Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 30
Found at i:2711900 original size:41 final size:41
Alignment explanation
Indices: 2711812--2711902 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
2711802 GTAAGTGTCG
* * ** * *
2711812 CATTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCG
1 CATTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCC
*
2711853 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCC
1 CATTGCGATAGTCAGTATCGCATTGCGATTTT-CAAATATCC
2711894 CATTGCGAT
1 CATTGCGAT
2711903 TTACTTATTC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 39 0.95
42 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (41 bp):
CATTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCC
Found at i:2711917 original size:20 final size:21
Alignment explanation
Indices: 2711870--2711921 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2711860 ATAGTCAGTA
*
2711870 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
2711891 TCCCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
2711911 TCGCATTGCGA
1 TCGCATTGCGA
2711922 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:2711963 original size:21 final size:22
Alignment explanation
Indices: 2711911--2711963 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
2711901 ATTTACTTAT
2711911 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
2711932 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2711953 TCGCATTGCGA
1 TCGCATTGCGA
2711964 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2714198 original size:3 final size:3
Alignment explanation
Indices: 2714190--2714264 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
2714180 TTTGATTTAT
* * * * *
2714190 TTA TTA TTA TTA TTA CTA TAA ATA TTA TTA TTA TTA TTA TAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2714238 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2714265 AATATATATA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:2714217 original size:21 final size:21
Alignment explanation
Indices: 2714191--2714264 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
2714181 TTGATTTATT
*
2714191 TATTATTATTATTACTATAAA
1 TATTATTATTATTATTATAAA
2714212 TATTATTATTATTATTATAAA
1 TATTATTATTATTATTATAAA
* *
2714233 TATTATTATTATTATTATTAT
1 TATTATTATTATTATTATAAA
2714254 TATTATTATTA
1 TATTATTATTA
2714265 AATATATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTATTATTATTATTATAAA
Found at i:2714273 original size:2 final size:2
Alignment explanation
Indices: 2714266--2714292 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2714256 TTATTATTAA
2714266 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 A
2714293 AATAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2731750 original size:13 final size:13
Alignment explanation
Indices: 2731732--2731780 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
2731722 TGCATCATAA
2731732 ATTTATGACGCGC
1 ATTTATGACGCGC
* *
2731745 ATTTATGACACAC
1 ATTTATGACGCGC
*
2731758 ATTTATGACGCGT
1 ATTTATGACGCGC
2731771 ATTTATGACG
1 ATTTATGACG
2731781 TTTATTGAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:2732022 original size:2 final size:2
Alignment explanation
Indices: 2732015--2732047 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
2732005 ATAATACTAA
2732015 AT AT AT AT AT AT AT AT AT AT CAT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT A
2732048 AGCATTCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2753191 original size:160 final size:162
Alignment explanation
Indices: 2752927--2753249 Score: 623
Period size: 160 Copynumber: 2.0 Consensus size: 162
2752917 GGATAAGATT
2752927 CATGTGCCTCCTTTTCCATTGAACATAATGACTGTACCATGACCATTCTCGATGTGGGGCAAGGA
1 CATGTGCCTCCTTTTCCATTGAACATAATGACTGTACCATGACCATTCTCGATGTGGGGCAAGGA
2752992 CGTCATTGGAGAAATTTCTCCAAATGCTTTAAATAGTCATAGTTTCATTATGGTGCCTATC-A-A
66 CGTCATTGGAGAAATTTCTCCAAATGCTTTAAATAGTCATAGTTTCATTATGGTGCCTATCAATA
2753055 TTTCACGAAGTGGGTATAGATTGCTTCCTACA
131 TTTCACGAAGTGGGTATAGATTGCTTCCTACA
2753087 CATGTGCCTCCTTTTCCATTGAACATAATGACTGTACCATGACCATTCTCGATGTGGGGCAAGGA
1 CATGTGCCTCCTTTTCCATTGAACATAATGACTGTACCATGACCATTCTCGATGTGGGGCAAGGA
2753152 CGTCATTGGAGAAATTTCTCCAAATGCTTTAAATAGTCATAGTTTCATTATGGTGCCTATCAATT
66 CGTCATTGGAGAAATTTCTCCAAATGCTTTAAATAGTCATAGTTTCATTATGGTGCCTATCAA-T
2753217 ATTTCACGAAGTGGGTATAGATTGCTTCCTACA
130 ATTTCACGAAGTGGGTATAGATTGCTTCCTACA
2753250 AAGTATCACG
Statistics
Matches: 160, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
160 126 0.79
161 1 0.01
163 33 0.21
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (162 bp):
CATGTGCCTCCTTTTCCATTGAACATAATGACTGTACCATGACCATTCTCGATGTGGGGCAAGGA
CGTCATTGGAGAAATTTCTCCAAATGCTTTAAATAGTCATAGTTTCATTATGGTGCCTATCAATA
TTTCACGAAGTGGGTATAGATTGCTTCCTACA
Found at i:2754008 original size:14 final size:14
Alignment explanation
Indices: 2753989--2754039 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
2753979 ATTATACTTG
2753989 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
*
2754003 AAGAAAAAATA-ATA
1 AAGAAAAAA-AGAAA
2754017 AA-AAAAAAAGAATA
1 AAGAAAAAAAGAA-A
*
2754031 AATAAAAAA
1 AAGAAAAAA
2754040 TGGGTTCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 1 0.03
13 7 0.23
14 16 0.52
15 7 0.23
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:2754024 original size:21 final size:21
Alignment explanation
Indices: 2753992--2754039 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2753982 ATACTTGAAG
2753992 AAAAAAAGAAAAAGAAAAAAT
1 AAAAAAAGAAAAAGAAAAAAT
*
2754013 AATAAAAA-AAAAAGAATAAAT
1 AA-AAAAAGAAAAAGAAAAAAT
2754034 AAAAAA
1 AAAAAA
2754040 TGGGTTCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 16 0.64
22 5 0.20
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.08
Consensus pattern (21 bp):
AAAAAAAGAAAAAGAAAAAAT
Found at i:2754030 original size:17 final size:17
Alignment explanation
Indices: 2754000--2754039 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2753990 AGAAAAAAAG
*
2754000 AAAAAGAAAAAAT-AAT
1 AAAAAAAAAAAATAAAT
2754016 AAAAAAAAAAGAATAAAT
1 AAAAAAAAAA-AATAAAT
2754034 AAAAAA
1 AAAAAA
2754040 TGGGTTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 3 0.14
18 9 0.43
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (17 bp):
AAAAAAAAAAAATAAAT
Found at i:2754557 original size:22 final size:21
Alignment explanation
Indices: 2754481--2754579 Score: 78
Period size: 23 Copynumber: 4.5 Consensus size: 21
2754471 AAAGAAAAGC
2754481 AGAATAAAAA-AGAAAAATAAATA
1 AGAA-AAAAACAGAAAAAT-AA-A
2754504 AGAATAAAAA-AGAAAAAATAAA
1 AGAA-AAAAACAG-AAAAATAAA
*
2754526 ATGAAGAAAACAGAAAAATGAAA
1 A-GAAAAAAACAGAAAAAT-AAA
* *
2754549 AGAGAAAAAA-AGAGAAATATA
1 AGA-AAAAAACAGAAAAATAAA
2754570 AGAAAAAAAC
1 AGAAAAAAAC
2754580 CGAAGTGAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
20 6 0.09
21 5 0.08
22 21 0.32
23 28 0.42
24 6 0.09
ACGTcount: A:0.76, C:0.02, G:0.13, T:0.09
Consensus pattern (21 bp):
AGAAAAAAACAGAAAAATAAA
Found at i:2754559 original size:24 final size:22
Alignment explanation
Indices: 2754462--2754567 Score: 97
Period size: 23 Copynumber: 4.6 Consensus size: 22
2754452 ACGGATGAAG
* *
2754462 AAAAAGGAAAAAGAAAAGCAGAAT
1 AAAAAAGAAAAATAAAA--AGAAT
2754486 AAAAAAGAAAAATAAATAAGAAT
1 AAAAAAGAAAAATAAA-AAGAAT
* *
2754509 AAAAAAGAAAAAATAAAATGAAG
1 AAAAAAG-AAAAATAAAAAGAAT
* *
2754532 AAAACAGAAAAATGAAAAGAGA-
1 AAAAAAGAAAAATAAAAAGA-AT
*
2754554 AAAAAAGAGAAATA
1 AAAAAAGAAAAATA
2754568 TAAGAAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
22 22 0.32
23 23 0.33
24 23 0.33
25 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (22 bp):
AAAAAAGAAAAATAAAAAGAAT
Found at i:2754627 original size:41 final size:41
Alignment explanation
Indices: 2754582--2754672 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
2754572 AAAAAAACCG
* * *
2754582 AAGTGAAAAATCGAAAGAGCTCTTTGAGAAGAGTGAATCTA
1 AAGTGAAAAATAGAAAGAGCGCTTTGAGAAGAGTAAATCTA
* *
2754623 AAGTGAAAACTAGAAAGGGCGCTTTGAGAAGAGTAAATCTA
1 AAGTGAAAAATAGAAAGAGCGCTTTGAGAAGAGTAAATCTA
*
2754664 AAGGGAAAA
1 AAGTGAAAA
2754673 CCTGAAAGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.19
Consensus pattern (41 bp):
AAGTGAAAAATAGAAAGAGCGCTTTGAGAAGAGTAAATCTA
Found at i:2754673 original size:41 final size:41
Alignment explanation
Indices: 2754594--2754688 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
2754584 GTGAAAAATC
* * * *
2754594 GAAAGAGCTCTTTGAGAAGAGTGAATCTAAAGTGAAAA-CT
1 GAAAGGGCGCTTTGAGAAGAGTAAATCTAAAGGGAAAACCT
2754634 AGAAAGGGCGCTTTGAGAAGAGTAAATCTAAAGGGAAAACCT
1 -GAAAGGGCGCTTTGAGAAGAGTAAATCTAAAGGGAAAACCT
2754676 GAAAGGGCGCTTT
1 GAAAGGGCGCTTT
2754689 AGAGCGTATG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 47 0.96
42 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20
Consensus pattern (41 bp):
GAAAGGGCGCTTTGAGAAGAGTAAATCTAAAGGGAAAACCT
Found at i:2759693 original size:54 final size:54
Alignment explanation
Indices: 2759630--2759943 Score: 421
Period size: 54 Copynumber: 5.8 Consensus size: 54
2759620 TTACATTATT
*
2759630 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTAGTGAATTACC
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACC
* * * *
2759684 GTATTGGCACTCTGTGTGCGACCCACTTAATTCATAATGTGTTTGTGAATTACC
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACC
* ** *
2759738 ATATTGGCACTATGTACGCAAGCCACGTAATTCATAATGAGTTTGTGAATTACC
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACC
* *
2759792 GTATTGGCACTATGTGTGCAACCCACGAAATTCATAATGAGTTTGTGAATTACT
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACC
* * ** *
2759846 TTATCGGCACTATGTGTGCAATTCACGTAATTCATAATGAGTTTGTGAATTATC
1 GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACC
* * *** *
2759900 GTATCGACACTATGTGTGCAAACCCATAAAATTTATAATGAGTT
1 GTATTGGCACTATGTGTGC-AACCCACGTAATTCATAATGAGTT
2759944 GAAATATTCA
Statistics
Matches: 225, Mismatches: 34, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
54 207 0.92
55 18 0.08
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (54 bp):
GTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACC
Found at i:2768045 original size:54 final size:54
Alignment explanation
Indices: 2767955--2768328 Score: 498
Period size: 54 Copynumber: 6.9 Consensus size: 54
2767945 TATATGTTGC
**
2767955 ATTACCGTATTGGCACTATGTGTGCAACCCGTGTAATTCATAATGAGTTTGTGA
1 ATTACCGTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGA
* * *
2768009 ATTATCGTATTGACACTATGTGTGCAACCCACGTAATTCATAATGACTTTGTGA
1 ATTACCGTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGA
* * * *
2768063 ATTACCGTATTGACACTATTTGTGCAACCCACGTAATTCATAATGAATTTTTGA
1 ATTACCGTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGA
* * * * * *
2768117 ATTATCGTATTGGCACTATATGTACAAACCACTTAATTCATAATGAGTTTTTGA
1 ATTACCGTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGA
* *
2768171 ATTACTGTATTGGCACTATGTGCGCAACCCACGTAATTCATAATGAGTTTGTGA
1 ATTACCGTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGA
* * *
2768225 ATTACCATATCGGCACTATGTGTGCAACCCACATAATTCATAATGAGTTTGTGA
1 ATTACCGTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGA
* * * * *
2768279 ATTACTGTATCGACACTATGTGTGCAAAACCACAG-AATTTATAATGAGTT
1 ATTACCGTATTGGCACTATGTGTGC-AACCCAC-GTAATTCATAATGAGTT
2768329 GAAATATTCA
Statistics
Matches: 283, Mismatches: 35, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
54 263 0.93
55 20 0.07
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (54 bp):
ATTACCGTATTGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGA
Found at i:2773545 original size:11 final size:11
Alignment explanation
Indices: 2773529--2773553 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2773519 ATACCAAAAA
2773529 GAAGTGCAAGT
1 GAAGTGCAAGT
2773540 GAAGTGCAAGT
1 GAAGTGCAAGT
2773551 GAA
1 GAA
2773554 AGAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:2773600 original size:24 final size:24
Alignment explanation
Indices: 2773573--2773628 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
2773563 AAAATCAGCA
* *
2773573 AAGAAAAGTCAAGCACTCCAAAAG
1 AAGAAAAATCAAGCACTCAAAAAG
2773597 AAGAAAAATCAAGCACTCAAAAAG
1 AAGAAAAATCAAGCACTCAAAAAG
2773621 AAGAAAAA
1 AAGAAAAA
2773629 GATAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.62, C:0.16, G:0.14, T:0.07
Consensus pattern (24 bp):
AAGAAAAATCAAGCACTCAAAAAG
Found at i:2773637 original size:17 final size:17
Alignment explanation
Indices: 2773615--2773658 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
2773605 TCAAGCACTC
*
2773615 AAAAAGAAGA-AAAAGA
1 AAAAAGAAAAGAAAAGA
2773631 TAAAAAGAAAAGAAAAG-
1 -AAAAAGAAAAGAAAAGA
2773648 AAAAAGAAAAG
1 AAAAAGAAAAG
2773659 TTGAAGCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 11 0.44
17 9 0.36
18 5 0.20
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAGA
Found at i:2788142 original size:54 final size:54
Alignment explanation
Indices: 2788073--2788183 Score: 222
Period size: 54 Copynumber: 2.1 Consensus size: 54
2788063 GAGTATCCTT
2788073 TTCTTAGGAGATTCTTAGGGTTTGAGAGAATAACTAGGTAAAGTATCCTTAGTA
1 TTCTTAGGAGATTCTTAGGGTTTGAGAGAATAACTAGGTAAAGTATCCTTAGTA
2788127 TTCTTAGGAGATTCTTAGGGTTTGAGAGAATAACTAGGTAAAGTATCCTTAGTA
1 TTCTTAGGAGATTCTTAGGGTTTGAGAGAATAACTAGGTAAAGTATCCTTAGTA
2788181 TTC
1 TTC
2788184 GAGAGAAACT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (54 bp):
TTCTTAGGAGATTCTTAGGGTTTGAGAGAATAACTAGGTAAAGTATCCTTAGTA
Found at i:2789041 original size:12 final size:13
Alignment explanation
Indices: 2788995--2789047 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
2788985 GTTAAGCATT
2788995 TTTATTTTACTTG
1 TTTATTTTACTTG
**
2789008 TTTATTTTTTTTG
1 TTTATTTTACTTG
*
2789021 TATTGTTTTACTTG
1 T-TTATTTTACTTG
*
2789035 -TTATTTTCCTTG
1 TTTATTTTACTTG
2789047 T
1 T
2789048 CTTTTTCATG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
12 10 0.32
13 12 0.39
14 9 0.29
ACGTcount: A:0.11, C:0.08, G:0.09, T:0.72
Consensus pattern (13 bp):
TTTATTTTACTTG
Found at i:2795381 original size:20 final size:19
Alignment explanation
Indices: 2795353--2795422 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
2795343 AGGGTGTCAA
*
2795353 AGTGTATCCATGCACCCTG
1 AGTGCATCCATGCACCCTG
2795372 CAGTGCATCCATGCA---T-
1 -AGTGCATCCATGCACCCTG
* *
2795388 TGTGCATCGATGCACCCTG
1 AGTGCATCCATGCACCCTG
2795407 TAGTGCATCCATGCAC
1 -AGTGCATCCATGCAC
2795423 TCAAACACCG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
15 12 0.30
17 1 0.03
18 1 0.03
20 26 0.65
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.26
Consensus pattern (19 bp):
AGTGCATCCATGCACCCTG
Found at i:2796112 original size:20 final size:20
Alignment explanation
Indices: 2796021--2796121 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
2796011 AGGGTGTCAA
* * *
2796021 AGTGTATCCATACACCCTGT
1 AGTGCATCCATACACTCTGC
* * *
2796041 AGTGTATCCATACACCCTGT
1 AGTGCATCCATACACTCTGC
2796061 AGTGCATCCATACACTCTGC
1 AGTGCATCCATACACTCTGC
*
2796081 AGTGCATCCATGCACTCTGC
1 AGTGCATCCATACACTCTGC
* *
2796101 AGTGCATCCATGCACTGTGC
1 AGTGCATCCATACACTCTGC
2796121 A
1 A
2796122 TCGATGCACC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.27
Consensus pattern (20 bp):
AGTGCATCCATACACTCTGC
Found at i:2796196 original size:20 final size:20
Alignment explanation
Indices: 2796171--2796208 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2796161 AATGCAATTA
* *
2796171 GTGCATCGATGCACCCTGTC
1 GTGCATCCATACACCCTGTC
2796191 GTGCATCCATACACCCTG
1 GTGCATCCATACACCCTG
2796209 GCTACAATGA
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:0.18, C:0.37, G:0.21, T:0.24
Consensus pattern (20 bp):
GTGCATCCATACACCCTGTC
Found at i:2798156 original size:133 final size:133
Alignment explanation
Indices: 2797860--2798231 Score: 469
Period size: 133 Copynumber: 2.8 Consensus size: 133
2797850 AATAATATTA
* * * * * *
2797860 AGAGAGAAAACGATAACATCTAATTATTTCCAATCGAGAATAAAGGACTTTTCATGCCTTAAAAC
1 AGAGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAACGACCTCTCATGCCTTAAAGC
* * * * * * *
2797925 AGTCATTTATTACCCCAATTGAAATGAAGAGATATCAC-ATTTTTTTTCTTAAAATTCAATATTG
66 AGTTATTTATTACTCCAACTGAAATGAAGAGATATTACTATTTTCTGTCTTAAAATTCAATATCG
*
2797989 ATT
131 ACT
* * * * * * *
2797992 CGAGTGAAAACGATAATATATGATTATTTCCAACCGGGAATAAATGACCTCTCATGGCTTAAAGC
1 AGAGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAACGACCTCTCATGCCTTAAAGC
* * * *
2798057 AATTATTTATCACTCCAACTGAAACGAGGAGATATTACTATTTTCTGTCTTAAAAATT-AATATC
66 AGTTATTTATTACTCCAACTGAAATGAAGAGATATTACTATTTTCTGTCTT-AAAATTCAATATC
2798121 GACT
130 GACT
* * *
2798125 AGAGTGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAACGACCTCTTATACCTTAAAGC
1 AGAGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAACGACCTCTCATGCCTTAAAGC
2798190 AGTTATTTATTACTCCAACTGAAATGAAGAGATATTACTATT
66 AGTTATTTATTACTCCAACTGAAATGAAGAGATATTACTATT
2798232 CTCATATCGA
Statistics
Matches: 200, Mismatches: 38, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
132 83 0.41
133 111 0.56
134 6 0.03
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (133 bp):
AGAGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAACGACCTCTCATGCCTTAAAGC
AGTTATTTATTACTCCAACTGAAATGAAGAGATATTACTATTTTCTGTCTTAAAATTCAATATCG
ACT
Found at i:2799291 original size:108 final size:108
Alignment explanation
Indices: 2799054--2799278 Score: 256
Period size: 108 Copynumber: 2.1 Consensus size: 108
2799044 ATCACTACGC
* * * *
2799054 ATGACCAAAATACAAAAACCACGCATAAA-TATGAGGGACTAAACAAAAAATAATCCTAAAAATA
1 ATGACCAAAATGCAAAAA-CATGC-TAAAGT-TGCGGGACTAAACAAAAAATAATACTAAAAATA
***
2799118 TATAACATGCATAAAAGTGGGTAAATTACAAAAACAGCCCCTACAG
63 TATAACATGCATAAAAACAGGTAAATTACAAAAACAGCCCCTACAG
* * *
2799164 ATGACTAAAATGCAAAAACATGCTAAAGTTGCGGGACTAAACAATAATTAA-ACTAAAAATATAT
1 ATGACCAAAATGCAAAAACATGCTAAAGTTGCGGGACTAAACAAAAAATAATACTAAAAATATAT
* * * * * *
2799228 AACATGCATAAGAAACATGTAAATTATAAAATCGGTCCCTACAT
66 AACATGCATAA-AAACAGGTAAATTACAAAAACAGCCCCTACAG
2799272 ATGACCA
1 ATGACCA
2799279 TTTTGCAAAA
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
107 23 0.24
108 52 0.54
109 5 0.05
110 16 0.17
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (108 bp):
ATGACCAAAATGCAAAAACATGCTAAAGTTGCGGGACTAAACAAAAAATAATACTAAAAATATAT
AACATGCATAAAAACAGGTAAATTACAAAAACAGCCCCTACAG
Found at i:2800083 original size:3 final size:3
Alignment explanation
Indices: 2800075--2800111 Score: 56
Period size: 3 Copynumber: 11.7 Consensus size: 3
2800065 AAGAAAAAAG
2800075 TAA TAA TAA TAAA TAA TAA TAAA TAA TAA TAA TAA TA
1 TAA TAA TAA T-AA TAA TAA T-AA TAA TAA TAA TAA TA
2800112 TTAAAAATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2800091 original size:10 final size:10
Alignment explanation
Indices: 2800076--2800116 Score: 66
Period size: 10 Copynumber: 4.2 Consensus size: 10
2800066 AGAAAAAAGT
2800076 AATAATAATA
1 AATAATAATA
2800086 AATAATAATA
1 AATAATAATA
2800096 AATAATAAT-
1 AATAATAATA
*
2800105 AATAATATTA
1 AATAATAATA
2800115 AA
1 AA
2800117 AATGGGATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AATAATAATA
Found at i:2800093 original size:13 final size:14
Alignment explanation
Indices: 2800075--2800112 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
2800065 AAGAAAAAAG
2800075 TAATAATAATA-AA
1 TAATAATAATATAA
2800088 TAATAATAA-ATAA
1 TAATAATAATATAA
2800101 TAATAATAATAT
1 TAATAATAATAT
2800113 TAAAAATGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.04
13 20 0.87
14 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:2800632 original size:31 final size:31
Alignment explanation
Indices: 2800597--2800675 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
2800587 ATTCAACGTC
*
2800597 TAAGTGACCGAAACTTAATAAAACGATAACA
1 TAAGTGACCAAAACTTAATAAAACGATAACA
* * **
2800628 TAAGTGACTACAACTTAATAAAACGATAATG
1 TAAGTGACCAAAACTTAATAAAACGATAACA
2800659 TAAGTGACCAAAACTTA
1 TAAGTGACCAAAACTTA
2800676 TGTTTTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAAACGATAACA
Found at i:2801293 original size:5 final size:6
Alignment explanation
Indices: 2801276--2801300 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2801266 ATAATTTAAA
2801276 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
2801301 TTATCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:2803550 original size:60 final size:60
Alignment explanation
Indices: 2803438--2803552 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
2803428 TAGCTTGGAA
* * * * *
2803438 TGAAATTGAAATGTTCAAAAAGTTTTGGGTTAATTTAGAATGAAGGTCATAGTTTGATGG
1 TGAAAATGAAATGTTCAAAAAGTTTTGGGCTAAGTTAGAATGAAGATAATAGTTTGATGG
2803498 TGAAAATGAAATGTTC-AAAAG-TTTGAGGACTAAGTTAGAATGATA-ATAATAGTTT
1 TGAAAATGAAATGTTCAAAAAGTTTTG-GG-CTAAGTTAGAATGA-AGATAATAGTTT
2803553 CAGATGAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
58 4 0.09
59 7 0.15
60 35 0.74
61 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (60 bp):
TGAAAATGAAATGTTCAAAAAGTTTTGGGCTAAGTTAGAATGAAGATAATAGTTTGATGG
Found at i:2804346 original size:21 final size:21
Alignment explanation
Indices: 2804320--2804367 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
2804310 CCGTCGTTTA
2804320 TAACTCATGTAATTACTCTTG
1 TAACTCATGTAATTACTCTTG
* *
2804341 TAACTCATGTAATTATTGTTG
1 TAACTCATGTAATTACTCTTG
2804362 TAACTC
1 TAACTC
2804368 TTATAACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (21 bp):
TAACTCATGTAATTACTCTTG
Found at i:2807045 original size:13 final size:13
Alignment explanation
Indices: 2807027--2807052 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2807017 ACATATTTGA
2807027 ACAGTCTTCATAT
1 ACAGTCTTCATAT
2807040 ACAGTCTTCATAT
1 ACAGTCTTCATAT
2807053 GCGCTTCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAGTCTTCATAT
Found at i:2808274 original size:48 final size:48
Alignment explanation
Indices: 2808203--2808300 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
2808193 TCAAGGCGAA
*
2808203 GATGTAAGGGTTAAGAGCCGACCCCTGGTGGAGTTCGATTTCCACCGG
1 GATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTTCGATTTCCACCGG
*
2808251 GATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTTTGATTTCCACCGG
1 GATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTTCGATTTCCACCGG
2808299 GA
1 GA
2808301 ATGCCTTGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (48 bp):
GATGTAAGGGCTAAGAGCCGACCCCTGGTGGAGTTCGATTTCCACCGG
Found at i:2811159 original size:20 final size:20
Alignment explanation
Indices: 2811134--2811172 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2811124 TGTGCATGCG
2811134 TCTATCTATATATATATATC
1 TCTATCTATATATATATATC
* *
2811154 TCTATCTATCTCTATATAT
1 TCTATCTATATATATATAT
2811173 ATATATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (20 bp):
TCTATCTATATATATATATC
Found at i:2813110 original size:2 final size:2
Alignment explanation
Indices: 2813103--2813166 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
2813093 CATTAAGCTA
2813103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2813145 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
2813167 GTATTGGCAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2834990 original size:39 final size:39
Alignment explanation
Indices: 2834941--2835015 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
2834931 CTTCTTTTTA
*
2834941 TTAGTTTTCTTCTTATGGTCTCTCATTCTCTCCTTTGTT
1 TTAGCTTTCTTCTTATGGTCTCTCATTCTCTCCTTTGTT
* *
2834980 TTAGCTTTCTTTTTCTGGTCTCTCATTCTCTCCTTT
1 TTAGCTTTCTTCTTATGGTCTCTCATTCTCTCCTTT
2835016 ATTTCACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.07, C:0.25, G:0.09, T:0.59
Consensus pattern (39 bp):
TTAGCTTTCTTCTTATGGTCTCTCATTCTCTCCTTTGTT
Found at i:2835731 original size:3 final size:3
Alignment explanation
Indices: 2835719--2835768 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
2835709 GTAACATTTT
* *
2835719 TAA T-A TAA TAA TAA TAG TAA T-A TAA TAA TAA T-A CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2835764 AAA TA
1 TAA TA
2835769 TGGGTGGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 5 0.13
3 33 0.87
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:2835733 original size:11 final size:11
Alignment explanation
Indices: 2835719--2835762 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
2835709 GTAACATTTT
2835719 TAAT-ATAATAA
1 TAATAATAAT-A
*
2835730 TAATAGTAATA
1 TAATAATAATA
2835741 TAATAATAATA
1 TAATAATAATA
*
2835752 CAATAATAATA
1 TAATAATAATA
2835763 AAAATATGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 25 0.86
12 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (11 bp):
TAATAATAATA
Found at i:2835741 original size:17 final size:17
Alignment explanation
Indices: 2835719--2835751 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2835709 GTAACATTTT
2835719 TAATATAATAATAATAG
1 TAATATAATAATAATAG
2835736 TAATATAATAATAATA
1 TAATATAATAATAATA
2835752 CAATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TAATATAATAATAATAG
Found at i:2835745 original size:14 final size:14
Alignment explanation
Indices: 2835719--2835763 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
2835709 GTAACATTTT
*
2835719 TAATATAATAATAA
1 TAATACAATAATAA
*
2835733 TAGTA-ATATAATAA
1 TAATACA-ATAATAA
2835747 TAATACAATAATAA
1 TAATACAATAATAA
2835761 TAA
1 TAA
2835764 AAATATGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (14 bp):
TAATACAATAATAA
Found at i:2835760 original size:17 final size:17
Alignment explanation
Indices: 2835720--2835768 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
2835710 TAACATTTTT
*
2835720 AATATAATAATAATAGT
1 AATATAATAATAATAGC
2835737 AATATAATAATAATA-C
1 AATATAATAATAATAGC
*
2835753 AATAATAATAAAAATA
1 AAT-ATAATAATAATA
2835769 TGGGTGGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 3 0.10
17 26 0.90
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
AATATAATAATAATAGC
Found at i:2843675 original size:13 final size:14
Alignment explanation
Indices: 2843658--2843692 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2843648 ACGCTAAACA
2843658 AAAATAAAGAATAG
1 AAAATAAAGAATAG
*
2843672 -AAATTAAGAATAG
1 AAAATAAAGAATAG
2843685 AAAATAAA
1 AAAATAAA
2843693 TTAAAGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (14 bp):
AAAATAAAGAATAG
Found at i:2844318 original size:21 final size:22
Alignment explanation
Indices: 2844278--2844323 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2844268 TTTTGAGAAT
*
2844278 TACTTTGATTTCTCATTTTG-A
1 TACTTTGATTTCCCATTTTGTA
2844299 TACTTTCGATTTCCCA-TTTGTA
1 TACTTT-GATTTCCCATTTTGTA
2844321 TAC
1 TAC
2844324 ATATGGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.52
Consensus pattern (22 bp):
TACTTTGATTTCCCATTTTGTA
Found at i:2844524 original size:20 final size:19
Alignment explanation
Indices: 2844443--2844525 Score: 130
Period size: 19 Copynumber: 4.4 Consensus size: 19
2844433 TGCCAAATAT
2844443 AGAAAATATAAAATTTTTC
1 AGAAAATATAAAATTTTTC
2844462 AGAAAATATAAAATTTTTC
1 AGAAAATATAAAATTTTTC
* *
2844481 AGAAAGTATAAAATTTTTT
1 AGAAAATATAAAATTTTTC
*
2844500 AGAAAATATAAAAATTTTC
1 AGAAAATATAAAATTTTTC
*
2844519 AGGAAAT
1 AGAAAAT
2844526 CAACGGTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 58 1.00
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (19 bp):
AGAAAATATAAAATTTTTC
Found at i:2854440 original size:20 final size:21
Alignment explanation
Indices: 2854411--2854453 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
2854401 GGTATCGATT
2854411 CCCTAAGAACAAT-ATTGATA
1 CCCTAAGAACAATCATTGATA
*
2854431 CCCTATGAACAATGCATTGATA
1 CCCTAAGAACAAT-CATTGATA
2854453 C
1 C
2854454 TACCTAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (21 bp):
CCCTAAGAACAATCATTGATA
Found at i:2855412 original size:21 final size:21
Alignment explanation
Indices: 2855386--2855430 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
2855376 TCAAACACTT
2855386 TATCCGAAACTACTAACCCGA
1 TATCCGAAACTACTAACCCGA
2855407 TATCCGAAACTACTAACCCGA
1 TATCCGAAACTACTAACCCGA
2855428 TAT
1 TAT
2855431 TCGGAGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.31, G:0.09, T:0.22
Consensus pattern (21 bp):
TATCCGAAACTACTAACCCGA
Found at i:2857151 original size:30 final size:30
Alignment explanation
Indices: 2857115--2857187 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
2857105 ATTGTTTCCC
2857115 AACCGAACTAATTCAATGACCGACCATTTT
1 AACCGAACTAATTCAATGACCGACCATTTT
* * *
2857145 AACCGAATTAATTCAATGATCGACCGTTTT
1 AACCGAACTAATTCAATGACCGACCATTTT
*
2857175 AACTGAACTAATT
1 AACCGAACTAATT
2857188 GATTTGGTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (30 bp):
AACCGAACTAATTCAATGACCGACCATTTT
Found at i:2857976 original size:15 final size:15
Alignment explanation
Indices: 2857956--2857998 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
2857946 AATATTTATT
2857956 TTTAAAATTATTTAA
1 TTTAAAATTATTTAA
* *
2857971 TTTAAAATAATATTAT
1 TTTAAAATTAT-TTAA
*
2857987 TTTTAAATTATT
1 TTTAAAATTATT
2857999 ATATAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAAAATTATTTAA
Found at i:2858006 original size:34 final size:33
Alignment explanation
Indices: 2857944--2858012 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
2857934 CTTATTTATT
*
2857944 ATAATATTTATTTTTAAAATTATTTAATTTAAA
1 ATAATATTTATTTTTAAAATTATATAATTTAAA
*
2857977 ATAATA-TTATTTTTAAATTATTATATAATTTTAA
1 ATAATATTTATTTTTAAA--ATTATATAATTTAAA
2858011 AT
1 AT
2858013 TATTGTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 11 0.34
33 6 0.19
34 15 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
ATAATATTTATTTTTAAAATTATATAATTTAAA
Found at i:2858022 original size:34 final size:31
Alignment explanation
Indices: 2857948--2858022 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 31
2857938 TTTATTATAA
*
2857948 TATTTATTTTTAAAATTATTTAATTTAAAAT
1 TATTTATTTTTAAAATTATATAATTTAAAAT
* *
2857979 AATATTATTTTTAAATTATTATATAATTTTAAAT
1 TAT-TTATTTTTAAA--ATTATATAATTTAAAAT
2858013 TATTGTATTT
1 TATT-TATTT
2858023 ATATTTTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 2 0.06
32 11 0.31
33 1 0.03
34 22 0.61
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
TATTTATTTTTAAAATTATATAATTTAAAAT
Found at i:2858250 original size:3 final size:3
Alignment explanation
Indices: 2858242--2858276 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2858232 TTCGTTTTCT
2858242 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2858277 TGTACATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2859286 original size:22 final size:22
Alignment explanation
Indices: 2859260--2859305 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2859250 CGTACACATT
*
2859260 AAGTTAAATTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
2859282 AAGTTAAACTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
2859304 AA
1 AA
2859306 AATATTATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (22 bp):
AAGTTAAACTATGATGGACTAA
Found at i:2860826 original size:3 final size:3
Alignment explanation
Indices: 2860809--2860859 Score: 59
Period size: 3 Copynumber: 16.3 Consensus size: 3
2860799 GCAAAAGTAA
*
2860809 AAT AAT AAAT AAAT AAT AAT AAT AAT AAT AAT AAT AAC AAT -AT AATT
1 AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
2860856 AAT A
1 AAT A
2860860 TTTATAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.72
4 10 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2861226 original size:55 final size:56
Alignment explanation
Indices: 2861049--2861363 Score: 267
Period size: 55 Copynumber: 5.8 Consensus size: 56
2861039 CCATTGGGTT
* * * ** * **
2861049 TGCTCCCTTTTGCTTCAGGGAGTATAAAACTCAAACAATCTTCATA-AAA-CAAGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCA-ACAAATCGTGTC
* * *
2861104 CGTTCTCTATTCCTTCAGAGAGTATAGGACT---A-AATCTTCAACAAAT-GTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAATCGTGTC
* * * * *
2861155 CGCTCCCCATTCCTTCAGAGAGTATAGGACTCGAATAATTTTCAAC-ATTCGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAATCGTGTC
* * * * *
2861210 TGCTCCCTATTTCTTCAGAGAGTATTA-GACTCGAACAATTTTC-ACTATTCATGTC
1 TGCTCCCTATTCCTTCAGAGAGTA-TAGGACTCGAACAATCTTCAACAAATCGTGTC
* * *
2861265 TGCTCCCTATTGCTTAAGAGAGTAT-GAGACTTGAACAATCTTCAAC-AATCGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAG-GACTCGAACAATCTTCAACAAATCGTGTC
* ** *
2861320 TGCTCTCTATTTGTTCAGAGAGTATAAGACTCGAACAATCTTCA
1 TGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCA
2861364 TTTGCTTCAC
Statistics
Matches: 215, Mismatches: 32, Indels: 26
0.79 0.12 0.10
Matches are distributed among these distances:
50 1 0.00
51 42 0.20
52 1 0.00
54 6 0.03
55 161 0.75
56 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (56 bp):
TGCTCCCTATTCCTTCAGAGAGTATAGGACTCGAACAATCTTCAACAAATCGTGTC
Found at i:2861317 original size:110 final size:110
Alignment explanation
Indices: 2861151--2861363 Score: 302
Period size: 110 Copynumber: 1.9 Consensus size: 110
2861141 TCAACAAATG
* * * *
2861151 TGTCCGCTCCCCATTCCTTCAGAGAGTATAGGACTCGAATAATTTTCAACATTCGTGTCTGCTCC
1 TGTCCGCTCCCCATTCCTTAAGAGAGTATAGGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
* *
2861216 CTATTTCTTCAGAGAGTATTAGACTCGAACAATTTTCACTATTCA
66 CTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCACTATTCA
* * * *
2861261 TGTCTGCTCCCTATTGCTTAAGAGAGTAT-GAGACTTGAACAATCTTCAACAATCGTGTCTGCTC
1 TGTCCGCTCCCCATTCCTTAAGAGAGTATAG-GACTCGAACAATCTTCAACAATCGTGTCTGCTC
* *
2861325 TCTATTTGTTCAGAGAGTATAAGACTCGAACAATCTTCA
65 CCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCA
2861364 TTTGCTTCAC
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
109 1 0.01
110 89 0.99
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (110 bp):
TGTCCGCTCCCCATTCCTTAAGAGAGTATAGGACTCGAACAATCTTCAACAATCGTGTCTGCTCC
CTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCACTATTCA
Found at i:2873893 original size:12 final size:12
Alignment explanation
Indices: 2873876--2873905 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
2873866 GGCTAAGGAA
2873876 ATATATATATGT
1 ATATATATATGT
2873888 ATATATATATGT
1 ATATATATATGT
2873900 ATATAT
1 ATATAT
2873906 GATAATCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (12 bp):
ATATATATATGT
Found at i:2873990 original size:22 final size:22
Alignment explanation
Indices: 2873964--2874009 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2873954 CGTACACATT
*
2873964 AAGTTAAATTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
2873986 AAGTTAAACTATGATGGACTAA
1 AAGTTAAACTATGATGGACTAA
2874008 AA
1 AA
2874010 CATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (22 bp):
AAGTTAAACTATGATGGACTAA
Found at i:2875322 original size:3 final size:3
Alignment explanation
Indices: 2875304--2875356 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
2875294 GCAAATGTAA
* *
2875304 AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT -AT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2875349 AATT AAT A
1 AA-T AAT A
2875357 TTTTTAAGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2876315 original size:30 final size:30
Alignment explanation
Indices: 2876279--2876352 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
2876269 AATTATTTCC
*
2876279 TAACCGAACTAATTCAATGACCGACCATTT
1 TAACCGAACTAATTCAATGACAGACCATTT
* * *
2876309 TAACCGAATTAATTCAATGATAGACCGTTT
1 TAACCGAACTAATTCAATGACAGACCATTT
*
2876339 TAACTGAACTAATT
1 TAACCGAACTAATT
2876353 GATTTGGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (30 bp):
TAACCGAACTAATTCAATGACAGACCATTT
Found at i:2876946 original size:22 final size:22
Alignment explanation
Indices: 2876918--2876962 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2876908 TAGTCACTCA
2876918 ACTAGACTACGCATATGTTTCT
1 ACTAGACTACGCATATGTTTCT
2876940 ACTAGACTACGCATATGTTTCT
1 ACTAGACTACGCATATGTTTCT
2876962 A
1 A
2876963 TTATATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (22 bp):
ACTAGACTACGCATATGTTTCT
Found at i:2877150 original size:23 final size:21
Alignment explanation
Indices: 2877124--2877181 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
2877114 ATTTGCTTAT
2877124 TTATTTAATATTTATTTTTAAAA
1 TTATTTAAT-TTTA-TTTTAAAA
*
2877147 TTATTTTATTTTATTTTAAAA
1 TTATTTAATTTTATTTTAAAA
*
2877168 TAATATTAATTTTA
1 TTAT-TTAATTTTA
2877182 AATTATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.35
22 12 0.39
23 8 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTTAATTTTATTTTAAAA
Found at i:2877198 original size:19 final size:18
Alignment explanation
Indices: 2877132--2877207 Score: 68
Period size: 17 Copynumber: 4.2 Consensus size: 18
2877122 ATTTATTTAA
*
2877132 TATTTATT--TTTAAAAT
1 TATTTATTAATTTTAAAT
* *
2877148 TATTTTATTTTATTTTAAAA
1 TA-TTTA-TTAATTTTAAAT
*
2877168 TA-ATATTAATTTTAAAT
1 TATTTATTAATTTTAAAT
2877185 TATTTATATAATTTTAAAT
1 TATTTAT-TAATTTTAAAT
2877204 TATT
1 TATT
2877208 AAATTTATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
16 2 0.04
17 16 0.33
18 7 0.15
19 15 0.31
20 8 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTATTAATTTTAAAT
Found at i:2877199 original size:36 final size:39
Alignment explanation
Indices: 2877129--2877202 Score: 100
Period size: 36 Copynumber: 2.0 Consensus size: 39
2877119 CTTATTTATT
* * *
2877129 TAATATTTATTTTTAAAATTATTTTATTTTATTTTAAAA
1 TAATATTTAATTTTAAAATTATTTTATATAATTTTAAAA
2877168 TAATA-TTAATTTT-AAATTA-TTTATATAATTTTAAA
1 TAATATTTAATTTTAAAATTATTTTATATAATTTTAAA
2877203 TTATTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 14 0.44
37 6 0.19
38 7 0.22
39 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (39 bp):
TAATATTTAATTTTAAAATTATTTTATATAATTTTAAAA
Found at i:2878687 original size:22 final size:22
Alignment explanation
Indices: 2878657--2878702 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2878647 CTTTAATCCT
*
2878657 TTTTCTTTTCTAATAATATTTA
1 TTTTATTTTCTAATAATATTTA
2878679 TTTTATTTTCTAATAATATTTA
1 TTTTATTTTCTAATAATATTTA
2878701 TT
1 TT
2878703 GTAAAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTATTTTCTAATAATATTTA
Found at i:2878884 original size:31 final size:31
Alignment explanation
Indices: 2878846--2878910 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
2878836 AAGCAGAGAC
*
2878846 TGAGGGATGATTTTACAGGATTTTTGGAAAA
1 TGAGGGATAATTTTACAGGATTTTTGGAAAA
* *
2878877 TGAGGGATAATTTTGCATGATTTTTGGAAAA
1 TGAGGGATAATTTTACAGGATTTTTGGAAAA
2878908 TGA
1 TGA
2878911 CTATTAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (31 bp):
TGAGGGATAATTTTACAGGATTTTTGGAAAA
Found at i:2879199 original size:26 final size:27
Alignment explanation
Indices: 2879170--2879229 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
2879160 ATTATAAATG
*
2879170 AAATATATAAATCTA-AATTATAATAA
1 AAATATATAAAACTATAATTATAATAA
*
2879196 AAATATA-AAAAGTATAATTATAATAA
1 AAATATATAAAACTATAATTATAATAA
2879222 AAATATAT
1 AAATATAT
2879230 TTTTATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (27 bp):
AAATATATAAAACTATAATTATAATAA
Found at i:2883423 original size:52 final size:53
Alignment explanation
Indices: 2883352--2883451 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 53
2883342 AGATTGGGCA
2883352 CACAGAAATAAGAAACTAGCATAGAGTT-GGGGGATTACAACTAATTACAAGT
1 CACAGAAATAAGAAACTAGCATAGAGTTGGGGGGATTACAACTAATTACAAGT
* * *
2883404 CACAGAAATAGGAAGCTAGCCTAGAGTTGGGGGGATTACAACTAATTA
1 CACAGAAATAAGAAACTAGCATAGAGTTGGGGGGATTACAACTAATTA
2883452 TAAGGATATT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 25 0.57
53 19 0.43
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (53 bp):
CACAGAAATAAGAAACTAGCATAGAGTTGGGGGGATTACAACTAATTACAAGT
Found at i:2883927 original size:19 final size:19
Alignment explanation
Indices: 2883903--2883948 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
2883893 TTTCTTGGAT
2883903 GACCAAGAAATAGGATAAC
1 GACCAAGAAATAGGATAAC
2883922 GACCAAGAAATAGGATAAC
1 GACCAAGAAATAGGATAAC
2883941 GACCAAGA
1 GACCAAGA
2883949 TAGACAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.52, C:0.17, G:0.22, T:0.09
Consensus pattern (19 bp):
GACCAAGAAATAGGATAAC
Found at i:2884271 original size:15 final size:15
Alignment explanation
Indices: 2884251--2884279 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2884241 GTCAGATTTC
2884251 CATCTGTAACAAGTG
1 CATCTGTAACAAGTG
2884266 CATCTGTAACAAGT
1 CATCTGTAACAAGT
2884280 AGTGTACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (15 bp):
CATCTGTAACAAGTG
Found at i:2887926 original size:52 final size:52
Alignment explanation
Indices: 2887865--2887966 Score: 150
Period size: 52 Copynumber: 2.0 Consensus size: 52
2887855 ATATTGGGCA
* * *
2887865 CACAGAAATAAGAAACTAGCCTAGAGTTGGGGGATTACAACTAATTACAAGG
1 CACAAAAATAAGAAACTAGCCTAGAGTTGGGGAATTAAAACTAATTACAAGG
* * *
2887917 CACAAAAATAGGAAGCTTGCCTAGAGTTGGGGAATTAAAACTAATTACAA
1 CACAAAAATAAGAAACTAGCCTAGAGTTGGGGAATTAAAACTAATTACAA
2887967 TGATATTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (52 bp):
CACAAAAATAAGAAACTAGCCTAGAGTTGGGGAATTAAAACTAATTACAAGG
Found at i:2888728 original size:91 final size:91
Alignment explanation
Indices: 2888573--2888754 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
2888563 CGTCTGGTTT
2888573 GGGGTTAAAACTTTTTCTGAACCATGGAGTTGCCATGATTCTCGCAGTCGAAATTCGATCTTTTG
1 GGGGTTAAAACTTTTTCTGAACCATGGAGTTGCCATGATTCTCGCAGTCGAAATTCGATCTTTTG
2888638 GATTAGGATTGGAGATTCTTGACAAC
66 GATTAGGATTGGAGATTCTTGACAAC
2888664 GGGGTTAAAACTTTTTCTGAACCATGGAGTTGCCATGATTCTCGCAGTCGAAATTCGATCTTTTG
1 GGGGTTAAAACTTTTTCTGAACCATGGAGTTGCCATGATTCTCGCAGTCGAAATTCGATCTTTTG
2888729 GATTAGGATTGGAGATTCTTGACAAC
66 GATTAGGATTGGAGATTCTTGACAAC
2888755 AACTTGGTGA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (91 bp):
GGGGTTAAAACTTTTTCTGAACCATGGAGTTGCCATGATTCTCGCAGTCGAAATTCGATCTTTTG
GATTAGGATTGGAGATTCTTGACAAC
Found at i:2896047 original size:53 final size:54
Alignment explanation
Indices: 2895979--2896108 Score: 208
Period size: 54 Copynumber: 2.4 Consensus size: 54
2895969 ATCGAATAAT
* *
2895979 AAAAGCAGCAACGTTTAGCAAAATTTAAGA-AAAAAACTAACAATTATTTTGTA
1 AAAAGCAGCAGCGTTTAGCAAAATTTAAAAGAAAAAACTAACAATTATTTTGTA
*
2896032 AAAAGCATCAGCGTTTAGCAAAATTTAAAAGAAAAAACTAACAATTATTTTGTA
1 AAAAGCAGCAGCGTTTAGCAAAATTTAAAAGAAAAAACTAACAATTATTTTGTA
* *
2896086 AAAAACAGCAGCGTTTAACAAAA
1 AAAAGCAGCAGCGTTTAGCAAAA
2896109 AATCAAAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
53 27 0.39
54 43 0.61
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.25
Consensus pattern (54 bp):
AAAAGCAGCAGCGTTTAGCAAAATTTAAAAGAAAAAACTAACAATTATTTTGTA
Found at i:2897442 original size:16 final size:16
Alignment explanation
Indices: 2897423--2897456 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2897413 TCTTTTACAT
2897423 TTAAAATAT-TTTATTA
1 TTAAAATATATTT-TTA
2897439 TTAAAATATATTTTTA
1 TTAAAATATATTTTTA
2897455 TT
1 TT
2897457 TATGGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAAAATATATTTTTA
Found at i:2899414 original size:3 final size:3
Alignment explanation
Indices: 2899406--2899455 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2899396 CTACCAAAAA
2899406 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
2899454 TA
1 TA
2899456 ATTTTGTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2903379 original size:28 final size:29
Alignment explanation
Indices: 2903348--2903402 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
2903338 ATTTACAATA
*
2903348 TTATATGATATTTAAAATAT-TATATGAT
1 TTATACGATATTTAAAATATCTATATGAT
* *
2903376 TTATACGATATTTTATATATCTATATG
1 TTATACGATATTTAAAATATCTATATG
2903403 TCTTACTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (29 bp):
TTATACGATATTTAAAATATCTATATGAT
Found at i:2903387 original size:19 final size:19
Alignment explanation
Indices: 2903330--2903375 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
2903320 TATATGTTAG
2903330 TATATGATATTTACAATAT
1 TATATGATATTTACAATAT
*
2903349 TATATGATATTTAAAATAT
1 TATATGATATTTACAATAT
2903368 TATATGAT
1 TATATGAT
2903376 TTATACGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (19 bp):
TATATGATATTTACAATAT
Found at i:2903551 original size:37 final size:37
Alignment explanation
Indices: 2903499--2903602 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
2903489 CTTTTCGTCC
*
2903499 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* *
2903536 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
2903573 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
2903603 CCATAAGCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:2904153 original size:14 final size:14
Alignment explanation
Indices: 2904114--2904162 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
2904104 TATTATATTA
2904114 TTTTTTTATCTATGT
1 TTTTTTTA-CTATGT
2904129 TTACTTATTTACTATGT
1 TT--TT-TTTACTATGT
*
2904146 TTTTTTTACTATAT
1 TTTTTTTACTATGT
2904160 TTT
1 TTT
2904163 CCTAACGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 12 0.40
15 4 0.13
17 10 0.33
18 4 0.13
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.69
Consensus pattern (14 bp):
TTTTTTTACTATGT
Found at i:2904259 original size:13 final size:13
Alignment explanation
Indices: 2904227--2904287 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
2904217 TTTTAGTTAA
* *
2904227 TATTATGTATATT
1 TATTATTTATTTT
2904240 TATTATTTATTTT
1 TATTATTTATTTT
*
2904253 TATTA-TTATTGT
1 TATTATTTATTTT
*
2904265 TACTATTTAGTATTT
1 TATTATTTA-T-TTT
2904280 TATATATT
1 TAT-TATT
2904288 ATACATGCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 10 0.26
13 19 0.50
14 1 0.03
15 4 0.11
16 4 0.11
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (13 bp):
TATTATTTATTTT
Found at i:2906372 original size:160 final size:160
Alignment explanation
Indices: 2906108--2906427 Score: 640
Period size: 160 Copynumber: 2.0 Consensus size: 160
2906098 CTGGAGCGAG
2906108 CCTACATCAAACACATCAAGAGTCAGCCTTTCAAGAACAGACTGGCTAAGATTGCAGGAGTTGAT
1 CCTACATCAAACACATCAAGAGTCAGCCTTTCAAGAACAGACTGGCTAAGATTGCAGGAGTTGAT
2906173 GAAAAGTGGGTGACTGACCGACTCCGAAACAAAGGTAACGGGCAAGGAATTCAGTGGATCCACAT
66 GAAAAGTGGGTGACTGACCGACTCCGAAACAAAGGTAACGGGCAAGGAATTCAGTGGATCCACAT
2906238 AAGGAAACTAATGAATGACCACCCTGATGA
131 AAGGAAACTAATGAATGACCACCCTGATGA
2906268 CCTACATCAAACACATCAAGAGTCAGCCTTTCAAGAACAGACTGGCTAAGATTGCAGGAGTTGAT
1 CCTACATCAAACACATCAAGAGTCAGCCTTTCAAGAACAGACTGGCTAAGATTGCAGGAGTTGAT
2906333 GAAAAGTGGGTGACTGACCGACTCCGAAACAAAGGTAACGGGCAAGGAATTCAGTGGATCCACAT
66 GAAAAGTGGGTGACTGACCGACTCCGAAACAAAGGTAACGGGCAAGGAATTCAGTGGATCCACAT
2906398 AAGGAAACTAATGAATGACCACCCTGATGA
131 AAGGAAACTAATGAATGACCACCCTGATGA
2906428 ATGGAAGACT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 160 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (160 bp):
CCTACATCAAACACATCAAGAGTCAGCCTTTCAAGAACAGACTGGCTAAGATTGCAGGAGTTGAT
GAAAAGTGGGTGACTGACCGACTCCGAAACAAAGGTAACGGGCAAGGAATTCAGTGGATCCACAT
AAGGAAACTAATGAATGACCACCCTGATGA
Found at i:2909224 original size:19 final size:18
Alignment explanation
Indices: 2909189--2909243 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
2909179 ACAAAAAGAG
2909189 CAAAAACAAAA-AAGAAAA
1 CAAAAA-AAAAGAAGAAAA
* *
2909207 GAAGCAAAAAAGAAGAAAA
1 CAA-AAAAAAAGAAGAAAA
*
2909226 CAAAAAAAAAGAATAAAA
1 CAAAAAAAAAGAAGAAAA
2909244 ATCAAAAAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.02
Consensus pattern (18 bp):
CAAAAAAAAAGAAGAAAA
Found at i:2909233 original size:16 final size:14
Alignment explanation
Indices: 2909178--2909232 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 14
2909168 ATTCAATCGG
*
2909178 AACAAAAAGAGCAAA
1 AACAAAAA-AGAAAA
2909193 AACAAAAAAGAAAA
1 AACAAAAAAGAAAA
2909207 GAAGCAAAAAAGAAGAA
1 -AA-CAAAAAAGAA-AA
2909224 AACAAAAAA
1 AACAAAAAA
2909233 AAAGAATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 5 0.14
15 17 0.47
16 12 0.33
17 2 0.06
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (14 bp):
AACAAAAAAGAAAA
Found at i:2910984 original size:106 final size:106
Alignment explanation
Indices: 2910824--2912236 Score: 2139
Period size: 106 Copynumber: 13.3 Consensus size: 106
2910814 GCCAACCGTG
* * * * *
2910824 ATTTCAACTCCACGAG-GGAGGATATTGTGCCACTCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCAC-AGCGAAGGATATTG-G--ACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * **
2910888 AGGGACGGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGAAA
62 AGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
2910933 ATTTCAACTTCACAGTGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
2910998 ACGGCTGGTTGTCAACAAACAACTTCTTAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
2911039 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGATGAAGCG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
2911104 ACCGCTGGTTGTCAATAAACAATTTCCCAATTTCATAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
2911145 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
2911210 ACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCTA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
2911251 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
2911316 ACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
2911357 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
2911422 ACTGCTGGTTGTCAACAAACAACTTTCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
2911463 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
2911528 ACCGCTTGTTGTCAATAAACAA-TTACCCAATTTTGGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTT-CCCAATTTCAGAGCCA
* *
2911569 ATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
2911634 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTTGGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
2911675 ATTTCAACTTCACAGCGAAGGATATTGGAATCCAGATAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
2911740 ACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
2911781 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
2911846 ACCACTGGTTGTCAACAAGCAACTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
2911887 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
2911952 ACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
2911993 ATTTCAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
2912058 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * * * * *
2912099 ATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAGTTTAACTTCACAACAAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * * *
2912164 ACGGCTGGTTGTCAACAAACAATTTCCCGATTCCAGAGCAA
66 ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
2912205 ATTTTAACTTCAC-GACGGAGGATATTGGACTC
1 ATTTCAACTTCACAG-CGAAGGATATTGGACTC
2912237 AGAACAATTC
Statistics
Matches: 1203, Mismatches: 97, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
105 2 0.00
106 1175 0.98
107 2 0.00
108 3 0.00
109 21 0.02
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
Found at i:2913493 original size:23 final size:23
Alignment explanation
Indices: 2913465--2913511 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
2913455 TGTATATATA
2913465 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTT-TTTCATT
2913488 TATTTATTATAATTTTTTTCATT
1 TATTTATTATAATTTTTTTCATT
2913511 T
1 T
2913512 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTATTATAATTTTTTTCATT
Found at i:2913802 original size:26 final size:28
Alignment explanation
Indices: 2913756--2913812 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 28
2913746 ATACAAACGT
2913756 TTTTATATTTATATATATATA-TATATTA
1 TTTTATATTTATATATATATACTAT-TTA
2913784 TTTTATTATTT-TAT-T-TATACTATTTA
1 TTTTA-TATTTATATATATATACTATTTA
2913810 TTT
1 TTT
2913813 ATTTTCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
26 10 0.37
27 4 0.15
28 8 0.30
29 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTATATTTATATATATATACTATTTA
Found at i:2920343 original size:2 final size:2
Alignment explanation
Indices: 2920336--2920391 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
2920326 TTTACATGTG
2920336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2920378 AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT
2920392 GATTGGTTGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2920501 original size:19 final size:18
Alignment explanation
Indices: 2920452--2920502 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
2920442 CTTTTACATG
2920452 TTTATACATTATTATATGA
1 TTTATACA-TATTATATGA
*
2920471 TACT-TACAATATTATATGA
1 T-TTATAC-ATATTATATGA
2920490 TTTATACGATATT
1 TTTATAC-ATATT
2920503 TTATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.04
19 23 0.88
20 2 0.08
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (18 bp):
TTTATACATATTATATGA
Found at i:2923287 original size:64 final size:62
Alignment explanation
Indices: 2923188--2923314 Score: 236
Period size: 64 Copynumber: 2.0 Consensus size: 62
2923178 AGTACCTAGA
2923188 TCCACCCAAGACGATGTGTGGAAGGCCCCCATACATCAGAATGCACATAATCAAGAATCCCT
1 TCCACCCAAGACGATGTGTGGAAGGCCCCCATACATCAGAATGCACATAATCAAGAATCCCT
2923250 TCCACCCAAAGACGATGTCGTGGAAGGCCCCCATACATCAGAATGCACATAATCAAGAATCCCT
1 TCCACCC-AAGACGATGT-GTGGAAGGCCCCCATACATCAGAATGCACATAATCAAGAATCCCT
2923314 T
1 T
2923315 GAGTTGTGTG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 7 0.11
63 10 0.16
64 46 0.73
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.18
Consensus pattern (62 bp):
TCCACCCAAGACGATGTGTGGAAGGCCCCCATACATCAGAATGCACATAATCAAGAATCCCT
Found at i:2929790 original size:2 final size:2
Alignment explanation
Indices: 2929783--2929899 Score: 117
Period size: 2 Copynumber: 58.5 Consensus size: 2
2929773 ATACATACAA
2929783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * * * *
2929825 AC AT AC AT AC AT AC AT AC AA AT AT AT AC AC AC AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
2929867 AT AT AC AT AT AT AC AT AG AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2929900 CTTTTTGTAG
Statistics
Matches: 96, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 96 1.00
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.38
Consensus pattern (2 bp):
AT
Found at i:2937839 original size:20 final size:20
Alignment explanation
Indices: 2937814--2937853 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2937804 AATCGATAAA
2937814 GTGTGAATTTGCTTGTTCAT
1 GTGTGAATTTGCTTGTTCAT
2937834 GTGTGAATTTGCTTGTTCAT
1 GTGTGAATTTGCTTGTTCAT
2937854 ATTTGACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.25, T:0.50
Consensus pattern (20 bp):
GTGTGAATTTGCTTGTTCAT
Found at i:2939452 original size:40 final size:40
Alignment explanation
Indices: 2939376--2939457 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
2939366 ACATTACAAG
* *
2939376 TTAGGTGGGAAAGGCCCGACCTCAGCACTACGGTGCATTA
1 TTAGGTGAGAAAGGCCCGACCTCAGCACTACGGTGCAATA
* * **
2939416 TTAGGTGAGCAAGGCTCGACCTCAGCACTATTGTGCAATA
1 TTAGGTGAGAAAGGCCCGACCTCAGCACTACGGTGCAATA
2939456 TT
1 TT
2939458 TGACTCCTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TTAGGTGAGAAAGGCCCGACCTCAGCACTACGGTGCAATA
Found at i:2939952 original size:2 final size:2
Alignment explanation
Indices: 2939945--2940005 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
2939935 TTTAATTATG
2939945 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2939986 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
2940006 CATGTGATAG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2948791 original size:18 final size:19
Alignment explanation
Indices: 2948753--2948798 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
2948743 AAGACAATGG
* *
2948753 AGAAAGAAAAGTAAAATAA
1 AGAAATAAAAGTAAAAGAA
2948772 AGAAATAAAA-TAAAAGAA
1 AGAAATAAAAGTAAAAGAA
*
2948790 AGGAATAAA
1 AGAAATAAA
2948799 TCAAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (19 bp):
AGAAATAAAAGTAAAAGAA
Found at i:2948935 original size:12 final size:12
Alignment explanation
Indices: 2948918--2948947 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2948908 TATACAAAAC
*
2948918 AAAATATGAATA
1 AAAATATAAATA
2948930 AAAATATAAATA
1 AAAATATAAATA
2948942 AAAATA
1 AAAATA
2948948 AAGGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (12 bp):
AAAATATAAATA
Found at i:2952798 original size:49 final size:50
Alignment explanation
Indices: 2952741--2952868 Score: 118
Period size: 56 Copynumber: 2.5 Consensus size: 50
2952731 TCATTACTAG
*
2952741 CACC-TTTCTACCAAAAATGCACCATTTTTCATCTAACTTGCATTAGTGA
1 CACCGTTTCTACCAAAAATGCACCATTTTTCATCTAACTTGCATCAGTGA
* ** *
2952790 CA-CTTTTCTGCAAAAAAAAAAAAATGCACCATTTTTCATCTAACTTGCATCAGTGG
1 CACCGTTTCT-------ACCAAAAATGCACCATTTTTCATCTAACTTGCATCAGTGA
*
2952846 CACCGTTT-TGCCAAAAATGCACC
1 CACCGTTTCTACCAAAAATGCACC
2952869 GTTAGGCATT
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
48 1 0.02
49 18 0.29
56 39 0.63
57 4 0.06
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (50 bp):
CACCGTTTCTACCAAAAATGCACCATTTTTCATCTAACTTGCATCAGTGA
Found at i:2952862 original size:56 final size:56
Alignment explanation
Indices: 2952753--2952862 Score: 168
Period size: 56 Copynumber: 2.0 Consensus size: 56
2952743 CCTTTCTACC
* *
2952753 AAAAATGCACCATTTTTCATCTAACTTGCATTAGTGACACTTTTCTGCAAAAAAAA
1 AAAAATGCACCATTTTTCATCTAACTTGCATCAGTGACACGTTTCTGCAAAAAAAA
* *
2952809 AAAAATGCACCATTTTTCATCTAACTTGCATCAGTGGCACCGTTT-TGCCAAAAA
1 AAAAATGCACCATTTTTCATCTAACTTGCATCAGTGACA-CGTTTCTGCAAAAAA
2952863 TGCACCGTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 45 0.92
57 4 0.08
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (56 bp):
AAAAATGCACCATTTTTCATCTAACTTGCATCAGTGACACGTTTCTGCAAAAAAAA
Found at i:2962958 original size:15 final size:16
Alignment explanation
Indices: 2962929--2962958 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2962919 TACTTTCACA
2962929 CTAAATCGTGTTCAAT
1 CTAAATCGTGTTCAAT
2962945 CTAAATCG-GTTCAA
1 CTAAATCGTGTTCAA
2962959 AAGACACCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (16 bp):
CTAAATCGTGTTCAAT
Found at i:2966126 original size:25 final size:24
Alignment explanation
Indices: 2966098--2966152 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
2966088 TTTAATCTAT
2966098 ATTTAATTTGAATTAATT-AAATAAC
1 ATTTAATTT--ATTAATTAAAATAAC
*
2966123 ATTTTATTTATTAATTCAAAATAAC
1 ATTTAATTTATTAATT-AAAATAAC
2966148 -TTTAA
1 ATTTAA
2966153 AAACCCTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 7 0.27
24 4 0.15
25 15 0.58
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (24 bp):
ATTTAATTTATTAATTAAAATAAC
Found at i:2966128 original size:77 final size:78
Alignment explanation
Indices: 2965984--2966128 Score: 197
Period size: 77 Copynumber: 1.9 Consensus size: 78
2965974 GTAAGCATCA
**
2965984 AAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATTTAATTCGGAATAATTAAATAAGTTT
1 AAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATTTAATTCGGAATAATTAAATAACATT
2966049 TTAAATAAACATT
66 TTAAATAAACATT
* * * *
2966062 AAAGATTGTAATTTAGATTATAAGTC-TTTAATCT-ATATTTAATT-TGAATTAATTAAATAACA
1 AAAGAATGTAATTTAGATTACAACTCTTTTAAT-TGATATTTAATTCGGAA-TAATTAAATAACA
2966124 TTTTA
64 TTTTA
2966129 TTTATTAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
76 3 0.05
77 32 0.54
78 24 0.41
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (78 bp):
AAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATTTAATTCGGAATAATTAAATAACATT
TTAAATAAACATT
Found at i:2968677 original size:49 final size:49
Alignment explanation
Indices: 2968623--2968773 Score: 189
Period size: 49 Copynumber: 3.1 Consensus size: 49
2968613 TTTTATGCTG
* *
2968623 AAATGCACCGTTATACATGTAA-TTGTCATTAGTGGCACCTTTCTGCCAA
1 AAATGCACCATTATACATCTAACTTG-CATTAGTGGCACCTTTCTGCCAA
* * **
2968672 CAATGCACAATT-TTTATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
1 AAATGCACCATTATACATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
** * *
2968720 AAATGCACCATTAGGCATTTAACTTGCATTAGTGGCACCTTTTTGCCAA
1 AAATGCACCATTATACATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
2968769 AAATG
1 AAATG
2968774 TACAGTTAGG
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
48 39 0.45
49 48 0.55
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (49 bp):
AAATGCACCATTATACATCTAACTTGCATTAGTGGCACCTTTCTGCCAA
Found at i:2968783 original size:49 final size:48
Alignment explanation
Indices: 2968649--2968793 Score: 193
Period size: 49 Copynumber: 3.0 Consensus size: 48
2968639 ATGTAATTGT
* *** *
2968649 CATTAGTGGCACCTTTCTGCCAACAATGCACAATT-TTTATCTAACTTG
1 CATTAGTGGCACCTTTCTGCCAAAAATGCAC-ATTAGGCATTTAACTTG
2968697 CATTAGTGGCACCTTTCTGCCAAAAATGCACCATTAGGCATTTAACTTG
1 CATTAGTGGCACCTTTCTGCCAAAAATGCA-CATTAGGCATTTAACTTG
* *
2968746 CATTAGTGGCACCTTTTTGCCAAAAATGTACAGTTAGGCATTTAACTT
1 CATTAGTGGCACCTTTCTGCCAAAAATGCACA-TTAGGCATTTAACTT
2968794 TAATTTAAGA
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
48 34 0.39
49 53 0.61
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (48 bp):
CATTAGTGGCACCTTTCTGCCAAAAATGCACATTAGGCATTTAACTTG
Found at i:2969313 original size:13 final size:13
Alignment explanation
Indices: 2969295--2969321 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2969285 ATAACTGTCT
2969295 CTTAGTATCGATA
1 CTTAGTATCGATA
2969308 CTTAGTATCGATA
1 CTTAGTATCGATA
2969321 C
1 C
2969322 CTACCTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (13 bp):
CTTAGTATCGATA
Found at i:2987445 original size:20 final size:20
Alignment explanation
Indices: 2987420--2987465 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2987410 ATTTTACTAA
2987420 GATTCGACCGTCAGAATTCT
1 GATTCGACCGTCAGAATTCT
*
2987440 GATTCGATCGTCAGAATTCT
1 GATTCGACCGTCAGAATTCT
2987460 GATTCG
1 GATTCG
2987466 TCTTATTCGT
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:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
GATTCGACCGTCAGAATTCT
Found at i:2995802 original size:14 final size:15
Alignment explanation
Indices: 2995772--2995803 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2995762 TCACAATCGC
2995772 GCAGGATTCCGGGGA
1 GCAGGATTCCGGGGA
2995787 GCAGGATTCC-GGGA
1 GCAGGATTCCGGGGA
2995801 GCA
1 GCA
2995804 CCGTGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.22, C:0.22, G:0.44, T:0.12
Consensus pattern (15 bp):
GCAGGATTCCGGGGA
Found at i:3010440 original size:207 final size:215
Alignment explanation
Indices: 3010181--3010602 Score: 788
Period size: 207 Copynumber: 2.0 Consensus size: 215
3010171 TGCAGAATAA
3010181 AAATGCATCAATATATAGATCATGAGTGATGCAACGTTATTCATTAATCAGATATGTCTCAGATA
1 AAATGCATCAATATATAGATCATGAGTGATGCAACGTTATTCATTAATCAGATATGTCTCAGATA
3010246 ATTGTAATCATGGTGCAT-TG-TTTCAAGCTGAACATAAAACATAATAGCATAATACATCGAAAA
66 ATTGTAATCATGGTGCATATGTTTTCAAGCTGAACATAAAACATAATAGCATAATACATCGAAAA
3010309 TATCAAACATGTCTAGAT-A-ACA-CTATAG-AAGATAATCAATA-CAATTAAGCC-TATGCTTC
131 TATCAAACATGTCTAGATAACACACCTATAGAAAGATAATCAATATCAATTAAGCCTTATGCTTC
3010368 CCACGGTCAGTGGTACTAGG
196 CCACGGTCAGTGGTACTAGG
3010388 AAATGCATCAATATATAGATCATGAGTGATGCAACGTTATTCATTAATCAGATATGTCTCAGATA
1 AAATGCATCAATATATAGATCATGAGTGATGCAACGTTATTCATTAATCAGATATGTCTCAGATA
3010453 ATTGTAATCATGGTGCATATGTTTTCAAGCTGAACATAAAACATAATAGCATAATACATCGAAAA
66 ATTGTAATCATGGTGCATATGTTTTCAAGCTGAACATAAAACATAATAGCATAATACATCGAAAA
3010518 TATCAAACATGTCTAGATAACACACCTATAGAAAGATAATCAATATCAATTAAGCCTTATGCTTC
131 TATCAAACATGTCTAGATAACACACCTATAGAAAGATAATCAATATCAATTAAGCCTTATGCTTC
3010583 CCACGGTCAGTGGTACTAGG
196 CCACGGTCAGTGGTACTAGG
3010603 TCCTGTAGAA
Statistics
Matches: 207, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
207 83 0.40
208 2 0.01
209 61 0.29
210 1 0.00
211 3 0.01
212 6 0.03
213 13 0.06
214 10 0.05
215 28 0.14
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (215 bp):
AAATGCATCAATATATAGATCATGAGTGATGCAACGTTATTCATTAATCAGATATGTCTCAGATA
ATTGTAATCATGGTGCATATGTTTTCAAGCTGAACATAAAACATAATAGCATAATACATCGAAAA
TATCAAACATGTCTAGATAACACACCTATAGAAAGATAATCAATATCAATTAAGCCTTATGCTTC
CCACGGTCAGTGGTACTAGG
Found at i:3010996 original size:14 final size:14
Alignment explanation
Indices: 3010977--3011012 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3010967 AATGATCAAA
*
3010977 GTCAACGGTCAATT
1 GTCAACGGTCAATG
*
3010991 GTCAACGATCAATG
1 GTCAACGGTCAATG
3011005 GTCAACGG
1 GTCAACGG
3011013 GTCGGGTCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (14 bp):
GTCAACGGTCAATG
Found at i:3011027 original size:17 final size:17
Alignment explanation
Indices: 3011005--3011043 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3010995 ACGATCAATG
3011005 GTCAACGGGTCGGGTCA
1 GTCAACGGGTCGGGTCA
*
3011022 GTCAACGGTTCGGGTCA
1 GTCAACGGGTCGGGTCA
3011039 GTCAA
1 GTCAA
3011044 TGAGTCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.36, T:0.21
Consensus pattern (17 bp):
GTCAACGGGTCGGGTCA
Found at i:3015076 original size:16 final size:16
Alignment explanation
Indices: 3015051--3015083 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3015041 TGCACTTCAC
3015051 TTTTTTTTCTTT-TTT
1 TTTTTTTTCTTTGTTT
3015066 TTTTCTTTTCTTTGTTT
1 TTTT-TTTTCTTTGTTT
3015083 T
1 T
3015084 CTTTGATAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (16 bp):
TTTTTTTTCTTTGTTT
Found at i:3015489 original size:2 final size:2
Alignment explanation
Indices: 3015482--3015506 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3015472 TTGGGCCCAT
3015482 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 T
3015507 GAACCACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3029806 original size:20 final size:20
Alignment explanation
Indices: 3029781--3029849 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
3029771 TTTCCCACGA
*
3029781 ATTTGTAAAACCTCCAGGTT
1 ATTTGTAAAACCTCCGGGTT
*
3029801 ATTTGTAAAACCTCCGGGTA
1 ATTTGTAAAACCTCCGGGTT
*
3029821 ATTTGTAAAGCCTCCGGGTT
1 ATTTGTAAAACCTCCGGGTT
3029841 ATTTGTAAA
1 ATTTGTAAA
3029850 GCTTTTGGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (20 bp):
ATTTGTAAAACCTCCGGGTT
Found at i:3029850 original size:20 final size:20
Alignment explanation
Indices: 3029780--3029879 Score: 110
Period size: 20 Copynumber: 5.0 Consensus size: 20
3029770 ATTTCCCACG
*
3029780 AATTTGTAAAACCTCCAGGT
1 AATTTGTAAAACCTCCGGGT
*
3029800 TATTTGTAAAACCTCCGGGT
1 AATTTGTAAAACCTCCGGGT
*
3029820 AATTTGTAAAGCCTCCGGGT
1 AATTTGTAAAACCTCCGGGT
* * * **
3029840 TATTTGTAAAGCTTTTGGGT
1 AATTTGTAAAACCTCCGGGT
* *
3029860 AATTTGTAAATCCTTCGGGT
1 AATTTGTAAAACCTCCGGGT
3029880 CATATATTAG
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (20 bp):
AATTTGTAAAACCTCCGGGT
Found at i:3029879 original size:40 final size:40
Alignment explanation
Indices: 3029780--3029879 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
3029770 ATTTCCCACG
*
3029780 AATTTGTAAAACCTCCAGGTTATTTGTAAAACCTCCGGGT
1 AATTTGTAAAACCTCCGGGTTATTTGTAAAACCTCCGGGT
* * * **
3029820 AATTTGTAAAGCCTCCGGGTTATTTGTAAAGCTTTTGGGT
1 AATTTGTAAAACCTCCGGGTTATTTGTAAAACCTCCGGGT
* *
3029860 AATTTGTAAATCCTTCGGGT
1 AATTTGTAAAACCTCCGGGT
3029880 CATATATTAG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (40 bp):
AATTTGTAAAACCTCCGGGTTATTTGTAAAACCTCCGGGT
Found at i:3030116 original size:35 final size:38
Alignment explanation
Indices: 3030026--3030120 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 38
3030016 GTAATACAAA
* *
3030026 TTCAACCTTCACAGAAAAGTAGTGAAGTAAATGCAATTC
1 TTCAA-CTTCACGGAAGAGTAGTGAAGTAAATGCAATTC
* * *
3030065 TCCAGTCTTCACGGAAGAGTAGTGAAGTCAAT-C-ATT-
1 TTCA-ACTTCACGGAAGAGTAGTGAAGTAAATGCAATTC
3030101 TTCAACTTCACGGAAGAGTA
1 TTCAACTTCACGGAAGAGTA
3030121 ATCCAATCTC
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
35 15 0.31
36 3 0.06
37 3 0.06
38 1 0.02
39 26 0.54
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (38 bp):
TTCAACTTCACGGAAGAGTAGTGAAGTAAATGCAATTC
Found at i:3030233 original size:39 final size:38
Alignment explanation
Indices: 3030178--3030366 Score: 217
Period size: 39 Copynumber: 5.1 Consensus size: 38
3030168 CTTCTCAAAT
*
3030178 AATGCAAAT-TCAACCTTCACGGAAGAGTAGTGAAGTA
1 AATGCAATTCTCAACCTTCACGGAAGAGTAGTGAAGTA
*
3030215 AATGCAATTCTGCAACCTTCACAGAAGAGTAGTGAAGTA
1 AATGCAATTCT-CAACCTTCACGGAAGAGTAGTGAAGTA
* *
3030254 AATGCAATTCTCCAGCCTTCACGGAAGAGTAGTGAAGTC
1 AATGCAATTCT-CAACCTTCACGGAAGAGTAGTGAAGTA
* *
3030293 AAT-C-ATTTTCAACCTTCACAGAAGAGTAGTGAAGT-
1 AATGCAATTCTCAACCTTCACGGAAGAGTAGTGAAGTA
* * ** * *
3030328 CATTCAA-GATCAACCTTCATGGAAGAGCAGTGAAGTA
1 AATGCAATTCTCAACCTTCACGGAAGAGTAGTGAAGTA
3030365 AA
1 AA
3030367 AGAGGTGCAA
Statistics
Matches: 131, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
35 2 0.02
36 49 0.37
37 14 0.11
38 2 0.02
39 64 0.49
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (38 bp):
AATGCAATTCTCAACCTTCACGGAAGAGTAGTGAAGTA
Found at i:3030244 original size:160 final size:164
Alignment explanation
Indices: 3029957--3030284 Score: 502
Period size: 160 Copynumber: 2.0 Consensus size: 164
3029947 AGAGTAGTGA
* * *
3029957 AGTAGTCCAATCTCGAGTCTGATCTTCATGGAAGAGTAGTGAAATTAGATTCTTATCAAGTAATA
1 AGTAATCCAATCTCGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTTATCAAATAATA
** *
3030022 CAAATTCAACCTTCACAGAAAAGTAGTGAAGTAAATGCAATTCTCCAGTCTTCACGGAAGAGTAG
66 CAAATTCAACCTTCACAGAAAAGTAGTGAAGTAAATGCAATTCTCCAACCTTCACAGAAGAGTAG
* *
3030087 TGAAGTCAAT-C-ATT-TTCA-ACTTCACGGAAG
131 TGAAGTAAATGCAATTCTCCAGACTTCACGGAAG
* *
3030117 AGTAATCCAATCTCGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTTCTCAAATAATG
1 AGTAATCCAATCTCGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTTATCAAATAATA
* * *
3030182 CAAATTCAACCTTCACGGAAGAGTAGTGAAGTAAATGCAATTCTGCAACCTTCACAGAAGAGTAG
66 CAAATTCAACCTTCACAGAAAAGTAGTGAAGTAAATGCAATTCTCCAACCTTCACAGAAGAGTAG
*
3030247 TGAAGTAAATGCAATTCTCCAGCCTTCACGGAAG
131 TGAAGTAAATGCAATTCTCCAGACTTCACGGAAG
3030281 AGTA
1 AGTA
3030285 GTGAAGTCAA
Statistics
Matches: 150, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
160 128 0.85
161 1 0.01
162 3 0.02
163 3 0.02
164 15 0.10
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (164 bp):
AGTAATCCAATCTCGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTTATCAAATAATA
CAAATTCAACCTTCACAGAAAAGTAGTGAAGTAAATGCAATTCTCCAACCTTCACAGAAGAGTAG
TGAAGTAAATGCAATTCTCCAGACTTCACGGAAG
Found at i:3030606 original size:14 final size:15
Alignment explanation
Indices: 3030587--3030639 Score: 74
Period size: 14 Copynumber: 3.5 Consensus size: 15
3030577 AGTCTCATAT
3030587 TTATA-TAATATTTA
1 TTATATTAATATTTA
3030601 TTATATTAATATTT-
1 TTATATTAATATTTA
3030615 TTATATTAATATATTA
1 TTATATTAATAT-TTA
3030631 TTATTATTA
1 TTA-TATTA
3030640 TTACAATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 17 0.49
15 10 0.29
16 3 0.09
17 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTAATATTTA
Done.