Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 55
Found at i:2934852 original size:19 final size:20
Alignment explanation
Indices: 2934806--2934865 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
2934796 TTCCCCTGTG
2934806 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
2934829 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
2934848 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2934866 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:2938707 original size:22 final size:21
Alignment explanation
Indices: 2938665--2938704 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2938655 GAGTTTGTTT
*
2938665 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2938686 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2938705 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2946975 original size:15 final size:15
Alignment explanation
Indices: 2946955--2946988 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2946945 CCGTAGGACC
2946955 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
2946970 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
2946985 ACTA
1 ACTA
2946989 AAGAACCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:2948616 original size:22 final size:22
Alignment explanation
Indices: 2948589--2948650 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 22
2948579 ATACAGTAAA
2948589 TAATATTATT-TATTATAAAACT
1 TAATATTATTAT-TTATAAAACT
*
2948611 TAATATTATTATTTATAAAATTT
1 TAATATTATTATTTATAAAA-CT
*
2948634 TAAAATTATGTATTTAT
1 TAATATTAT-TATTTAT
2948651 TATTAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 18 0.51
23 10 0.29
24 7 0.20
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATATTATTATTTATAAAACT
Found at i:2949533 original size:131 final size:130
Alignment explanation
Indices: 2949291--2949631 Score: 513
Period size: 131 Copynumber: 2.6 Consensus size: 130
2949281 AATTCTAAGA
*
2949291 GAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCATT
1 GAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAAT
* * *
2949356 CATTCATTACTCCAATCGAAATAAAGAGATATCACTATTCCATCTT-AAAACTCAATATTGATTT
66 CATTCATTACTCCAATCAAAATAAAGAGATATCACAATTCCATCTTAAAAAATCAATATTGATTT
* * * *
2949420 GAGTGAAAATGATAATATCTAATGATTTTCAATTGAGAATAAATGACCTCTCACGCCTTAAAGCA
1 GA--GAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * *
2949485 ATCATTCATTACTTCAATCAAAATAAAGAGATATCACAATTTCGTCTTAAAAAATCAATATTGAT
64 ATCATTCATTACTCCAATCAAAATAAAGAGATATCACAATTCCATCTTAAAAAATCAATATTGAT
2949550 TT
129 TT
* * * * *
2949552 GAGAGAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATTCCTTAAAACAGT
1 GAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAAT
2949617 CATTCATTACTCCAA
66 CATTCATTACTCCAA
2949632 CCGAAATAGA
Statistics
Matches: 188, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
129 2 0.01
130 68 0.36
131 99 0.53
132 19 0.10
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (130 bp):
GAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAAT
CATTCATTACTCCAATCAAAATAAAGAGATATCACAATTCCATCTTAAAAAATCAATATTGATTT
Found at i:2951246 original size:36 final size:38
Alignment explanation
Indices: 2951181--2951256 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
2951171 TATATATATA
*
2951181 TATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATACAACAAAGTATTAATAAAATAGAA-AAGC
*
2951219 TATATATATACAACAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATACAACAAAGTATTAATAAAATAGAAAAGC
2951255 TA
1 TA
2951257 CCCTCTTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 12 0.34
37 7 0.20
38 16 0.46
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (38 bp):
TATATATATACAACAAAGTATTAATAAAATAGAAAAGC
Found at i:2951510 original size:2 final size:2
Alignment explanation
Indices: 2951458--2951494 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2951448 AACAAAAATA
2951458 AT AT 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 AT AT A
2951495 AAGTTATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2951680 original size:2 final size:2
Alignment explanation
Indices: 2951673--2951705 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2951663 TTAAACAAAC
2951673 AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2951706 GTAAAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2951776 original size:18 final size:17
Alignment explanation
Indices: 2951755--2951797 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2951745 ATATGTATGT
2951755 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
2951773 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
2951790 ATAA-AATA
1 ATAATAATA
2951798 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:2953271 original size:106 final size:106
Alignment explanation
Indices: 2953086--2953616 Score: 855
Period size: 106 Copynumber: 5.0 Consensus size: 106
2953076 GTATTGTTCT
* * * * * * *
2953086 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTATTTGTTGTCAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
2953151 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
*
2953192 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
2953257 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* ** **
2953298 GAGTCTAATGCCCTTTACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
2953363 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
** *
2953404 GAGTCCAATGCCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
2953469 CCAGCCTTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * *
2953510 GATTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGATGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
2953575 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
2953616 G
1 G
2953617 GGTGGCGCGA
Statistics
Matches: 396, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 396 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:2954531 original size:36 final size:38
Alignment explanation
Indices: 2954477--2954553 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 38
2954467 GAAACAAATT
* **
2954477 CAAAGGTTTTTTTCCAAGGGAATTTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACTGTCTCAAGAGAGA
2954515 CAAA-GTTTGTTT-CAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACTGTCTCAAGAGAGA
2954551 CAA
1 CAA
2954554 TGGTGAGAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 25 0.69
37 7 0.19
38 4 0.11
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (38 bp):
CAAAGGTTTGTTTCCAAGGGAAACTGTCTCAAGAGAGA
Found at i:2955070 original size:18 final size:18
Alignment explanation
Indices: 2955039--2955074 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2955029 TATTGAATCC
*
2955039 CCAAAGATGACCCAATAT
1 CCAAAAATGACCCAATAT
*
2955057 CCAAAAATGCCCCAATAT
1 CCAAAAATGACCCAATAT
2955075 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGACCCAATAT
Found at i:2956157 original size:10 final size:10
Alignment explanation
Indices: 2956137--2956197 Score: 63
Period size: 10 Copynumber: 5.8 Consensus size: 10
2956127 TTCCTTTTGA
2956137 TTTTTGCTTCT
1 TTTTTG-TTCT
2956148 TTTCTT-TTCT
1 TTT-TTGTTCT
2956158 TTTTTGTTCT
1 TTTTTGTTCT
2956168 TGTTTT-TTCT
1 T-TTTTGTTCT
2956178 TTTTTGCTTCT
1 TTTTTG-TTCT
2956189 TTTCTTGTT
1 TTT-TTGTT
2956198 TGTTCTTGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
9 6 0.14
10 17 0.39
11 16 0.36
12 5 0.11
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (10 bp):
TTTTTGTTCT
Found at i:2956167 original size:20 final size:21
Alignment explanation
Indices: 2956137--2956194 Score: 93
Period size: 20 Copynumber: 2.8 Consensus size: 21
2956127 TTCCTTTTGA
2956137 TTTTTGCTTCTTTTCTTTTCT
1 TTTTTGCTTCTTTTCTTTTCT
2956158 TTTTTG-TTCTTGTT-TTTTCT
1 TTTTTGCTTCTT-TTCTTTTCT
2956178 TTTTTGCTTCTTTTCTT
1 TTTTTGCTTCTTTTCTT
2956195 GTTTGTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 19 0.56
21 15 0.44
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTGCTTCTTTTCTTTTCT
Found at i:2959673 original size:9 final size:10
Alignment explanation
Indices: 2959650--2959681 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
2959640 ACAGTTAGTA
2959650 AAATAAAAAT
1 AAATAAAAAT
2959660 AAATAAAAAT
1 AAATAAAAAT
2959670 -AATAAAAA-
1 AAATAAAAAT
2959678 AAAT
1 AAAT
2959682 CGCAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 11 0.52
10 10 0.48
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:2960802 original size:38 final size:40
Alignment explanation
Indices: 2960733--2960812 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
2960723 TATATATATA
*
2960733 TATATATATATACATCAAAGTATTAATAAAATA-AATAAGC
1 TATATATATATACAACAAAGTATTAATAAAATAGAA-AAGC
*
2960773 TATATATATATACAACAAA-TATTTA-AAAATAGAAAAGC
1 TATATATATATACAACAAAGTATTAATAAAATAGAAAAGC
2960811 TA
1 TA
2960813 CCCTCTCACT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.31
Consensus pattern (40 bp):
TATATATATATACAACAAAGTATTAATAAAATAGAAAAGC
Found at i:2961068 original size:2 final size:2
Alignment explanation
Indices: 2961024--2961052 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2961014 AATAAAAATA
2961024 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 A
2961053 AAGTTATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2962776 original size:44 final size:44
Alignment explanation
Indices: 2962727--2962991 Score: 395
Period size: 44 Copynumber: 6.0 Consensus size: 44
2962717 CTGCTCTAAA
* * *
2962727 ATAAATGAAATTGTATAACGGTGCATTATTGGCAGAAAGGTGAC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * *
2962771 ATAAATGAAAATGTATAATGGTGCATTATTGGCATAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
2962815 ATAAATGAATATGCATAACGGTGCATTATTGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
2962859 ATAAATGAATATGCATAATGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
2962903 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAATGTGAC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
2962947 ATAAATGAAAATGCATAACGGTACATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
2962991 A
1 A
2962992 CTCATGGTAT
Statistics
Matches: 201, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 201 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:2962832 original size:25 final size:25
Alignment explanation
Indices: 2962802--2962876 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
2962792 TGCATTATTG
2962802 GCATAAATGTGCCATAAATGAATAT
1 GCATAAATGTGCCATAAATGAATAT
**
2962827 GCATAACGGTG-CAT---T--AT-T
1 GCATAAATGTGCCATAAATGAATAT
*
2962845 GGCAGAAATGTGCCATAAATGAATAT
1 -GCATAAATGTGCCATAAATGAATAT
2962871 GCATAA
1 GCATAA
2962877 TGGTGCATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
18 1 0.03
19 10 0.28
20 3 0.08
21 1 0.03
23 1 0.03
24 3 0.08
25 16 0.44
26 1 0.03
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (25 bp):
GCATAAATGTGCCATAAATGAATAT
Found at i:2965024 original size:27 final size:28
Alignment explanation
Indices: 2964989--2965041 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
2964979 ATTATATTAA
2964989 TATTAAATACA-TAAATAATATTATTCAT
1 TATTAAATA-ATTAAATAATATTATTCAT
*
2965017 TATT-AATAATTTAATAATATTATTC
1 TATTAAATAATTAAATAATATTATTC
2965042 TATAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 18 0.78
28 4 0.17
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (28 bp):
TATTAAATAATTAAATAATATTATTCAT
Found at i:2965055 original size:24 final size:26
Alignment explanation
Indices: 2964983--2965056 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 26
2964973 TATATTATTA
*
2964983 TATTAATATTAAATACATA-AATAATAT
1 TATTCATATTAAA-A-ATATAATAATAT
* *
2965010 TATTCATTATTAATAATTTAATAATAT
1 TATTCA-TATTAAAAATATAATAATAT
2965037 TATTC-TA-TAAAAATATAATA
1 TATTCATATTAAAAATATAATA
2965057 TCTTATATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 11 0.28
25 2 0.05
26 2 0.05
27 19 0.47
28 6 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (26 bp):
TATTCATATTAAAAATATAATAATAT
Found at i:2965111 original size:16 final size:17
Alignment explanation
Indices: 2965087--2965134 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
2965077 ATTGAGTATT
2965087 TTATTATAATATTAAAA
1 TTATTATAATATTAAAA
* *
2965104 TT-TTATAAAATT-ATA
1 TTATTATAATATTAAAA
2965119 TTATTATAAATATTAA
1 TTATTAT-AATATTAA
2965135 TAAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 7 0.28
18 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATTATAATATTAAAA
Found at i:2965137 original size:26 final size:24
Alignment explanation
Indices: 2965089--2965140 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2965079 TGAGTATTTT
*
2965089 ATTATAATATTAAAATTTTATAAA
1 ATTATAATATTAAAATTTAATAAA
*
2965113 ATTATATTATTATAAATATTAATAAA
1 ATTATAATATTA-AAAT-TTAATAAA
2965139 AT
1 AT
2965141 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.46
25 4 0.17
26 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTATAATATTAAAATTTAATAAA
Found at i:2965148 original size:10 final size:11
Alignment explanation
Indices: 2965096--2965177 Score: 51
Period size: 11 Copynumber: 7.1 Consensus size: 11
2965086 TTTATTATAA
*
2965096 TATTAAAATTT
1 TATTAAAATAT
*
2965107 TATAAAATTATAT
1 TATTAAA--ATAT
2965120 TATTATAAATAT
1 TATTA-AAATAT
*
2965132 TAATAAAATAT
1 TATTAAAATAT
*
2965143 T-TTAAATATTT
1 TATTAAA-ATAT
*
2965154 TGATTGAAATGA-
1 T-ATTAAAAT-AT
2965166 TATTAAAATAT
1 TATTAAAATAT
2965177 T
1 T
2965178 TTATTAATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
10 5 0.09
11 25 0.46
12 11 0.20
13 11 0.20
14 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (11 bp):
TATTAAAATAT
Found at i:2965701 original size:27 final size:28
Alignment explanation
Indices: 2965671--2965728 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
2965661 TTAAAAACTG
* *
2965671 TTTGTA-TGAATAAGTATAACTTTTCTT
1 TTTGTAGTGAAAAAGTACAACTTTTCTT
2965698 TTTGTAGGTGAAAAAGTACAACTTTTCTT
1 TTTGTA-GTGAAAAAGTACAACTTTTCTT
2965727 TT
1 TT
2965729 ATTTTTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 6 0.22
29 21 0.78
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (28 bp):
TTTGTAGTGAAAAAGTACAACTTTTCTT
Found at i:2966050 original size:30 final size:27
Alignment explanation
Indices: 2965995--2966061 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 27
2965985 ACAAATACTC
2965995 AAAATATTATTATTTTATATATTTAATA
1 AAAATA-TATTATTTTATATATTTAATA
**
2966023 TTAATATATTATTTTAGTATCATTTTAATA
1 AAAATATATTATTTTA-TAT-A-TTTAATA
2966053 AAAATATAT
1 AAAATATAT
2966062 ATTATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 10 0.31
28 7 0.22
29 1 0.03
30 14 0.44
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (27 bp):
AAAATATATTATTTTATATATTTAATA
Found at i:2966151 original size:25 final size:26
Alignment explanation
Indices: 2966117--2966192 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 26
2966107 ATTTTTTTAG
* *
2966117 TATTGTAATAATAT-ATCAATTATAT
1 TATTATAATAATATAATAAATTATAT
* *
2966142 TATTATAAT-ATATAATAAATTTTTT
1 TATTATAATAATATAATAAATTATAT
*
2966167 TATTTTAATAATAAATAATAAATTAT
1 TATTATAATAAT--ATAATAAATTAT
2966193 TTCTTAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
24 4 0.10
25 24 0.59
26 2 0.05
28 11 0.27
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (26 bp):
TATTATAATAATATAATAAATTATAT
Found at i:2966179 original size:28 final size:31
Alignment explanation
Indices: 2966146--2966204 Score: 88
Period size: 28 Copynumber: 2.0 Consensus size: 31
2966136 TTATATTATT
*
2966146 ATAATATATAATAAATT-TTT-TT-ATTTTA
1 ATAATAAATAATAAATTATTTCTTAATTTTA
2966174 ATAATAAATAATAAATTATTTCTTAATTTTA
1 ATAATAAATAATAAATTATTTCTTAATTTTA
2966205 TATTATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 16 0.59
29 3 0.11
30 2 0.07
31 6 0.22
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (31 bp):
ATAATAAATAATAAATTATTTCTTAATTTTA
Found at i:2968736 original size:21 final size:20
Alignment explanation
Indices: 2968668--2968737 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
2968658 AAAATACCCT
**
2968668 AGTATCGATACTCCTATGGGG
1 AGTATCGATACT-CTATGCTG
* *
2968689 AGTATCAATACTC-CTGCCTTG
1 AGTATCGATACTCTATG-C-TG
2968710 -GTATCGATACTCTATGACTG
1 AGTATCGATACTCTATG-CTG
2968730 AGTATCGA
1 AGTATCGA
2968738 AACTAACTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.05
20 14 0.37
21 22 0.58
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTCTATGCTG
Found at i:2969790 original size:15 final size:15
Alignment explanation
Indices: 2969770--2969822 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
2969760 CAATTTGTTT
2969770 AACCCAATTAACTTA
1 AACCCAATTAACTTA
*
2969785 AACCC-ATTAAATATTA
1 AACCCAATT-AA-CTTA
2969801 AAGTCCCAATTAACTTA
1 AA--CCCAATTAACTTA
2969818 AACCC
1 AACCC
2969823 CTGAAAGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 3 0.10
15 10 0.32
16 5 0.16
17 5 0.16
18 5 0.16
19 3 0.10
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.26
Consensus pattern (15 bp):
AACCCAATTAACTTA
Found at i:2976043 original size:217 final size:216
Alignment explanation
Indices: 2975777--2976690 Score: 1448
Period size: 217 Copynumber: 4.3 Consensus size: 216
2975767 ATTTAAGAAT
2975777 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
2975842 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATAGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
** * *
2975907 CCATTTAAAATTTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAAGTATGTATCAATTTCAG
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGT-AAAAAGTATGGATCAATTTCAG
*
2975972 ATGCAAATAAATTTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
*
2975994 TAAATTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
2976059 GGGTCAAATCA-AAATAATTTTAAATTGTGATGTTGAAATTAATAC-AAAAAGTACTAAATTATA
66 GGATCAAAT-AGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATA
* * * * *
2976122 CTCATATAAAAAGTTATGGGCCAATTAAAAAATAGAATTAAGTAAAAAGTATGGATCACTTTCAT
130 CCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAAAAAGTATGGATCAATTTCAG
2976187 ATGCAAATAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
*
2976209 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATTAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
2976274 GGATCAAATAGAAATAAATTTAAATTGTGATGTTAAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATAGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * *
2976339 CCATTTAAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAG
131 CCATTT-AAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAAAAAGTATGGATCAATTTCAG
2976404 ATGCAAATAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
* *
2976426 TAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAATTAAACAACACA-A---A--AT
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
2976485 GGATCAAATAGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATAC
66 GGATCAAATAGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * * *
2976550 TCATTTAAAAAGTTATGGGCCAATTAATAAATAGAAATAAGTAATAAGTATGGGTCAATTTTAGA
131 CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAAAAAGTATGGATCAATTTCAGA
* *
2976615 TGCAAATAAAATGTGGATGAC
196 TGCAAATAAAATTTGGAGGAC
*
2976636 TAAATTGAACAGATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
2976691 AAAGGGATCA
Statistics
Matches: 652, Mismatches: 41, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
210 128 0.20
211 66 0.10
213 1 0.00
214 1 0.00
215 143 0.22
216 81 0.12
217 232 0.36
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATAGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAAAAAGTATGGATCAATTTCAGA
TGCAAATAAAATTTGGAGGAC
Found at i:2976778 original size:2 final size:2
Alignment explanation
Indices: 2976773--2977064 Score: 87
Period size: 2 Copynumber: 147.0 Consensus size: 2
2976763 AAAACAACTA
*
2976773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
2976815 AT GT A- AT AT AA ACT AT AT AGT TT TT AT AT AT AT -T AT GT AT AA
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * * *
2976857 ACT AT AT AT ACC AT GT AT AA ACT AT A- AT ACC AT AT AGT TT AT AT
1 A-T AT AT AT A-T AT AT AT AT A-T AT AT AT A-T AT AT A-T AT AT AT
* * * *
2976901 AT GA- ACT AT AT AG A- AT CT AC AT AGT TT AT AT AT GA- AT -T AT
1 AT -AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT -AT AT AT AT
* * * * *
2976941 AT AT AA ACT AT AC A- AT TT AT AT TT AT AT AT -T AT GT AT A- AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
2976981 -T AT AA AT A- AT AT AT AT -T GT AT AA AT -T AT AT AGT TT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
2977019 A- AT AT AA ACT AT AT AGT TT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
2977061 AT AT
1 AT AT
2977065 GATTTAGGGT
Statistics
Matches: 209, Mismatches: 49, Indels: 64
0.65 0.15 0.20
Matches are distributed among these distances:
1 17 0.08
2 177 0.85
3 15 0.07
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2976960 original size:31 final size:31
Alignment explanation
Indices: 2976894--2976962 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
2976884 TACCATATAG
* * *
2976894 TTTATATATGAACTATATAGAATCTACATAG
1 TTTATATATGAACTATATAGAAACTACACAA
* * *
2976925 TTTATATATGAATTATATATAAACTATACAA
1 TTTATATATGAACTATATAGAAACTACACAA
2976956 TTTATAT
1 TTTATAT
2976963 TTATATATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (31 bp):
TTTATATATGAACTATATAGAAACTACACAA
Found at i:2976978 original size:17 final size:17
Alignment explanation
Indices: 2976958--2977062 Score: 65
Period size: 17 Copynumber: 6.3 Consensus size: 17
2976948 CTATACAATT
* *
2976958 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
2976975 TATAATTATAAATAATA
1 TATATTTATAAATTATA
2976992 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
* *
2977010 TA-GTTTATTAA-TATA
1 TATATTTATAAATTATA
* **
2977025 -A-ACTATATAGTTTATA
1 TATA-TTTATAAATTATA
* *
2977041 TATATATATATATTATA
1 TATATTTATAAATTATA
2977058 TATAT
1 TATAT
2977063 ATGATTTAGG
Statistics
Matches: 68, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
14 1 0.01
15 8 0.12
16 9 0.13
17 37 0.54
18 13 0.19
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:2977060 original size:9 final size:9
Alignment explanation
Indices: 2976958--2977062 Score: 67
Period size: 9 Copynumber: 11.6 Consensus size: 9
2976948 CTATACAATT
2976958 TATATT-TA
1 TATATTATA
*
2976966 TATATTATG
1 TATATTATA
2976975 TATAATTATA
1 TAT-ATTATA
*
2976985 -A-ATAATA
1 TATATTATA
*
2976992 TATATTGTA
1 TATATTATA
*
2977001 TAAATTATA
1 TATATTATA
2977010 TAGTTTATTAATA
1 TA---TATT-ATA
* *
2977023 TAAACTATA
1 TATATTATA
2977032 TAGT-TTATA
1 TA-TATTATA
2977041 TATA-TATA
1 TATATTATA
2977049 TATATTATA
1 TATATTATA
2977058 TATAT
1 TATAT
2977063 ATGATTTAGG
Statistics
Matches: 74, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
7 5 0.07
8 16 0.22
9 38 0.51
10 7 0.09
12 3 0.04
13 5 0.07
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (9 bp):
TATATTATA
Found at i:2977077 original size:7 final size:7
Alignment explanation
Indices: 2977067--2977130 Score: 58
Period size: 7 Copynumber: 9.1 Consensus size: 7
2977057 ATATATATGA
2977067 TTTAGGG
1 TTTAGGG
2977074 TTTAGGG
1 TTTAGGG
**
2977081 TTTATAG
1 TTTAGGG
**
2977088 TTTATAG
1 TTTAGGG
**
2977095 TTTATAG
1 TTTAGGG
2977102 TTTA-GG
1 TTTAGGG
2977108 TATTAGGG
1 T-TTAGGG
2977116 TTTAGGG
1 TTTAGGG
2977123 TTTAGGG
1 TTTAGGG
2977130 T
1 T
2977131 GTATATTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
6 2 0.04
7 47 0.90
8 3 0.06
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:2977181 original size:20 final size:20
Alignment explanation
Indices: 2977156--2977228 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 20
2977146 TATAAACTAC
2977156 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
*
2977176 ATACTATATTTTATACTATTTAT
1 ATACTATA-ATT-TA-TATTTAT
*
2977199 ATAAACTATAGTTTATATTTAT
1 AT--ACTATAATTTATATTTAT
*
2977221 ATATTATA
1 ATACTATA
2977229 TATATGAACT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 13 0.29
21 2 0.04
22 11 0.24
23 11 0.24
24 2 0.04
25 6 0.13
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.53
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:2977199 original size:23 final size:24
Alignment explanation
Indices: 2977169--2977215 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
2977159 CTATAATTTA
*
2977169 TATTTATAT-ACTATATTTTATAC
1 TATTTATATAACTATAGTTTATAC
2977192 TATTTATATAAACTATAGTTTATA
1 TATTTATAT-AACTATAGTTTATA
2977216 TTTATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
25 12 0.57
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (24 bp):
TATTTATATAACTATAGTTTATAC
Found at i:2977301 original size:2 final size:2
Alignment explanation
Indices: 2977294--2977366 Score: 58
Period size: 2 Copynumber: 34.0 Consensus size: 2
2977284 ACATATGACC
* *
2977294 TA TA TA TA TA TA TA CTA TA GTT TA TA TT TA TA TA CTA TA TA T-
1 TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA
*
2977336 TA TA TA TA AA CTA TA TA TA CTA TA TA GTA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
2977367 ATTTACATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
1 1 0.02
2 47 0.81
3 10 0.17
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2977319 original size:22 final size:22
Alignment explanation
Indices: 2977294--2977343 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
2977284 ACATATGACC
2977294 TATATATATATATACTATAGT-T
1 TATATATATATATACTATA-TAT
2977316 TATAT-T-TATATACTATATAT
1 TATATATATATATACTATATAT
2977336 TATATATA
1 TATATATA
2977344 AACTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.04
20 17 0.68
21 2 0.08
22 5 0.20
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
TATATATATATATACTATATAT
Found at i:2977343 original size:18 final size:18
Alignment explanation
Indices: 2977173--2977753 Score: 138
Period size: 18 Copynumber: 31.8 Consensus size: 18
2977163 AATTTATATT
*
2977173 TATATACTATATTTTATA
1 TATATACTATATATTATA
* * *
2977191 CTATTTA-TATAAACTATA
1 -TATATACTATATATTATA
* *
2977209 GTTTATATTTATATATTATA
1 -TATATA-CTATATATTATA
*
2977229 TATATGAACTATAGT-TTACA
1 TATAT--ACTATA-TATTATA
*
2977249 TATGA-ACTATAGT-TTACA
1 TAT-ATACTATA-TATTATA
*
2977267 TATAAACTATATAGTT-TA
1 TATATACTATATA-TTATA
* *
2977285 CATATGAC-CTATA-TATA
1 TATAT-ACTATATATTATA
2977302 TATATACTATAGT-TTATA
1 TATATACTATA-TATTATA
2977320 TTTATATACTATATATTATA
1 --TATATACTATATATTATA
*
2977340 TATAAACTATATATACTATA
1 TATATACTATATAT--TATA
* * *
2977360 TAGTATAATTTACATATGAACTA
1 TA-TAT-A-CTATATAT-TA-TA
** * *
2977383 TATATAAAACCATA-TAAA
1 TATATACTA-TATATTATA
*
2977401 CTATATACTATAGT-TGATATT
1 -TATATACTATA-TAT--TATA
**
2977422 TATATACTATATAAAATAA
1 TATATACTATATATTAT-A
*
2977441 TTTATACTATAGTA-TATA
1 TATATACTATA-TATTATA
*
2977459 TA-A-ACCATAT-TATATA
1 TATATACTATATAT-TATA
*
2977475 TATAAACTATATATTATA
1 TATATACTATATATTATA
*
2977493 TAGT-T-C-AT-TAGTATA
1 TA-TATACTATATATTATA
* *
2977508 TATAAACTATATAATATA
1 TATATACTATATATTATA
* * **
2977526 TATAAAGTATATGGTATA
1 TATATACTATATATTATA
* * *
2977544 TATAAACTACACATTATA
1 TATATACTATATATTATA
* *
2977562 TATAT-TTCAT-TAGTATA
1 TATATACT-ATATATTATA
*
2977579 TATAAACTATATATTATA
1 TATATACTATATATTATA
*
2977597 TAGT-T-C-AT-TAGTATA
1 TA-TATACTATATATTATA
* *
2977612 TATAAACTATATAGTATA
1 TATATACTATATATTATA
* *
2977630 TGTAAACTATATATTATA
1 TATATACTATATATTATA
* *
2977648 TAGTTCATTACTATATATAACA
1 TA--T-A-TACTATATATTATA
* **
2977670 TATATAGTATATGGTATA
1 TATATACTATATATTATA
* *
2977688 TACAAACTATATATTATA
1 TATATACTATATATTATA
*
2977706 TAGT-T-C-AT-TACTATA
1 TA-TATACTATATATTATA
* * **
2977721 TATAAATTATATAGCATA
1 TATATACTATATATTATA
*
2977739 TATAAACTATATATT
1 TATATACTATATATT
2977754 GAAAAGTTCA
Statistics
Matches: 413, Mismatches: 90, Indels: 119
0.66 0.14 0.19
Matches are distributed among these distances:
14 3 0.01
15 25 0.06
16 22 0.05
17 33 0.08
18 191 0.46
19 40 0.10
20 58 0.14
21 13 0.03
22 18 0.04
23 10 0.02
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (18 bp):
TATATACTATATATTATA
Found at i:2977349 original size:38 final size:37
Alignment explanation
Indices: 2977187--2977350 Score: 129
Period size: 33 Copynumber: 4.6 Consensus size: 37
2977177 TACTATATTT
2977187 TATACTATT-TATATAAACTATAGTTTATATT-TATA-
1 TATA-TATTATATATAAACTATAGTTTATATTATATAC
* *
2977222 TAT-TA-TATATATGAACTATAGTTTACA-TATGA-AC
1 TATATATTATATATAAACTATAGTTTATATTAT-ATAC
* * *
2977256 TATAGT-TTACATATAAACTATATAGTTTACA-TATGA-CC
1 TATA-TATTATATATAAAC--TATAGTTTATATTAT-ATAC
2977294 TATATA-TATATAT--ACTATAGTTTATATTTATATAC
1 TATATATTATATATAAACTATAGTTTATA-TTATATAC
2977329 TATATATTATATATAAACTATA
1 TATATATTATATATAAACTATA
2977351 TATACTATAT
Statistics
Matches: 105, Mismatches: 8, Indels: 29
0.74 0.06 0.20
Matches are distributed among these distances:
32 2 0.02
33 32 0.30
34 5 0.05
35 15 0.14
36 17 0.16
37 7 0.07
38 27 0.26
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (37 bp):
TATATATTATATATAAACTATAGTTTATATTATATAC
Found at i:2977505 original size:51 final size:52
Alignment explanation
Indices: 2977450--2977784 Score: 324
Period size: 51 Copynumber: 6.4 Consensus size: 52
2977440 ATTTATACTA
*
2977450 TAGTATATATAAACCATATTA-TATATATAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATTAGTATATATAAACTATATATTATATAGTTCAT
* * ** ** *
2977501 TAGTATATATAAACTATA-TAATATATATAAAGTATATGGTATATA-TAAAC
1 TAGTATATATAAACTATATTAGTATATATAAACTATATATTATATAGTTCAT
** * *
2977551 TACACATTATATATA-TTTCATTAGTATATATAAACTATATATTATATAGTTCAT
1 TA-GTA-TATATAAACTAT-ATTAGTATATATAAACTATATATTATATAGTTCAT
*
2977605 TAGTATATATAAACTATA-TAGTATATGTAAACTATATATTATATAGTTCAT
1 TAGTATATATAAACTATATTAGTATATATAAACTATATATTATATAGTTCAT
* * *
2977656 TACTATATATAACATATATAGTATATGGTATATACAAACTATATATTATATAGTTCAT
1 TAGTATATATAA-A-CTATA-T-TA--GTATATATAAACTATATATTATATAGTTCAT
* * * *
2977714 TACTATATATAAATTATA-TAGCATATATAAACTATATATTGA-AAAGTTCAT
1 TAGTATATATAAACTATATTAGTATATATAAACTATATATT-ATATAGTTCAT
* *
2977765 TAATATATTATAACCTATAT
1 TAGTATA-TATAAACTATAT
2977785 ATTAATTTAT
Statistics
Matches: 233, Mismatches: 34, Indels: 32
0.78 0.11 0.11
Matches are distributed among these distances:
50 6 0.03
51 116 0.50
52 27 0.12
53 32 0.14
54 4 0.02
56 6 0.03
57 1 0.00
58 41 0.18
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (52 bp):
TAGTATATATAAACTATATTAGTATATATAAACTATATATTATATAGTTCAT
Found at i:2977571 original size:71 final size:69
Alignment explanation
Indices: 2977448--2977598 Score: 203
Period size: 71 Copynumber: 2.2 Consensus size: 69
2977438 TAATTTATAC
* * * *
2977448 TATAGTATATATAAACCATATTATATATATAAACTATATATTATATAGTTCATTAGTATATATAA
1 TATAATATATATAAACCATATGATATATATAAACTACACATTATATAGTTCATTAGTATATATAA
2977513 ACTA
66 ACTA
** * *
2977517 TATAATATATATAAAGTATATGGTATATATAAACTACACATTATATATATTTCATTAGTATATAT
1 TATAATATATATAAACCATATGATATATATAAACTACACA-T-TATATAGTTCATTAGTATATAT
2977582 AAACTA
64 AAACTA
*
2977588 TATATTATATA
1 TATAATATATA
2977599 GTTCATTAGT
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
69 33 0.46
70 1 0.01
71 37 0.52
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (69 bp):
TATAATATATATAAACCATATGATATATATAAACTACACATTATATAGTTCATTAGTATATATAA
ACTA
Found at i:2977732 original size:58 final size:58
Alignment explanation
Indices: 2977619--2977740 Score: 192
Period size: 58 Copynumber: 2.1 Consensus size: 58
2977609 ATATATAAAC
**
2977619 TATATAGTATATGTAAACTATATATTATATAGTTCATTACTATATATAACATATATAG
1 TATATAGTATATACAAACTATATATTATATAGTTCATTACTATATATAACATATATAG
*
2977677 TATATGGTATATACAAACTATATATTATATAGTTCATTACTATATATAA-ATTATATAG
1 TATATAGTATATACAAACTATATATTATATAGTTCATTACTATATATAACA-TATATAG
*
2977735 CATATA
1 TATATA
2977741 TAAACTATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 1 0.02
58 57 0.98
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (58 bp):
TATATAGTATATACAAACTATATATTATATAGTTCATTACTATATATAACATATATAG
Found at i:2977732 original size:109 final size:110
Alignment explanation
Indices: 2977574--2977785 Score: 329
Period size: 109 Copynumber: 1.9 Consensus size: 110
2977564 TATTTCATTA
* * * *
2977574 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATGTAAACTA
1 GTATATACAAACTATATATTATATAGTTCATTACTATATATAAACTATATAGCATATATAAACTA
* *
2977639 TATATT-ATATAGTTCATTACTATA-TATAACATATATAGTATATG
66 TATATTGA-AAAGTTCATTAATATATTATAACATATATAGTATATG
*
2977683 GTATATACAAACTATATATTATATAGTTCATTACTATATATAAATTATATAGCATATATAAACTA
1 GTATATACAAACTATATATTATATAGTTCATTACTATATATAAACTATATAGCATATATAAACTA
*
2977748 TATATTGAAAAGTTCATTAATATATTATAACCTATATA
66 TATATTGAAAAGTTCATTAATATATTATAACATATATA
2977786 TTAATTTATT
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
109 80 0.86
110 13 0.14
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (110 bp):
GTATATACAAACTATATATTATATAGTTCATTACTATATATAAACTATATAGCATATATAAACTA
TATATTGAAAAGTTCATTAATATATTATAACATATATAGTATATG
Found at i:2977935 original size:60 final size:61
Alignment explanation
Indices: 2977845--2977985 Score: 178
Period size: 60 Copynumber: 2.3 Consensus size: 61
2977835 TATAAGGATC
* * *
2977845 AAATTGAATAAATTTTAAATATGAAACTTAAATTAATAAACTGTAAT-ATTAAATTTGGACT
1 AAATTGAACAAATTTAAAATATGAAACTTAAATTAATAAACTG-AATCATTAAATTTAGACT
* * * * * *
2977906 AAATTGAA-AAATTTGAAATGTGAAGCTTAAATTAATATATTGCATCATTAAATTTAGACT
1 AAATTGAACAAATTTAAAATATGAAACTTAAATTAATAAACTGAATCATTAAATTTAGACT
2977966 AAATTGAACAAATTTAAAAT
1 AAATTGAACAAATTTAAAAT
2977986 TACAATACCA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 2 0.03
60 50 0.71
61 18 0.26
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (61 bp):
AAATTGAACAAATTTAAAATATGAAACTTAAATTAATAAACTGAATCATTAAATTTAGACT
Found at i:2978196 original size:11 final size:11
Alignment explanation
Indices: 2978180--2978206 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2978170 AAATCAATCG
2978180 TGTTCTTCATT
1 TGTTCTTCATT
2978191 TGTTCTTCATT
1 TGTTCTTCATT
2978202 TGTTC
1 TGTTC
2978207 ATCCAGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.19, G:0.11, T:0.63
Consensus pattern (11 bp):
TGTTCTTCATT
Found at i:2978388 original size:112 final size:112
Alignment explanation
Indices: 2978191--2978511 Score: 450
Period size: 112 Copynumber: 2.9 Consensus size: 112
2978181 GTTCTTCATT
* *
2978191 TGTTCTTCATTTGTTCATCCAGTTCATCCCCAAAAGCCTCATTTGATCTTCAAAAACACCTAAAC
1 TGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAAC
* *
2978256 CAAAACATTTTCTTATTTTTTTCGATCAAACGCCCAAA-ATTCTTCCG
66 CAAAACATTTT-TTGTTTTTTTCGATCAAACACCCAAATATTCTTCCG
* *
2978303 TGTTCTTCATTTGTTCTTCCAATTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAAC
1 TGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAAC
*
2978368 CAAAACA-TTTTTGTGTTTTTTCTATCAAACACCCAAATATTCTTCCG
66 CAAAACATTTTTTGT-TTTTTTCGATCAAACACCCAAATATTCTTCCG
* * *
2978415 TATTCTTCATTTGTTCATCCAGTTGTTCCCCAAAACCCT-ACTTTAATCTTCAAAAACACCTAAA
1 TGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCA-TTTGATCTTCAAAAACACCTAAA
* * ** *
2978479 CACAAACCATATCATGTTTATTTCGATCAAACA
65 C-CAAAACATTTTTTGTTTTTTTCGATCAAACA
2978512 GCCGTAAATT
Statistics
Matches: 186, Mismatches: 18, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
110 3 0.02
111 24 0.13
112 135 0.73
113 20 0.11
114 4 0.02
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (112 bp):
TGTTCTTCATTTGTTCATCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCTAAAC
CAAAACATTTTTTGTTTTTTTCGATCAAACACCCAAATATTCTTCCG
Found at i:2978799 original size:16 final size:17
Alignment explanation
Indices: 2978751--2978823 Score: 67
Period size: 17 Copynumber: 4.1 Consensus size: 17
2978741 CCCTAACCCT
2978751 CCCAAACATAAACCCAAA
1 CCCAAAC-TAAACCCAAA
* * *
2978769 TCCAAATTGAACCCAAA
1 CCCAAACTAAACCCAAA
2978786 CCCAAACT-AACCCAAA
1 CCCAAACTAAACCCAAA
*
2978802 CCTAAACCCTAAACCCTAAA
1 CCCAAA--CTAAACCC-AAA
2978822 CC
1 CC
2978824 ATAACCCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
16 13 0.29
17 15 0.33
18 7 0.16
19 5 0.11
20 5 0.11
ACGTcount: A:0.48, C:0.40, G:0.01, T:0.11
Consensus pattern (17 bp):
CCCAAACTAAACCCAAA
Found at i:2978814 original size:7 final size:7
Alignment explanation
Indices: 2978794--2978883 Score: 98
Period size: 7 Copynumber: 13.4 Consensus size: 7
2978784 AACCCAAACT
2978794 AACCC-A
1 AACCCTA
2978800 AA-CCTA
1 AACCCTA
2978806 AACCCTA
1 AACCCTA
2978813 AACCCTA
1 AACCCTA
*
2978820 AACCAT-
1 AACCCTA
2978826 AACCCTA
1 AACCCTA
*
2978833 AACCCCA
1 AACCCTA
***
2978840 AATTATA
1 AACCCTA
2978847 AACCCTA
1 AACCCTA
*
2978854 AACTCTA
1 AACCCTA
2978861 AACCC-A
1 AACCCTA
2978867 AACCCTA
1 AACCCTA
2978874 AACCCTA
1 AACCCTA
2978881 AAC
1 AAC
2978884 TCTACACTAT
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
5 2 0.03
6 16 0.24
7 50 0.74
ACGTcount: A:0.47, C:0.39, G:0.00, T:0.14
Consensus pattern (7 bp):
AACCCTA
Found at i:2978829 original size:20 final size:21
Alignment explanation
Indices: 2978794--2978883 Score: 107
Period size: 20 Copynumber: 4.5 Consensus size: 21
2978784 AACCCAAACT
2978794 AACCC-AAACC-TAAACCCTA
1 AACCCTAAACCATAAACCCTA
2978813 AACCCTAAACCAT-AACCCTA
1 AACCCTAAACCATAAACCCTA
* **
2978833 AACCCCAAATTATAAACCCTA
1 AACCCTAAACCATAAACCCTA
* *
2978854 AACTCTAAACC-CAAACCCTA
1 AACCCTAAACCATAAACCCTA
2978874 AACCCTAAAC
1 AACCCTAAAC
2978884 TCTACACTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
19 5 0.08
20 39 0.66
21 15 0.25
ACGTcount: A:0.47, C:0.39, G:0.00, T:0.14
Consensus pattern (21 bp):
AACCCTAAACCATAAACCCTA
Found at i:2978878 original size:27 final size:27
Alignment explanation
Indices: 2978783--2978887 Score: 105
Period size: 27 Copynumber: 4.0 Consensus size: 27
2978773 AATTGAACCC
2978783 AAACCCAAA--CT-AACCC-AAAC-CT
1 AAACCCAAACCCTAAACCCTAAACTCT
* *
2978805 AAACCCTAAACCCTAAACCAT-AACCCT
1 AAACCC-AAACCCTAAACCCTAAACTCT
***
2978832 AAACCCCAAATTATAAACCCTAAACTCT
1 AAA-CCCAAACCCTAAACCCTAAACTCT
2978860 AAACCCAAACCCTAAACCCTAAACTCT
1 AAACCCAAACCCTAAACCCTAAACTCT
2978887 A
1 A
2978888 CACTATTCGA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
22 6 0.09
23 3 0.05
25 2 0.03
26 7 0.11
27 37 0.56
28 11 0.17
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (27 bp):
AAACCCAAACCCTAAACCCTAAACTCT
Found at i:2979120 original size:2 final size:2
Alignment explanation
Indices: 2979113--2979146 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2979103 TATATGTTTG
2979113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2979147 TGTTTATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2979213 original size:31 final size:31
Alignment explanation
Indices: 2979148--2979485 Score: 410
Period size: 31 Copynumber: 11.0 Consensus size: 31
2979138 TATATATATT
* * * * *
2979148 GTTTATTGATGTTGATATATAT-ATATACTT
1 GTTTATTGCTGTTGATGTAAATGATGTACTG
* * *
2979178 GTTTACTGTTGTTGATGTAAATGATATACTG
1 GTTTATTGCTGTTGATGTAAATGATGTACTG
* * *
2979209 GTTTATTACTGTTGATGTAAATGATATACTA
1 GTTTATTGCTGTTGATGTAAATGATGTACTG
* *
2979240 GTTTATTGCTATTGATGTAAATCATGTACTG
1 GTTTATTGCTGTTGATGTAAATGATGTACTG
* *
2979271 GTTTATTGTTGTTAATGTAAATGATGTACT-
1 GTTTATTGCTGTTGATGTAAATGATGTACTG
*
2979301 GTTTATTGTTGTTGATGTAAATGATGTACTG
1 GTTTATTGCTGTTGATGTAAATGATGTACTG
* * *
2979332 GTTTATTGCTGTTAATGTAAGTGATGTATTG
1 GTTTATTGCTGTTGATGTAAATGATGTACTG
* * *
2979363 TTTTATTGTTGTTGATGTAAATGATGTATTG
1 GTTTATTGCTGTTGATGTAAATGATGTACTG
* * *
2979394 GTTTATTGCTGTTGATGTAATTGGTGTATTG
1 GTTTATTGCTGTTGATGTAAATGATGTACTG
*
2979425 TTTTATTGCTGTTGATGTAAATGATGTACTG
1 GTTTATTGCTGTTGATGTAAATGATGTACTG
* *
2979456 GTTTATTGATGTTGATGTAAATTATGTACT
1 GTTTATTGCTGTTGATGTAAATGATGTACT
2979486 AGTGTTGGAA
Statistics
Matches: 268, Mismatches: 38, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
30 47 0.18
31 221 0.82
ACGTcount: A:0.25, C:0.04, G:0.22, T:0.49
Consensus pattern (31 bp):
GTTTATTGCTGTTGATGTAAATGATGTACTG
Found at i:2980229 original size:21 final size:21
Alignment explanation
Indices: 2980203--2980258 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2980193 TAGTGGCAGA
2980203 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGG
*
2980224 TGCATGGATGCACTGCGGGGG
1 TGCATGGATGCACTGCAGGGG
2980245 TGCATGGATGCACT
1 TGCATGGATGCACT
2980259 TTGACTCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.20, G:0.41, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGG
Found at i:2980507 original size:21 final size:21
Alignment explanation
Indices: 2980484--2980522 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2980474 TGTTTAATGA
2980484 AAAAT-ATACCAATTGTTAAC
1 AAAATGATACCAATTGTTAAC
*
2980504 AAAATGATATCAATTGTTA
1 AAAATGATACCAATTGTTA
2980523 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (21 bp):
AAAATGATACCAATTGTTAAC
Found at i:2983598 original size:20 final size:20
Alignment explanation
Indices: 2983573--2983627 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
2983563 TTGCAGCCTT
2983573 GGTGCATGGATGCACAAAAG
1 GGTGCATGGATGCACAAAAG
* *
2983593 GGTGCATGGATCCACAACAG
1 GGTGCATGGATGCACAAAAG
2983613 GGTGCATGGATGCAC
1 GGTGCATGGATGCAC
2983628 TAATTGCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.29, C:0.20, G:0.35, T:0.16
Consensus pattern (20 bp):
GGTGCATGGATGCACAAAAG
Found at i:2983715 original size:21 final size:21
Alignment explanation
Indices: 2983689--2983748 Score: 120
Period size: 21 Copynumber: 2.9 Consensus size: 21
2983679 ACTAGTGGCA
2983689 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
2983710 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
2983731 GGTGCATGGATGCACTGC
1 GGTGCATGGATGCACTGC
2983749 GACACCCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.20, G:0.42, T:0.20
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:2983927 original size:31 final size:31
Alignment explanation
Indices: 2983892--2984314 Score: 519
Period size: 31 Copynumber: 13.7 Consensus size: 31
2983882 AATTCAACTA
2983892 GTTTATTGTTGTTGATGTAAATGATGTACTG
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
*
2983923 GTTTATTGCTGTTGATGTTAAAT-ATGTACTG
1 GTTTATTGTTGTTGATG-TAAATGATGTACTG
2983954 GTTTATTGTTGTTGATGTAAATGATGTACTG
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
* * *
2983985 GTTTATTGTTGTTGATGTTAATTATGTACTA
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
* *
2984016 GTTTATTGTTGTTAATGTAAATGATGTATTG
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
* *
2984047 GTTTATTGTTGTTGATGTAAATAATGTAATG
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
* * *
2984078 GTTTATTGATGTTGATGTAAATTATGTATTG
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
* * * *
2984109 GTTTATTGCTGCTGATATAAATGATGTATTG
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
* * *
2984140 GTTTATTGTTGTTGATGTTAATTATGTACTA
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
* * *
2984171 GTTTATTATTGTTGATGTTAATTATGTACTG
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
* * *
2984202 CTTTATTGATGTTGATGTAAATGATGTATTG
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
* * *
2984233 GTTTATT-TCTGTTGATTTAAATGATATACTA
1 GTTTATTGT-TGTTGATGTAAATGATGTACTG
* * * *
2984264 GTTTATTGCTGTTGATGTTAATTATGTGCTG
1 GTTTATTGTTGTTGATGTAAATGATGTACTG
*
2984295 GTTTATTGTTG-TAATGTAAA
1 GTTTATTGTTGTTGATGTAAA
2984315 CTAACCATGT
Statistics
Matches: 337, Mismatches: 51, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
30 12 0.04
31 320 0.95
32 5 0.01
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (31 bp):
GTTTATTGTTGTTGATGTAAATGATGTACTG
Found at i:2984051 original size:93 final size:93
Alignment explanation
Indices: 2983888--2984302 Score: 582
Period size: 93 Copynumber: 4.5 Consensus size: 93
2983878 ACATAATTCA
* * *
2983888 ACTAGTTTATTGTTGTTGATGTAAATGATGTACTGGTTTATTGCTGTTGATGTTAAAT-ATGTAC
1 ACTAGTTTATTGTTGTTGATGTTAATTATGTACTGGTTTATTGCTGTTGATG-TAAATGATGTAT
2983952 TGGTTTATTGTTGTTGATGTAAATGATGT
65 TGGTTTATTGTTGTTGATGTAAATGATGT
* * * *
2983981 ACTGGTTTATTGTTGTTGATGTTAATTATGTACTAGTTTATTGTTGTTAATGTAAATGATGTATT
1 ACTAGTTTATTGTTGTTGATGTTAATTATGTACTGGTTTATTGCTGTTGATGTAAATGATGTATT
*
2984046 GGTTTATTGTTGTTGATGTAAATAATGT
66 GGTTTATTGTTGTTGATGTAAATGATGT
* * * * * * *
2984074 AATGGTTTATTGATGTTGATGTAAATTATGTATTGGTTTATTGCTGCTGATATAAATGATGTATT
1 ACTAGTTTATTGTTGTTGATGTTAATTATGTACTGGTTTATTGCTGTTGATGTAAATGATGTATT
* *
2984139 GGTTTATTGTTGTTGATGTTAATTATGT
66 GGTTTATTGTTGTTGATGTAAATGATGT
* * *
2984167 ACTAGTTTATTATTGTTGATGTTAATTATGTACTGCTTTATTGATGTTGATGTAAATGATGTATT
1 ACTAGTTTATTGTTGTTGATGTTAATTATGTACTGGTTTATTGCTGTTGATGTAAATGATGTATT
* *
2984232 GGTTTATT-TCTGTTGATTTAAATGATAT
66 GGTTTATTGT-TGTTGATGTAAATGATGT
* *
2984260 ACTAGTTTATTGCTGTTGATGTTAATTATGTGCTGGTTTATTG
1 ACTAGTTTATTGTTGTTGATGTTAATTATGTACTGGTTTATTG
2984303 TTGTAATGTA
Statistics
Matches: 283, Mismatches: 37, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
92 6 0.02
93 277 0.98
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.51
Consensus pattern (93 bp):
ACTAGTTTATTGTTGTTGATGTTAATTATGTACTGGTTTATTGCTGTTGATGTAAATGATGTATT
GGTTTATTGTTGTTGATGTAAATGATGT
Found at i:2986548 original size:20 final size:20
Alignment explanation
Indices: 2986523--2986568 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2986513 TAACCTAATA
2986523 ATATTTTATATTTATTATGT
1 ATATTTTATATTTATTATGT
2986543 ATATTTTATATTTATTATGT
1 ATATTTTATATTTATTATGT
*
2986563 TTATTT
1 ATATTT
2986569 AATAAAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
ATATTTTATATTTATTATGT
Found at i:2986708 original size:20 final size:20
Alignment explanation
Indices: 2986658--2986718 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
2986648 TGCTTGATTC
* *
2986658 TGCTTGCTTCCGTTTTATAT
1 TGCTTGCTTCTGTTTGATAT
*
2986678 TGTTTGCTTCTGTTTGATAT
1 TGCTTGCTTCTGTTTGATAT
**
2986698 TGCTTGCTTCTACTTGATAT
1 TGCTTGCTTCTGTTTGATAT
2986718 T
1 T
2986719 TGTAAGGGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.56
Consensus pattern (20 bp):
TGCTTGCTTCTGTTTGATAT
Found at i:2987472 original size:15 final size:17
Alignment explanation
Indices: 2987441--2987472 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2987431 TCAAATTATA
2987441 ATATACAAATTATAATT
1 ATATACAAATTATAATT
2987458 ATATA-AAATTA-AATT
1 ATATACAAATTATAATT
2987473 TCAAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 6 0.40
17 5 0.33
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATACAAATTATAATT
Found at i:2987579 original size:17 final size:17
Alignment explanation
Indices: 2987539--2987572 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2987529 AAGAGTAATC
2987539 ATAA-TTAATTATCATA
1 ATAATTTAATTATCATA
2987555 ATAATTTAATTATCATA
1 ATAATTTAATTATCATA
2987572 A
1 A
2987573 GTTTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATTTAATTATCATA
Found at i:2990460 original size:2 final size:2
Alignment explanation
Indices: 2990453--2990495 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2990443 GATCGGAGTT
2990453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2990495 T
1 T
2990496 GTTCAAACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2991439 original size:14 final size:14
Alignment explanation
Indices: 2991422--2991454 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2991412 ATTTCTATGT
*
2991422 AGGGAATTATTTGC
1 AGGGAATTATTTAC
2991436 AGGGAATTATTTAC
1 AGGGAATTATTTAC
2991450 AGGGA
1 AGGGA
2991455 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:2993226 original size:20 final size:21
Alignment explanation
Indices: 2993201--2993239 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2993191 TTTGTGGCCC
2993201 TTTCTAGCC-GTTGGGGATAA
1 TTTCTAGCCAGTTGGGGATAA
*
2993221 TTTCTAGCCATTTGGGGAT
1 TTTCTAGCCAGTTGGGGAT
2993240 GTTTTATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.38
Consensus pattern (21 bp):
TTTCTAGCCAGTTGGGGATAA
Found at i:2995674 original size:2 final size:2
Alignment explanation
Indices: 2995667--2995704 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2995657 CCACCCCGAT
2995667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2995705 TTTATATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2997490 original size:16 final size:17
Alignment explanation
Indices: 2997464--2997499 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2997454 TAATTAATAA
*
2997464 ATTTAAAATATAAAATC
1 ATTTAAAATATAAAAAC
2997481 ATTT-AAATATAAAAAC
1 ATTTAAAATATAAAAAC
2997497 ATT
1 ATT
2997500 GAATATCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTTAAAATATAAAAAC
Found at i:3001408 original size:22 final size:22
Alignment explanation
Indices: 3001378--3001441 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
3001368 AGTCGAGGGT
*
3001378 TACATAGGTCCTTCGAGACATA
1 TACATAGGTCATTCGAGACATA
* *
3001400 TACAGAGGTAATTCGAGACATA
1 TACATAGGTCATTCGAGACATA
*
3001422 TACATAGGTCATTCGGGACA
1 TACATAGGTCATTCGAGACA
3001442 AATTTCACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (22 bp):
TACATAGGTCATTCGAGACATA
Found at i:3009326 original size:11 final size:11
Alignment explanation
Indices: 3009298--3009327 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
3009288 TTTTCTTTCA
3009298 TTTGCATCATT
1 TTTGCATCATT
3009309 TTT-CATCATT
1 TTTGCATCATT
3009319 TTTGCATCA
1 TTTGCATCA
3009328 GATTTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (11 bp):
TTTGCATCATT
Found at i:3013609 original size:103 final size:101
Alignment explanation
Indices: 3013448--3013685 Score: 284
Period size: 103 Copynumber: 2.3 Consensus size: 101
3013438 CTTAAGATAA
* * * * * *
3013448 TTTCTCTCAAAATAAATTTCGTCTCGCTTGAAACATTTTTCCTTTGAGTTACAAATTTTAAAATT
1 TTTCTCTAAAAATAAA-TTCGTCTCGCTTGAGACAATTCTCCCTTAAGTTAC-AATTTTAAAATT
3013513 GCTTCACTTGAAACAAAATTAATCTCACTTGAGATTGT
64 GCTTCACTTGAAACAAAATTAATCTCACTTGAGATTGT
* * *
3013551 TTTCTCTAAAAATAAATTCCATCTCGCTTGAGACAATTCTCCCTTAAGATGTAC-ATTTTGAATT
1 TTTCTCTAAAAATAAATT-CGTCTCGCTTGAGACAATTCTCCCTTAAG-T-TACAATTTTAAAAT
* * * *
3013615 TGTTTCACTTGAAACAAAGTTCATTTCACTTGAGATTGT
63 TGCTTCACTTGAAACAAAATTAATCTCACTTGAGATTGT
*
3013654 TTT-TCTAAAAA-AAATTCGTCTCACTTGAGACA
1 TTTCTCTAAAAATAAATTCGTCTCGCTTGAGACA
3013686 GTCTTCCTCA
Statistics
Matches: 117, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
100 14 0.12
101 5 0.04
102 10 0.09
103 84 0.72
104 1 0.01
105 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (101 bp):
TTTCTCTAAAAATAAATTCGTCTCGCTTGAGACAATTCTCCCTTAAGTTACAATTTTAAAATTGC
TTCACTTGAAACAAAATTAATCTCACTTGAGATTGT
Found at i:3013895 original size:37 final size:34
Alignment explanation
Indices: 3013804--3013904 Score: 94
Period size: 37 Copynumber: 2.8 Consensus size: 34
3013794 ACAAAATTAA
* *
3013804 TCTCACTTGAGATTGTTTCTTTTAAAACAAATTTG
1 TCTCACTTGAGA-AGTTTCTCTTAAAACAAATTTG
* * *
3013839 TCTCGCTTGGGGAAATTTCTCTTAAAACAAAGTTTTG
1 TCTCACTT-GAGAAGTTTCTCTTAAAACAAA--TTTG
* *
3013876 TCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TCTCACTTGAGA-AGTTTCTCTTAAAACA
3013905 CACAAAAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
35 22 0.42
36 6 0.11
37 25 0.47
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.41
Consensus pattern (34 bp):
TCTCACTTGAGAAGTTTCTCTTAAAACAAATTTG
Found at i:3013925 original size:16 final size:16
Alignment explanation
Indices: 3013900--3013930 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3013890 GTTTCTCTTG
*
3013900 AAACACACAAAAAAAC
1 AAACAAACAAAAAAAC
3013916 AAACAAACAAAAAAA
1 AAACAAACAAAAAAA
3013931 ATCTTTGAGT
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:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (16 bp):
AAACAAACAAAAAAAC
Found at i:3013977 original size:22 final size:22
Alignment explanation
Indices: 3013949--3014027 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
3013939 GTCTGTTTAC
3013949 CTTGAAACAAAGTTTTGTCTCT
1 CTTGAAACAAAGTTTTGTCTCT
* *
3013971 CTTGAAACAAAAATCTTTGAGTCTGTTTCC
1 CTTGAAAC-AAAGT-TTT--GTC----TCT
3014001 CTTGAAACAAAGTTTTGTCTCT
1 CTTGAAACAAAGTTTTGTCTCT
3014023 CTTGA
1 CTTGA
3014028 GATAATTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
22 15 0.33
23 4 0.09
24 3 0.07
26 6 0.13
28 3 0.07
29 4 0.09
30 10 0.22
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (22 bp):
CTTGAAACAAAGTTTTGTCTCT
Found at i:3013992 original size:52 final size:52
Alignment explanation
Indices: 3013927--3014027 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
3013917 AACAAACAAA
3013927 AAAAATCTTTGAGTCTGTTTACCTTGAAACAAAGTTTTGTCTCTCTTGAAAC
1 AAAAATCTTTGAGTCTGTTTACCTTGAAACAAAGTTTTGTCTCTCTTGAAAC
*
3013979 AAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGA
1 AAAAATCTTTGAGTCTGTTTACCTTGAAACAAAGTTTTGTCTCTCTTGA
3014028 GATAATTTCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (52 bp):
AAAAATCTTTGAGTCTGTTTACCTTGAAACAAAGTTTTGTCTCTCTTGAAAC
Found at i:3014044 original size:67 final size:67
Alignment explanation
Indices: 3013968--3014282 Score: 549
Period size: 67 Copynumber: 4.7 Consensus size: 67
3013958 AAGTTTTGTC
* *
3013968 TCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAA
1 TCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
3014033 TT
66 TT
3014035 TCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
3014100 TT
66 TT
* *
3014102 TCTCTTGAAACAAAAATCTTTGAGTATGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAG
1 TCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
3014167 TT
66 TT
* *
3014169 TCTCTTGAAACAAAAATCTTTAAGTCTGTTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
3014234 TT
66 TT
3014236 TCTCTTGAAACAAAAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAA
1 TCTCTTGAAAC---AAAAATCTTTGAGTCTGTTTCCCTTGAAACAAA
3014283 TTATCCCTAA
Statistics
Matches: 236, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
67 204 0.86
70 32 0.14
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.38
Consensus pattern (67 bp):
TCTCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
TT
Found at i:3014544 original size:134 final size:133
Alignment explanation
Indices: 3014285--3014682 Score: 514
Period size: 134 Copynumber: 3.0 Consensus size: 133
3014275 GAAACAAATT
* * * ** *
3014285 ATCCCTAAGATGGCCAGCCGTCCTTATCACGTAGGAATTGTGTCATCCACCGACCATATCTCCTC
1 ATCCCTAAGATGGCCAGTCATCCTCATCACGTAGGAACAGTGTCATCCACCGACCATATCTCTTC
* * * *
3014350 ATCACGTAGGAGCCGC-ATCAACCTTAGATAACCAGTCATCCTCATCACGTAGAAAACGTGTTAT
66 ATCACGTAGGAGTCGCGATCAACCTTAGATAACCA-ACATCCTCATCACGTAGGAACCGTGTTAT
3014414 CATC
130 CATC
* * *
3014418 ATCCCTACAGATGTCCAGTCTTCCTCATCACGTAGGAACAATGTCATCCACCGACCATATCTCTT
1 ATCCCTA-AGATGGCCAGTCATCCTCATCACGTAGGAACAGTGTCATCCACCGACCATATCTCTT
** * * *
3014483 CATCTTGTAGGAGTCGCGAT-AACCTTAAATAACCAACCGTCCTCATCAAGTAGGAACCGTGTTA
65 CATCACGTAGGAGTCGCGATCAACCTTAGATAACCAA-CATCCTCATCACGTAGGAACCGTGTTA
3014547 TCATC
129 TCATC
*
3014552 ATCCCTGAAGATGGCTAGTCATCCTCATCACGTAGGAACAGTGTCATCCACCGACCATATCTCTT
1 ATCCCT-AAGATGGCCAGTCATCCTCATCACGTAGGAACAGTGTCATCCACCGACCATATCTCTT
* * * * *
3014617 CATCACGTAGGAGTCGTG-TCACCCTTAGATAGCTAGACTTCCTCATCACGTAGGAACCGTGTTA
65 CATCACGTAGGAGTCGCGATCAACCTTAGATAACCA-ACATCCTCATCACGTAGGAACCGTGTTA
3014681 TC
129 TC
3014683 TCCAAAATTA
Statistics
Matches: 229, Mismatches: 30, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
133 8 0.03
134 217 0.95
135 4 0.02
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (133 bp):
ATCCCTAAGATGGCCAGTCATCCTCATCACGTAGGAACAGTGTCATCCACCGACCATATCTCTTC
ATCACGTAGGAGTCGCGATCAACCTTAGATAACCAACATCCTCATCACGTAGGAACCGTGTTATC
ATC
Found at i:3015007 original size:18 final size:18
Alignment explanation
Indices: 3014984--3015021 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3014974 TACAGTTATT
3014984 AGTGTTAGAGAGCTTTAG
1 AGTGTTAGAGAGCTTTAG
3015002 AGTGTTAGAGAGCTTTAG
1 AGTGTTAGAGAGCTTTAG
3015020 AG
1 AG
3015022 GTGTACTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (18 bp):
AGTGTTAGAGAGCTTTAG
Found at i:3019201 original size:20 final size:20
Alignment explanation
Indices: 3019176--3019242 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
3019166 ACTGTTTGGA
3019176 CTCCATACCAAAGGA-TTGTT
1 CTCCATACCAAAGGACTTG-T
*
3019196 CTCCATACCGAAGGACTTGT
1 CTCCATACCAAAGGACTTGT
* *
3019216 CTCCATA-CATAATGACTGGT
1 CTCCATACCA-AAGGACTTGT
3019236 CTCCATA
1 CTCCATA
3019243 TCGATGAACG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 37 0.90
21 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
CTCCATACCAAAGGACTTGT
Found at i:3030649 original size:37 final size:37
Alignment explanation
Indices: 3030540--3030652 Score: 163
Period size: 37 Copynumber: 3.1 Consensus size: 37
3030530 AACATAACGT
* * * *
3030540 TAGATTTTTACTAGGATTTAAACTCCTAAAAATATAA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
* *
3030577 TAGAGTTTTACTATAATTCAAACTCTTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
*
3030614 TATAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
3030651 TA
1 TA
3030653 CATAAGCATT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
Found at i:3031088 original size:63 final size:64
Alignment explanation
Indices: 3030970--3031090 Score: 208
Period size: 64 Copynumber: 1.9 Consensus size: 64
3030960 AGGAGGGGGG
**
3030970 AAAATTCAATTTTATATATTTTATTTTTTTCTTACTATTATTATTATATATACTTCATCTTTAA
1 AAAATTCAATTTTATATATTTTATTTTTTTCAAACTATTATTATTATATATACTTCATCTTTAA
*
3031034 AAAATTCAATTTTTTATATTTTATTTTTTT-AAACTATTATTATTATATATACTTCAT
1 AAAATTCAATTTTATATATTTTATTTTTTTCAAACTATTATTATTATATATACTTCAT
3031091 TATTATTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
63 25 0.46
64 29 0.54
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (64 bp):
AAAATTCAATTTTATATATTTTATTTTTTTCAAACTATTATTATTATATATACTTCATCTTTAA
Found at i:3031118 original size:19 final size:18
Alignment explanation
Indices: 3031091--3031134 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
3031081 TATACTTCAT
*
3031091 TATTATTATTATATTTTA
1 TATTTTTATTATATTTTA
* *
3031109 TATGTTTTATTTTGTTTTA
1 TAT-TTTTATTATATTTTA
3031128 TATTTTT
1 TATTTTT
3031135 TTAATTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (18 bp):
TATTTTTATTATATTTTA
Found at i:3031127 original size:63 final size:63
Alignment explanation
Indices: 3030970--3031090 Score: 192
Period size: 63 Copynumber: 1.9 Consensus size: 63
3030960 AGGAGGGGGG
*
3030970 AAAATTCAATTTTATATATTTTATTTTTTTCT-TACTATTATTATTATATATACTTCATCTTTAA
1 AAAATTCAATTTTATATATTTTATTTTTTT-TAAACTATTATTATTATATATACTTCATCTTT-A
*
3031034 AAAATTCAATTTTTTATATTTTA-TTTTTTTAAACTATTATTATTATATATACTTCAT
1 AAAATTCAATTTTATATATTTTATTTTTTTTAAACTATTATTATTATATATACTTCAT
3031091 TATTATTATT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
62 1 0.02
63 31 0.57
64 22 0.41
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (63 bp):
AAAATTCAATTTTATATATTTTATTTTTTTTAAACTATTATTATTATATATACTTCATCTTTA
Found at i:3031457 original size:20 final size:20
Alignment explanation
Indices: 3031434--3031627 Score: 183
Period size: 20 Copynumber: 9.5 Consensus size: 20
3031424 AACTCTAGTT
* *
3031434 TCGCAACACAGTTTCCAAAA
1 TCGCAACGCGGTTTCCAAAA
* * * *
3031454 TCGCAACACGATTTTCAAAT
1 TCGCAACGCGGTTTCCAAAA
* * *
3031474 TCACAACGCGATTCTCTAAAA
1 TCGCAACGCGGTT-TCCAAAA
* *
3031495 TCGCAATGCGGTTTTCAAAA
1 TCGCAACGCGGTTTCCAAAA
**
3031515 TCGCAACGC-AATTCTCAAAA
1 TCGCAACGCGGTTTC-CAAAA
*
3031535 TCGCAACGCGGTTCTCCAAAT
1 TCGCAACGCGGTT-TCCAAAA
*
3031556 TCGCAACGCGATTCTCCAAAA
1 TCGCAACGCGGTT-TCCAAAA
* *
3031577 TCGCAACGCGGTTTTCAAAT
1 TCGCAACGCGGTTTCCAAAA
3031597 TCGCAACGCGGTTCTCCAAAA
1 TCGCAACGCGGTT-TCCAAAA
3031618 TCGCAACGCG
1 TCGCAACGCG
3031628 TTGCGAAAAT
Statistics
Matches: 141, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
19 2 0.01
20 72 0.51
21 65 0.46
22 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGGTTTCCAAAA
Found at i:3031497 original size:41 final size:41
Alignment explanation
Indices: 3031447--3031627 Score: 265
Period size: 41 Copynumber: 4.4 Consensus size: 41
3031437 CAACACAGTT
* * *
3031447 TCCAAAATCGCAACACGATTTTCAAATTCACAACGCGATTC
1 TCCAAAATCGCAACGCGGTTTTCAAATTCGCAACGCGATTC
* * * *
3031488 TCTAAAATCGCAATGCGGTTTTCAAAATCGCAACGCAATTC
1 TCCAAAATCGCAACGCGGTTTTCAAATTCGCAACGCGATTC
*
3031529 T-CAAAATCGCAACGCGGTTCTCCAAATTCGCAACGCGATTC
1 TCCAAAATCGCAACGCGGTT-TTCAAATTCGCAACGCGATTC
*
3031570 TCCAAAATCGCAACGCGGTTTTCAAATTCGCAACGCGGTTC
1 TCCAAAATCGCAACGCGGTTTTCAAATTCGCAACGCGATTC
3031611 TCCAAAATCGCAACGCG
1 TCCAAAATCGCAACGCG
3031628 TTGCGAAAAT
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
40 16 0.13
41 90 0.73
42 18 0.15
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.23
Consensus pattern (41 bp):
TCCAAAATCGCAACGCGGTTTTCAAATTCGCAACGCGATTC
Found at i:3031672 original size:20 final size:20
Alignment explanation
Indices: 3031647--3031695 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
3031637 TAAACGCGCT
*
3031647 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTCTGTG
3031667 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
3031687 TTGCGAATT
1 TTGCGAATT
3031696 ACAAATTCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.12, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:3031709 original size:20 final size:20
Alignment explanation
Indices: 3031686--3031735 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3031676 TGACTTCTGT
3031686 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
* *
3031706 GTTGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGC
3031726 GTTGCGAATT
1 GTTGCGAATT
3031736 TGGAAACTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:3031884 original size:8 final size:8
Alignment explanation
Indices: 3031884--3031913 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
3031874 ATATACATAT
3031884 ATATATAC
1 ATATATAC
3031892 ATATATAC
1 ATATATAC
3031900 ATATATAC
1 ATATATAC
3031908 ATATAT
1 ATATAT
3031914 TTTATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATATAC
Found at i:3031889 original size:12 final size:12
Alignment explanation
Indices: 3031872--3031913 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3031862 TTATTATTTC
3031872 ATATATACATAT
1 ATATATACATAT
3031884 ATATATACATAT
1 ATATATACATAT
* * *
3031896 ATACATATATAC
1 ATATATACATAT
3031908 ATATAT
1 ATATAT
3031914 TTTATTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATACATAT
Found at i:3037331 original size:20 final size:20
Alignment explanation
Indices: 3037302--3037339 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3037292 CCCCTTCAAA
*
3037302 GGGGGAATCGGTTCCCTCAG
1 GGGGGAATCGATTCCCTCAG
*
3037322 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
3037340 TGCACCAAAA
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:0.13, C:0.26, G:0.39, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAG
Found at i:3043998 original size:14 final size:13
Alignment explanation
Indices: 3043957--3044009 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
3043947 AGATCCAATC
*
3043957 AGAGCAAAAAAAA
1 AGAGAAAAAAAAA
*
3043970 AGAGAAAAAACAA
1 AGAGAAAAAAAAA
3043983 AGAGAAAATAAAAA
1 AGAGAAAA-AAAAA
3043997 AGAGAAACAAAAA
1 AGAGAAA-AAAAA
3044010 CCAAGGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
13 19 0.54
14 15 0.43
15 1 0.03
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (13 bp):
AGAGAAAAAAAAA
Found at i:3045127 original size:32 final size:32
Alignment explanation
Indices: 3045058--3045119 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3045048 ACCTTTGAAG
* * *
3045058 ATTCAACATCAAATGTTGGGGCATTTTTGGAA
1 ATTCAACATCAAATATTGGGGCATCTTCGGAA
*
3045090 ATTCAACATCGAATATTGGGGCATCTTCGG
1 ATTCAACATCAAATATTGGGGCATCTTCGG
3045120 GTATTCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (32 bp):
ATTCAACATCAAATATTGGGGCATCTTCGGAA
Found at i:3046567 original size:37 final size:37
Alignment explanation
Indices: 3046457--3046568 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
3046447 AACATAACGT
* * *
3046457 TAGAGTTTTACTAGGATTTAAACTCCTAAAAATAGAA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
3046494 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
3046531 TAGAGTTTTACTATGATTCAAACTCCTAAAACTAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
3046568 T
1 T
3046569 CCATATGCAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:3047027 original size:20 final size:20
Alignment explanation
Indices: 3046990--3047028 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3046980 TGTTTTATCT
*
3046990 TTTTTTAAAATTTATTATTA
1 TTTTTTAAAAATTATTATTA
3047010 TTTTTTAAAACATT-TTATT
1 TTTTTTAAAA-ATTATTATT
3047029 TATATGCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTTAAAAATTATTATTA
Found at i:3047125 original size:3 final size:3
Alignment explanation
Indices: 3047119--3047187 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
3047109 TATCTATACG
3047119 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3047167 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
3047188 ATATACATTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3047326 original size:3 final size:3
Alignment explanation
Indices: 3047318--3047365 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
3047308 TTACTTACTG
3047318 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3047364 TT
1 TT
3047366 TATTTCTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3047580 original size:28 final size:26
Alignment explanation
Indices: 3047555--3047614 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
3047545 TCGTATTCAT
3047555 TTTTATCTTCACTC-TTTTTTTTATTC
1 TTTTAT-TTCACTCGTTTTTTTTATTC
** *
3047581 TTTTATTTCGGTCGTTTTTTTTATTT
1 TTTTATTTCACTCGTTTTTTTTATTC
3047607 TCTTTATT
1 T-TTTATT
3047615 CTATTTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 5 0.17
26 18 0.62
27 6 0.21
ACGTcount: A:0.10, C:0.13, G:0.05, T:0.72
Consensus pattern (26 bp):
TTTTATTTCACTCGTTTTTTTTATTC
Found at i:3047621 original size:18 final size:18
Alignment explanation
Indices: 3047600--3047639 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3047590 GGTCGTTTTT
3047600 TTTATTTTC-TTTATTCTA
1 TTTATTTTCATTT-TTCTA
*
3047618 TTTATTTTCATTTTTTTA
1 TTTATTTTCATTTTTCTA
3047636 TTTA
1 TTTA
3047640 ACACGTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTTTCATTTTTCTA
Found at i:3049778 original size:16 final size:17
Alignment explanation
Indices: 3049751--3049796 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
3049741 TAGTAATTTA
3049751 TTTAATTATTTTAATTG
1 TTTAATTATTTTAATTG
*
3049768 TTTAA-TATTTTAATTA
1 TTTAATTATTTTAATTG
* *
3049784 ATTAATTTTTTTA
1 TTTAATTATTTTA
3049797 CATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTAATTATTTTAATTG
Found at i:3058546 original size:17 final size:17
Alignment explanation
Indices: 3058524--3058557 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3058514 TGGGAATAGG
3058524 GTTTTGTTATTGTTGTT
1 GTTTTGTTATTGTTGTT
*
3058541 GTTTTGTTGTTGTTGTT
1 GTTTTGTTATTGTTGTT
3058558 AATATTAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.00, G:0.26, T:0.71
Consensus pattern (17 bp):
GTTTTGTTATTGTTGTT
Found at i:3062480 original size:113 final size:113
Alignment explanation
Indices: 3062282--3062848 Score: 836
Period size: 112 Copynumber: 5.1 Consensus size: 113
3062272 TTGTTGGTTT
* * * * *
3062282 GTGTCGATACTTTATAAAAATATATTGATCTATAACAATATAACAAGTAAAAAAAATGATAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
* * *
3062347 CGGTCAATAAATGACAAAACATGTAAAGCGCTACTGGATATATTGAAA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
3062395 GTGTCGATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
3062460 CGGTCTATAAATGACAAAACAGGT-AA-----A---G--ATATTGAAA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
3062497 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
*
3062561 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
3062609 ATGCCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATAACAAAAT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
* * *
3062673 TGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
3062721 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACATGTAAAAAAAATGACAAAAT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
* * *
3062786 CGGTCTATAAATAACAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
3062834 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
3062849 TATAAGTATC
Statistics
Matches: 418, Mismatches: 24, Indels: 24
0.90 0.05 0.05
Matches are distributed among these distances:
101 40 0.10
102 58 0.14
104 1 0.00
107 2 0.00
110 1 0.00
112 159 0.38
113 157 0.38
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (113 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:3063034 original size:182 final size:182
Alignment explanation
Indices: 3062720--3063174 Score: 748
Period size: 182 Copynumber: 2.5 Consensus size: 182
3062710 ATATGTTGAT
* * *
3062720 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACATGTAAAAAAAATGACAAAA
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAATATGACAAAA
** * * * *
3062785 TCGGTCTATAAATAACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATT
65 TCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTCTATT
* *
3062850 ATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAACACTAATAA
130 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACACCAATAA
*
3062903 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
3062968 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTCTATTA
66 CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTCTATTA
* *
3063033 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
131 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACACCAATAA
*
3063085 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
* *
3063150 CGATCTCGAAATGACAAAATCGGTA
66 CGGTCTCGAAATGACAAAACCGGTA
3063175 GTAAAAAAGT
Statistics
Matches: 254, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
182 207 0.81
183 47 0.19
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
CGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTCTATTA
TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAACACCAATAA
Found at i:3064232 original size:26 final size:24
Alignment explanation
Indices: 3064197--3064265 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 24
3064187 GTCTACAAAA
3064197 ATAT-TTTATTTTATTATATATATAT
1 ATATATTTATTTTATTAT-TAT-TAT
3064222 ATATATTTA-TTTATTATTATTAT
1 ATATATTTATTTTATTATTATTAT
3064245 -TATTATTATATTTTTATTATT
1 ATA-TATT-TA-TTTTATTATT
3064266 TTTGCAGGCC
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 5 0.13
25 12 0.31
26 13 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATATATTTATTTTATTATTATTAT
Found at i:3064240 original size:3 final size:3
Alignment explanation
Indices: 3064198--3064265 Score: 54
Period size: 3 Copynumber: 22.3 Consensus size: 3
3064188 TCTACAAAAA
3064198 TAT T-T TAT T-T TAT TA- TAT ATAT ATAT ATATT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TA-T TA-T TAT TAT TAT
*
3064242 TAT TAT TAT TA- TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3064266 TTTGCAGGCC
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
2 8 0.14
3 32 0.56
4 16 0.28
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3064811 original size:32 final size:32
Alignment explanation
Indices: 3064733--3064831 Score: 87
Period size: 32 Copynumber: 3.1 Consensus size: 32
3064723 TCTCCTAATT
* * * * *
3064733 TTAATATTTTTTTATTTCTTTTTACATTGTTA
1 TTAATATTATTATATTTATTTTTTCATTATTA
*
3064765 -T-ATATATATATATATTTATTTTTTCATTTTTA
1 TTAATAT-TAT-TATATTTATTTTTTCATTATTA
3064797 TTAATATTATTATATTAATATTTTTT-ATTATTA
1 TTAATATTATTATATT--TATTTTTTCATTATTA
3064830 TT
1 TT
3064832 TTCTCATGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
30 4 0.07
31 3 0.05
32 24 0.44
33 12 0.22
34 12 0.22
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (32 bp):
TTAATATTATTATATTTATTTTTTCATTATTA
Found at i:3068724 original size:110 final size:110
Alignment explanation
Indices: 3068526--3069511 Score: 1496
Period size: 110 Copynumber: 9.0 Consensus size: 110
3068516 GATGGTGGTT
* * * *
3068526 GCTCCACTTCACAGCGAAGGGGTGACTGACGGTCAACAAATAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
3068591 AATTTCAACTTCACAACGAATGATATTGTACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
**
3068636 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAACTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
3068701 AATTTTAACTTCACAACGAATGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
3068746 GCTCAACTTCACAGTGAAGGGGCGACTGACTGTCAACAAACAATTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
3068811 AATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
3068856 GCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAAAAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * * * * *
3068921 AATTTCAATTTCACAACGAATGATATTGGAATTGAGATAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
3068966 GCTCAACTTCACAGCGAAGGGGCGACTGACTGCCAACAAACAGCTTTTCAATTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
3069031 AATTTCAACTTCACACCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
3069076 GCTCAACTTCACAGTGAAAGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
3069141 AATTTCAACTTCACAGCGAATGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
3069186 GCTCAACTTCACAGTGAAGGGGCGACTGACTGTCAACAAATAACTTTTCAATTTCATTTAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
3069251 AATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
3069296 GCTCAATTTCACAGTGAAGGGGTGACTGACTGTCAACAATCAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
3069361 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACATCGCAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
3069406 GCTCAACTTCACAGCGAAGGGGCGACTTG-CTATCAACAAATAACTTTCCAG--T--TTCAGAGT
1 GCTCAACTTCACAGCGAAGGGGCGAC-TGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * * *
3069466 CAATTTCAACTTCACGGCGAAGGATATTGGTCTCGAAACATCACAA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
3069512 ATATTTGGAT
Statistics
Matches: 806, Mismatches: 69, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
106 50 0.06
108 1 0.00
110 753 0.93
111 2 0.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:3069867 original size:84 final size:83
Alignment explanation
Indices: 3069618--3070385 Score: 701
Period size: 84 Copynumber: 9.3 Consensus size: 83
3069608 AATCGTGCCC
** * * * *
3069618 ACCAAAGGTCTTCGAATTCGACTACGCTCAGCTCCAAGGCACATCATTGGCAGTATAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* * ***
3069683 CAAGAATGGTTATCTACCA
66 CGAGAAGGGTTATCT-GTG
** * * * * *
3069702 ACTGAAGACCCTT-GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAA
1 ACCAAAGA-CCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAA
* *
3069766 GGCTAGAAGGGTTATCTGTG
64 GTCGAGAAGGGTTATCTGTG
* * * * *
3069786 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGACATATCATTTGCAACATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
* **
3069851 TCGAGAAGGATTATCTGCCA
65 TCGAGAAGGGTTATCTG-TG
* * * *
3069871 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCACCAAGACACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
*
3069936 CGAGAAGGGCTATC--TG
66 CGAGAAGGGTTATCTGTG
* * * * * * *
3069952 -CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAG
* * *
3070016 GCTATAAGGGTTATCTGTG
65 TCGAGAAGGGTTATCTGTG
* * * **
3070035 ACCAAAAGACCTTCGAGTTTGACTATACTCAGCTCCAAGGCATATCATTTATAGCATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
**
3070100 TCGAGAAGGGTTATCTGCCA
65 TCGAGAAGGGTTATCTG-TG
* * *
3070120 ACCAAAGACCTTCGAGTTCGACTACGCTCATCTCCAAGGCACATCATTTGTAGCATAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
3070185 CGAGAAGGGCTA--TATG
66 CGAGAAGGGTTATCTGTG
* * * * * * * *
3070201 -CCAAAGACCCTAGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACGGCATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAG
* * *
3070265 GCTAGAAGGGTTATCTGTC
65 TCGAGAAGGGTTATCTGTG
* * * * *
3070284 AACAAAGACCTTCAAGTTCGACTCCACTCAGCTCAAAGGCACCATCATTTGCAGCATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCA-CATCATTTGCAGCATAACTTAAG
* * * *
3070349 GCAAGAAGGGCTA--TATG
65 TCGAGAAGGGTTATCTGTG
3070366 -CCAAAGACCTTCGAGTTCGA
1 ACCAAAGACCTTCGAGTTCGA
3070386 TTCCATTCAG
Statistics
Matches: 552, Mismatches: 116, Indels: 35
0.79 0.17 0.05
Matches are distributed among these distances:
80 54 0.10
81 89 0.16
82 3 0.01
83 11 0.02
84 301 0.55
85 94 0.17
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (83 bp):
ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
CGAGAAGGGTTATCTGTG
Found at i:3070068 original size:249 final size:249
Alignment explanation
Indices: 3069613--3070385 Score: 1097
Period size: 249 Copynumber: 3.1 Consensus size: 249
3069603 AAGGGAATCG
* ** * * *
3069613 TGCCCACCAAAGGTCTTCGAATTCGACTACGCTCAGCTCCAAGGCACATCATTGGCAGTATAACT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* * * * *
3069678 TAAGTCAAGAATGGTTATCTACCAACTGAAGACCCTTGAGTTCGATTACACTCAGCTTCGAGGGC
66 TAAGTCGAGAAGGGCTATCTGCC-A---AAGACCCTAGAGTTCGATTACACTCAGCTTCGAGGGC
3069743 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGA
127 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGA
* * * * *
3069808 CTACGCTCAGCTCTAAGACATATCATTTGCAACATAACTTAAGTCGAGAAGGATTATC
192 CTACACTCAGCTCAAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* * *
3069866 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCACCAAGACACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
*
3069931 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTAGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * *
3069996 CATTTACAACATAACTCAAGGCTATAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGACTAT
131 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
* **
3070061 ACTCAGCTCCAAGGCATATCATTTATAGCATAACTTAAGTCGAGAAGGGTTATC
196 ACTCAGCTCAAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* *
3070115 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCATCTCCAAGGCACATCATTTGTAGCATAACT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
*
3070180 TAAGTCGAGAAGGGCTATATGCCAAAGACCCTAGAGTTCGATTACACTCAGCTTCGAGGGCACAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTAGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * * *
3070245 CATTTACGGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTCAAGTTCGACTCC
131 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
* * * * * *
3070309 ACTCAGCTCAAAGGCACCATCATTTGCAGCATAACTCAAGGCAAGAAGGGCTATA
196 ACTCAGCTCAAAGGCA-TATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
3070364 TG----CCAAAGACCTTCGAGTTCGA
1 TGCCAACCAAAGACCTTCGAGTTCGA
3070386 TTCCATTCAG
Statistics
Matches: 469, Mismatches: 50, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
245 20 0.04
248 33 0.07
249 340 0.72
252 1 0.00
253 75 0.16
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (249 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
TAAGTCGAGAAGGGCTATCTGCCAAAGACCCTAGAGTTCGATTACACTCAGCTTCGAGGGCACAT
CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
ACTCAGCTCAAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
Found at i:3070386 original size:165 final size:164
Alignment explanation
Indices: 3069627--3070404 Score: 760
Period size: 165 Copynumber: 4.7 Consensus size: 164
3069617 CACCAAAGGT
* * * *
3069627 CTTCGAATTCGACTACGCTCAGCTCCAAGGCACATCATTGGCAGTATAACTTAAGTCAAGAATGG
1 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGG
* *
3069692 TTATCTACCAACTGAAGACCCTT-GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAG
66 TTATATGCC-A---AAGA-CCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAG
* * *
3069756 CATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGAC
126 CATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGAC
* * * * * *
3069796 CTTCGAGTTCGACTACGCTCAGCTCTAAGACATATCATTTGCAACATAACTTAAGTCGAGAAGGA
1 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGG
* * * * * * * *
3069861 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-ACCAAGACACATCATTTGCAGC
66 TTATATG----CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGC
* * * *
3069925 ATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGAC
127 ATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGAC
* * * * * * * * * * *
3069960 CCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTATAAGG
1 CTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGG
* * * * * * * *
3070025 GTTATCTGTGACCAAAAGACCTTCGAGTTTGACTATACTCAGC-TCCAAGGCATATCATTTATAG
65 GTTA--TATG-CC-AAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAG
* * *
3070089 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
126 CATAACTCAAGGCGAGAAGGGTTATCTGTCAA-CAAAGAC
* * *
3070129 CTTCGAGTTCGACTACGCTCATCTCCAAGGCACATCATTTGTAGCATAACTTAAGTCGAGAAGGG
1 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGG
* * * *
3070194 CTATATGCCAAAGACCCTAGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACGGCATAA
66 TTATATGCCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
*
3070259 CTCAAGGCTAGAAGGGTTATCTGTCAACAAAGAC
131 CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGAC
* * * * * *
3070293 CTTCAAGTTCGACTCCACTCAGCTCAAAGGCACCATCATTTGCAGCATAACTCAAGGCAAGAAGG
1 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAACTTAAGTCAAGAAGG
* * *
3070358 GCTATATGCCAAAGACCTTCGAGTTCGATTCCATTCAG-TTCGAGGGC
65 GTTATATGCCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGC
3070405 GTATCAACCA
Statistics
Matches: 504, Mismatches: 90, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
164 96 0.19
165 212 0.42
166 4 0.01
167 3 0.01
168 78 0.15
169 108 0.21
172 1 0.00
173 2 0.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (164 bp):
CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGG
TTATATGCCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAA
CTCAAGGCGAGAAGGGTTATCTGTCAACAAAGAC
Found at i:3070747 original size:2 final size:2
Alignment explanation
Indices: 3070735--3070807 Score: 118
Period size: 2 Copynumber: 38.5 Consensus size: 2
3070725 AACATTTTAT
3070735 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3070776 TA TA TA TA TA TA TA TA TA TA T- TA T- TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3070808 TTTTATTATT
Statistics
Matches: 67, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
1 4 0.06
2 63 0.94
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3071281 original size:2 final size:2
Alignment explanation
Indices: 3071274--3071310 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3071264 TTTACATTGT
3071274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3071311 TCATTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3071352 original size:24 final size:24
Alignment explanation
Indices: 3071297--3071354 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
3071287 ATATATATAT
*
3071297 ATATATATATATATTCATTTTTATTA
1 ATAT-TAT-TATATTAATTTTTATTA
3071323 ATATTATTATATTAATATTTT-TTA
1 ATATTATTATATTAAT-TTTTATTA
*
3071347 TTATTATT
1 ATATTATT
3071355 TTCTCATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 18 0.62
25 7 0.24
26 4 0.14
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATTATTATATTAATTTTTATTA
Found at i:3073054 original size:20 final size:20
Alignment explanation
Indices: 3073029--3073094 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
3073019 AATTTGTAAA
*
3073029 TCGCAACACAGAAGTCAATT
1 TCGCAACACAGAAGTCAAAT
* **
3073049 TCGCAACGC-GATTTCCAAAT
1 TCGCAACACAGAAGT-CAAAT
*
3073069 TCGCAATACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
3073089 TCGCAA
1 TCGCAA
3073095 AGCGCGTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 3 0.08
20 30 0.83
21 3 0.08
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:3073685 original size:20 final size:20
Alignment explanation
Indices: 3073650--3073743 Score: 69
Period size: 20 Copynumber: 5.0 Consensus size: 20
3073640 AAATCGAAAC
*
3073650 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
3073669 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
3073689 GC-AGTTTTC----T--CGTT
1 GCGA-TTTTCATTTTCGCGTT
* * *
3073703 ACGATTTTCATTTTTGAGTT
1 GCGATTTTCATTTTCGCGTT
* *
3073723 GTGATTTTCATTTTCACGTT
1 GCGATTTTCATTTTCGCGTT
3073743 G
1 G
3073744 TGAATTTAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 1 0.02
18 1 0.02
19 9 0.16
20 36 0.62
ACGTcount: A:0.13, C:0.16, G:0.20, T:0.51
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:3073757 original size:20 final size:20
Alignment explanation
Indices: 3073720--3073758 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3073710 TCATTTTTGA
* * *
3073720 GTTGTGATTTTCATTTTCAC
1 GTTGTGAATTTAAGTTTCAC
3073740 GTTGTGAATTTAAGTTTCA
1 GTTGTGAATTTAAGTTTCA
3073759 GAAACTACTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGTGAATTTAAGTTTCAC
Found at i:3075949 original size:21 final size:21
Alignment explanation
Indices: 3075902--3076020 Score: 107
Period size: 21 Copynumber: 5.7 Consensus size: 21
3075892 GATTCACCTG
* * *
3075902 TCATCATTCAAGAGGCGCATC
1 TCATCGTTCAAGAGGCCCCTC
*
3075923 -CTATCGTTCAAGAGGCCCCTT
1 TC-ATCGTTCAAGAGGCCCCTC
*
3075944 TCATCGTTCAAGATGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
3075965 CCACCGTTCAAGAGGCCTCTG
1 TCATCGTTCAAGAGGCCCCTC
*
3075986 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
3076007 -CAACCGTTCAAGAG
1 TC-ATCGTTCAAGAG
3076021 CCTGATTCAC
Statistics
Matches: 78, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
20 2 0.03
21 75 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:3075954 original size:42 final size:42
Alignment explanation
Indices: 3075898--3076020 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 42
3075888 GCTCGATTCA
* * * *
3075898 CCTGTCATCATTCAAGAGGCGCATCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCCCATCCCACCGTTCAAGAGGCC
* * *
3075940 CCTTTCATCGTTCAAGATGCCCCTCCCACCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCCCATCCCACCGTTCAAGAGGCC
* *
3075982 TCTGTCATCGTTCAAGAGGTCCC-TCCAACCGTTCAAGAG
1 CCTGTCATCGTTCAAGAGG-CCCATCCCACCGTTCAAGAG
3076021 CCTGATTCAC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
42 66 0.96
43 3 0.04
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGCCCATCCCACCGTTCAAGAGGCC
Found at i:3077455 original size:50 final size:50
Alignment explanation
Indices: 3077400--3077506 Score: 178
Period size: 50 Copynumber: 2.1 Consensus size: 50
3077390 TGTAAAAGTC
* *
3077400 GATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTCTTGTTTAATT
1 GATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTATTTAATT
* *
3077450 GATTTGTTTAATTGATGTGTAAATAAGAATTATTTTTTGCTTATTTAATT
1 GATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTATTTAATT
3077500 GATTTGT
1 GATTTGT
3077507 AAAAGTTGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (50 bp):
GATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTATTTAATT
Done.