
3868546 TATATATGTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACATAG
Found at i:3868592 original size:21 final size:21
Alignment explanation
Indices: 3868568--3868624 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
3868558 AAATGACCAA
*
3868568 ATATATGTCCCGAAGGATT-GC
1 ATATATGTCCCGAAGG-TTCAC
* *
3868589 ATATATGTTCCAAAGGTTCAC
1 ATATATGTCCCGAAGGTTCAC
3868610 ATATATGTCCCGAAG
1 ATATATGTCCCGAAG
3868625 AACCGTGTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (21 bp):
ATATATGTCCCGAAGGTTCAC
Found at i:3871470 original size:21 final size:21
Alignment explanation
Indices: 3871444--3871557 Score: 129
Period size: 21 Copynumber: 5.4 Consensus size: 21
3871434 CATATAAAAT
*
3871444 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATATA
*
3871465 TGTCCCGAAAGACCACATATA
1 TGTCCCGAAGGACCACATATA
**
3871486 TGTCCCGAAATACCACATATA
1 TGTCCCGAAGGACCACATATA
* **
3871507 TGTCCCAAAGGACTGCATATA
1 TGTCCCGAAGGACCACATATA
* * * *
3871528 TGTTCCAAAGGATCACTTATA
1 TGTCCCGAAGGACCACATATA
3871549 TGTCCCGAA
1 TGTCCCGAA
3871558 AAACCGCGTA
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 78 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:3872588 original size:20 final size:20
Alignment explanation
Indices: 3872560--3872657 Score: 115
Period size: 20 Copynumber: 4.8 Consensus size: 20
3872550 TCAACGTTCG
3872560 AATCGCGTTGCGAATTACAA
1 AATCGCGTTGCGAATTACAA
* ** **
3872580 AACCGCGTTGTTAATTTGGAA
1 AATCGCGTTGCGAA-TTACAA
**
3872601 AATCTTGTTGCGAATTACAA
1 AATCGCGTTGCGAATTACAA
*
3872621 AATCACGTTGCGAATTACAA
1 AATCGCGTTGCGAATTACAA
3872641 AATCGCGTTGCGAATTA
1 AATCGCGTTGCGAATTA
3872658 GGAAAATTGA
Statistics
Matches: 62, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 49 0.79
21 13 0.21
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
AATCGCGTTGCGAATTACAA
Found at i:3872673 original size:61 final size:60
Alignment explanation
Indices: 3872560--3872676 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 60
3872550 TCAACGTTCG
* ** *
3872560 AATCGCGTTGCGAATTACAAAACCGCGTTGTTAATTTGGAAAATCTTGTTGCGAATTACAA
1 AATCACGTTGCGAATTACAAAACCGCGTTGCGAATTAGGAAAA-CTTGTTGCGAATTACAA
*
3872621 AATCACGTTGCGAATTACAAAATCGCGTTGCGAATTAGGAAAA-TTGAATTGCGAAT
1 AATCACGTTGCGAATTACAAAACCGCGTTGCGAATTAGGAAAACTTG--TTGCGAAT
3872677 CTGGGAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 3 0.06
61 46 0.94
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (60 bp):
AATCACGTTGCGAATTACAAAACCGCGTTGCGAATTAGGAAAACTTGTTGCGAATTACAA
Found at i:3872694 original size:22 final size:22
Alignment explanation
Indices: 3872562--3872705 Score: 81
Period size: 20 Copynumber: 6.9 Consensus size: 22
3872552 AACGTTCGAA
*
3872562 TCGCGTTGCGAATTA-CAAAA-
1 TCGCGTTGCGAATTAGGAAAAT
* ** *
3872582 CCGCGTTGTTAATTTGGAAAA-
1 TCGCGTTGCGAATTAGGAAAAT
** *
3872603 TCTTGTTGCGAATTA-CAAAA-
1 TCGCGTTGCGAATTAGGAAAAT
* *
3872623 TCACGTTGCGAATTA-CAAAA-
1 TCGCGTTGCGAATTAGGAAAAT
3872643 TCGCGTTGCGAATTAGGAAAAT
1 TCGCGTTGCGAATTAGGAAAAT
** *
3872665 T-GAATTGCGAATCT-GGGAAAT
1 TCGCGTTGCGAAT-TAGGAAAAT
* *
3872686 TCGCGTTGCGAGTTTGGAAA
1 TCGCGTTGCGAATTAGGAAA
3872706 CTGTGTTGTG
Statistics
Matches: 95, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
20 47 0.49
21 34 0.36
22 14 0.15
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (22 bp):
TCGCGTTGCGAATTAGGAAAAT
Found at i:3874787 original size:23 final size:22
Alignment explanation
Indices: 3874743--3874788 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3874733 AATTTCTTAG
* **
3874743 TTTATTTAGGTTTTTATTTATT
1 TTTATTTACGTTTTTACCTATT
3874765 TTTATTTTACGTTTTTACCTATT
1 TTTA-TTTACGTTTTTACCTATT
3874788 T
1 T
3874789 AAATATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.70
Consensus pattern (22 bp):
TTTATTTACGTTTTTACCTATT
Found at i:3879202 original size:24 final size:23
Alignment explanation
Indices: 3879146--3879211 Score: 60
Period size: 24 Copynumber: 2.8 Consensus size: 23
3879136 CTATGTGGTC
* * *
3879146 CTTCGGTTCATTTCTATGTGGCA
1 CTTCGGTGCATTTCTACGCGGCA
* *
3879169 CTTTGATGCATGTTCTACGCGGCA
1 CTTCGGTGCAT-TTCTACGCGGCA
*
3879193 CTTCGGTGCAATTTATACG
1 CTTCGGTGC-ATTTCTACG
3879212 AGCTGTGGTG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
23 8 0.24
24 23 0.70
25 2 0.06
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (23 bp):
CTTCGGTGCATTTCTACGCGGCA
Found at i:3881094 original size:6 final size:6
Alignment explanation
Indices: 3881083--3881127 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
3881073 GATATCTCAG
* * *
3881083 AGAGGA AGAGGA AGAGGT AGAGGA AGAGGA AGAGGT AGGGGA AGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGAGGA AGA
3881128 AATCAGTCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.51, T:0.04
Consensus pattern (6 bp):
AGAGGA
Found at i:3881106 original size:18 final size:18
Alignment explanation
Indices: 3881083--3881127 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
3881073 GATATCTCAG
3881083 AGAGGAAGAGGAAGAGGT
1 AGAGGAAGAGGAAGAGGT
3881101 AGAGGAAGAGGAAGAGGT
1 AGAGGAAGAGGAAGAGGT
*
3881119 AGGGGAAGA
1 AGAGGAAGA
3881128 AATCAGTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.51, T:0.04
Consensus pattern (18 bp):
AGAGGAAGAGGAAGAGGT
Found at i:3887605 original size:23 final size:23
Alignment explanation
Indices: 3887574--3887672 Score: 92
Period size: 23 Copynumber: 4.3 Consensus size: 23
3887564 GTCGAGGGTT
*
3887574 TACGCGGTCCTTCGGGACAATTC
1 TACGTGGTCCTTCGGGACAATTC
* * *
3887597 TACGTGGTCATTCGAGACATTTC
1 TACGTGGTCCTTCGGGACAATTC
** *
3887620 TACACGGTCCTTTGGGACATATT-
1 TACGTGGTCCTTCGGGACA-ATTC
* *
3887643 TATGTGGTCCTTCGGGACATTTC
1 TACGTGGTCCTTCGGGACAATTC
*
3887666 TATGTGG
1 TACGTGG
3887673 CACTTTGGTT
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
22 2 0.03
23 55 0.93
24 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.34
Consensus pattern (23 bp):
TACGTGGTCCTTCGGGACAATTC
Found at i:3887631 original size:46 final size:46
Alignment explanation
Indices: 3887578--3887667 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
3887568 AGGGTTTACG
3887578 CGGTCCTTCGGGACA-ATTCTACGTGGTCATTCGAGACATTTCTACA
1 CGGTCCTTCGGGACATATT-TACGTGGTCATTCGAGACATTTCTACA
* * * *
3887624 CGGTCCTTTGGGACATATTTATGTGGTCCTTCGGGACATTTCTA
1 CGGTCCTTCGGGACATATTTACGTGGTCATTCGAGACATTTCTA
3887668 TGTGGCACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 36 0.92
47 3 0.08
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (46 bp):
CGGTCCTTCGGGACATATTTACGTGGTCATTCGAGACATTTCTACA
Found at i:3890958 original size:17 final size:18
Alignment explanation
Indices: 3890919--3890967 Score: 82
Period size: 17 Copynumber: 2.8 Consensus size: 18
3890909 TGTTTCTGAG
3890919 GGAATTGGAATCTGTTAA
1 GGAATTGGAATCTGTTAA
*
3890937 GGAATTGGAATCTG-TCA
1 GGAATTGGAATCTGTTAA
3890954 GGAATTGGAATCTG
1 GGAATTGGAATCTG
3890968 AATCTGAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (18 bp):
GGAATTGGAATCTGTTAA
Found at i:3896590 original size:138 final size:138
Alignment explanation
Indices: 3896336--3896596 Score: 293
Period size: 138 Copynumber: 1.9 Consensus size: 138
3896326 ACTTAATATA
* * * *
3896336 TATCGGGTCAGATCAGGTTTTTATCTCAAAAATCAGATCGAGTGGAGTACTCTTAAATTCGGGTC
1 TATCGGGTCAGATCAAGTTTTTATCTCAAAAATCAGATCGAGTGGAATACTCTTAAACTCAGGTC
* * * * *
3896401 GAGTCATATGAGGATGTATGTGTTTAATCTTCGGATTGAGTTCGGATGAGTCCAAAATTCGATTT
66 GAGTCAGATGAAGATGAAGGTGTTTAATCTTC-GATTGAGTTCGGATGAGTCAAAAATTCGATTT
3896466 GTGTGTGTT
130 GTGTGTGTT
*
3896475 TATCGGGTCAGATCAAGTTTTT-TCTACAAAAAT-GGATC-AGATGGAATAC-CTCTAAACTCAG
1 TATCGGGTCAGATCAAGTTTTTATCT-CAAAAATCAGATCGAG-TGGAATACTCT-TAAACTCAG
* *
3896536 GTCGAGTTAGATGTAAG-TGAAGGTGTTTAAGTCTT-GATTCTAGTTC-GAGTGAGTCAAAAAT
63 GTCGAGTCAGATG-AAGATGAAGGTGTTTAA-TCTTCGATT-GAGTTCGGA-TGAGTCAAAAAT
3896597 CTTATCCGAC
Statistics
Matches: 103, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
137 10 0.10
138 59 0.57
139 34 0.33
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (138 bp):
TATCGGGTCAGATCAAGTTTTTATCTCAAAAATCAGATCGAGTGGAATACTCTTAAACTCAGGTC
GAGTCAGATGAAGATGAAGGTGTTTAATCTTCGATTGAGTTCGGATGAGTCAAAAATTCGATTTG
TGTGTGTT
Found at i:3898101 original size:19 final size:19
Alignment explanation
Indices: 3898077--3898114 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3898067 TGCATGTAAT
3898077 CTGAGTAAACAACAGTTAG
1 CTGAGTAAACAACAGTTAG
* *
3898096 CTGAGTCAGCAACAGTTAG
1 CTGAGTAAACAACAGTTAG
3898115 GAGTTTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (19 bp):
CTGAGTAAACAACAGTTAG
Found at i:3914595 original size:14 final size:14
Alignment explanation
Indices: 3914576--3914615 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3914566 CGGTTTCTAC
3914576 AAAATAAA-AATAAA
1 AAAATAAATAA-AAA
3914590 AAAATAAATAAAAA
1 AAAATAAATAAAAA
*
3914604 TAAATAAATAAA
1 AAAATAAATAAA
3914616 TTAAACACGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATAAATAAAAA
Found at i:3914598 original size:18 final size:18
Alignment explanation
Indices: 3914577--3914616 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3914567 GGTTTCTACA
3914577 AAATAAAAATAAAAAAAT
1 AAATAAAAATAAAAAAAT
*
3914595 AAATAAAAATAAATAAAT
1 AAATAAAAATAAAAAAAT
3914613 AAAT
1 AAAT
3914617 TAAACACGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAATAAAAATAAAAAAAT
Found at i:3914604 original size:10 final size:10
Alignment explanation
Indices: 3914577--3914611 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
3914567 GGTTTCTACA
3914577 AAATAAAAAT
1 AAATAAAAAT
3914587 -AA-AAAAAT
1 AAATAAAAAT
3914595 AAATAAAAAT
1 AAATAAAAAT
3914605 AAATAAA
1 AAATAAA
3914612 TAAATTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.26
9 4 0.17
10 13 0.57
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:3914654 original size:13 final size:13
Alignment explanation
Indices: 3914636--3914661 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3914626 CTGGTTGAAC
3914636 AAAAATAAAAATT
1 AAAAATAAAAATT
3914649 AAAAATAAAAATT
1 AAAAATAAAAATT
3914662 TAACGGAAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATAAAAATT
Found at i:3926514 original size:24 final size:24
Alignment explanation
Indices: 3926487--3926540 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3926477 GTTATTATGG
3926487 ATGATTAAGTGTTTGCTTTAATGA
1 ATGATTAAGTGTTTGCTTTAATGA
*
3926511 ATGATTAATTGTTTGCTTTAATGA
1 ATGATTAAGTGTTTGCTTTAATGA
3926535 ATGATT
1 ATGATT
3926541 TGCGTTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.48
Consensus pattern (24 bp):
ATGATTAAGTGTTTGCTTTAATGA
Found at i:3928158 original size:60 final size:60
Alignment explanation
Indices: 3928023--3928158 Score: 141
Period size: 60 Copynumber: 2.3 Consensus size: 60
3928013 TAGTTGAGTG
* * * *
3928023 ATCATTTTGTAATTTTTAATAGTCGAATGACTTAACAAAGCAACATTCTATAATCGGAGG
1 ATCATTTTATAACTTTTAATAGTCGAATGACTTAACAAAGCAACATTCTATAATCAGAGA
* * * ** * *
3928083 ATGATTTTGTAACTTTTAATAGTCGAATGACTTAATAAAGCATTA-TCATATAGTTAGAGA
1 ATCATTTTATAACTTTTAATAGTCGAATGACTTAACAAAGCAACATTC-TATAATCAGAGA
3928143 ATCA-TTTATATACTTT
1 ATCATTTTATA-ACTTT
3928159 ACCCTAAATC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 7 0.11
60 56 0.89
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (60 bp):
ATCATTTTATAACTTTTAATAGTCGAATGACTTAACAAAGCAACATTCTATAATCAGAGA
Found at i:3928891 original size:44 final size:44
Alignment explanation
Indices: 3928816--3929230 Score: 288
Period size: 44 Copynumber: 9.9 Consensus size: 44
3928806 AGATCGAAGC
* * * * *
3928816 CTCAATTATAAAAGTA-TAATTGAGATTGAAAAACCTTAGGGGT
1 CTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGT
**
3928859 CTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGAC
1 CTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGT
* * * * *
3928903 CTCAATTATAAAGTTAAAAGAGTGACATT-AAACAA-TTAGGGGT
1 CTCAATTATAAAGGTAGAA-AGTGAGATTGAAAAAACTTAAGGGT
* * * ***
3928946 CTCAAATATAAAGGTAGAAATTGAGAATGAAAAAACTTAAAAAT
1 CTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGT
* *
3928990 CTCAATTGTAAATGTAGAAAGTGAGATTGAAAAAACTTAAGGGT
1 CTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGT
* * *
3929034 CTCAATTATAAAGTTAAAAAGTGGGATT---AAAA--T-A----
1 CTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGT
* * *
3929068 C-CAATTATAAAGGTAGAAAGTGAGAGTGAAAAAACTTAAAGGC
1 CTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGT
* * * *
3929111 CTCAATTATAAA-GT-TAAATTGGGA-T-AAAAAA-TTAA-GGA
1 CTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGT
* * *
3929149 CATCAATTATAAAGGTA-AAA-TAAGGATTG-AAAAA-TTAA-AGA
1 C-TCAATTATAAAGGTAGAAAGTGA-GATTGAAAAAACTTAAGGGT
* *
3929190 CTTCAATTATAAAGATAAAAAGTGAGATTGAATAAAA-TTAA
1 C-TCAATTATAAAGGTAGAAAGTGAGATTGAA-AAAACTTAA
3929231 AACATTATTT
Statistics
Matches: 295, Mismatches: 52, Indels: 49
0.74 0.13 0.12
Matches are distributed among these distances:
33 22 0.07
34 1 0.00
36 4 0.01
38 5 0.02
39 18 0.06
40 13 0.04
41 32 0.11
42 21 0.07
43 47 0.16
44 124 0.42
45 8 0.03
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (44 bp):
CTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGT
Found at i:3928961 original size:87 final size:88
Alignment explanation
Indices: 3928815--3929065 Score: 278
Period size: 87 Copynumber: 2.9 Consensus size: 88
3928805 GAGATCGAAG
* * * * *
3928815 CCTCAATTATAAAAGT-ATAATTGAGATTGAAAAACCTTAGGGGTCTCAATTATAAAGGTAGAAA
1 CCTCAATTATAAATGTAAAAAGTGACATTGAAAAAACTTAGGGGTCTCAATTATAAAGGTAGAAA
**
3928879 GTGAGATTGAAAAAACTTAAGGA
66 GTGAGATTGAAAAAACTTAAAAA
* *
3928902 CCTCAATTATAAA-GTTAAAAGAGTGACATT-AAACAA-TTAGGGGTCTCAAATATAAAGGTAGA
1 CCTCAATTATAAATG-TAAAA-AGTGACATTGAAAAAACTTAGGGGTCTCAATTATAAAGGTAGA
* *
3928964 AATTGAGAATGAAAAAACTTAAAAA
64 AAGTGAGATTGAAAAAACTTAAAAA
* * * * * * *
3928989 TCTCAATTGTAAATGTAGAAAGTGAGATTGAAAAAACTTAAGGGTCTCAATTATAAAGTTAAAAA
1 CCTCAATTATAAATGTAAAAAGTGACATTGAAAAAACTTAGGGGTCTCAATTATAAAGGTAGAAA
*
3929054 GTGGGATT-AAAA
66 GTGAGATTGAAAA
3929066 TACCAATTAT
Statistics
Matches: 136, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
86 9 0.07
87 84 0.62
88 36 0.26
89 7 0.05
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.26
Consensus pattern (88 bp):
CCTCAATTATAAATGTAAAAAGTGACATTGAAAAAACTTAGGGGTCTCAATTATAAAGGTAGAAA
GTGAGATTGAAAAAACTTAAAAA
Found at i:3928993 original size:131 final size:120
Alignment explanation
Indices: 3928948--3929168 Score: 261
Period size: 121 Copynumber: 1.9 Consensus size: 120
3928938 TTAGGGGTCT
* *
3928948 CAAATATAAAGGTAGAAATTGAGAATGAAAAAACTTAAAAATCTCAATTGTAAATGTAGAAAGTG
1 CAAATATAAAGGTAGAAAGTGAGAATGAAAAAACTTAAAAATCTCAATTATAAA-GTAGAAAGTG
** **
3929013 AGATTGAAAAAACTTAAGGGTCTCAATTATAAAGTTAAAAAGTGGGATTAAAATAC
65 AGATTGAAAAAACTTAAGGACCTCAATTATAAAGTTAAAAAGTGACATTAAAATAC
* * *** * * *
3929069 CAATTATAAAGGTAGAAAGTGAGAGTGAAAAAACTTAAAGGCCTCAATTATAAAGT-TAAATTGG
1 CAAATATAAAGGTAGAAAGTGAGAATGAAAAAACTTAAAAATCTCAATTATAAAGTAGAAAGTGA
* *
3929133 GA-T-AAAAAA-TTAAGGACATCAATTATAAAGGTAAAA
66 GATTGAAAAAACTTAAGGACCTCAATTATAAAGTTAAAA
3929169 TAAGGATTGA
Statistics
Matches: 86, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
116 23 0.27
117 6 0.07
118 1 0.01
119 7 0.08
120 2 0.02
121 47 0.55
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.25
Consensus pattern (120 bp):
CAAATATAAAGGTAGAAAGTGAGAATGAAAAAACTTAAAAATCTCAATTATAAAGTAGAAAGTGA
GATTGAAAAAACTTAAGGACCTCAATTATAAAGTTAAAAAGTGACATTAAAATAC
Found at i:3929196 original size:41 final size:40
Alignment explanation
Indices: 3929069--3929209 Score: 124
Period size: 41 Copynumber: 3.4 Consensus size: 40
3929059 ATTAAAATAC
* * *
3929069 CAATTATAAAGGTAGAAAGTGA-GAGTGAAAAAACTTAAAGGCCT
1 CAATTATAAAGGTA-AAA-TAAGGA-TG-AAAAA-TTAAAGACAT
* ** * *
3929113 CAATTATAAA-GTTAAATTGGGATAAAAAATTAAGGACAT
1 CAATTATAAAGGTAAAATAAGGATGAAAAATTAAAGACAT
*
3929152 CAATTATAAAGGTAAAATAAGGATTGAAAAATTAAAGACTT
1 CAATTATAAAGGTAAAATAAGGA-TGAAAAATTAAAGACAT
*
3929193 CAATTATAAAGATAAAA
1 CAATTATAAAGGTAAAA
3929210 AGTGAGATTG
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
39 17 0.21
40 14 0.17
41 32 0.40
42 5 0.06
43 2 0.03
44 10 0.12
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.25
Consensus pattern (40 bp):
CAATTATAAAGGTAAAATAAGGATGAAAAATTAAAGACAT
Found at i:3929261 original size:43 final size:41
Alignment explanation
Indices: 3929137--3929270 Score: 123
Period size: 41 Copynumber: 3.2 Consensus size: 41
3929127 AATTGGGATA
* * *
3929137 AAAAATTAAGGACATCAATTATAAAGGT-AAAATAAGGATTG
1 AAAAATTAAAGACTTCAATTATAAAAGTAAAAATAA-GATTG
*
3929178 AAAAATTAAAGACTTCAATTAT-AAAGATAAAAAGTGAGATTG
1 AAAAATTAAAGACTTCAATTATAAAAG-TAAAAA-TAAGATTG
* *
3929220 AATAAAATTAAA-ACATT-ATTTATAAAAGTAAAAACTAAGATTT
1 -A-AAAATTAAAGAC-TTCAATTATAAAAGTAAAAA-TAAGATTG
3929263 AAAAATTA
1 AAAAATTA
3929271 GGAGCCTAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
40 3 0.04
41 28 0.36
42 10 0.13
43 22 0.28
44 15 0.19
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (41 bp):
AAAAATTAAAGACTTCAATTATAAAAGTAAAAATAAGATTG
Found at i:3931368 original size:21 final size:23
Alignment explanation
Indices: 3931344--3931386 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3931334 TAATAGATTA
3931344 ATATATA-AT-TTTAAAAATATG
1 ATATATATATATTTAAAAATATG
* *
3931365 ATATTTATTTATTTAAAAATAT
1 ATATATATATATTTAAAAATAT
3931387 CAGAAAATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATATATATATTTAAAAATATG
Found at i:3932865 original size:3 final size:3
Alignment explanation
Indices: 3932857--3932928 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
3932847 TAAATGTATT
3932857 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3932905 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
3932929 AAGTGAAAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3933202 original size:76 final size:76
Alignment explanation
Indices: 3933110--3933926 Score: 1517
Period size: 76 Copynumber: 10.8 Consensus size: 76
3933100 AGGCTTTAAG
* * *
3933110 ATCAAAAAGCTTCCGAAGTCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
*
3933175 GTTTTGAAAAC
66 GCTTTGAAAAC
*
3933186 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
3933251 GCTTTGAAAAC
66 GCTTTGAAAAC
* * *
3933262 ATCAGAAAGCTCCCGAAGTCTTTTTGGAAACATCATGTACTGTAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
3933327 GCTTTGAAAAC
66 GCTTTGAAAAC
3933338 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
*
3933403 GCTTTAAAAAC
66 GCTTTGAAAAC
*
3933414 ATCAAAAAGCTCCCGAAGGATTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
3933479 GCTTTGAAAAC
66 GCTTTGAAAAC
*
3933490 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
3933555 GCTTTGAAAAC
66 GCTTTGAAAAC
3933566 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
3933631 GCTTTGAAAAC
66 GCTTTGAAAAC
*
3933642 ATCAAAAAGCTCTCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
3933707 GCTTTGAAAAC
66 GCTTTGAAAAC
3933718 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
3933783 GCTTTGAAAAC
66 GCTTTGAAAAC
*
3933794 ATCAAAAAGCTCACGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
3933859 GCTTTGAAAAC
66 GCTTTGAAAAC
3933870 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
3933927 TGGGAAATAG
Statistics
Matches: 719, Mismatches: 22, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 719 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAG
GCTTTGAAAAC
Found at i:3934632 original size:22 final size:22
Alignment explanation
Indices: 3934604--3934682 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
3934594 AATAAAGCTT
*
3934604 TCATCTTTGAAAAGTGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3934626 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3934648 TCATCTTTGAAAAAAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3934670 TCATCTTTGAAAA
1 TCATCTTTGAAAA
3934683 ATGTAGATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3939296 original size:16 final size:18
Alignment explanation
Indices: 3939267--3939304 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
3939257 CTTGATTCAA
3939267 TTTTCTCCTCTTTTT-CT
1 TTTTCTCCTCTTTTTCCT
*
3939284 TTTTC-CCTTTTTTTCCT
1 TTTTCTCCTCTTTTTCCT
3939301 TTTT
1 TTTT
3939305 TTTTTGCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTCTCCTCTTTTTCCT
Found at i:3942147 original size:27 final size:27
Alignment explanation
Indices: 3942117--3942172 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
3942107 GTAATTATGT
3942117 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGTAAATACAAACGTA
* * *
3942144 AAAAATGCAAATGTAAATGCAAATGTA
1 AAAAATGAAAATGTAAATACAAACGTA
3942171 AA
1 AA
3942173 TATGTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGTAAATACAAACGTA
Found at i:3942161 original size:12 final size:12
Alignment explanation
Indices: 3942146--3942173 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3942136 CAAACGTAAA
3942146 AAATGCAAATGT
1 AAATGCAAATGT
3942158 AAATGCAAATGT
1 AAATGCAAATGT
3942170 AAAT
1 AAAT
3942174 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:3942266 original size:7 final size:7
Alignment explanation
Indices: 3942232--3942273 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
3942222 ATAAAAGTAT
3942232 AAATGCA
1 AAATGCA
* *
3942239 CAATGAA
1 AAATGCA
3942246 AAATGCA
1 AAATGCA
3942253 AAGATGCA
1 AA-ATGCA
3942261 AAATGC-
1 AAATGCA
3942267 AAATGCA
1 AAATGCA
3942274 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:3944358 original size:21 final size:23
Alignment explanation
Indices: 3944334--3944376 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3944324 TAATAGATTA
3944334 ATATATA-AT-TTTAAAAATATG
1 ATATATATATATTTAAAAATATG
* *
3944355 ATATTTATTTATTTAAAAATAT
1 ATATATATATATTTAAAAATAT
3944377 CATAAAATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATATATATATTTAAAAATATG
Found at i:3944466 original size:144 final size:143
Alignment explanation
Indices: 3944211--3944471 Score: 321
Period size: 144 Copynumber: 1.8 Consensus size: 143
3944201 TATAAATAAA
* * * *
3944211 ATATTTATTTATTTAAAAATATCAGAAAATGACTTCTAGGTGCCTTAAGACAGCTCTTTTCTTTG
1 ATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGTGCCTTAAGACAGCTCCTTTCTTTA
* *
3944276 ATATTAAAAAATAAATAATTAATTAAGACATTTTTCTAAAAATAATAATAATAGATTAATATATA
66 ATATTAAAAAATAAATAAATAATTAAGACATTTTTATAAAAATAAT-ATAATAGATTAATATATA
3944341 ATTTTAAAAATATG
130 ATTTTAAAAATATG
* * ** * *
3944355 ATATTTATTTATTTAAAAATATCATAAAATGGACATCCAGTTGTTTTAAGTCTGC-CCTTTC-TT
1 ATATTTATTTATTTAAAAATATCAGAAAAT-GACATCCAGGTGCCTTAAGACAGCTCCTTTCTTT
* * * *
3944418 AATATTAAAAAATAAATAAAT-ATTAATATATATATTTATAATACTAATATAATA
65 AATATTAAAAAATAAATAAATAATTAAGACAT-T-TTTATAAAAATAATATAATA
3944472 AAATAATAAT
Statistics
Matches: 98, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
142 8 0.08
143 28 0.29
144 45 0.46
145 17 0.17
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.41
Consensus pattern (143 bp):
ATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGTGCCTTAAGACAGCTCCTTTCTTTA
ATATTAAAAAATAAATAAATAATTAAGACATTTTTATAAAAATAATATAATAGATTAATATATAA
TTTTAAAAATATG
Found at i:3945858 original size:3 final size:3
Alignment explanation
Indices: 3945850--3945883 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
3945840 TAAATGTATT
*
3945850 TAA TAA TAA TAA TAA TAA TAA TAAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
3945884 AAGTGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3955234 original size:48 final size:48
Alignment explanation
Indices: 3955182--3955366 Score: 169
Period size: 48 Copynumber: 3.9 Consensus size: 48
3955172 GCAAACTCTT
*
3955182 TTTATGCAACAACCGGCG-TTGCCGCCTCCTAAAGAAACGCAGACGTTG
1 TTTATGCAACCACCGGCGCTT-CCGCCTCCTAAAGAAACGCAGACGTTG
* * * * *
3955230 TTTATGCAACCGCCGACGCATCCGCCTCCGAAAGAAACGCA-ACCTCTG
1 TTTATGCAACCACCGGCGCTTCCGCCTCCTAAAGAAACGCAGACGT-TG
* * * * *
3955278 TTTATGCAGCCACCGGCGCCTT-CGCCTCATAAGGAAACGCAGACGCTA
1 TTTATGCAACCACCGGCG-CTTCCGCCTCCTAAAGAAACGCAGACGTTG
* *** * *
3955326 TTTATGCAACCGCCGTTACCTCCACCTCCTAAAGAAACGCA
1 TTTATGCAACCACCGGCGCTTCCGCCTCCTAAAGAAACGCA
3955367 ACCGCTATTT
Statistics
Matches: 107, Mismatches: 25, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
47 5 0.05
48 97 0.91
49 5 0.05
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.19
Consensus pattern (48 bp):
TTTATGCAACCACCGGCGCTTCCGCCTCCTAAAGAAACGCAGACGTTG
Found at i:3955321 original size:96 final size:94
Alignment explanation
Indices: 3955157--3955369 Score: 259
Period size: 96 Copynumber: 2.2 Consensus size: 94
3955147 TCATGCAACA
* * * *
3955157 GCCTCCGAAAGAGACGCAAACTCTTTTTATGCAACAACCGGCGTTGCCGCCTCCTAAAGAAACGC
1 GCCTCCGAAAGAAACGCAACCTCTGTTTATGCAACAACCGGCGTT-CCGCCTCATAAAGAAACGC
* *
3955222 AGACGTTGTTTATGCAACCGCCG-ACGCATCC
65 AGACGCTATTTATGCAACCGCCGTAC-C-TCC
* * *
3955253 GCCTCCGAAAGAAACGCAACCTCTGTTTATGCAGCCACCGGCGCCTT-CGCCTCATAAGGAAACG
1 GCCTCCGAAAGAAACGCAACCTCTGTTTATGCAACAACCGGCG--TTCCGCCTCATAAAGAAACG
3955317 CAGACGCTATTTATGCAACCGCCGTTACCTCC
64 CAGACGCTATTTATGCAACCGCCG-TACCTCC
* *
3955349 ACCTCCTAAAGAAACGCAACC
1 GCCTCCGAAAGAAACGCAACC
3955370 GCTATTTGCG
Statistics
Matches: 102, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
96 97 0.95
97 1 0.01
98 4 0.04
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (94 bp):
GCCTCCGAAAGAAACGCAACCTCTGTTTATGCAACAACCGGCGTTCCGCCTCATAAAGAAACGCA
GACGCTATTTATGCAACCGCCGTACCTCC
Found at i:3958855 original size:20 final size:20
Alignment explanation
Indices: 3958823--3958885 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
3958813 ATATTGACTT
*
3958823 GACCCGAAAATCAACCGATCC
1 GACCCG-AAATCAATCGATCC
3958844 GACCCGAAATCAATCGATCC
1 GACCCGAAATCAATCGATCC
*
3958864 GATCCGAAATCAATCGATCC
1 GACCCGAAATCAATCGATCC
3958884 GA
1 GA
3958886 TATTGACCCG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 34 0.85
21 6 0.15
ACGTcount: A:0.37, C:0.33, G:0.16, T:0.14
Consensus pattern (20 bp):
GACCCGAAATCAATCGATCC
Found at i:3959044 original size:64 final size:64
Alignment explanation
Indices: 3958903--3959046 Score: 191
Period size: 64 Copynumber: 2.3 Consensus size: 64
3958893 CCGACCTGAT
* * **
3958903 ACCCAAACCT-ACCCGACTTACTATAAACTCGAATAAAACCGAAACCCGAAATGATCTGACTCG
1 ACCCAAACCTGACCCGACTTACTATAAACCCGAATAAAACCGAAACCCGAAATGACCCAACTCG
** * ** *
3958966 ACCCGGACCCGACCCGACTTACTATAAACCCGAATAAAACCGAAACTTGAAATGACCCAATTCG
1 ACCCAAACCTGACCCGACTTACTATAAACCCGAATAAAACCGAAACCCGAAATGACCCAACTCG
3959030 ACCCAAACCTGACCCGA
1 ACCCAAACCTGACCCGA
3959047 ACCGAACCCG
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
63 7 0.10
64 60 0.90
ACGTcount: A:0.38, C:0.34, G:0.12, T:0.15
Consensus pattern (64 bp):
ACCCAAACCTGACCCGACTTACTATAAACCCGAATAAAACCGAAACCCGAAATGACCCAACTCG
Found at i:3960295 original size:33 final size:33
Alignment explanation
Indices: 3960222--3960300 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
3960212 TCCAACAATG
* * *
3960222 CCAGATTTGCCAAAGCCTTAACTTCCTAAAGTT
1 CCAGAGTTGCCAAAGCCTGAACTTCCTAAAGTC
*
3960255 CCAGAGTTGCCAAAGCCTGAA-TTGCCTAAGGTC
1 CCAGAGTTGCCAAAGCCTGAACTT-CCTAAAGTC
* *
3960288 CCTGAGTTTCCAA
1 CCAGAGTTGCCAA
3960301 CAGTGCCGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 2 0.05
33 37 0.95
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.27
Consensus pattern (33 bp):
CCAGAGTTGCCAAAGCCTGAACTTCCTAAAGTC
Found at i:3961403 original size:36 final size:36
Alignment explanation
Indices: 3961362--3961501 Score: 201
Period size: 36 Copynumber: 3.9 Consensus size: 36
3961352 ATTTATCCAT
3961362 TATCAGATTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGATTTGATACATTCGTGTATCAATGTTATCA
* **
3961398 TATCAGCTTTGGCACATTCGTGTATCAATGTTATCA
1 TATCAGATTTGATACATTCGTGTATCAATGTTATCA
*
3961434 TATCA-ACTTTGATACATTTGTGTATCAATGTTATCA
1 TATCAGA-TTTGATACATTCGTGTATCAATGTTATCA
* * *
3961470 TATCAGCTTGGGTACATTCGTGTATCAATGTT
1 TATCAGATTTGATACATTCGTGTATCAATGTT
3961502 CAGCACCGTT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
36 91 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (36 bp):
TATCAGATTTGATACATTCGTGTATCAATGTTATCA
Found at i:3962948 original size:36 final size:36
Alignment explanation
Indices: 3962902--3963039 Score: 224
Period size: 36 Copynumber: 3.9 Consensus size: 36
3962892 ATTTATCCAT
*
3962902 TATCAACTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
*
3962938 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
*
3962974 TATCAGCTTTGATATATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
* *
3963010 TAT-AGCTTTGGTACATTCATGTATCAATGT
1 TATCAGCTTTGATACATTCGTGTATCAATGT
3963040 CCAGCACCGT
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 24 0.25
36 71 0.75
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (36 bp):
TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
Found at i:3969420 original size:36 final size:36
Alignment explanation
Indices: 3969374--3969505 Score: 192
Period size: 36 Copynumber: 3.7 Consensus size: 36
3969364 CATTAATAGA
* *
3969374 TTTGATACATTCGTGTATCAATGTTATCATATCATC
1 TTTGGTACATTCGTGTATCAATGTTATCATATCAGC
* * * *
3969410 TTTGGCACATTCATATATCAATGTTATCATATAAGC
1 TTTGGTACATTCGTGTATCAATGTTATCATATCAGC
* *
3969446 TTTGATGCATTCGTGTATCAATGTTATCATATCAGC
1 TTTGGTACATTCGTGTATCAATGTTATCATATCAGC
3969482 TTTGGTACATTCGTGTATCAATGT
1 TTTGGTACATTCGTGTATCAATGT
3969506 CCAGAAACGT
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 82 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTGGTACATTCGTGTATCAATGTTATCATATCAGC
Found at i:3971112 original size:21 final size:21
Alignment explanation
Indices: 3971088--3971139 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
3971078 TGGGAGCGTA
3971088 TGGTGCATCGATGCATAGGCT
1 TGGTGCATCGATGCATAGGCT
3971109 TGGTGCATCGATGCATAGGCT
1 TGGTGCATCGATGCATAGGCT
*
3971130 TTGTGCATCG
1 TGGTGCATCG
3971140 GTACACTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (21 bp):
TGGTGCATCGATGCATAGGCT
Found at i:3971282 original size:65 final size:64
Alignment explanation
Indices: 3971205--3971353 Score: 174
Period size: 65 Copynumber: 2.3 Consensus size: 64
3971195 TACACTAGGG
* *** *
3971205 TGTGCATCGGTGCACAAATTTGCTTCGATGTTTCAA-AAATAGCCGGGGTACATCGATGCATGAC
1 TGTGCATCGGTGCACAAAATCAATTCGATGTTTCAATAAA-AGCCGGAGTACATCGATGCATG-C
3971269 T
64 T
* * * * *
3971270 TGTGCATTGGTGCACAAAATCAATTCGATGTTTCAATAAAATCCTGAGTGCATCGATGCATGGT
1 TGTGCATCGGTGCACAAAATCAATTCGATGTTTCAATAAAAGCCGGAGTACATCGATGCATGCT
*
3971334 TGTGCATCGGTGCATAAAAT
1 TGTGCATCGGTGCACAAAAT
3971354 GCATTCAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 19 0.27
65 49 0.69
66 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (64 bp):
TGTGCATCGGTGCACAAAATCAATTCGATGTTTCAATAAAAGCCGGAGTACATCGATGCATGCT
Found at i:3974072 original size:21 final size:22
Alignment explanation
Indices: 3974019--3974099 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 22
3974009 GCATAGCGGA
3974019 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
3974041 CGTGCATCGATGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
3974063 GTGAATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
3974085 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
3974100 TAACTAGTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.32
22 5 0.10
23 29 0.58
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:3982006 original size:14 final size:15
Alignment explanation
Indices: 3981966--3981999 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3981956 CCCTGTGTTG
*
3981966 ATAATTATAATAATA
1 ATAATTATTATAATA
3981981 ATAATTATTATAAT-
1 ATAATTATTATAATA
3981995 ATAAT
1 ATAAT
3982000 ATTTATATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATTATTATAATA
Found at i:3984075 original size:12 final size:12
Alignment explanation
Indices: 3984058--3984083 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3984048 TAACAAAATG
3984058 CCGATTTTCTCA
1 CCGATTTTCTCA
3984070 CCGATTTTCTCA
1 CCGATTTTCTCA
3984082 CC
1 CC
3984084 AAACACTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (12 bp):
CCGATTTTCTCA
Found at i:3985097 original size:17 final size:17
Alignment explanation
Indices: 3985075--3985113 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3985065 TGACCGGTCT
3985075 GACCCTACCCGTTGA-CC
1 GACCCTACCCG-TGACCC
*
3985092 GACCCTTCCCGTGACCC
1 GACCCTACCCGTGACCC
3985109 GACCC
1 GACCC
3985114 AGTGACATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.15, C:0.51, G:0.18, T:0.15
Consensus pattern (17 bp):
GACCCTACCCGTGACCC
Found at i:3985208 original size:57 final size:55
Alignment explanation
Indices: 3985115--3985300 Score: 214
Period size: 57 Copynumber: 3.3 Consensus size: 55
3985105 ACCCGACCCA
* * * *
3985115 GTGACATTCT-GAGATTTTTTGAAAATGTGACATTCTGGGAAATATTTGAAAAAAT
1 GTGACATTCTGGAAATATTTTAAAAATGTGACATTCTGGGAAATATTTG-AAAAAG
*
3985170 GTGACATTCTGGGAAATATTTTAAAAAGGTGACATTCTGGGAAATATTTTTG-AAAAG
1 GTGACATTCT-GGAAATATTTTAAAAATGTGACATTCTGGGAAATA--TTTGAAAAAG
* * *
3985227 GTGATATTCTAGGAAATATTTTAAAAAATGTGACATTCTGAGAATTATTTTGAAAAAG
1 GTGACATTCT-GGAAATATTTT-AAAAATGTGACATTCTGGGAAATA-TTTGAAAAAG
*
3985285 GTGACATTTTGGAAAT
1 GTGACATTCTGGAAAT
3985301 TTTCGAATGT
Statistics
Matches: 113, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
55 10 0.09
57 65 0.58
58 34 0.30
59 4 0.04
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.35
Consensus pattern (55 bp):
GTGACATTCTGGAAATATTTTAAAAATGTGACATTCTGGGAAATATTTGAAAAAG
Found at i:3985257 original size:86 final size:85
Alignment explanation
Indices: 3985115--3985303 Score: 274
Period size: 86 Copynumber: 2.2 Consensus size: 85
3985105 ACCCGACCCA
* * *
3985115 GTGACATTCT-GAGATTTTTTGAAAATGTGACATTCTGGGAAATATTTGAAAAAATGTGACATTC
1 GTGACATTCTGGAAATTTTTTGAAAAGGTGACATTCTAGGAAATATTTGAAAAAATGTGACATTC
*
3985179 TGGGAAATATTTT-AAAAAG
66 TGAGAAATATTTTGAAAAAG
* *
3985198 GTGACATTCTGGGAAATATTTTTGAAAAGGTGATATTCTAGGAAATATTTTAAAAAATGTGACAT
1 GTGACATTCT-GGAAAT-TTTTTGAAAAGGTGACATTCTAGGAAATATTTGAAAAAATGTGACAT
*
3985263 TCTGAGAATTATTTTGAAAAAG
64 TCTGAGAAATATTTTGAAAAAG
*
3985285 GTGACATTTTGGAAATTTT
1 GTGACATTCTGGAAATTTT
3985304 CGAATGTGAA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
83 10 0.11
85 7 0.07
86 62 0.66
87 15 0.16
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (85 bp):
GTGACATTCTGGAAATTTTTTGAAAAGGTGACATTCTAGGAAATATTTGAAAAAATGTGACATTC
TGAGAAATATTTTGAAAAAG
Found at i:3985301 original size:29 final size:29
Alignment explanation
Indices: 3985115--3985300 Score: 206
Period size: 29 Copynumber: 6.6 Consensus size: 29
3985105 ACCCGACCCA
* * *
3985115 GTGACATTCT--GAGATTTTTTG-AAAAT
1 GTGACATTCTGGGAAATATTTTGAAAAAG
*
3985141 GTGACATTCTGGGAAATA-TTTGAAAAAAT
1 GTGACATTCTGGGAAATATTTTG-AAAAAG
3985170 GTGACATTCTGGGAAATATTTT-AAAAAG
1 GTGACATTCTGGGAAATATTTTGAAAAAG
3985198 GTGACATTCTGGGAAATATTTTTG-AAAAG
1 GTGACATTCTGGGAAATA-TTTTGAAAAAG
* * * *
3985227 GTGATATTCTAGGAAATATTTTAAAAAAT
1 GTGACATTCTGGGAAATATTTTGAAAAAG
* *
3985256 GTGACATTCTGAGAATTATTTTGAAAAAG
1 GTGACATTCTGGGAAATATTTTGAAAAAG
*
3985285 GTGACATT-TTGGAAAT
1 GTGACATTCTGGGAAAT
3985301 TTTCGAATGT
Statistics
Matches: 136, Mismatches: 16, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
26 10 0.07
27 4 0.03
28 36 0.26
29 83 0.61
30 3 0.02
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.35
Consensus pattern (29 bp):
GTGACATTCTGGGAAATATTTTGAAAAAG
Found at i:3992638 original size:30 final size:29
Alignment explanation
Indices: 3992523--3992683 Score: 168
Period size: 29 Copynumber: 5.6 Consensus size: 29
3992513 ACCCGACCCA
* * *
3992523 GTGACATTT-GGGAAT-TTTTGTGAAAAAT
1 GTGACATTTAGGAAATATTTTG-AAAAAAG
* *
3992551 GTGACATTTGGGAAATATTTT-AAAAAAT
1 GTGACATTTAGGAAATATTTTGAAAAAAG
*
3992579 GTGACATTCTAGAAAATATTTTG-AAAAAG
1 GTGACATT-TAGGAAATATTTTGAAAAAAG
3992608 GTGACATTCTAGGAAATATTTTGAAAAAAG
1 GTGACATT-TAGGAAATATTTTGAAAAAAG
* *
3992638 GTGACATTTTGAGAATTATTTTGAAAAAAG
1 GTGACATTTAG-GAAATATTTTGAAAAAAG
* *
3992668 TTGACATTTTGGAAAT
1 GTGACATTTAGGAAAT
3992684 TTTCGAATGT
Statistics
Matches: 117, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
28 23 0.20
29 49 0.42
30 45 0.38
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (29 bp):
GTGACATTTAGGAAATATTTTGAAAAAAG
Found at i:3992642 original size:59 final size:57
Alignment explanation
Indices: 3992543--3992683 Score: 176
Period size: 59 Copynumber: 2.4 Consensus size: 57
3992533 GGAATTTTTG
* * *
3992543 TGAAAAATGTGACATTTGGGAAATATTTTAAAAAATGTGACATTCTAGA-AAATATTT
1 TGAAAAAGGTGACATTTAGGAAATATTTTAAAAAAGGTGACATT-TAGAGAAATATTT
* *
3992600 TGAAAAAGGTGACATTCTAGGAAATATTTTGAAAAAAGGTGACATTTTGAGAATTATTT
1 TGAAAAAGGTGACATT-TAGGAAATATTTT-AAAAAAGGTGACATTTAGAGAAATATTT
* *
3992659 TGAAAAAAGTTGACATTTTGGAAAT
1 TG-AAAAAGGTGACATTTAGGAAAT
3992684 TTTCGAATGT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
57 15 0.21
58 15 0.21
59 30 0.41
60 13 0.18
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (57 bp):
TGAAAAAGGTGACATTTAGGAAATATTTTAAAAAAGGTGACATTTAGAGAAATATTT
Found at i:3994645 original size:17 final size:17
Alignment explanation
Indices: 3994619--3994669 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
3994609 GTTGAAAATG
*
3994619 TATAATAAAATAAATAA
1 TATAAAAAAATAAATAA
3994636 TATAAAAAAAGTAAA-AA
1 TATAAAAAAA-TAAATAA
*
3994653 TAATAAAATAATAAATA
1 T-ATAAAAAAATAAATA
3994670 TTAATAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (17 bp):
TATAAAAAAATAAATAA
Found at i:3994674 original size:18 final size:17
Alignment explanation
Indices: 3994619--3994688 Score: 60
Period size: 16 Copynumber: 4.3 Consensus size: 17
3994609 GTTGAAAATG
3994619 TATAATAAAATAA-ATAA
1 TATAATAAAATAATA-AA
*
3994636 TATAA-AAAA-AGTAAA
1 TATAATAAAATAATAAA
*
3994651 AATAATAAAATAATAAA
1 TATAATAAAATAATAAA
*
3994668 TAT--TAATAGTAATAAA
1 TATAATAA-AATAATAAA
3994684 TATAA
1 TATAA
3994689 GAGGGGGATT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
15 10 0.24
16 20 0.48
17 12 0.29
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TATAATAAAATAATAAA
Found at i:3994737 original size:18 final size:18
Alignment explanation
Indices: 3994716--3994758 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3994706 ATTGTTTTTA
*
3994716 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
3994734 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
3994752 AAATAAA
1 AAATAAA
3994759 CAAATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:3996029 original size:15 final size:15
Alignment explanation
Indices: 3996009--3996065 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
3995999 TGTTCCCAAG
*
3996009 TTACCATAACCAGAA
1 TTACCAAAACCAGAA
*
3996024 TTACCAAAAGTTCCTGAA
1 TTACCAAAA---CCAGAA
*
3996042 TTACCAAAACCAGAG
1 TTACCAAAACCAGAA
3996057 TTACCAAAA
1 TTACCAAAA
3996066 ATTTCTGAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 21 0.60
18 14 0.40
ACGTcount: A:0.46, C:0.25, G:0.09, T:0.21
Consensus pattern (15 bp):
TTACCAAAACCAGAA
Found at i:3996030 original size:33 final size:33
Alignment explanation
Indices: 3995988--3996147 Score: 130
Period size: 33 Copynumber: 4.9 Consensus size: 33
3995978 CAAAGCTCCT
* *
3995988 GAATTACCAAATGTTCC-CAAGTTACCATAACCA
1 GAATTACCAAAAGTTCCTCAA-TTACCAAAACCA
*
3996021 GAATTACCAAAAGTTCCTGAATTACCAAAACCA
1 GAATTACCAAAAGTTCCTCAATTACCAAAACCA
* * * * * *
3996054 GAGTTACCAAAAATTTCTGAGTTACCAAAGCCA
1 GAATTACCAAAAGTTCCTCAATTACCAAAACCA
* * * *
3996087 AAATTACCTAAA-TTCCTGAGA-TACCAAAACTA
1 GAATTACCAAAAGTTCCTCA-ATTACCAAAACCA
* *
3996119 GAATTACCCAAAA-CTCCTGAATTACCAAA
1 GAATTA-CCAAAAGTTCCTCAATTACCAAA
3996148 CATGAAATAC
Statistics
Matches: 105, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
32 21 0.20
33 82 0.78
34 2 0.02
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.23
Consensus pattern (33 bp):
GAATTACCAAAAGTTCCTCAATTACCAAAACCA
Found at i:3996044 original size:18 final size:18
Alignment explanation
Indices: 3995979--3996050 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 18
3995969 TGATGCGACC
*
3995979 AAAGCTCCTGAATTACCA
1 AAAGTTCCTGAATTACCA
* *
3995997 AATGTTCC-CAAGTTACCA
1 AAAGTTCCTGAA-TTACCA
* *
3996015 TAA---CCAGAATTACCA
1 AAAGTTCCTGAATTACCA
3996030 AAAGTTCCTGAATTACCA
1 AAAGTTCCTGAATTACCA
3996048 AAA
1 AAA
3996051 CCAGAGTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
15 10 0.24
16 2 0.05
17 2 0.05
18 27 0.66
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.24
Consensus pattern (18 bp):
AAAGTTCCTGAATTACCA
Found at i:3996144 original size:65 final size:65
Alignment explanation
Indices: 3996009--3996148 Score: 167
Period size: 65 Copynumber: 2.1 Consensus size: 65
3995999 TGTTCCCAAG
* * * *
3996009 TTACCATAACCAGAATTACCAAAAGTTCCTGAATTACCAAAACCAGAGTTACCAAAAATTTCTGA
1 TTACCA-AACCAAAATTACCAAAAGTTCCTGAATTACCAAAACCAGAATTACCAAAAACTCCTGA
*
3996074 G
65 A
* * *
3996075 TTACCAAAGCCAAAATTACCTAAA-TTCCTGAGA-TACCAAAACTAGAATTACCCAAAACTCCTG
1 TTACCAAA-CCAAAATTACCAAAAGTTCCTGA-ATTACCAAAACCAGAATTACCAAAAACTCCTG
3996138 AA
64 AA
3996140 TTACCAAAC
1 TTACCAAAC
3996149 ATGAAATACC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
64 1 0.02
65 43 0.67
66 20 0.31
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.23
Consensus pattern (65 bp):
TTACCAAACCAAAATTACCAAAAGTTCCTGAATTACCAAAACCAGAATTACCAAAAACTCCTGAA
Found at i:3996473 original size:2 final size:2
Alignment explanation
Indices: 3996466--3996505 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3996456 AATTCATGTA
3996466 AT AT AT AT AT AT AT AT AT -T 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 AT AT AT AT A
3996506 GGTATTATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3997442 original size:13 final size:13
Alignment explanation
Indices: 3997424--3997456 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3997414 TAAAAAAACT
*
3997424 TTTAAAAGTGTTG
1 TTTAAAAGTATTG
3997437 TTTAAAAGTATTG
1 TTTAAAAGTATTG
3997450 TTTAAAA
1 TTTAAAA
3997457 TTTAACTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (13 bp):
TTTAAAAGTATTG
Found at i:3998165 original size:23 final size:20
Alignment explanation
Indices: 3998115--3998168 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
3998105 ATAACAATAA
3998115 CTGTCTTTGTGACATGTTCT
1 CTGTCTTTGTGACATGTTCT
* *
3998135 CTGCCTTTGTTACATGTTTATCT
1 CTGTCTTTGTGACATG--T-TCT
3998158 CTGTCTTTGTG
1 CTGTCTTTGTG
3998169 GCACATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 14 0.52
22 1 0.04
23 12 0.44
ACGTcount: A:0.09, C:0.20, G:0.19, T:0.52
Consensus pattern (20 bp):
CTGTCTTTGTGACATGTTCT
Found at i:3998892 original size:21 final size:21
Alignment explanation
Indices: 3998842--3998888 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
3998832 AATTTTATTT
3998842 ATTTTTAAGTAATTAAAATAA
1 ATTTTTAAGTAATTAAAATAA
* * *
3998863 ATTATTAAGTAA-TAAATTAT
1 ATTTTTAAGTAATTAAAATAA
3998883 ATTTTT
1 ATTTTT
3998889 TAAGAACGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTTTTAAGTAATTAAAATAA
Found at i:4000125 original size:17 final size:18
Alignment explanation
Indices: 4000088--4000125 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4000078 ATAATTGCCT
*
4000088 AAAATTCCTGAGGTGACC
1 AAAATTCCTGAGATGACC
*
4000106 AAAATTCCTGA-ATTACC
1 AAAATTCCTGAGATGACC
4000123 AAA
1 AAA
4000126 TTTTCCCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (18 bp):
AAAATTCCTGAGATGACC
Found at i:4000666 original size:41 final size:42
Alignment explanation
Indices: 4000612--4000804 Score: 122
Period size: 41 Copynumber: 4.4 Consensus size: 42
4000602 TGAGGTCGAA
* * *
4000612 AAAAACTAGGGGCCTCAAATATAAATGTA-TAATTGAGATTG
1 AAAAACTAGGGGCCTCAAATATAAAGGTAGAAAGTGAGATTG
*
4000653 AAAAACTTA-GGGCCTCAATTATAAAGGTAGAAAGTGAGATTG
1 AAAAAC-TAGGGGCCTCAAATATAAAGGTAGAAAGTGAGATTG
* * * * ** * *
4000695 AAAAAAATTAAGAG-CTTAAATTATAAAATTTTAAAAAAAGTGAGATTA
1 --AAAAACTAGGGGCCTCAAA-TAT-AAA-GGT--AGAAAGTGAGATTG
* * * *
4000743 AAAAATTAGGGTCCTCAATTATAAAGGTAGAAATTGAGATTG
1 AAAAACTAGGGGCCTCAAATATAAAGGTAGAAAGTGAGATTG
*
4000785 AAAAAACTTAAGGGCCTCAA
1 -AAAAAC-TAGGGGCCTCAA
4000805 TTGTAAAGTT
Statistics
Matches: 114, Mismatches: 25, Indels: 23
0.70 0.15 0.14
Matches are distributed among these distances:
41 24 0.21
42 23 0.20
43 11 0.10
44 21 0.18
45 6 0.05
46 13 0.11
47 4 0.04
48 12 0.11
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (42 bp):
AAAAACTAGGGGCCTCAAATATAAAGGTAGAAAGTGAGATTG
Found at i:4000762 original size:90 final size:86
Alignment explanation
Indices: 4000645--4000906 Score: 269
Period size: 90 Copynumber: 3.0 Consensus size: 86
4000635 AATGTATAAT
*
4000645 TGAGATTGAAAAACTTAGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAAGAGC
1 TGAGATT-AAAAAATTAGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAAGAGC
* *
4000710 TTAAATTATAAAATTTTAAAAAAAG
65 CTAAATTAT-AAA-GTT-AAAAAAG
* * *
4000735 TGAGATTAAAAAATTAGGGTCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAACTTAAGGGC
1 TGAGATTAAAAAATTAGGG-CCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAAGAGC
* *
4000800 CTCAATTGTAAAGTTAAAAAAG
65 CTAAATTATAAAGTTAAAAAAG
* * * * * * * * *
4000822 CGGGATTAAAAAATTATGGCCCTCAATTGTAAAGTTAAAAAGCGGGATT--AAAAAATTATG-GC
1 TGAGATTAAAAAATTA-GGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAAGAG-
* *
4000884 CCTCAATTATAAAGTTAGAAAAG
64 CCTAAATTATAAAGTTAAAAAAG
4000907 GTAGAAAGTG
Statistics
Matches: 148, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
84 1 0.01
85 30 0.20
87 44 0.30
88 4 0.03
89 14 0.09
90 55 0.37
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (86 bp):
TGAGATTAAAAAATTAGGGCCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAAGAGCC
TAAATTATAAAGTTAAAAAAG
Found at i:4000803 original size:44 final size:43
Alignment explanation
Indices: 4000611--4000990 Score: 243
Period size: 42 Copynumber: 8.5 Consensus size: 43
4000601 TTGAGGTCGA
* * * * * *
4000611 AAAAAACTAGGGGCCTCAAATATAAATGT-ATAATTGAGATTG
1 AAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTG
* *
4000653 AAAAACTT-AGGGCCTCAATTATAAAGGTAGAAAGTGAGATTG
1 AAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTG
* * * **
4000695 AAAAAAATTAAGAGCTTAAATTATAAAATTTTAAAAAAAGTGAGATT-
1 -AAAAAATTAAGGGCCTCAATTAT-AAA-GGT--AAAAAGTGAGATTG
* *
4000742 AAAAAATT-AGGGTCCTCAATTATAAAGGTAGAAATTGAGATTG
1 AAAAAATTAAGGG-CCTCAATTATAAAGGTAAAAAGTGAGATTG
* * * *
4000785 AAAAAACTTAAGGGCCTCAATTGTAAAGTTAAAAAAGCGGGATT-
1 AAAAAA-TTAAGGGCCTCAATTATAAAGGT-AAAAAGTGAGATTG
* * * * * *
4000829 AAAAAATTATGGCCCTCAATTGTAAAGTTAAAAAGCGGGATT-
1 AAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTG
* * *
4000871 AAAAAATTATGGCCCTCAATTATAAAGTTAGAAAAGGTAGAAAGTGAGATTG
1 AAAAAATTAAGGGCCTCAA-T-T--A--T---AAAGGTAAAAAGTGAGATTG
* *
4000923 AAAAAACTTAAGGGCCTCAATTATAAAGTTAAAAAAAAATGAGATT-
1 AAAAAA-TTAAGGGCCTCAATTATAAAGGT---AAAAAGTGAGATTG
*
4000969 AAAAAATTAGGGGCCTCAATTA
1 AAAAAATTAAGGGCCTCAATTA
4000991 AAAAAGGGGA
Statistics
Matches: 271, Mismatches: 41, Indels: 49
0.75 0.11 0.14
Matches are distributed among these distances:
41 17 0.06
42 59 0.22
43 35 0.13
44 40 0.15
45 37 0.14
46 23 0.08
47 12 0.04
48 13 0.05
49 1 0.00
51 16 0.06
52 7 0.03
53 11 0.04
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (43 bp):
AAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTG
Found at i:4000876 original size:87 final size:85
Alignment explanation
Indices: 4000646--4000906 Score: 247
Period size: 87 Copynumber: 3.0 Consensus size: 85
4000636 ATGTATAATT
* * *
4000646 GAGATTGAAAAACTTAGGG-CCTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAAATTAAGAG-
1 GAGATT-AAAAAATTAGGGCCCTCAATTATAAAGGTAAAAAGCGAGATT--AAAAAATTAAG-GC
* * * *
4000709 CTTAAATTATAAAATTTTAAAAAAAGT
62 CCTCAATTAT-AAA-GTT-AAAAAAGC
* * ** *
4000736 GAGATTAAAAAATTAGGGTCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAACTTAAGGGCC
1 GAGATTAAAAAATTAGGGCCCTCAATTATAAAGGTAAAAAGCGAGATT-AAAAAA-TTAAGGCCC
*
4000801 TCAATTGTAAAGTTAAAAAAGC
64 TCAATTATAAAGTTAAAAAAGC
* * * * * *
4000823 GGGATTAAAAAATTATGGCCCTCAATTGTAAAGTTAAAAAGCGGGATTAAAAAATTATGGCCCTC
1 GAGATTAAAAAATTAGGGCCCTCAATTATAAAGGTAAAAAGCGAGATTAAAAAATTAAGGCCCTC
*
4000888 AATTATAAAGTTAGAAAAG
66 AATTATAAAGTTAAAAAAG
4000907 GTAGAAAGTG
Statistics
Matches: 147, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
85 26 0.18
86 6 0.04
87 46 0.31
88 2 0.01
89 21 0.14
90 46 0.31
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (85 bp):
GAGATTAAAAAATTAGGGCCCTCAATTATAAAGGTAAAAAGCGAGATTAAAAAATTAAGGCCCTC
AATTATAAAGTTAAAAAAGC
Found at i:4001022 original size:34 final size:34
Alignment explanation
Indices: 4000956--4001024 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
4000946 TAAAGTTAAA
* * *
4000956 AAAAAATGAGATTAAAAAATTAGGGGCCTCAATT
1 AAAAAAGGAGATTAAAAAATTAGAGACCTCAATT
* * *
4000990 AAAAAAGGGGATTGAAAAATTAGAGACTTCAATT
1 AAAAAAGGAGATTAAAAAATTAGAGACCTCAATT
4001024 A
1 A
4001025 TAAAGATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (34 bp):
AAAAAAGGAGATTAAAAAATTAGAGACCTCAATT
Found at i:4001034 original size:138 final size:135
Alignment explanation
Indices: 4000765--4001037 Score: 344
Period size: 138 Copynumber: 2.0 Consensus size: 135
4000755 CCTCAATTAT
* * * *
4000765 AAAGGTAGAAATTGAGATTGAAAAAACTTAAGGGCCTCAATTGTAAAGTTAAAAAAGCGGGATTA
1 AAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGCCTCAATTATAAAGTTAAAAAAACGAGATTA
* *
4000830 AAAAATTATGGCCCTCAATTGTAAAGTTAAAAAGCGGGATTAAAAAATTATGGCCCTCAATTATA
66 AAAAATTAGGGCCCTCAATTGT-AA--TAAAAAGCGGGATTAAAAAATTATGGACCTCAATTATA
4000895 AAGTTAGA
128 AAGTTAGA
*
4000903 AAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGCCTCAATTATAAAGTTAAAAAAAAATGAGAT
1 AAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGCCTCAATTATAAAGTT--AAAAAAACGAGAT
* * *
4000968 TAAAAAATTAGGGGCCTCAA-T-T-A-AAAAAG-GGGATTGAAAAATTA-GAGACTTCAATTATA
64 TAAAAAATTAGGGCCCTCAATTGTAATAAAAAGCGGGATTAAAAAATTATG-GACCTCAATTATA
*
4001027 AAGATA-A
128 AAGTTAGA
4001034 AAAG
1 AAAG
4001038 TGAGATTGAA
Statistics
Matches: 121, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
131 6 0.05
132 30 0.25
133 6 0.05
136 1 0.01
138 49 0.40
139 1 0.01
140 28 0.23
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.24
Consensus pattern (135 bp):
AAAGGTAGAAAGTGAGATTGAAAAAACTTAAGGGCCTCAATTATAAAGTTAAAAAAACGAGATTA
AAAAATTAGGGCCCTCAATTGTAATAAAAAGCGGGATTAAAAAATTATGGACCTCAATTATAAAG
TTAGA
Found at i:4001504 original size:18 final size:18
Alignment explanation
Indices: 4001478--4001512 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4001468 AAATCAGAAT
* *
4001478 TGCCTAAAGTTCCTGAGA
1 TGCCCAAAGCTCCTGAGA
4001496 TGCCCAAAGCTCCTGAG
1 TGCCCAAAGCTCCTGAG
4001513 TTATCAAAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (18 bp):
TGCCCAAAGCTCCTGAGA
Found at i:4001538 original size:18 final size:18
Alignment explanation
Indices: 4001483--4001538 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
4001473 AGAATTGCCT
* *
4001483 AAAGTTCCTGAGA-TGCCC
1 AAAGTTCCTGA-ATTACCA
* * *
4001501 AAAGCTCCTGAGTTATCA
1 AAAGTTCCTGAATTACCA
4001519 AAAGTTCCTGAATTACCA
1 AAAGTTCCTGAATTACCA
4001537 AA
1 AA
4001539 GCTAGAATTG
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (18 bp):
AAAGTTCCTGAATTACCA
Found at i:4001622 original size:69 final size:68
Alignment explanation
Indices: 4001463--4001631 Score: 178
Period size: 69 Copynumber: 2.4 Consensus size: 68
4001453 GTTCAAAAGT
* * * *
4001463 TACCGAAATCAGAATTGCCTAAAGTTCCTGAGATGCCCAAAGCTCCTGAGTTATCAAAAGTTCCT
1 TACC-AAATCAGAATTGCCTAAAGTTCCTGAGATGACCAAAGCTCCTAAATTACCAAAAGTTCCT
*
4001528 GAAT
65 GAAG
* * *
4001532 TACCAAAGCTAGAATTGCCTAAAGTTCTCT-AGGTGACCAAAGCTCCTAAATTACCAAATGTTCC
1 TACCAAATC-AGAATTGCCTAAAGTTC-CTGAGATGACCAAAGCTCCTAAATTACCAAAAGTTCC
*
4001596 TGAGG
64 TGAAG
* * * *
4001601 TGCCAAAATCATAATTTCCTAAAATTCCTGA
1 TACC-AAATCAGAATTGCCTAAAGTTCCTGA
4001632 ATTTTCAAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
68 6 0.07
69 70 0.85
70 6 0.07
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (68 bp):
TACCAAATCAGAATTGCCTAAAGTTCCTGAGATGACCAAAGCTCCTAAATTACCAAAAGTTCCTG
AAG
Found at i:4005898 original size:33 final size:33
Alignment explanation
Indices: 4005856--4005957 Score: 132
Period size: 33 Copynumber: 3.1 Consensus size: 33
4005846 TCGGAAATTT
4005856 CAAAGCCTGAAATACCTAAGGTTCCTGAGTTGC
1 CAAAGCCTGAAATACCTAAGGTTCCTGAGTTGC
* * *
4005889 CAAAGCCTGAATTGCCTAAGATTCCTGAGTTGC
1 CAAAGCCTGAAATACCTAAGGTTCCTGAGTTGC
* * * * *
4005922 CAAAGCCCGAAGTTCCTAAGGTTCCCGAGTTTC
1 CAAAGCCTGAAATACCTAAGGTTCCTGAGTTGC
4005955 CAA
1 CAA
4005958 CAATGCCAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (33 bp):
CAAAGCCTGAAATACCTAAGGTTCCTGAGTTGC
Found at i:4005903 original size:15 final size:15
Alignment explanation
Indices: 4005879--4005928 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
4005869 ACCTAAGGTT
4005879 CCTGAGTTGCCAAAG
1 CCTGAGTTGCCAAAG
* *
4005894 CCTGAATTGCCTAAGATT
1 CCTGAGTTGCC-AA-A-G
4005912 CCTGAGTTGCCAAAG
1 CCTGAGTTGCCAAAG
4005927 CC
1 CC
4005929 CGAAGTTCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 12 0.43
16 3 0.11
17 3 0.11
18 10 0.36
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (15 bp):
CCTGAGTTGCCAAAG
Found at i:4005921 original size:18 final size:18
Alignment explanation
Indices: 4005870--4005922 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
4005860 GCCTGAAATA
*
4005870 CCTAAGGTTCCTGAGTTG
1 CCTAAGATTCCTGAGTTG
* *
4005888 CC-AA-A-GCCTGAATTG
1 CCTAAGATTCCTGAGTTG
4005903 CCTAAGATTCCTGAGTTG
1 CCTAAGATTCCTGAGTTG
4005921 CC
1 CC
4005923 AAAGCCCGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 3 0.11
18 12 0.44
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (18 bp):
CCTAAGATTCCTGAGTTG
Found at i:4006086 original size:18 final size:18
Alignment explanation
Indices: 4006056--4006099 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4006046 ATCGAAGTCA
4006056 GAATTACCCAAAGCTCCT
1 GAATTACCCAAAGCTCCT
* * *
4006074 GAGTTACCTAAAGTTCCT
1 GAATTACCCAAAGCTCCT
4006092 GAATTACC
1 GAATTACC
4006100 GAAACCAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (18 bp):
GAATTACCCAAAGCTCCT
Found at i:4006120 original size:33 final size:33
Alignment explanation
Indices: 4006077--4006304 Score: 160
Period size: 33 Copynumber: 6.8 Consensus size: 33
4006067 AGCTCCTGAG
*
4006077 TTACCTAAAGTTCCTGAATTACCGAAACCAGAA
1 TTACCTAAAGTTCCTGAATTACCAAAACCAGAA
* * *
4006110 TTGCCTAAAGTTCCT-AATGCGACCAAAGCTCCTA-AA
1 TTACCTAAAGTTCCTGAAT--TACCAAA--ACC-AGAA
* *
4006146 TTACC-AAACGTTCCCGAGTTACCAAAACCAGAA
1 TTACCTAAA-GTTCCTGAATTACCAAAACCAGAA
* * *
4006179 TTACCTAAAGTTCATGAATTACCGAAACCAGAG
1 TTACCTAAAGTTCCTGAATTACCAAAACCAGAA
* * ** * **
4006212 TTACCAAAAATTCCTGAGCTACCTAAGTCAGAA
1 TTACCTAAAGTTCCTGAATTACCAAAACCAGAA
* *
4006245 TTACCTAAAATTCCTGAGA-TACCAAAACCAGAG
1 TTACCTAAAGTTCCTGA-ATTACCAAAACCAGAA
** *
4006278 TTAACC-AAAACTCCCGAATTACCAAAA
1 TT-ACCTAAAGTTCCTGAATTACCAAAA
4006305 ACTAAATTAC
Statistics
Matches: 152, Mismatches: 31, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
32 5 0.03
33 111 0.73
34 11 0.07
35 9 0.06
36 13 0.09
37 3 0.02
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.22
Consensus pattern (33 bp):
TTACCTAAAGTTCCTGAATTACCAAAACCAGAA
Found at i:4006141 original size:69 final size:69
Alignment explanation
Indices: 4006063--4006191 Score: 188
Period size: 69 Copynumber: 1.9 Consensus size: 69
4006053 TCAGAATTAC
* * * * *
4006063 CCAAAGCTCCTGAGTTACCTAAA-GTTCCTGAATTACCGAAACCAGAATTGCCTAAAGTTCCTAA
1 CCAAAGCTCCTAAATTACC-AAACGTTCCCGAATTACCAAAACCAGAATTACCTAAAGTTCCTAA
4006127 TGCGA
65 TGCGA
*
4006132 CCAAAGCTCCTAAATTACCAAACGTTCCCGAGTTACCAAAACCAGAATTACCTAAAGTTC
1 CCAAAGCTCCTAAATTACCAAACGTTCCCGAATTACCAAAACCAGAATTACCTAAAGTTC
4006192 ATGAATTACC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 3 0.06
69 50 0.94
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (69 bp):
CCAAAGCTCCTAAATTACCAAACGTTCCCGAATTACCAAAACCAGAATTACCTAAAGTTCCTAAT
GCGA
Found at i:4008000 original size:22 final size:22
Alignment explanation
Indices: 4007972--4008024 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
4007962 AAAAATCCGT
4007972 AACTCGAATTCGCCAATTTCGC
1 AACTCGAATTCGCCAATTTCGC
*
4007994 AACTCGAATTCGCCAATTTTGC
1 AACTCGAATTCGCCAATTTCGC
4008016 AACTC-AATT
1 AACTCGAATT
4008025 ACCGATATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.30
Consensus pattern (22 bp):
AACTCGAATTCGCCAATTTCGC
Found at i:4008166 original size:22 final size:21
Alignment explanation
Indices: 4008141--4008194 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
4008131 TGAAAACTGA
4008141 GTTGCGAATTTGGGAAATTCGT
1 GTTGCGAATTTGGG-AATTCGT
* *
4008163 GTTGCGAAATT-GGAGTTCGT
1 GTTGCGAATTTGGGAATTCGT
4008183 GTTGCGAATTTG
1 GTTGCGAATTTG
4008195 AAATCGCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.57
21 2 0.07
22 10 0.36
ACGTcount: A:0.20, C:0.09, G:0.33, T:0.37
Consensus pattern (21 bp):
GTTGCGAATTTGGGAATTCGT
Found at i:4008438 original size:21 final size:21
Alignment explanation
Indices: 4008384--4008438 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
4008374 ACGTCACTTA
*
4008384 TAAAAATATTTTAAAATTTAT
1 TAAAAATATATTAAAATTTAT
*
4008405 TATTAAATA-ATTAAAATTT-T
1 TA-AAAATATATTAAAATTTAT
4008425 TAAAATATATATTA
1 TAAAA-ATATATTA
4008439 TTTTATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.07
20 6 0.21
21 15 0.54
22 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAAATATATTAAAATTTAT
Found at i:4008807 original size:13 final size:13
Alignment explanation
Indices: 4008791--4008831 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
4008781 GAATTTATTT
4008791 AAAAATTGAAAAA
1 AAAAATTGAAAAA
4008804 AAAAATTGAAAAA
1 AAAAATTGAAAAA
4008817 AAAGAA--GAAAAA
1 AAA-AATTGAAAAA
4008829 AAA
1 AAA
4008832 CAGTCCCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.33
13 16 0.59
14 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (13 bp):
AAAAATTGAAAAA
Found at i:4013003 original size:3 final size:3
Alignment explanation
Indices: 4012985--4013029 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
4012975 GTAAAATGTG
* *
4012985 TAA TAA TAT TAA -AA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4013030 TTTTTAAGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4013544 original size:131 final size:133
Alignment explanation
Indices: 4013221--4013551 Score: 348
Period size: 134 Copynumber: 2.5 Consensus size: 133
4013211 GTCTAAGGGT
* * * *
4013221 ACGCTACTCCTACGTGATGAGGAGATTTGGTCGGTGGATGAAACGGTTCCTACGCGAGGAGGA-G
1 ACGCTGCTCCTACGTGATGAGGAGATTTGATCGGTGGATGAAAC-GTTCCTACGTGATGAGGACG
* * ** *
4013285 GACTGGAAATCTTTAGGGATGATGATAACAAGGTTCCTATGCGATGAGGACGGTTGGTTATCTAG
65 GACTAGAAATCTTTAGGGA-GATGATAACAAGGTTCCTAAGCGATGAGGACGACTGATTATCTAG
4013350 AGGTG
129 AGGTG
* * * * * * *
4013355 ACACAGCTCCTACGTGATAAGGAGATATGTTCGGGGGATGAAACGATTCTTACGTGATGAGGACG
1 ACGCTGCTCCTACGTGATGAGGAGATTTGATCGGTGGATGAAACG-TTCCTACGTGATGAGGACG
* * * * *
4013420 G-TTAGTAATCTTTA-GG-G-TGATAACATGGTTCCTAAGTGATGAGGACGACTGATTATCTAGG
65 GACTAGAAATCTTTAGGGAGATGATAACAAGGTTCCTAAGCGATGAGGACGACTGATTATCTAGA
4013481 GGTTG
130 GG-TG
* * * * *
4013486 ACGCTGCTCCTATGTGATGAGGAGATTTGATCGATAGATGACACAGTTCCTACATGATGAGGACG
1 ACGCTGCTCCTACGTGATGAGGAGATTTGATCGGTGGATGAAAC-GTTCCTACGTGATGAGGACG
4013551 G
65 G
4013552 CTGGCCATCT
Statistics
Matches: 161, Mismatches: 32, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
130 39 0.24
131 55 0.34
132 1 0.01
133 3 0.02
134 61 0.38
135 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.27
Consensus pattern (133 bp):
ACGCTGCTCCTACGTGATGAGGAGATTTGATCGGTGGATGAAACGTTCCTACGTGATGAGGACGG
ACTAGAAATCTTTAGGGAGATGATAACAAGGTTCCTAAGCGATGAGGACGACTGATTATCTAGAG
GTG
Found at i:4013562 original size:131 final size:132
Alignment explanation
Indices: 4013221--4013564 Score: 354
Period size: 131 Copynumber: 2.6 Consensus size: 132
4013211 GTCTAAGGGT
* * * *
4013221 ACGCTACTCCTACGTGATGAGGAGATTTGGTCGGTGGATGAAACGGTTCCTACGCGAGGAGGA-G
1 ACGCTGCTCCTACGTGATGAGGAGATTTGATCGGTGGATGAAAC-GTTCCTACGTGATGAGGACG
* ** *
4013285 GACTGGAAATCTTTAGGGATGATGATAACAAGGTTCCTATGCGATGAGGACGGTTGGTTATCTAG
65 G-CTGGAAATCTTTAGGGA-GATGATAACAAGGTTCCTAAGCGATGAGGACGACTGATTATCTAG
4013350 AGGTG
128 AGGTG
* * * * * * *
4013355 ACACAGCTCCTACGTGATAAGGAGATATGTTCGGGGGATGAAACGATTCTTACGTGATGAGGACG
1 ACGCTGCTCCTACGTGATGAGGAGATTTGATCGGTGGATGAAACG-TTCCTACGTGATGAGGACG
* * * * * *
4013420 GTTAGTAATCTTTA-GG-G-TGATAACATGGTTCCTAAGTGATGAGGACGACTGATTATCTAGGG
65 GCTGGAAATCTTTAGGGAGATGATAACAAGGTTCCTAAGCGATGAGGACGACTGATTATCTAGAG
4013482 GTTG
130 G-TG
* * * * *
4013486 ACGCTGCTCCTATGTGATGAGGAGATTTGATCGATAGATGACACAGTTCCTACATGATGAGGACG
1 ACGCTGCTCCTACGTGATGAGGAGATTTGATCGGTGGATGAAAC-GTTCCTACGTGATGAGGACG
**
4013551 GCTGGCCATCTTTA
65 GCTGGAAATCTTTA
4013565 AGGATTTGTT
Statistics
Matches: 170, Mismatches: 36, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
130 39 0.23
131 64 0.38
132 1 0.01
133 3 0.02
134 61 0.36
135 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (132 bp):
ACGCTGCTCCTACGTGATGAGGAGATTTGATCGGTGGATGAAACGTTCCTACGTGATGAGGACGG
CTGGAAATCTTTAGGGAGATGATAACAAGGTTCCTAAGCGATGAGGACGACTGATTATCTAGAGG
TG
Found at i:4013678 original size:65 final size:65
Alignment explanation
Indices: 4013571--4013919 Score: 590
Period size: 65 Copynumber: 5.4 Consensus size: 65
4013561 TTTAAGGATT
* *
4013571 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
* * * *
4013636 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATCCATTTCAAGGGAAACAATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
*
4013701 TGTTACAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
* * * *
4013766 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACAATTTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
*
4013831 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
4013896 TGTTTCAAGAGAAACTGTCTCAAG
1 TGTTTCAAGAGAAACTGTCTCAAG
4013920 CGAGCCGAAT
Statistics
Matches: 262, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 262 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGA
Found at i:4015474 original size:12 final size:12
Alignment explanation
Indices: 4015459--4015529 Score: 63
Period size: 13 Copynumber: 5.7 Consensus size: 12
4015449 TTTTGTTCTA
4015459 TTTTTTCTTTGT
1 TTTTTTCTTTGT
* *
4015471 TTTTTGTTTTTCT
1 TTTTT-TCTTTGT
*
4015484 TTTTGTCTTTGT
1 TTTTTTCTTTGT
*
4015496 TTTTCTT-TGTTTT
1 TTTT-TTCT-TTGT
4015509 TTTATTTCTTTGT
1 TTT-TTTCTTTGT
4015522 TTTTTTCT
1 TTTTTTCT
4015530 CTTTGCTTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
12 20 0.43
13 24 0.52
14 2 0.04
ACGTcount: A:0.01, C:0.08, G:0.08, T:0.82
Consensus pattern (12 bp):
TTTTTTCTTTGT
Found at i:4015499 original size:35 final size:34
Alignment explanation
Indices: 4015447--4015519 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 34
4015437 TTTGCATGTG
*
4015447 CTTTTTGTTCTATTTTTTCTTTGTTTTTTGTTTTT
1 CTTTTTGTTCTATTTTTTCTTTGTTTTTT-TATTT
*
4015482 CTTTTTG-TCTTTGTTTTTCTTTGTTTTTTTATTT
1 CTTTTTGTTCTAT-TTTTTCTTTGTTTTTTTATTT
4015516 CTTT
1 CTTT
4015520 GTTTTTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 12 0.34
35 23 0.66
ACGTcount: A:0.03, C:0.10, G:0.08, T:0.79
Consensus pattern (34 bp):
CTTTTTGTTCTATTTTTTCTTTGTTTTTTTATTT
Found at i:4020766 original size:3 final size:3
Alignment explanation
Indices: 4020758--4020820 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
4020748 GCAAAATGTG
4020758 AAT AAT AAT AAT AAT 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 AAT AAT
4020806 AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT A
4020821 GTTTTTTAAG
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4021495 original size:25 final size:25
Alignment explanation
Indices: 4021460--4021509 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4021450 CCGAGAAGCA
*
4021460 GGGAAGTCGAAATCGTTTTCATGAT
1 GGGAAGACGAAATCGTTTTCATGAT
4021485 GGGAAGACGAAATCGTTTTCATGAT
1 GGGAAGACGAAATCGTTTTCATGAT
4021510 CACAGTGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (25 bp):
GGGAAGACGAAATCGTTTTCATGAT
Found at i:4026436 original size:112 final size:112
Alignment explanation
Indices: 4026126--4026722 Score: 860
Period size: 112 Copynumber: 5.3 Consensus size: 112
4026116 AACTTTCAAC
* ** * * * *
4026126 AAAGTATCGATACATGTACA-AAAAGTATCTATATTTTCAACATATTAGGTAG-TC-TTACCGGT
1 AAAGTATCGATACATTTTTATAAAA-TATCGATACTTTCAACATATCAGGTAGCTCTTTATCGGT
* * *
4026188 TTTGTCATAATGAAACTAATTTTTTCATATTTTTATATGTTATATTGT
65 TTTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGT
* ** * *
4026236 AAAGTATCGATACATTTTTATAAAAAGGATATATACTTTCAACATATCAGGTAGTTCTTTATCGA
1 AAAGTATCGATACATTTTTAT-AAAA-TATCGATACTTTCAACATATCAGGTAGCTCTTTATCGG
* * *
4026301 TTTTGTCATTATGAAACT-AGTTTTGCCATATTTTTACATATTATATTGT
64 TTTTGTCATAATGAAACTGA-TTTTGTCATATTTTTACATGTTATATTGT
*
4026350 AAAGTATCGATACATTTTTATAAAATATCGATACTTTCAACATATTAGGTAGCTCTTTATCGGTT
1 AAAGTATCGATACATTTTTATAAAATATCGATACTTTCAACATATCAGGTAGCTCTTTATCGGTT
*
4026415 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
66 TTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGT
* * *
4026462 AAAGTATCGATACATTTTTATAAAATATCAATACTTTCAACATATCAAGTAGCTCTTTATCGATT
1 AAAGTATCGATACATTTTTATAAAATATCGATACTTTCAACATATCAGGTAGCTCTTTATCGGTT
*
4026527 TTGTCATAATGAAACTGATTTTGTCATATTTTTACCTGTTATATTGT
66 TTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGT
* * *
4026574 AAAGTATCGATACATTTTTGTAAAGTATCGATACTTTCAACATATCAGGTAGCTCTTTACCGGTT
1 AAAGTATCGATACATTTTTATAAAATATCGATACTTTCAACATATCAGGTAGCTCTTTATCGGTT
*
4026639 TTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGA
66 TTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGT
* *
4026686 AAAGTATCGATACATTTTTATAAAGTATAGATACTTT
1 AAAGTATCGATACATTTTTATAAAATATCGATACTTT
4026723 ATATGCGCTA
Statistics
Matches: 441, Mismatches: 40, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
110 17 0.04
112 349 0.79
113 7 0.02
114 68 0.15
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (112 bp):
AAAGTATCGATACATTTTTATAAAATATCGATACTTTCAACATATCAGGTAGCTCTTTATCGGTT
TTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGT
Found at i:4026929 original size:77 final size:73
Alignment explanation
Indices: 4026802--4026980 Score: 259
Period size: 77 Copynumber: 2.4 Consensus size: 73
4026792 TTTTACATAT
* * * *
4026802 CCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACTGTTTACATTATTAGCAACCT
1 CCGGTAGGTA-TTTAATGTAATAGGTAGCGCATATTTTTGTTACCGTTTACATTATTAACAACCT
4026867 TCAAAAAAAAAA
65 T---AAAAAAAA
4026879 CCGGTAGGTATTTTAATGTAATAGGTAGCGCATATTTTTGTTACCGTTTACATTATTAACAACCT
1 CCGGTAGGTA-TTTAATGTAATAGGTAGCGCATATTTTTGTTACCGTTTACATTATTAACAACCT
4026944 TAAAAAAAA
65 TAAAAAAAA
*
4026953 CCGATAGGTATTTAATTGTAATAGGTAG
1 CCGGTAGGTATTTAA-TGTAATAGGTAG
4026981 TTTAAATTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
73 5 0.05
74 29 0.31
77 61 0.64
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (73 bp):
CCGGTAGGTATTTAATGTAATAGGTAGCGCATATTTTTGTTACCGTTTACATTATTAACAACCTT
AAAAAAAA
Found at i:4027212 original size:23 final size:23
Alignment explanation
Indices: 4027185--4027232 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
4027175 TAAGTAATTA
** *
4027185 ACCTATTTTATTATATAAGTGCT
1 ACCTATTACATTATATAAGCGCT
*
4027208 ACCTATTACGTTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
4027231 AC
1 AC
4027233 GTAATATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:4027243 original size:23 final size:23
Alignment explanation
Indices: 4027195--4027244 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4027185 ACCTATTTTA
* *
4027195 TTATATAAGTGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
* *
4027218 TTATATAAGCGCTACGTAATATG
1 TTATATAAGCGCTACCTAATACG
4027241 TTAT
1 TTAT
4027245 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:4027415 original size:158 final size:158
Alignment explanation
Indices: 4027066--4027403 Score: 525
Period size: 158 Copynumber: 2.1 Consensus size: 158
4027056 TTTGTTACAA
* *
4027066 AAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTTCAGTAACTAACCGGTTATATTATCCT
1 AAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTTCAATAAATAACCGGTTATATTATCCT
** * *
4027131 TGATAACATTTTAAGCGTTTATTTAATATGTTGTAATAACAAATTAAGTAATTAACCTATTTTAT
66 TGATAACATTTTAAGCGTTTACCTAATATGTTATAATAACAAATTAAGTAATTAACATATTTTAT
*
4027196 TATATAAGTGCTACCTATTACGTTATAT
131 TATATAAGTGCTACCTATTACATTATAT
* * * * *
4027224 AAGCGCTACGTAATATGTTATTGTGCTTGATAATGTTTTCAATAAATAACCTGTTATGTTATCTT
1 AAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTTCAATAAATAACCGGTTATATTATCCT
*
4027289 TGGTAACATTTT-AGACGTTTACCTAATATGTTATAATAACAAATTAAGTAATTAACATATTTTA
66 TGATAACATTTTAAG-CGTTTACCTAATATGTTATAATAACAAATTAAGTAATTAACATATTTTA
4027353 TTATATAAGTGCTACCTATTACATTATAT
130 TTATATAAGTGCTACCTATTACATTATAT
* *
4027382 GAGCTCTACCTAATATGTTATT
1 AAGCGCTACCTAATATGTTATT
4027404 TTATTTTATA
Statistics
Matches: 163, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
157 2 0.01
158 161 0.99
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (158 bp):
AAGCGCTACCTAATATGTTATTATGCTTGATAATGTTTTCAATAAATAACCGGTTATATTATCCT
TGATAACATTTTAAGCGTTTACCTAATATGTTATAATAACAAATTAAGTAATTAACATATTTTAT
TATATAAGTGCTACCTATTACATTATAT
Found at i:4033077 original size:22 final size:21
Alignment explanation
Indices: 4033051--4033092 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
4033041 TGGCTACAGA
*
4033051 ATTGATTGTCTTGATGGATGAT
1 ATTGATGGTCTTGAT-GATGAT
*
4033073 ATTGATGGTGTTGATGATGA
1 ATTGATGGTCTTGATGATGA
4033093 AATGAAGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.02, G:0.31, T:0.43
Consensus pattern (21 bp):
ATTGATGGTCTTGATGATGAT
Done.