Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 31
Found at i:3492636 original size:114 final size:114
Alignment explanation
Indices: 3492426--3492649 Score: 369
Period size: 114 Copynumber: 2.0 Consensus size: 114
3492416 GGCCCTGCCT
3492426 CCCTCAGCCCTGTCTCCCTCATACATACAACAATAATTTAACGTAAATTGAAGGCGTGAAAATGA
1 CCCTCAGCCCTGTCTCCCTCATACATACAACAATAATTTAACGTAAATTGAAGGCGTGAAAATGA
3492491 TGCAATAATTCACGTAAATTACAGGCATGATTTGCAACAATAGTTCGAC
66 TGCAATAATTCACGTAAATTACAGGCATGATTTGCAACAATAGTTCGAC
* * *
3492540 CCCTCAGCCCTGTCTCCCTCATGCATGCAATAATAATTTAACGTAAATTGAAGGCGTGAAAATGC
1 CCCTCAGCCCTGTCTCCCTCATACATACAACAATAATTTAACGTAAATTGAAGGCGTGAAAATG-
* ** *
3492605 A-GCAATAATTCACGTAAATTGCAGGTGTGATTTGCAGCAATAGTT
65 ATGCAATAATTCACGTAAATTACAGGCATGATTTGCAACAATAGTT
3492650 TGACATGGTG
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 101 0.99
115 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (114 bp):
CCCTCAGCCCTGTCTCCCTCATACATACAACAATAATTTAACGTAAATTGAAGGCGTGAAAATGA
TGCAATAATTCACGTAAATTACAGGCATGATTTGCAACAATAGTTCGAC
Found at i:3492985 original size:15 final size:15
Alignment explanation
Indices: 3492965--3493053 Score: 95
Period size: 15 Copynumber: 6.5 Consensus size: 15
3492955 GGTACGTTTA
3492965 AGAAGAAAGAAAGGG
1 AGAAGAAAGAAAGGG
*
3492980 AGAAGAAGGAAA--G
1 AGAAGAAAGAAAGGG
3492993 -GAAG-AAGAAAGGG
1 AGAAGAAAGAAAGGG
*
3493006 AGAAGAAGGAAA--G
1 AGAAGAAAGAAAGGG
3493019 -GAAG-AAGAAAGGG
1 AGAAGAAAGAAAGGG
*
3493032 AGAAAAAAGAAAGGG
1 AGAAGAAAGAAAGGG
3493047 AGAAGAA
1 AGAAGAA
3493054 TGGGAGAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
11 10 0.17
12 8 0.13
13 4 0.07
14 7 0.12
15 31 0.52
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (15 bp):
AGAAGAAAGAAAGGG
Found at i:3493002 original size:11 final size:11
Alignment explanation
Indices: 3492981--3493040 Score: 57
Period size: 11 Copynumber: 5.0 Consensus size: 11
3492971 AAGAAAGGGA
3492981 GAAGAAGGAAAG
1 GAAGAA-GAAAG
3492993 GAAGAAGAAAGGG
1 GAAGAAGAAA--G
3493006 AGAAGAAGGAAAG
1 -GAAGAA-GAAAG
3493019 GAAGAAGAAAG
1 GAAGAAGAAAG
* *
3493030 GGAGAAAAAAG
1 GAAGAAGAAAG
3493041 AAAGGGAGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
11 18 0.43
12 12 0.29
13 2 0.05
14 6 0.14
15 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (11 bp):
GAAGAAGAAAG
Found at i:3493003 original size:26 final size:26
Alignment explanation
Indices: 3492966--3493091 Score: 180
Period size: 26 Copynumber: 4.8 Consensus size: 26
3492956 GTACGTTTAA
3492966 GAAGAAAGAAAGGGAGAAGAAGGAAAG
1 GAAG-AAGAAAGGGAGAAGAAGGAAAG
3492993 GAAGAAGAAAGGGAGAAGAAGGAAAG
1 GAAGAAGAAAGGGAGAAGAAGGAAAG
* *
3493019 GAAGAAGAAAGGGAGAAAAAAGAAAG
1 GAAGAAGAAAGGGAGAAGAAGGAAAG
* * *
3493045 GGAGAAGAATGGGAGAAAAAGGAAAG
1 GAAGAAGAAAGGGAGAAGAAGGAAAG
* *
3493071 GAATAAGAAAGGGTGAAGAAG
1 GAAGAAGAAAGGGAGAAGAAG
3493092 AGATCGGGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
26 85 0.96
27 4 0.04
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (26 bp):
GAAGAAGAAAGGGAGAAGAAGGAAAG
Found at i:3493025 original size:41 final size:40
Alignment explanation
Indices: 3492965--3493091 Score: 127
Period size: 41 Copynumber: 3.2 Consensus size: 40
3492955 GGTACGTTTA
* *
3492965 AGAAGAAAGAAAGGGAGAAGAAGGAAAGGAAGAAGAAAGGG
1 AGAAGAAGGAAA-GGAGAAGAAGGAAAGGAAAAAGAAAGGG
* *
3493006 AGAAGAAGGAAAGGAAGAAGAAAGG-GAGAAAAAAGAAAGGG
1 AGAAGAAGGAAAGG-AGAAG-AAGGAAAGGAAAAAGAAAGGG
* * *
3493047 AGAAGAATG---GGAGAAAAAGGAAAGGAATAAGAAAGGG
1 AGAAGAAGGAAAGGAGAAGAAGGAAAGGAAAAAGAAAGGG
*
3493084 TGAAGAAG
1 AGAAGAAG
3493092 AGATCGGGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
36 4 0.06
37 23 0.32
38 2 0.03
40 2 0.03
41 37 0.51
42 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.02
Consensus pattern (40 bp):
AGAAGAAGGAAAGGAGAAGAAGGAAAGGAAAAAGAAAGGG
Found at i:3493052 original size:11 final size:11
Alignment explanation
Indices: 3492983--3493066 Score: 53
Period size: 11 Copynumber: 6.9 Consensus size: 11
3492973 GAAAGGGAGA
*
3492983 AGAAGGAAAGGA
1 AGAA-GAAAGGG
3492995 AGAAGAAAGGGAG
1 AGAAGAAA-GG-G
*
3493008 AAGAAGGAAAGGA
1 -AGAA-GAAAGGG
3493021 AGAAGAAAGGG
1 AGAAGAAAGGG
3493032 AGAAAAAAGAAAGGG
1 AG----AAGAAAGGG
*
3493047 AGAAGAATGGG
1 AGAAGAAAGGG
3493058 AGAA-AAAGG
1 AGAAGAAAGG
3493067 AAAGGAATAA
Statistics
Matches: 59, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
10 4 0.07
11 24 0.41
12 10 0.17
14 6 0.10
15 15 0.25
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.01
Consensus pattern (11 bp):
AGAAGAAAGGG
Found at i:3493170 original size:28 final size:29
Alignment explanation
Indices: 3493130--3493194 Score: 107
Period size: 28 Copynumber: 2.3 Consensus size: 29
3493120 AATTTAAATC
*
3493130 ATTAGTTTGTTAGTTTAAGTT-ATATTAT
1 ATTAGTTTGTTAGATTAAGTTAATATTAT
3493158 ATTAGTTTGTTAGATTAAGTTAATATTAT
1 ATTAGTTTGTTAGATTAAGTTAATATTAT
3493187 ATTA-TTTG
1 ATTAGTTTG
3493195 AAAAATTAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 24 0.69
29 11 0.31
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (29 bp):
ATTAGTTTGTTAGATTAAGTTAATATTAT
Found at i:3493202 original size:28 final size:29
Alignment explanation
Indices: 3493144--3493208 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
3493134 GTTTGTTAGT
** *
3493144 TTAAGTT-ATATTATATTAGTTTGTTAGA
1 TTAAGTTAATATTATATTAGTTTGAAAAA
3493172 TTAAGTTAATATTATATTA-TTTGAAAAA
1 TTAAGTTAATATTATATTAGTTTGAAAAA
3493200 TT-AGTTAAT
1 TTAAGTTAAT
3493209 TAGTTTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 7 0.21
28 15 0.45
29 11 0.33
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (29 bp):
TTAAGTTAATATTATATTAGTTTGAAAAA
Found at i:3496431 original size:23 final size:22
Alignment explanation
Indices: 3496388--3496428 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3496378 AATAAAGTTG
3496388 ATTTAAATCAAATAATATAATTA
1 ATTTAAAT-AAATAATATAATTA
3496411 ATTTAAAT-AATAAT-TAAT
1 ATTTAAATAAATAATATAAT
3496429 AATAACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
23 8 0.44
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTTAAATAAATAATATAATTA
Found at i:3497449 original size:21 final size:21
Alignment explanation
Indices: 3497425--3497479 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3497415 TCAAATATTT
3497425 AATAATAATAATAATTCATTA
1 AATAATAATAATAATTCATTA
** * *
3497446 AATACAT-ATTTTATTTTATTA
1 AATA-ATAATAATAATTCATTA
3497467 AATAATAATAATA
1 AATAATAATAATA
3497480 CCATTATTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAATAATAATAATTCATTA
Found at i:3497765 original size:23 final size:22
Alignment explanation
Indices: 3497738--3497783 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
3497728 AGAACATCAT
3497738 TTAAACTAACAAACTAATATAAC
1 TTAAACTAACAAACTAAT-TAAC
3497761 TTAAACTAACAAACTAATTAAC
1 TTAAACTAACAAACTAATTAAC
3497783 T
1 T
3497784 AAATCTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.28
Consensus pattern (22 bp):
TTAAACTAACAAACTAATTAAC
Found at i:3497901 original size:17 final size:17
Alignment explanation
Indices: 3497881--3497917 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3497871 TTCTTCTATG
3497881 TTCCTTTCCTTTCTCTC
1 TTCCTTTCCTTTCTCTC
3497898 TTCCTTTCCTTTCTCTC
1 TTCCTTTCCTTTCTCTC
3497915 TTC
1 TTC
3497918 TCCCTTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (17 bp):
TTCCTTTCCTTTCTCTC
Found at i:3497923 original size:15 final size:15
Alignment explanation
Indices: 3497888--3497933 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
3497878 ATGTTCCTTT
*
3497888 CCTTTCTCTCTTCCTTT
1 CCTTTCTCTCTT-C-TC
3497905 CCTTTCTCTCTTCTC
1 CCTTTCTCTCTTCTC
*
3497920 CCTTTCTTTCTTCT
1 CCTTTCTCTCTTCT
3497934 GCTCAATGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 14 0.52
16 1 0.04
17 12 0.44
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
CCTTTCTCTCTTCTC
Found at i:3498193 original size:29 final size:29
Alignment explanation
Indices: 3498141--3498251 Score: 125
Period size: 31 Copynumber: 3.7 Consensus size: 29
3498131 TTCGAGCTGC
* * *
3498141 CTGCATGGTGACCTACAAGGTCGC-AGCGA
1 CTGCATGGCGACCTACAAGCTCGCTTG-GA
* *
3498170 CTGTATGGCGACCTATAAGCTCGCTTGGA
1 CTGCATGGCGACCTACAAGCTCGCTTGGA
3498199 CTGCATGGCGACCAATACAAGCTCGCTTGGA
1 CTGCATGGCGACC--TACAAGCTCGCTTGGA
3498230 CTGCATGGCGACCAATACAAGC
1 CTGCATGGCGACC--TACAAGC
3498252 ACTGTATCGT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
29 34 0.47
30 1 0.01
31 37 0.51
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (29 bp):
CTGCATGGCGACCTACAAGCTCGCTTGGA
Found at i:3498224 original size:31 final size:31
Alignment explanation
Indices: 3498168--3498251 Score: 136
Period size: 31 Copynumber: 2.8 Consensus size: 31
3498158 AGGTCGCAGC
* *
3498168 GACTGTATGGCGACC--TATAAGCTCGCTTG
1 GACTGCATGGCGACCAATACAAGCTCGCTTG
3498197 GACTGCATGGCGACCAATACAAGCTCGCTTG
1 GACTGCATGGCGACCAATACAAGCTCGCTTG
3498228 GACTGCATGGCGACCAATACAAGC
1 GACTGCATGGCGACCAATACAAGC
3498252 ACTGTATCGT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.27
31 37 0.73
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.20
Consensus pattern (31 bp):
GACTGCATGGCGACCAATACAAGCTCGCTTG
Found at i:3498886 original size:18 final size:18
Alignment explanation
Indices: 3498863--3498897 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3498853 ATTTTTATTG
3498863 AATAAAAATAATATTTTA
1 AATAAAAATAATATTTTA
* *
3498881 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
3498898 GGGACATGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATAAAAATAATATTTTA
Found at i:3502758 original size:40 final size:36
Alignment explanation
Indices: 3502710--3502799 Score: 85
Period size: 40 Copynumber: 2.4 Consensus size: 36
3502700 AATTTCGTCC
*
3502710 TTTATATATATATATTTTTAAATATATTTTATTTATT
1 TTTATATATATATATTTTTAAATATATTATA-TTATT
* **
3502747 TATT-TACTATATTCATTTTTTTATTTATATTATATTATT
1 T-TTATA-TATA-T-ATATTTTTAAATATATTATATTATT
3502786 TTTAT-TATATATAT
1 TTTATATATATATAT
3502800 CTTATATCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
35 3 0.07
36 1 0.02
37 7 0.16
38 8 0.19
39 8 0.19
40 16 0.37
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (36 bp):
TTTATATATATATATTTTTAAATATATTATATTATT
Found at i:3502786 original size:14 final size:14
Alignment explanation
Indices: 3502767--3502806 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
3502757 ATTCATTTTT
3502767 TTATTTATATTATA
1 TTATTTATATTATA
*
3502781 TTATTTTTATTATA
1 TTATTTATATTATA
3502795 TATATCTTATAT
1 T-TAT-TTATAT
3502807 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:3502982 original size:13 final size:13
Alignment explanation
Indices: 3502964--3502988 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3502954 TTACTTTATT
3502964 TTATTTTTTTCTA
1 TTATTTTTTTCTA
3502977 TTATTTTTTTCT
1 TTATTTTTTTCT
3502989 TAATATCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTTTTCTA
Found at i:3506342 original size:13 final size:12
Alignment explanation
Indices: 3506309--3506350 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 12
3506299 ACAAAAAGAG
3506309 AAAAAAGAGAAA
1 AAAAAAGAGAAA
3506321 AAAGCAAAGAGAAA
1 AAA--AAAGAGAAA
3506335 ATAAAAAGAGAAA
1 A-AAAAAGAGAAA
3506348 AAA
1 AAA
3506351 TAAATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 5 0.19
13 10 0.37
14 10 0.37
15 2 0.07
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (12 bp):
AAAAAAGAGAAA
Found at i:3506367 original size:37 final size:36
Alignment explanation
Indices: 3506302--3506377 Score: 82
Period size: 37 Copynumber: 2.1 Consensus size: 36
3506292 AATCAGAACA
* *
3506302 AAAAGAGAAAAAAGAGAAAAAAGCAAAGAGAAAATA
1 AAAAGAGAAAAAAGAGAAAAAAGCAAAGAAAAAAGA
* **
3506338 AAAAGAGAAAAAATA-AATGAAAATTAAAGAAAAAAGA
1 AAAAGAGAAAAAAGAGAA--AAAAGCAAAGAAAAAAGA
3506375 AAA
1 AAA
3506378 CAAGATGCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
35 2 0.06
36 14 0.42
37 17 0.52
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (36 bp):
AAAAGAGAAAAAAGAGAAAAAAGCAAAGAAAAAAGA
Found at i:3506541 original size:8 final size:8
Alignment explanation
Indices: 3506528--3506553 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3506518 ACAATCATTT
3506528 CTGAATCA
1 CTGAATCA
3506536 CTGAATCA
1 CTGAATCA
3506544 CTGAATCA
1 CTGAATCA
3506552 CT
1 CT
3506554 CCACTCGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (8 bp):
CTGAATCA
Found at i:3508038 original size:37 final size:38
Alignment explanation
Indices: 3507977--3508051 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
3507967 GAAGATTTTA
* * * *
3507977 TCTCGCTTGAGATAGTTTCCCTTGAAACA-AAATATTG
1 TCTCCCTTGAGACAGGTTCCCTTGAAACATAAACATTG
*
3508014 TCTCCCTTGAGACAGGTTCTCTTGAAACATAAACATTG
1 TCTCCCTTGAGACAGGTTCCCTTGAAACATAAACATTG
3508052 AAAACATTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (38 bp):
TCTCCCTTGAGACAGGTTCCCTTGAAACATAAACATTG
Found at i:3508125 original size:37 final size:37
Alignment explanation
Indices: 3508058--3508144 Score: 131
Period size: 37 Copynumber: 2.4 Consensus size: 37
3508048 ATTGAAAACA
* *
3508058 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
3508094 TTTCCCTTCAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
3508131 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
3508145 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:3508207 original size:36 final size:36
Alignment explanation
Indices: 3508160--3508385 Score: 207
Period size: 36 Copynumber: 6.4 Consensus size: 36
3508150 ATTGAAAACA
*
3508160 TTTCCCTTGAAATAAATTTCATCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
**
3508196 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
* *
3508232 TTTCCCTTGAATCAAA-TT-A----T-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACA-G
*** *
3508261 TTTTATTTGAAACAAATTTCATCTCTCTTGAGACAA
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
** * * **
3508297 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCATCTCTCTTGAGACAG
* * * *
3508334 TTTCTCTTAAAACAAATTTCGTTTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
3508370 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
3508386 ATCTTTGAAT
Statistics
Matches: 153, Mismatches: 27, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
28 2 0.01
29 17 0.11
30 3 0.02
31 1 0.01
35 3 0.02
36 96 0.63
37 31 0.20
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCATCTCTCTTGAGACAG
Found at i:3508274 original size:203 final size:204
Alignment explanation
Indices: 3507971--3508347 Score: 479
Period size: 203 Copynumber: 1.9 Consensus size: 204
3507961 TAAAATGAAG
* * *
3507971 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGGTTCTCT
1 ATTTCATCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGGTTCCCT
* ** * *
3508036 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCT
66 TGAAACATAAACATTGAAAACATTTCACTTGAAACAAATTTCATCTCTCTTGAGACAATTTCCCT
*
3508101 TCAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCC
131 TCAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAACATTTCCC
3508166 TTGAAATAA
196 TTGAAATAA
* * * *
3508175 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCT
1 ATTTCATCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGGTTCCCT
* ** * ** * * **
3508239 TGAATCA-AATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCTCTTGAGACAATTTCTT
66 TGAAACATAAACA-TTGAAAACATTTCACTTGAAACAAATTTCATCTCTCTTGAGACAATTTCCC
** * * *
3508303 TTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACA
130 TTCAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACA
3508348 AATTTCGTTT
Statistics
Matches: 144, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
202 3 0.02
203 110 0.76
204 31 0.22
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (204 bp):
ATTTCATCTCGCTTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGGTTCCCT
TGAAACATAAACATTGAAAACATTTCACTTGAAACAAATTTCATCTCTCTTGAGACAATTTCCCT
TCAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACATAAACATTGAAAACATTTCCC
TTGAAATAA
Found at i:3508278 original size:101 final size:102
Alignment explanation
Indices: 3507971--3508347 Score: 470
Period size: 102 Copynumber: 3.7 Consensus size: 102
3507961 TAAAATGAAG
* * * * *
3507971 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGGTTCTCT
1 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
3508036 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
** * *
3508073 ATTTTGTCTCTCTTGAGATAGTTTCCCTTCAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
*
3508138 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
* *
3508175 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCT
1 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
* ** * ** ***
3508239 TGAATCA-AATTATTTGAATATGTTTTATTTGAAACAA
66 TGAAACATAAACA-TTGAAAACATTTCCCTTGAAACAA
* ** * * * *
3508276 ATTTCATCTCTCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCT
1 ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
*
3508341 TAAAACA
66 TGAAACA
3508348 AATTTCGTTT
Statistics
Matches: 243, Mismatches: 30, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
100 3 0.01
101 81 0.33
102 159 0.65
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (102 bp):
ATTTCATCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
Found at i:3508429 original size:138 final size:138
Alignment explanation
Indices: 3508181--3508439 Score: 360
Period size: 138 Copynumber: 1.9 Consensus size: 138
3508171 ATAAATTTCA
* * *
3508181 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAATCA
1 TCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
* * * *
3508246 AATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCTCTTGAGACAATTTCTTTTGGAACT
66 AAATATTTGAATATGTTTTATCTAAAACAAATTTCATCTCCCTTGAGACAATTTCTTTTGGAACT
3508311 AAGTTTTG
131 AAGTTTTG
* *
3508319 TCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTCGTTTCTCTTGAGACAGTTTCCCTTGAAACA
1 TCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
* * ** *
3508384 AAATCTTTGAAT-T-TATTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAATATTTGAATATGT-TTTAT-CTAAAACAAATTTCATCTCCCTTGAGACAATTTCT
3508440 CTTGAAACAC
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
136 1 0.01
137 5 0.05
138 99 0.94
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (138 bp):
TCTCTCTTGAGACAGTTTCCCTTAAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
AAATATTTGAATATGTTTTATCTAAAACAAATTTCATCTCCCTTGAGACAATTTCTTTTGGAACT
AAGTTTTG
Found at i:3508513 original size:67 final size:67
Alignment explanation
Indices: 3508334--3508515 Score: 246
Period size: 65 Copynumber: 2.7 Consensus size: 67
3508324 CTTGAGACAG
* * * * *
3508334 TTTCTCTTAAAACAAATTTCGTTTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATT
1 TTTCCCTTAAAACAAATTTTGTTTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTAAATT
3508397 TA
66 TA
*
3508399 TTTCTCC-TAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTAAAT
1 TTTC-CCTTAAAACAAATTTTGTTTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTAAAT
3508463 TTA
65 TTA
* *
3508466 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTTT-TCATGAAACA
1 TTTCCCTTAAAAC-AAATTTTGTTTCCCTTGAGACAGTTTCTCTTGAAACA
3508516 ACATATATCT
Statistics
Matches: 103, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
65 38 0.37
66 5 0.05
67 36 0.35
68 24 0.23
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (67 bp):
TTTCCCTTAAAACAAATTTTGTTTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTTAAATT
TA
Found at i:3509430 original size:110 final size:110
Alignment explanation
Indices: 3509232--3509467 Score: 313
Period size: 110 Copynumber: 2.2 Consensus size: 110
3509222 GCTTTCTAGT
* * *
3509232 TTCAGAGCCAATTTCAACTTAACAGTGAGGGATATTGGACTCAAGATAACACAAGCTCAAATTCA
1 TTCAGAGCCAATTTCAACTTAACAGTGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* *
3509297 TAACGAAGGGGGGACTGATTGTCAATAAACAACTTTTCAGTTTCA
66 TAACGAAGGGGGGACTGACTGTCAACAAACAACTTTTCAGTTTCA
* * * *
3509342 TTCAGAGTCAATTTCAGCTTCACAGTGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTAACAGTGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* *
3509407 TAGCGAAGGGGCGGA-TGACTGTCAACAAACAA-TTTCCCAG-TTC-
66 TAACGAAGGGG-GGACTGACTGTCAACAAACAACTTT-TCAGTTTCA
3509450 --CAGAGCCAATTTCAACTT
1 TTCAGAGCCAATTTCAACTT
3509468 CACGACGGAG
Statistics
Matches: 111, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
106 16 0.14
109 6 0.05
110 86 0.77
111 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTAACAGTGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
TAACGAAGGGGGGACTGACTGTCAACAAACAACTTTTCAGTTTCA
Found at i:3510944 original size:37 final size:37
Alignment explanation
Indices: 3510895--3510973 Score: 85
Period size: 37 Copynumber: 2.1 Consensus size: 37
3510885 TTTTGTCCCA
*
3510895 TATATATATTTTTAATTTTATT-TATT-TATTTATT-TA
1 TATATATATTTTT--TTATATTATATTATATTTATTATA
3510931 CTATAT-TACTTTTTTTATATTATATTATATTTATTATA
1 -TATATATA-TTTTTTTATATTATATTATATTTATTATA
3510969 TATAT
1 TATAT
3510974 CTTATATCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
35 6 0.16
36 6 0.16
37 23 0.62
38 2 0.05
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (37 bp):
TATATATATTTTTTTATATTATATTATATTTATTATA
Found at i:3510967 original size:19 final size:19
Alignment explanation
Indices: 3510913--3510994 Score: 66
Period size: 19 Copynumber: 4.4 Consensus size: 19
3510903 TTTTTAATTT
3510913 TATT-TATT-TATTTATT-
1 TATTATATTATATTTATTA
* *
3510929 TACTATATTACT-TTTTTTA
1 TATTATATTA-TATTTATTA
3510948 TATTATATTATATTTATTA
1 TATTATATTATATTTATTA
* *
3510967 TATATATCTTATA-TCATTA
1 TAT-TATATTATATTTATTA
3510986 TATATATAT
1 TAT-TATAT
3510995 ATGTATAGAT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.06
17 4 0.08
18 6 0.11
19 32 0.60
20 8 0.15
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATATTATATTTATTA
Found at i:3510978 original size:14 final size:14
Alignment explanation
Indices: 3510894--3510969 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 14
3510884 ATTTTGTCCC
3510894 ATATATATATTT-TT
1 ATAT-TATATTTATT
*
3510908 A-ATTTTATTTATT
1 ATATTATATTTATT
*
3510921 -TATT-TATTTACT
1 ATATTATATTTATT
*
3510933 ATATTACT-TTTTTT
1 ATATTA-TATTTATT
3510947 ATATTATATTATATT
1 ATATTATATT-TATT
3510962 -TATTATAT
1 ATATTATAT
3510970 ATATCTTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
12 13 0.26
13 12 0.24
14 21 0.42
15 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTATATTTATT
Found at i:3512319 original size:12 final size:11
Alignment explanation
Indices: 3512289--3512322 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3512279 CAAGACCCAA
*
3512289 TTTTATTTCAT
1 TTTTATTTAAT
3512300 TTTTATTTAAT
1 TTTTATTTAAT
3512311 TTATTATTTAAT
1 TT-TTATTTAAT
3512323 ATTAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTATTTAAT
Found at i:3512375 original size:22 final size:22
Alignment explanation
Indices: 3512349--3512396 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3512339 TTCTATATAT
*
3512349 TATAATATAT-TAGATTATTATC
1 TATAATAT-TCTAAATTATTATC
3512371 TATAATATTCTAAATTATTATC
1 TATAATATTCTAAATTATTATC
3512393 TATA
1 TATA
3512397 TAAATTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (22 bp):
TATAATATTCTAAATTATTATC
Found at i:3512422 original size:18 final size:19
Alignment explanation
Indices: 3512389--3512428 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
3512379 TCTAAATTAT
3512389 TATCTATATAAATTATCTA
1 TATCTATATAAATTATCTA
3512408 TATCTATAT-AATTATCTA
1 TATCTATATAAATTATCTA
3512426 TAT
1 TAT
3512429 AATTAGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (19 bp):
TATCTATATAAATTATCTA
Found at i:3512425 original size:12 final size:12
Alignment explanation
Indices: 3512408--3512433 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3512398 AAATTATCTA
3512408 TATCTATATAAT
1 TATCTATATAAT
3512420 TATCTATATAAT
1 TATCTATATAAT
3512432 TA
1 TA
3512434 GATAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TATCTATATAAT
Found at i:3512728 original size:13 final size:13
Alignment explanation
Indices: 3512705--3512753 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
3512695 ATAATAATCA
3512705 ATTATTTAATATTT
1 ATTA-TTAATATTT
3512719 ATTATTAATATTT
1 ATTATTAATATTT
*
3512732 ATTATTAAATTATTG
1 ATTATT-AA-TATTT
3512747 ATTATTA
1 ATTATTA
3512754 TCAATTTTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 15 0.47
14 7 0.22
15 10 0.31
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
ATTATTAATATTT
Found at i:3512885 original size:17 final size:17
Alignment explanation
Indices: 3512863--3512899 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3512853 TTGCTGTGTA
3512863 CCTTAAAATAACCATTC
1 CCTTAAAATAACCATTC
3512880 CCTTAAAATAACCATTC
1 CCTTAAAATAACCATTC
3512897 CCT
1 CCT
3512900 CAAGACCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.30
Consensus pattern (17 bp):
CCTTAAAATAACCATTC
Found at i:3527444 original size:31 final size:31
Alignment explanation
Indices: 3527395--3527456 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
3527385 TTTCAATCAG
3527395 AAATTTAAAAAATCAACATTTTA-AGTTGCGT
1 AAATTTAAAAAATCAACATTTTAGA-TTGCGT
*
3527426 AAATGTTAAAAACT-AACATTTTAGATTGCGT
1 AAAT-TTAAAAAATCAACATTTTAGATTGCGT
3527457 TCACCGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (31 bp):
AAATTTAAAAAATCAACATTTTAGATTGCGT
Found at i:3528076 original size:31 final size:32
Alignment explanation
Indices: 3528026--3528088 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
3528016 TTTCAATCAG
3528026 AAATGTTAAAAAATCAACATTTTA-AGTTGCGT
1 AAATGTTAAAAAATCAACATTTTAGA-TTGCGT
*
3528058 AAATGTTAAAAACT-AACATTTTAGATTGCGT
1 AAATGTTAAAAAATCAACATTTTAGATTGCGT
3528089 TCAACCGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (32 bp):
AAATGTTAAAAAATCAACATTTTAGATTGCGT
Found at i:3528077 original size:632 final size:621
Alignment explanation
Indices: 3526879--3528134 Score: 2331
Period size: 632 Copynumber: 2.0 Consensus size: 621
3526869 TATAACCTCC
3526879 TTAGTTTTAAGGGACATATGAATAACAACCAATTAAATTCAGCATTCCACTTAGCCTAGGCTTTT
1 TTAGTTTTAAGGGACATATGAATAACAACCAATTAAATTCAGCATTCCACTTAGCCTAGGCTTTT
3526944 AGAAAAACTTTATCAATCTTGACACTATAAAATGTTGGAAAACTTTTGAGAATCTAAAGGAAAAT
66 AGAAAAACTTTATCAATCTTGACACTATAAAATGTTGGAAAACTTTTGAGAATCTAAAGGAAAAT
3527009 ACATAAGCAATCCAGAAAAGTAATTAATCGAGCTTTAAAAACAGCTTTGGGGGTAGAATCAATGT
131 ACATAAGCAATCCAGAAAAGTAATTAATCGAGCTTTAAAAACAGCTTTGGGGGTAGAATCAATGT
3527074 GATAATTTCGTTTAGATGGGTCTGATCGTTGATTTGAGTTAATAATTTTAAAAATACTTTTTGTA
196 GATAATTTCGTTTAGATGGGTCTGATCGTTGATTTGAGTTAATAATTTTAAAAATACTTTTTGTA
3527139 TTGATGTTTGCAACATGCGCATGTTAGTTCAGTGTGATAAGGCATTTTGTTTAGATTTAGAGTCT
261 TTGATGTTTGCAACATGCGCATGTTAGTTCAGTGTGATAAGGCATTTTGTTTAGATTTAGAGTCT
*
3527204 CTTGAAATTCGATGGGACTTTTTTGGACCTTCAATCTTCAATATTCCCTTTTGTTTATGTTTACG
326 CTTGAAATTCGATGGGACTTTTTTGGACATTCAATCTTCAATATTCCCTTTTGTTTATGTTTACG
3527269 CTTTTTCTTTTATTTTGAGAATGTAGCAGCAAAATTTAGGTTAAGGAAAGATACAATCAAAATGT
391 CTTTTTCTTTTATTTTGAGAATGTAGCAGCAAAATTTAGGTTAAGGAAAGATACAATCAAAATGT
3527334 TAAGAAAATTATAATATTTTCGGTTGACAATTGGAAATATTACATTTTCGATTTCAATCAGAAAT
456 TAAGAAAATTATAATATTTTCGGTTGACAATTGGAAATATTACATTTTCGATTTCAATCAGAAAT
3527399 TTAAAAAATCAACATTTTAAGTTGCGTAAATGTTAAAAACTAACATTTTAGATTGCGTTC-ACCG
521 TTAAAAAATCAACATTTTAAGTTGCGTAAATGTTAAAAACTAACATTTTAGATTGCGTTCAACCG
3527463 AAAATATTAAGATTTTTTAATA-TTCGATTGCGCAT
586 AAAATATTAAGATTTTTTAATATTTCGATTGCGCAT
3527498 TTAGTTTTAAGGGACATATGAATAAC-ACCAATTAAAATTCAGCATTCCACTTAGCCTAGGCTTT
1 TTAGTTTTAAGGGACATATGAATAACAACCAATT-AAATTCAGCATTCCACTTAGCCTAGGCTTT
3527562 TAGAAAAACTTTATCAATCATTGACACTATAAAATGTTGGAAAACTTTTGAGAATCTAAAGGAAA
65 TAGAAAAACTTTATCAATC-TTGACACTATAAAATGTTGGAAAACTTTTGAGAATCTAAAGGAAA
3527627 ATACATAAGCAATCCCAGAAAAGTAATTAAGTCGAGCTTTAAAAACAGCTTTGGGGGTAGAATCA
129 ATACATAAGCAAT-CCAGAAAAGTAATTAA-TCGAGCTTTAAAAACAGCTTTGGGGGTAGAATCA
3527692 ATGTGATAATTATCGTTTAGATGGGTCTGATCGATTGATTTGAGTTAATAATTTTAAAAATACTT
192 ATGTGATAATT-TCGTTTAGATGGGTCTGATCG-TTGATTTGAGTTAATAATTTTAAAAATACTT
3527757 TTTGTATTGATGTTTGCAACATGCGCAATGTTAGTTCAGTGTGATAAGGCATTTTTGTTTAGATT
255 TTTGTATTGATGTTTGCAACATGCGC-ATGTTAGTTCAGTGTGATAAGGCA-TTTTGTTTAGATT
3527822 TAGAGTCTCTTGAAATTCGATGGGAGACTTTTTTGGACATTCAATCTTCAATATTCCCTTTTGTT
318 TAGAGTCTCTTGAAATTCGAT-GG-GACTTTTTTGGACATTCAATCTTCAATATTCCCTTTTGTT
3527887 TATGTTTACGCTTTTTTCTTTTATTTTGAGAATGTAGCAGCAAAATTTAAGGTTAAGGAAAGATA
381 TATGTTTACGC-TTTTTCTTTTATTTTGAGAATGTAGCAGCAAAATTT-AGGTTAAGGAAAGATA
3527952 CAATCGAAAATGTTAAGAAAAATTATAATATTTTCGGTTGACAATT-GAAATATTACATTTTCGA
444 CAATC-AAAATGTTAAG-AAAATTATAATATTTTCGGTTGACAATTGGAAATATTACATTTTCGA
3528016 TTTCAATCAGAAATGTTAAAAAATCAACATTTTAAGTTGCGTAAATGTTAAAAACTAACATTTTA
507 TTTCAATCAGAAAT-TTAAAAAATCAACATTTTAAGTTGCGTAAATGTTAAAAACTAACATTTTA
3528081 GATTGCGTTCAACCGAAAATATTAAGATTTTTTAATATTTTCGATTGCGCAT
571 GATTGCGTTCAACCGAAAATATTAAGATTTTTTAATA-TTTCGATTGCGCAT
3528133 TT
1 TT
3528135 TATTAACCTT
Statistics
Matches: 618, Mismatches: 1, Indels: 20
0.97 0.00 0.03
Matches are distributed among these distances:
618 7 0.01
619 75 0.12
620 58 0.09
621 16 0.03
622 45 0.07
623 21 0.03
624 57 0.09
625 24 0.04
626 34 0.06
627 2 0.00
628 50 0.08
629 36 0.06
630 21 0.03
631 43 0.07
632 88 0.14
633 26 0.04
635 15 0.02
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (621 bp):
TTAGTTTTAAGGGACATATGAATAACAACCAATTAAATTCAGCATTCCACTTAGCCTAGGCTTTT
AGAAAAACTTTATCAATCTTGACACTATAAAATGTTGGAAAACTTTTGAGAATCTAAAGGAAAAT
ACATAAGCAATCCAGAAAAGTAATTAATCGAGCTTTAAAAACAGCTTTGGGGGTAGAATCAATGT
GATAATTTCGTTTAGATGGGTCTGATCGTTGATTTGAGTTAATAATTTTAAAAATACTTTTTGTA
TTGATGTTTGCAACATGCGCATGTTAGTTCAGTGTGATAAGGCATTTTGTTTAGATTTAGAGTCT
CTTGAAATTCGATGGGACTTTTTTGGACATTCAATCTTCAATATTCCCTTTTGTTTATGTTTACG
CTTTTTCTTTTATTTTGAGAATGTAGCAGCAAAATTTAGGTTAAGGAAAGATACAATCAAAATGT
TAAGAAAATTATAATATTTTCGGTTGACAATTGGAAATATTACATTTTCGATTTCAATCAGAAAT
TTAAAAAATCAACATTTTAAGTTGCGTAAATGTTAAAAACTAACATTTTAGATTGCGTTCAACCG
AAAATATTAAGATTTTTTAATATTTCGATTGCGCAT
Found at i:3532380 original size:17 final size:17
Alignment explanation
Indices: 3532358--3532390 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3532348 TCAACCAAAA
3532358 TATATTATATT-TATTTC
1 TATATT-TATTATATTTC
3532375 TATATTTATTATATTT
1 TATATTTATTATATTT
3532391 ATTTTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TATATTTATTATATTTC
Found at i:3539956 original size:34 final size:34
Alignment explanation
Indices: 3539903--3540004 Score: 113
Period size: 34 Copynumber: 3.1 Consensus size: 34
3539893 GTTTTTCGTG
*
3539903 AAAAGAATCTTT-AAGTCGTTTCTTTTGAAACAAA
1 AAAAAAATCTTTGAA-TCGTTTCTTTTGAAACAAA
3539937 AAAAAAATCTTTGAATCGTTTCTTTTGAAAC---
1 AAAAAAATCTTTGAATCGTTTCTTTTGAAACAAA
* ** *
3539968 ACAATCATCTTTGACTCTGTTTCTTTTGAAACAAA
1 AAAAAAATCTTTGAATC-GTTTCTTTTGAAACAAA
3540003 AA
1 AA
3540005 TCTTTGAGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
31 13 0.23
32 14 0.25
34 27 0.47
35 3 0.05
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (34 bp):
AAAAAAATCTTTGAATCGTTTCTTTTGAAACAAA
Found at i:3540010 original size:30 final size:30
Alignment explanation
Indices: 3539908--3540060 Score: 132
Period size: 30 Copynumber: 4.9 Consensus size: 30
3539898 TCGTGAAAAG
*
3539908 AATCTTTAAGTC-GTTTCTTTTGAAACAAAAAAAA
1 AATCTTTGAGTCTGTTTCTTTTGAAAC-----AAA
*
3539942 AATCTTTGAATC-GTTTCTTTTGAAACACAA
1 AATCTTTGAGTCTGTTTCTTTTGAAACA-AA
* *
3539972 TCATCTTTGACTCTGTTTCTTTTGAAACAAA
1 -AATCTTTGAGTCTGTTTCTTTTGAAACAAA
* *
3540003 AATCTTTGAGTTTGATTT-TCTTGAAACAAA
1 AATCTTTGAGTCTG-TTTCTTTTGAAACAAA
* * *
3540033 ATTCTTCGAGTTTGTTTCTTTTGAAACA
1 AATCTTTGAGTCTGTTTCTTTTGAAACA
3540061 TCACCTTTGA
Statistics
Matches: 103, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
29 4 0.04
30 45 0.44
31 15 0.15
32 15 0.15
34 24 0.23
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.42
Consensus pattern (30 bp):
AATCTTTGAGTCTGTTTCTTTTGAAACAAA
Found at i:3540333 original size:133 final size:133
Alignment explanation
Indices: 3540094--3540370 Score: 317
Period size: 133 Copynumber: 2.1 Consensus size: 133
3540084 GAAACCATTA
* ** *
3540094 TCCCTAAAGATGGCCTGCCATCCTCATCATGTAGGAACCATGTCATCCACTTACCAGACATCCTT
1 TCCCTAAAGATGGCATGCCATCCTCATCATGTAGGAACCATGTCATCCACCGACCAGACATCCTC
* * ** *
3540159 ATCACGTAGGAGCCATGTCACTTCTGATAACCAACTTTCCTCATCATGTTGGAACCGTGTTATCA
66 ATCACGTAGGAGCCATGTCACTCCTGATAACCAACTATCCTCATCACATAGGAACCGTGTTATCA
3540224 CCC
131 CCC
* * ** *
3540227 TCCCTAAAGATGGCATGTCGTCCTCATCATGTAGGAACTGTGTCATCC-CCGACCAGACCTCCTC
1 TCCCTAAAGATGGCATGCCATCCTCATCATGTAGGAACCATGTCATCCACCGACCAGACATCCTC
* * * *
3540291 ATCACGTAGGAGTCGTGTCAC-CCATAGATAACC-AGTCATCCTCATCGCATAGGAACCGTGTTA
66 ATCACGTAGGAGCCATGTCACTCC-T-GATAACCAACT-ATCCTCATCACATAGGAACCGTGTTA
*
3540354 TCGCCC
128 TCACCC
* *
3540360 TTCTTAAAGAT
1 TCCCTAAAGAT
3540371 TGCCAGAACT
Statistics
Matches: 120, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
131 1 0.01
132 34 0.28
133 85 0.71
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (133 bp):
TCCCTAAAGATGGCATGCCATCCTCATCATGTAGGAACCATGTCATCCACCGACCAGACATCCTC
ATCACGTAGGAGCCATGTCACTCCTGATAACCAACTATCCTCATCACATAGGAACCGTGTTATCA
CCC
Found at i:3540437 original size:91 final size:91
Alignment explanation
Indices: 3540329--3540533 Score: 284
Period size: 91 Copynumber: 2.3 Consensus size: 91
3540319 TAACCAGTCA
* * * *
3540329 TCCTCATCGCATAGGAACCGTGTTATCGCCCTTCTTAAAGATTGCCAGAACTCTTTATCACGTAT
1 TCCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
** * *
3540394 GAGTTGTGTTATCCACCGACCAGACC
66 GAGCCGTGTCATCCACCGACCAAACC
* *
3540420 TCCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCTAGAACTCTTCATCACTTAT
1 TCCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
* *
3540485 GAGCCGTGTCATCTACCGACCAAATC
66 GAGCCGTGTCATCCACCGACCAAACC
* *
3540511 TCCTCATCACGTAGGAGCCGTGT
1 TCCTCATCGCGTAGGAACCGTGT
3540534 CACCCTTAGA
Statistics
Matches: 100, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 100 1.00
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (91 bp):
TCCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
GAGCCGTGTCATCCACCGACCAAACC
Found at i:3545633 original size:24 final size:20
Alignment explanation
Indices: 3545580--3545637 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
3545570 TTCCCCTTGA
*
3545580 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
3545600 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
3545623 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
3545638 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:3545734 original size:64 final size:63
Alignment explanation
Indices: 3545625--3545761 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 63
3545615 TCTTTAACAT
* *
3545625 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCAT-TTTAAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATG-TTTCATCTTTAAA-GA
* * * * ** *
3545689 GTGCATCGATGCACT-CCTTATGCATCGATGCACTACTTGCATTCGATGTTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCGATACACCAATCACATTCGATGTTTCATCTTTAAAGA
3545752 GTGCATCGAT
1 GTGCATCGAT
3545762 ACACATTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
63 18 0.29
64 44 0.71
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATGTTTCATCTTTAAAGA
Found at i:3550278 original size:24 final size:20
Alignment explanation
Indices: 3550225--3550282 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
3550215 TTCCCCTTGA
*
3550225 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
3550245 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
3550268 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
3550283 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:3550382 original size:64 final size:63
Alignment explanation
Indices: 3550270--3550406 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 63
3550260 TCTTTAACAT
* *
3550270 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACCTTCGATGTTTTCAT-TTTAAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATG-TTTCATCTTTAAA-GA
* * * ** * *
3550334 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTTGATGTTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCGATACACCAATCACATTCGATGTTTCATCTTTAAAGA
3550397 GTGCATCGAT
1 GTGCATCGAT
3550407 ACACATTGAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
63 18 0.29
64 44 0.71
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACCAATCACATTCGATGTTTCATCTTTAAAGA
Found at i:3550423 original size:21 final size:21
Alignment explanation
Indices: 3550397--3550436 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3550387 TCTTTAAAGA
3550397 GTGCATCGATACACATTGAAT
1 GTGCATCGATACACATTGAAT
*
3550418 GTGCATCGATACACCTTGA
1 GTGCATCGATACACATTGA
3550437 CCATAATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (21 bp):
GTGCATCGATACACATTGAAT
Found at i:3552389 original size:2 final size:2
Alignment explanation
Indices: 3552382--3552430 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3552372 TCCGTATACA
3552382 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
*
3552424 AT GT AT A
1 AT AT AT A
3552431 CATAAAGCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3552549 original size:2 final size:2
Alignment explanation
Indices: 3552542--3552589 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
3552532 GTTATAACCA
* *
3552542 AT AT AT AT GT AT AC A- 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
*
3552583 AT GT AT A
1 AT AT AT A
3552590 CAATAAAGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3553155 original size:17 final size:17
Alignment explanation
Indices: 3553133--3553171 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
3553123 TTGATATTTG
3553133 TCAAAGATTTACAGCTA
1 TCAAAGATTTACAGCTA
3553150 TCAAAGATTTACAGCTA
1 TCAAAGATTTACAGCTA
3553167 TCAAA
1 TCAAA
3553172 TATTAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (17 bp):
TCAAAGATTTACAGCTA
Found at i:3554249 original size:66 final size:67
Alignment explanation
Indices: 3554165--3554320 Score: 178
Period size: 66 Copynumber: 2.4 Consensus size: 67
3554155 TCATTATCCT
* * * * * *
3554165 TTGAGT-TGTTT-CTCTTGAAACAATTTTTTTTCTC-CATTGAGATAGTTTTTTTTG-AGAAAAA
1 TTGAGTCTGTTTCCT-TTGAAACAAATTCTTGTCTCTC-TAGAGATAGTTTTTCTTGAAAAAAAA
3554226 ATCA
64 ATCA
3554230 TTGAGTCTGTTTCCTTTGAAACAAATTCTTGTCTCTCTAGAGATAGTTTTTCTTGAAAAAAAAAT
1 TTGAGTCTGTTTCCTTTGAAACAAATTCTTGTCTCTCTAGAGATAGTTTTTCTTGAAAAAAAAAT
*
3554295 CT
66 CA
* *
3554297 TTGAGTC-GTTTCTTTTTAAACAAA
1 TTGAGTCTGTTTCCTTTGAAACAAA
3554321 AAAAATCTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
65 6 0.08
66 53 0.68
67 19 0.24
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (67 bp):
TTGAGTCTGTTTCCTTTGAAACAAATTCTTGTCTCTCTAGAGATAGTTTTTCTTGAAAAAAAAAT
CA
Found at i:3554327 original size:32 final size:32
Alignment explanation
Indices: 3554286--3554415 Score: 133
Period size: 32 Copynumber: 4.1 Consensus size: 32
3554276 TTTTTCTTGA
*
3554286 AAAAAAAATCTTTGAGTCGTTTCTTTTTAAAC
1 AAAAAAAATCTTTGAGTCGTTTCTTTTGAAAC
* *
3554318 AAAAAAAATCTTTGAGTCATTTTTTTTGAAAC
1 AAAAAAAATCTTTGAGTCGTTTCTTTTGAAAC
** **
3554350 -ACCATCATCTTTGAGTCTGTTTCTTTTGAAAC
1 AAAAAAAATCTTTGAGTC-GTTTCTTTTGAAAC
* *
3554382 ---AAAAATCTTTGAGTTTGTTTCTCTTGAAAC
1 AAAAAAAATCTTTGAG-TCGTTTCTTTTGAAAC
3554412 AAAA
1 AAAA
3554416 GACTTTTAGT
Statistics
Matches: 79, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
30 23 0.29
31 14 0.18
32 41 0.52
33 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (32 bp):
AAAAAAAATCTTTGAGTCGTTTCTTTTGAAAC
Found at i:3554392 original size:30 final size:30
Alignment explanation
Indices: 3554282--3554455 Score: 160
Period size: 30 Copynumber: 5.7 Consensus size: 30
3554272 ATAGTTTTTC
*
3554282 TTGAAAAAAAAATCTTTGAGTC-GTTTCTT
1 TTGAAACAAAAATCTTTGAGTCTGTTTCTT
*
3554311 TTTAAACAAAAAAAATCTTTGAGTCAT-TTT-TT
1 TTGAAAC---AAAAATCTTTGAGTC-TGTTTCTT
**
3554343 TTGAAACACCATCATCTTTGAGTCTGTTTCTT
1 TTGAAACA--AAAATCTTTGAGTCTGTTTCTT
* *
3554375 TTGAAACAAAAATCTTTGAGTTTGTTTCTC
1 TTGAAACAAAAATCTTTGAGTCTGTTTCTT
* *
3554405 TTGAAACAAAAGA-CTTTTAGTTTGTTTCTT
1 TTGAAACAAAA-ATCTTTGAGTCTGTTTCTT
**
3554435 TTGAAAC-ATCATCTTTGAGTC
1 TTGAAACAAAAATCTTTGAGTC
3554456 AATTTCCCTT
Statistics
Matches: 119, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.01
29 14 0.12
30 52 0.44
31 16 0.13
32 33 0.28
33 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (30 bp):
TTGAAACAAAAATCTTTGAGTCTGTTTCTT
Found at i:3554468 original size:59 final size:60
Alignment explanation
Indices: 3554281--3554470 Score: 154
Period size: 59 Copynumber: 3.1 Consensus size: 60
3554271 GATAGTTTTT
* * **
3554281 CTTGAAA-AAAAAATCTTTGAGTC-GTTTCTTTTTAAACAAAAAAAATCTTTGAGTC-ATTTTT
1 CTTGAAACAAAAGA-CTTTGAGTCTGTTTCTTTTGAAAC---AAAAATCTTTGAGTCAATTTCC
* * ** *** *
3554342 TTTGAAACACCATCATCTTTGAGTCTGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
1 CTTGAAACA-AAAGA-CTTTGAGTCTGTTTCTTTTGAAACAAAAATCTTTGAGTCAATTTCC
* * **
3554404 CTTGAAACAAAAGACTTTTAGTTTGTTTCTTTTGAAAC-ATCATCTTTGAGTCAATTTCC
1 CTTGAAACAAAAGACTTTGAGTCTGTTTCTTTTGAAACAAAAATCTTTGAGTCAATTTCC
3554463 CTTGAAAC
1 CTTGAAAC
3554471 CATTATCCCT
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
59 23 0.22
60 22 0.21
61 22 0.21
62 13 0.12
63 12 0.11
64 13 0.12
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (60 bp):
CTTGAAACAAAAGACTTTGAGTCTGTTTCTTTTGAAACAAAAATCTTTGAGTCAATTTCC
Found at i:3554862 original size:134 final size:133
Alignment explanation
Indices: 3554496--3554894 Score: 462
Period size: 134 Copynumber: 3.0 Consensus size: 133
3554486 TGGCATGCCA
* * * * * * *
3554496 TCCTCATCACGTAGGAACCGTGTTATCACCCTCCCTAAAGATGG-TATACCATCATCATCATGTA
1 TCCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCTAAAAC-TCTTCATCACGTA
* *
3554560 -GAAACCGTGTCATCC-CTCGACCAGACCTCCTCATCACGCAGGAGCCGTGTCACCCCTAGATAA
65 TG-AGCCGTGTCATCCAC-CGACCAGACCTCCTCATCACGTAGGAG-CGTGTCACCCCTAGATAA
*
3554623 CCAGTCG
127 CCAGGCG
* * * *
3554630 TCCTCATCGCATAGGAACCGTGTTATTGCCCTTCCTAAAGATGGCCAGAACTCTTCATCACGTAT
1 TCCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCTAAAACTCTTCATCACGTAT
* * * *
3554695 GAGCCATGTCATCTACTGACCAAACCTCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAACCA
66 GAGCCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAG-CGTGTCACCCCTAGATAACCA
3554760 GGCG
130 GGCG
3554764 TCCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCTAAAACTCTTCATCACGTAT
1 TCCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCTAAAACTCTTCATCACGTAT
** * * * * * * * * *
3554829 GAGTTGTGTAATCCACCAACTAGATCTCATCATCATGTAGGAGCTGTGTCACTCTTAGACAACCA
66 GAGCCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGC-GTGTCACCCCTAGATAACCA
3554894 G
130 G
3554895 ACCTCTTCAT
Statistics
Matches: 224, Mismatches: 37, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
133 1 0.00
134 218 0.97
135 5 0.02
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (133 bp):
TCCTCATCGCGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCTAAAACTCTTCATCACGTAT
GAGCCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCGTGTCACCCCTAGATAACCAG
GCG
Found at i:3559989 original size:31 final size:32
Alignment explanation
Indices: 3559951--3560027 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 32
3559941 TAACTTCGAG
3559951 TGATCAATTTGTAACAA-ATCAATAACATTAA
1 TGATCAATTTGTAACAAGATCAATAACATTAA
* ** *
3559982 TGATCAATTTATAA-AAGATTGATAACATTAG
1 TGATCAATTTGTAACAAGATCAATAACATTAA
* *
3560013 TGACCGATTTGTAAC
1 TGATCAATTTGTAAC
3560028 TTTTGAAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 2 0.05
31 35 0.95
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.34
Consensus pattern (32 bp):
TGATCAATTTGTAACAAGATCAATAACATTAA
Found at i:3561356 original size:30 final size:30
Alignment explanation
Indices: 3561321--3561385 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
3561311 TTATACCTTT
3561321 GAAACAAATAATAATTAACTGACTAAAATA
1 GAAACAAATAATAATTAACTGACTAAAATA
3561351 GAAACAAATAATAATTAACTGACTAAAATA
1 GAAACAAATAATAATTAACTGACTAAAATA
3561381 GAAAC
1 GAAAC
3561386 TATGCAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.22
Consensus pattern (30 bp):
GAAACAAATAATAATTAACTGACTAAAATA
Found at i:3561440 original size:8 final size:8
Alignment explanation
Indices: 3561427--3561464 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
3561417 TTACCCTTTA
3561427 TTTTTAAT
1 TTTTTAAT
*
3561435 TTTTTATT
1 TTTTTAAT
*
3561443 TTTTTATT
1 TTTTTAAT
3561451 TTTTTAAT
1 TTTTTAAT
3561459 TTTTTA
1 TTTTTA
3561465 CACGAGTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTAAT
Found at i:3562732 original size:338 final size:344
Alignment explanation
Indices: 3562060--3562747 Score: 849
Period size: 338 Copynumber: 2.0 Consensus size: 344
3562050 ATAATGAAAA
* * * *
3562060 ACATAAATATCTTGTTAACAAAAGAGAGGGTAAACTACGCTTTTAGTCACACATTTATTCTTGTA
1 ACATAAATATCATGTTAACAAAAGAAAGAGTAAACTACGCTTTTAGTCACACATCTATTCTTGTA
* * * * *
3562125 ATTCTGTTTTAACCATCCAACTATTTTTGTTAAATTATATATAATGTTATATTTTAGTTTTATTT
66 ATTATGTTTTAACCATCCAACTATTTTTGTTAAATCATACATAATGTTATATTTTAATTTCATTT
* * ** * *
3562190 TGATCACCTACTGTTAAAAAATAAATAGAACCATTGATATGTCATTATAAGATAGTGTCACGTCA
131 CGATCACCTACTGTTAAAAAATAAACAGAACCATTGATATGTCAGGATAAGATAATGTCACATCA
* * *
3562255 TCATTGAAAAAATGTAAAAAAATGTCACACCAGCCGTTATATTTATTTTTTTAACCGTAGGTGAT
196 TCAGTGAAAAAATGTAAAAAAATATCACACCAACCGTTATATTTATTTTTTTAACCGTAGGTGAT
* * * *
3562320 CAAAACGAAAAGTTAGATATGATTTTAAAAAAAGAATAATTGAGTGTCCAAAATGAAATCCTAGG
261 CAAAACGAAAAGTTAAATATGATTTTAAAAAAAGAAAAATAGAGTGTCCAAAATGAAATCCCAGG
3562385 AAAAGATGAGTGACTAAAT
326 AAAAGATGAGTGACTAAAT
* * **
3562404 GCATAAATATCATGTTAA-AAAAGAAAGAGTAAATTA-TTTATTTAGTCACACATCTATTCTTGC
1 ACATAAATATCATGTTAACAAAAGAAAGAGTAAACTACGCT-TTTAGTCACACATCTATTCTTG-
* * * * *
3562467 T-GTTATGTTTTGATCATTCAAC-ATTTTT-TTAAATCATACATAATGTTATGTTTTAATTTCAT
64 TAATTATGTTTTAACCATCCAACTATTTTTGTTAAATCATACATAATGTTATATTTTAATTTCAT
* * *
3562529 TTCGGTTA-CTACTGTTAAAAAATAAACAGAACCATTTATATGTCAGGATAAGATAATGTCACAT
129 TTCGATCACCTACTGTTAAAAAATAAACAGAACCATTGATATGTCAGGATAAGATAATGTCACAT
* * ** *
3562593 CATCAGTGGAAAAA-GTAAAAAATTATCACACCAATTGTTATATTTA-TTTTTTAA-CGTTGGGT
194 CATCAGTGAAAAAATGTAAAAAAATATCACACCAACCGTTATATTTATTTTTTTAACCG-TAGGT
* * * *
3562655 GATCAAAATGGAACA-TTAAATATGATTTTGAAAAAAGAAAAATAGAGTGTTCAAAACT-AAATC
258 GATCAAAA-CGAAAAGTTAAATATGATTTTAAAAAAAGAAAAATAGAGTGTCCAAAA-TGAAATC
* *
3562718 CCAGGAATAGATGAGTTACTAAAT
321 CCAGGAAAAGATGAGTGACTAAAT
3562742 ACATAA
1 ACATAA
3562748 TTTATACTAA
Statistics
Matches: 293, Mismatches: 46, Indels: 16
0.83 0.13 0.05
Matches are distributed among these distances:
337 2 0.01
338 87 0.30
339 32 0.11
340 62 0.21
341 34 0.12
342 7 0.02
343 52 0.18
344 17 0.06
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (344 bp):
ACATAAATATCATGTTAACAAAAGAAAGAGTAAACTACGCTTTTAGTCACACATCTATTCTTGTA
ATTATGTTTTAACCATCCAACTATTTTTGTTAAATCATACATAATGTTATATTTTAATTTCATTT
CGATCACCTACTGTTAAAAAATAAACAGAACCATTGATATGTCAGGATAAGATAATGTCACATCA
TCAGTGAAAAAATGTAAAAAAATATCACACCAACCGTTATATTTATTTTTTTAACCGTAGGTGAT
CAAAACGAAAAGTTAAATATGATTTTAAAAAAAGAAAAATAGAGTGTCCAAAATGAAATCCCAGG
AAAAGATGAGTGACTAAAT
Found at i:3564631 original size:32 final size:29
Alignment explanation
Indices: 3564568--3564632 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 29
3564558 AATGTTAGGT
* *
3564568 CCTTATTTGATATTTTTGAAATGTTAAAC
1 CCTTATTTGATATTTTTAAAAAGTTAAAC
*
3564597 CCTTATTTGAGTATATTTTAAAAAAGTTAGAC
1 CCTTATTTGA-TAT-TTTT-AAAAAGTTAAAC
3564629 CCTT
1 CCTT
3564633 GATCATTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 10 0.33
30 3 0.10
31 4 0.13
32 13 0.43
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (29 bp):
CCTTATTTGATATTTTTAAAAAGTTAAAC
Found at i:3568985 original size:29 final size:29
Alignment explanation
Indices: 3568950--3569027 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
3568940 CTTTAATATT
3568950 TTATAAATATTAAAAATTTA-AAAATAATA
1 TTATAAATA-TAAAAATTTACAAAATAATA
* * *
3568979 TTATAAACATAAAAAATATAGCATAATAATA
1 TTATAAATAT-AAAAATTTA-CAAAATAATA
3569010 TTATAAATA-AAAAATTTA
1 TTATAAATATAAAAATTTA
3569028 GGTTTAAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
28 1 0.02
29 24 0.59
31 16 0.39
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (29 bp):
TTATAAATATAAAAATTTACAAAATAATA
Found at i:3583947 original size:40 final size:41
Alignment explanation
Indices: 3583876--3583954 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 41
3583866 GGGATTGATG
*
3583876 ATTGAGCTAATTGTATGTTCAATTTTGGGTTCAATCAATCA
1 ATTGAACTAATTGTATGTTCAATTTTGGGTTCAATCAATCA
3583917 ATTGAACTAATTGTAT-TTCAATTTTGGGTTCAATCAAT
1 ATTGAACTAATTGTATGTTCAATTTTGGGTTCAATCAAT
3583955 ATCATTGGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 22 0.59
41 15 0.41
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (41 bp):
ATTGAACTAATTGTATGTTCAATTTTGGGTTCAATCAATCA
Found at i:3591097 original size:17 final size:17
Alignment explanation
Indices: 3591075--3591108 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3591065 ATGGTTTAGG
3591075 TGATTTTAAGTTCAAAA
1 TGATTTTAAGTTCAAAA
* *
3591092 TGATTTTCAGTTTAAAA
1 TGATTTTAAGTTCAAAA
3591109 AGAGTACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
TGATTTTAAGTTCAAAA
Found at i:3596193 original size:54 final size:54
Alignment explanation
Indices: 3596131--3596252 Score: 235
Period size: 54 Copynumber: 2.3 Consensus size: 54
3596121 TTGTATGAGT
3596131 GTGTATCGATACCCTCAAACATCGAATGCAATTTGTGTATCGGTACACTGAGGA
1 GTGTATCGATACCCTCAAACATCGAATGCAATTTGTGTATCGGTACACTGAGGA
*
3596185 GTGTATCGATACCCTCAAACATCGAATGTAATTTGTGTATCGGTACACTGAGGA
1 GTGTATCGATACCCTCAAACATCGAATGCAATTTGTGTATCGGTACACTGAGGA
3596239 GTGTATCGATACCC
1 GTGTATCGATACCC
3596253 CCTGTTATAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (54 bp):
GTGTATCGATACCCTCAAACATCGAATGCAATTTGTGTATCGGTACACTGAGGA
Found at i:3596630 original size:21 final size:20
Alignment explanation
Indices: 3596590--3596636 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
3596580 GATTATGTGT
*
3596590 TATGAACTTTGATAAGTGAA
1 TATGAACTTCGATAAGTGAA
*
3596610 TATGAACTTCGAATCAGTGAA
1 TATGAACTTCG-ATAAGTGAA
*
3596631 TGTGAA
1 TATGAA
3596637 TATACTCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (20 bp):
TATGAACTTCGATAAGTGAA
Found at i:3596804 original size:22 final size:21
Alignment explanation
Indices: 3596773--3596832 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
3596763 GAGGGTCTAC
3596773 GTGGCACTTCGGTGCAACCTAT
1 GTGGCACTTCGGTGCAA-CTAT
*
3596795 GTGGTC-CTTCGG-GACAATTAT
1 GTGG-CACTTCGGTG-CAACTAT
3596816 GTGGCACTTCGGTGCAA
1 GTGGCACTTCGGTGCAA
3596833 ATTACGAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
20 1 0.03
21 17 0.52
22 14 0.42
23 1 0.03
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.28
Consensus pattern (21 bp):
GTGGCACTTCGGTGCAACTAT
Found at i:3597094 original size:39 final size:40
Alignment explanation
Indices: 3597017--3597096 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
3597007 CAAATAAGAT
3597017 TCATGATAATAAGTTAGCACTATTATTTTGCCTTACTAAG
1 TCATGATAATAAGTTAGCACTATTATTTTGCCTTACTAAG
3597057 TCATGATAATAAGTTAGCACTA-TATTTTGCCTTACTAAG
1 TCATGATAATAAGTTAGCACTATTATTTTGCCTTACTAAG
3597096 T
1 T
3597097 ATCGACTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 18 0.45
40 22 0.55
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (40 bp):
TCATGATAATAAGTTAGCACTATTATTTTGCCTTACTAAG
Found at i:3597406 original size:3 final size:3
Alignment explanation
Indices: 3597398--3597519 Score: 167
Period size: 3 Copynumber: 40.7 Consensus size: 3
3597388 TTTATCCATT
* * *
3597398 TTA TTA TTA TTA TTA TTA ATA TTA ATA TTA TTA TTA TCA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3597445 TTA TTA TTA TTA -TA TTA TTA TTA TTA GTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
3597490 ATA TTA TATA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
3597520 TAACAAATAA
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
2 4 0.04
3 96 0.91
4 5 0.05
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3598831 original size:18 final size:18
Alignment explanation
Indices: 3598795--3598834 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3598785 TGATATTTTT
**
3598795 ATATTATTATATTGTTAA
1 ATATTATTATATTCATAA
*
3598813 ATATTTTTATATTCATAA
1 ATATTATTATATTCATAA
3598831 ATAT
1 ATAT
3598835 AATAAATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (18 bp):
ATATTATTATATTCATAA
Found at i:3599564 original size:13 final size:15
Alignment explanation
Indices: 3599533--3599569 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3599523 ATATATGTTT
3599533 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
3599548 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
3599561 TA-TTTATTT
1 TATTTTATTT
3599570 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:3610126 original size:31 final size:32
Alignment explanation
Indices: 3610081--3610156 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
3610071 TATTATGCTT
* *
3610081 GAAAAAAAAAAAAAAAAAAAAAAAAAGAGAAA
1 GAAAAAGAAAAAAAAAAAAAAAAAAAGAAAAA
*** *
3610113 G-AAAAGAAAAAAAAAGGGAAAAGAAGAAAAA
1 GAAAAAGAAAAAAAAAAAAAAAAAAAGAAAAA
3610144 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
3610157 GGGGGTCAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 25 0.68
32 12 0.32
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (32 bp):
GAAAAAGAAAAAAAAAAAAAAAAAAAGAAAAA
Found at i:3610143 original size:1 final size:1
Alignment explanation
Indices: 3610082--3610127 Score: 56
Period size: 1 Copynumber: 46.0 Consensus size: 1
3610072 ATTATGCTTG
* * * *
3610082 AAAAAAAAAAAAAAAAAAAAAAAAAGAGAAAGAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3610128 GGGAAAAGAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:3610147 original size:6 final size:6
Alignment explanation
Indices: 3610081--3610155 Score: 63
Period size: 5 Copynumber: 13.0 Consensus size: 6
3610071 TATTATGCTT
*
3610081 GAAAAA -AAAAA -AAAAA -AAAAA -AAAAA GAGAAA G-AAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
*
3610124 -AAAAGG GAAAAGAA GAAAAA GAAAAA GAAAAA
1 GAAAA-A G-AAA-AA GAAAAA GAAAAA GAAAAA
3610156 AGGGGGTCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
5 28 0.47
6 23 0.39
7 3 0.05
8 4 0.07
9 1 0.02
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:3611180 original size:52 final size:52
Alignment explanation
Indices: 3611097--3611717 Score: 1079
Period size: 52 Copynumber: 12.0 Consensus size: 52
3611087 ATATGTGCTC
3611097 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* *
3611149 CATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTAGA-AGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
3611200 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
3611252 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
3611303 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
3611355 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
3611406 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* * *
3611458 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGATTAGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
3611510 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
3611562 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
3611613 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* **
3611665 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTAACAGAA
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
3611717 C
1 C
3611718 CAATCAGTGA
Statistics
Matches: 542, Mismatches: 23, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
51 196 0.36
52 346 0.64
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
Found at i:3611276 original size:103 final size:103
Alignment explanation
Indices: 3611097--3611708 Score: 1161
Period size: 103 Copynumber: 5.9 Consensus size: 103
3611087 ATATGTGCTC
*
3611097 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
*
3611162 GGAAGTGTTCTTTAAGTTATCTGATCTGGTTAGAAGAA
66 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAA
3611200 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
3611265 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAA
66 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAA
3611303 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
3611368 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAA
66 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAA
3611406 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
* *
3611471 GGAAGTGTTCTTTGAGTTATCTAATCTGATTAGACAGAA
66 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAA
3611510 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
3611575 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAA
66 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAA
*
3611613 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
*
3611678 GGAAGTGTTCTTTGAGTTATTTGATCTGGTT
66 GGAAGTGTTCTTTGAGTTATCTGATCTGGTT
3611709 TAACAGAACC
Statistics
Matches: 500, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
103 399 0.80
104 101 0.20
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (103 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
GGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAA
Found at i:3611379 original size:155 final size:156
Alignment explanation
Indices: 3611097--3611705 Score: 1082
Period size: 155 Copynumber: 3.9 Consensus size: 156
3611087 ATATGTGCTC
*
3611097 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCT
* *
3611162 GGAAGTGTTCTTTAAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTGGAAGTGTTCTTT
66 GGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTT
3611226 GAGTTATCTGATCTGATTGGACAGAA
131 GAGTTATCTGATCTGATTGGACAGAA
3611252 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCT
*
3611316 GGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTT
66 GGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTT
* *
3611381 GAGTTATCTGATCTGGTTAGA-AGAA
131 GAGTTATCTGATCTGATTGGACAGAA
* *
3611406 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCT
*
3611471 GGAAGTGTTCTTTGAGTTATCTAATCTGATTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTT
66 GGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTT
3611536 GAGTTATCTGATCTGATTGGACAGAA
131 GAGTTATCTGATCTGATTGGACAGAA
3611562 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCT
1 CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCT
* *
3611626 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTT
66 GGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTT
*
3611691 GAGTTATTTGATCTG
131 GAGTTATCTGATCTG
3611706 GTTTAACAGA
Statistics
Matches: 433, Mismatches: 18, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
154 97 0.22
155 287 0.66
156 49 0.11
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (156 bp):
CATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCATCTTCT
GGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAACATAGCATCTTCTGGAAGTGTTCTTT
GAGTTATCTGATCTGATTGGACAGAA
Found at i:3611815 original size:52 final size:52
Alignment explanation
Indices: 3611753--3611890 Score: 233
Period size: 52 Copynumber: 2.7 Consensus size: 52
3611743 TTGCCAATAT
*
3611753 CATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGATTGGA-CATAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG-TTGGATCATAACATAG
*
3611805 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTGATCATAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTGGATCATAACATAG
*
3611857 CATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
3611891 CGAAGAAGTG
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
51 4 0.05
52 78 0.95
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (52 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTGGATCATAACATAG
Found at i:3612656 original size:118 final size:118
Alignment explanation
Indices: 3612448--3613140 Score: 1127
Period size: 118 Copynumber: 5.9 Consensus size: 118
3612438 CAAAGATTCA
3612448 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
3612513 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
3612566 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
3612631 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
3612684 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
3612749 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * *
3612802 AATTCATCATTTAATGGATCAACATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
* * * *
3612867 GAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTA
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * * *
3612920 AATTCATCATTTGGTGGATCATCTTTTCCAGAG-AA-AGTTCATAATGAAAAGAA--C-TCATCT
1 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
* * *
3612980 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTA
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* ** *
3613033 AATTCATCATTTGATGGATCAACATGGCCAAAG-AA-AGTTCATGAATGAGAAGAA--C-TCATC
1 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCAT-AATGAGAAGAACTCGTCATC
*
3613093 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
3613141 GTTTGATATC
Statistics
Matches: 550, Mismatches: 24, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
113 92 0.17
114 63 0.11
116 17 0.03
117 2 0.00
118 376 0.68
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (118 bp):
AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:3613444 original size:3 final size:3
Alignment explanation
Indices: 3613436--3613560 Score: 178
Period size: 3 Copynumber: 40.7 Consensus size: 3
3613426 TTTATCCATT
* * *
3613436 TTA TTA TTA TTA TTA TATA TTA ATA TTA TTA TTA TCA TTA TTA ATA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3613482 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
*
3613528 TTA ATA TTA TATA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
3613561 TAACAAATAA
Statistics
Matches: 109, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
3 101 0.93
4 8 0.07
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3614889 original size:18 final size:18
Alignment explanation
Indices: 3614853--3614892 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3614843 TGATATTTTT
**
3614853 ATATTATTATATTGTTAA
1 ATATTATTATATTCATAA
*
3614871 ATATTTTTATATTCATAA
1 ATATTATTATATTCATAA
3614889 ATAT
1 ATAT
3614893 AATAAATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (18 bp):
ATATTATTATATTCATAA
Found at i:3618783 original size:18 final size:19
Alignment explanation
Indices: 3618760--3618795 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3618750 AATATAAAAA
*
3618760 TGGTATCGGTACC-TAAGG
1 TGGTATCGATACCATAAGG
3618778 TGGTATCGATACCATAAG
1 TGGTATCGATACCATAAG
3618796 AGGGTAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (19 bp):
TGGTATCGATACCATAAGG
Found at i:3620190 original size:30 final size:30
Alignment explanation
Indices: 3620154--3620225 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
3620144 CCCGAAGGAC
*
3620154 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
3620184 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
3620214 CTGTCCATAGGT
1 CTATCCAGAGGT
3620226 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:3620250 original size:31 final size:31
Alignment explanation
Indices: 3620212--3620335 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 31
3620202 GATCCTCGGC
*
3620212 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTTCCGAAGAACATAGGTA
* **
3620243 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTTCCGAAGAACATAGGTA
* * *
3620274 TACTGTCCATATGTGT-CGAA-AGACATATGTA
1 AACTGTCCATAGGT-TCCGAAGA-ACATAGGTA
* ** *
3620305 ATTCTGTCCATATATTCCGTAG-ACATAGGTA
1 A-ACTGTCCATAGGTTCCGAAGAACATAGGTA
3620336 TACCCTCGAC
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
30 1 0.01
31 59 0.79
32 15 0.20
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
AACTGTCCATAGGTTCCGAAGAACATAGGTA
Found at i:3621634 original size:64 final size:64
Alignment explanation
Indices: 3621482--3621638 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
3621472 CAATAAGGGT
* * * **
3621482 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATACATTCGATGTTGTATTATTATTAGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATACATTCAATGTTCTATTATTAAAAGG
* * * *
3621546 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCAATGTTTCTATT-TTAAAA
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATACATTCAATG-TTCTATTATTAAAA
3621608 -G
63 GG
3621609 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
3621639 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
63 3 0.04
64 62 0.82
65 11 0.14
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATACATTCAATGTTCTATTATTAAAAGG
Found at i:3622235 original size:2 final size:2
Alignment explanation
Indices: 3622230--3622259 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3622220 ATCTTTATCC
3622230 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
3622260 CATTATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3622487 original size:42 final size:41
Alignment explanation
Indices: 3622440--3622592 Score: 182
Period size: 42 Copynumber: 3.7 Consensus size: 41
3622430 GGGTTTTACA
* **
3622440 ATGTGGTCATTCGGGATATATATGTAATCCTTTGGAACATAT
1 ATGTGGTCATTCGGGACATATATGTGGTCCTTTGG-ACATAT
* * * *
3622482 ATGTGGTTATTCGAGACACATATTTGGTCCTTTGGA-ATAT
1 ATGTGGTCATTCGGGACATATATGTGGTCCTTTGGACATAT
* * * *
3622522 ATTTGGTCTTTCGGGACATATATGTGGTCCTTCGGGACATCT
1 ATGTGGTCATTCGGGACATATATGTGGTCCTT-TGGACATAT
3622564 ATGTGGTCATTCGGGACATATATGTGGTC
1 ATGTGGTCATTCGGGACATATATGTGGTC
3622593 ATTCGGAACA
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 30 0.33
41 4 0.04
42 58 0.63
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (41 bp):
ATGTGGTCATTCGGGACATATATGTGGTCCTTTGGACATAT
Found at i:3622504 original size:21 final size:21
Alignment explanation
Indices: 3622440--3622598 Score: 160
Period size: 21 Copynumber: 7.7 Consensus size: 21
3622430 GGGTTTTACA
*
3622440 ATGTGGTCATTCGGGATATAT
1 ATGTGGTCATTCGGGACATAT
** * * *
3622461 ATGTAATCCTTTGGAACATAT
1 ATGTGGTCATTCGGGACATAT
* * *
3622482 ATGTGGTTATTCGAGACACAT
1 ATGTGGTCATTCGGGACATAT
* * *
3622503 ATTTGGTCCTT-TGGA-ATAT
1 ATGTGGTCATTCGGGACATAT
* *
3622522 ATTTGGTCTTTCGGGACATAT
1 ATGTGGTCATTCGGGACATAT
* *
3622543 ATGTGGTCCTTCGGGACATCT
1 ATGTGGTCATTCGGGACATAT
3622564 ATGTGGTCATTCGGGACATAT
1 ATGTGGTCATTCGGGACATAT
3622585 ATGTGGTCATTCGG
1 ATGTGGTCATTCGG
3622599 AACAAATTCT
Statistics
Matches: 109, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
19 13 0.12
20 5 0.05
21 91 0.83
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (21 bp):
ATGTGGTCATTCGGGACATAT
Found at i:3622571 original size:61 final size:63
Alignment explanation
Indices: 3622440--3622598 Score: 162
Period size: 61 Copynumber: 2.6 Consensus size: 63
3622430 GGGTTTTACA
* ** * * * *
3622440 ATGTGGTCATTCGGGATATATATGTAATCCTTTGGAACATATATGTGGTTATTCGAGACACAT
1 ATGTGGTCATTCGGGACATATATGTGGTCATTCGGGACATATATGTGGTCATTCGAGACACAT
* * * * * * *
3622503 ATTTGGTCCTT-TGGA-ATATATTTGGTCTTTCGGGACATATATGTGGTCCTTCGGGACATC-T
1 ATGTGGTCATTCGGGACATATATGTGGTCATTCGGGACATATATGTGGTCATTCGAGACA-CAT
3622564 ATGTGGTCATTCGGGACATATATGTGGTCATTCGG
1 ATGTGGTCATTCGGGACATATATGTGGTCATTCGG
3622599 AACAAATTCT
Statistics
Matches: 76, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
61 44 0.58
62 7 0.09
63 25 0.33
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.38
Consensus pattern (63 bp):
ATGTGGTCATTCGGGACATATATGTGGTCATTCGGGACATATATGTGGTCATTCGAGACACAT
Found at i:3628655 original size:30 final size:30
Alignment explanation
Indices: 3628619--3628676 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3628609 AAGGATGCAC
*
3628619 GCACCGAATATACATAATTTTAATGGGTTG
1 GCACCGAATATACATAATTTCAATGGGTTG
* *
3628649 GCACCGAATGTGCATAATTTCAATGGGT
1 GCACCGAATATACATAATTTCAATGGGT
3628677 CGTCAATTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (30 bp):
GCACCGAATATACATAATTTCAATGGGTTG
Found at i:3633144 original size:30 final size:30
Alignment explanation
Indices: 3633098--3633160 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
3633088 AAGGATGCAC
3633098 GCACCGAATATGCATAATTTCAATGGGTTG
1 GCACCGAATATGCATAATTTCAATGGGTTG
* *
3633128 GCACTGAATGTGCATAATTTCAATGGGTTG
1 GCACCGAATATGCATAATTTCAATGGGTTG
3633158 GCA
1 GCA
3633161 ATTGTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (30 bp):
GCACCGAATATGCATAATTTCAATGGGTTG
Found at i:3633868 original size:26 final size:25
Alignment explanation
Indices: 3633819--3633868 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
3633809 TTACTTATTT
*
3633819 TGATCAAAAAATACTTTTAAGTATG
1 TGATCAAAAAATAATTTTAAGTATG
* *
3633844 TGATCAAAATGATAATTTTAGGTAT
1 TGATCAAAA-AATAATTTTAAGTAT
3633869 TTATTTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (25 bp):
TGATCAAAAAATAATTTTAAGTATG
Found at i:3636121 original size:21 final size:21
Alignment explanation
Indices: 3636097--3636212 Score: 123
Period size: 21 Copynumber: 5.6 Consensus size: 21
3636087 TTTGGAATAA
*
3636097 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
3636118 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
3636138 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
3636159 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* *
3636180 ATCGCAACGCGAACTTCGAAT
1 ATCGCAATGCGAACTTCGACT
*
3636201 ATCGCATTGCGA
1 ATCGCAATGCGA
3636213 TTTACATATT
Statistics
Matches: 80, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
20 17 0.21
21 63 0.79
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:3636255 original size:21 final size:21
Alignment explanation
Indices: 3636221--3636378 Score: 171
Period size: 21 Copynumber: 7.6 Consensus size: 21
3636211 GATTTACATA
*
3636221 TTCGCATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
3636242 TTCACATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
3636263 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
3636284 TTCGCGTTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* * *
3636304 TATCACATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
3636325 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
3636346 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
3636367 TTCG-AGTTGCGA
1 TTCGCA-TTGCGA
3636379 ATCTGGAAAC
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
20 16 0.14
21 98 0.85
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:3638100 original size:19 final size:19
Alignment explanation
Indices: 3638076--3638117 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3638066 TAGGTCTCCA
3638076 GGAGCACACGGCGACCTAT
1 GGAGCACACGGCGACCTAT
***
3638095 GGAGCATTTGGCGACCTAT
1 GGAGCACACGGCGACCTAT
3638114 GGAG
1 GGAG
3638118 TTGCAATAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.17
Consensus pattern (19 bp):
GGAGCACACGGCGACCTAT
Found at i:3639296 original size:104 final size:104
Alignment explanation
Indices: 3639115--3639346 Score: 374
Period size: 104 Copynumber: 2.2 Consensus size: 104
3639105 AAGTCGTCGG
*
3639115 GAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAATTACCGATATAGGTAATCACTGTT
1 GAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAATTACCGATATAGGTAATAACTGTT
*
3639180 ACTTATGGGAAATAAAGGAAACCAATGCTTGAACATTTC
66 ACTTATGAGAAATAAAGGAAACCAATGCTTGAACATTTC
* *
3639219 GAGGACTTGGCGACCTATGGAGGTTTCGACTAAAATCCTAATTACCGATTTAGGTAATAACTGTT
1 GAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAATTACCGATATAGGTAATAACTGTT
* ** * *
3639284 ATTTATGAGAAATCTAGGAAACCAATGCTTGAACGTTTG
66 ACTTATGAGAAATAAAGGAAACCAATGCTTGAACATTTC
*
3639323 GAGGACTTGGCAACCTATGGAGGT
1 GAGGACTTGGCGACCTATGGAGGT
3639347 CGCCTAGAGT
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 118 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (104 bp):
GAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAATTACCGATATAGGTAATAACTGTT
ACTTATGAGAAATAAAGGAAACCAATGCTTGAACATTTC
Found at i:3644322 original size:21 final size:21
Alignment explanation
Indices: 3644293--3644345 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3644283 ATTCTGACTA
3644293 TCGCATTGCGATCTTCCAAAT
1 TCGCATTGCGATCTTCCAAAT
* * *
3644314 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATCTTCCAAAT
*
3644335 TCGCAATGCGA
1 TCGCATTGCGA
3644346 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATCTTCCAAAT
Found at i:3644360 original size:20 final size:20
Alignment explanation
Indices: 3644335--3644395 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
3644325 TTTTCCTAAT
3644335 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3644355 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
3644375 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
3644395 T
1 T
3644396 TGTAATTCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:3644430 original size:20 final size:20
Alignment explanation
Indices: 3644407--3644480 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
3644397 GTAATTCGAA
* *
3644407 TCTGACTATTGCAACGAAAT
1 TCTGACTATCGCAACGAGAT
3644427 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
3644447 TCTGACTATCGCAAC-ACGAT
1 TCTGACTATCGCAACGA-GAT
* *
3644467 TATGACTATTGCAA
1 TCTGACTATCGCAA
3644481 TACTGAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (20 bp):
TCTGACTATCGCAACGAGAT
Found at i:3645339 original size:24 final size:24
Alignment explanation
Indices: 3645312--3645370 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
3645302 AGTCAGTATT
3645312 CGAAATTTGATCTCGGTCAATACC
1 CGAAATTTGATCTCGGTCAATACC
* *
3645336 CGAACTTTGATCTTGGTCAATACC
1 CGAAATTTGATCTCGGTCAATACC
*
3645360 CGAATTTTGAT
1 CGAAATTTGAT
3645371 GATGAAACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTCGGTCAATACC
Found at i:3647736 original size:20 final size:20
Alignment explanation
Indices: 3647711--3647804 Score: 145
Period size: 20 Copynumber: 4.7 Consensus size: 20
3647701 GACATTCATT
3647711 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
3647731 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
3647751 TGACTATCACAACGTGGAAA
1 TGACTATCGCAACGCGGAAA
3647771 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
3647791 TGACTATCGCAACG
1 TGACTATCGCAACG
3647805 AGAGAATCGC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 64 0.96
21 3 0.04
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:3648039 original size:14 final size:14
Alignment explanation
Indices: 3648020--3648070 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
3648010 CATCAATTAA
3648020 ACAAATCAACATTT
1 ACAAATCAACATTT
3648034 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3648048 ACAAATCATCTTTT
1 ACAAATCAACATTT
3648062 ACAAATCAA
1 ACAAATCAA
3648071 TTAAACAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3649558 original size:42 final size:42
Alignment explanation
Indices: 3649451--3649562 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
3649441 TATAAAATGT
* * * *
3649451 TGGGAG-GGACCTCTTCAACGACGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACGA
* * ** *
3649493 TGGGAGGGGACTCTTGATGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
3649535 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
3649563 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:3650065 original size:20 final size:20
Alignment explanation
Indices: 3650042--3650186 Score: 131
Period size: 20 Copynumber: 7.5 Consensus size: 20
3650032 GAAACTTAAA
3650042 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
3650062 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* * ** *
3650082 ATTGCAATGCGAATTTGACA
1 ATCGCAACGCGAAAATGACT
*
3650102 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
3650116 ATCGCAATGCGCGAAAATGACT
1 ATCGCAA--CGCGAAAATGACT
3650138 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
3650158 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3650178 ATCGCAACG
1 ATCGCAACG
3650187 AGAGAATCGC
Statistics
Matches: 100, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
14 7 0.07
16 2 0.02
17 1 0.01
18 4 0.04
19 2 0.02
20 77 0.77
22 7 0.07
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3650138 original size:76 final size:76
Alignment explanation
Indices: 3650041--3650202 Score: 274
Period size: 76 Copynumber: 2.2 Consensus size: 76
3650031 TGAAACTTAA
* *
3650041 AATCGCAA--CGCGAAAATGACTATCGCAACACGGAAATGACTATTGCAATGCGAATTTGACAAT
1 AATCGCAATGCGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAATGCGAATTTGACAAT
3650104 CGCAACGAGAG
66 CGCAACGAGAG
* *
3650115 AATCGCAATGCGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCGAATTTGACTAT
1 AATCGCAATGCGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAATGCGAATTTGACAAT
3650180 CGCAACGAGAG
66 CGCAACGAGAG
3650191 AATCGCAATGCG
1 AATCGCAATGCG
3650203 ATTTTCATTT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
74 8 0.10
76 74 0.90
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (76 bp):
AATCGCAATGCGCGAAAATGACTATCGCAACACGAAAATGACTATCGCAATGCGAATTTGACAAT
CGCAACGAGAG
Found at i:3650236 original size:20 final size:20
Alignment explanation
Indices: 3650211--3650283 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
3650201 CGATTTTCAT
*
3650211 TTCGCATTACGATAGTCAAA
1 TTCGCATTGCGATAGTCAAA
**
3650231 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCAAA
**
3650251 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCAAA
*
3650271 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
3650284 TTTGTTGTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCAAA
Found at i:3650265 original size:40 final size:39
Alignment explanation
Indices: 3650193--3650283 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 39
3650183 AACGAGAGAA
* **
3650193 TCGCAATGCGATTTTCATTTCGCATTACGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTCGCATTACGATAGTCAAAT
* **
3650232 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCA-TTTCGCATTACGATAGTCAAAT
*
3650272 TCGCGTTGCGAT
1 TCGCATTGCGAT
3650284 TTTGTTGTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 14 0.32
40 30 0.68
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (39 bp):
TCGCATTGCGATAGTCATTTCGCATTACGATAGTCAAAT
Found at i:3650293 original size:14 final size:14
Alignment explanation
Indices: 3650268--3650325 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
3650258 TGCGATAGTC
*
3650268 ATTTTCGCGTTGCG
1 ATTTTCTCGTTGCG
* * *
3650282 ATTTTGTTGTTGTG
1 ATTTTCTCGTTGCG
3650296 ATTTTCTCGTTGCG
1 ATTTTCTCGTTGCG
3650310 ATTTTCTCGTTGCG
1 ATTTTCTCGTTGCG
3650324 AT
1 AT
3650326 AGTAAACTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.52
Consensus pattern (14 bp):
ATTTTCTCGTTGCG
Found at i:3652228 original size:20 final size:20
Alignment explanation
Indices: 3652207--3652387 Score: 144
Period size: 20 Copynumber: 9.4 Consensus size: 20
3652197 TGAAACTTAA
*
3652207 AATCGCAACACGAAAATGAA
1 AATCGCAACACGAAAATGAC
3652227 AATCGCAACACGAAAATGAC
1 AATCGCAACACGAAAATGAC
*
3652247 TATCGCAACACGAAAATGAC
1 AATCGCAACACGAAAATGAC
* * **
3652267 TATCGCAACGCGAATTTGAC
1 AATCGCAACACGAAAATGAC
* *
3652287 TATCGC-A-ACG-CAA-G--
1 AATCGCAACACGAAAATGAC
* *
3652301 AATCGCAACGCG-AAATGAA
1 AATCGCAACACGAAAATGAC
3652320 AATCGCAACACGAAAATGAC
1 AATCGCAACACGAAAATGAC
* * **
3652340 TATCGCAACGCGAATTTGAC
1 AATCGCAACACGAAAATGAC
* * * *
3652360 TATTGCAACGCG-AAATGAA
1 AATCGCAACACGAAAATGAC
3652379 AATCGCAAC
1 AATCGCAAC
3652388 GACAGAATCG
Statistics
Matches: 131, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
14 5 0.04
15 1 0.01
16 5 0.04
17 1 0.01
18 2 0.02
19 23 0.18
20 94 0.72
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (20 bp):
AATCGCAACACGAAAATGAC
Found at i:3652347 original size:73 final size:74
Alignment explanation
Indices: 3652227--3652370 Score: 245
Period size: 73 Copynumber: 2.0 Consensus size: 74
3652217 CGAAAATGAA
**
3652227 AATCGCAACACGAAAATGACTATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCG
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCG
3652292 CAACGCAAG
66 CAACGCAAG
* *
3652301 AATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATTG
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCG
3652365 CAACGC
66 CAACGC
3652371 GAAATGAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 55 0.83
74 11 0.17
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (74 bp):
AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCG
CAACGCAAG
Found at i:3652368 original size:93 final size:93
Alignment explanation
Indices: 3652207--3652399 Score: 282
Period size: 93 Copynumber: 2.1 Consensus size: 93
3652197 TGAAACTTAA
3652207 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAAAATGACTATCG
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAAAATGACTATCG
* **
3652272 CAACGCGAATTTGACTATCGCAACG-CAAG
66 CAACGCGAA-ATGAAAATCGCAACGAC-AG
* * ** *
3652301 AATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATTG
1 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAAAATGACTATCG
3652365 CAACGCGAAATGAAAATCGCAACGACAG
66 CAACGCGAAATGAAAATCGCAACGACAG
3652393 AATCGCA
1 AATCGCA
3652400 TTGCGATAGT
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
92 21 0.23
93 58 0.64
94 11 0.12
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (93 bp):
AATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACTATCGCAACACGAAAATGACTATCG
CAACGCGAAATGAAAATCGCAACGACAG
Found at i:3652785 original size:22 final size:22
Alignment explanation
Indices: 3652724--3652789 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
3652714 TAACCGTGAA
* ** *
3652724 TGATTTCGCCGGAGATGAAGCC
1 TGATTTCGTCGGAGATGGGGAC
*
3652746 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
3652768 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
3652790 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:3653013 original size:20 final size:20
Alignment explanation
Indices: 3652967--3653033 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3652957 GCTATGTAAA
* *
3652967 TCGCATTGCGATAGT-CAGAT
1 TCGCATTGCGAT-TTACATAT
*
3652987 TCACATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *
3653007 TTGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
3653027 TCGCATT
1 TCGCATT
3653034 ACGAATTAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:3653451 original size:28 final size:30
Alignment explanation
Indices: 3653403--3653473 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 30
3653393 CCCTAAATTG
*
3653403 TTTTTGAAATTTT-TAGGAATTT-AGGAGT
1 TTTTTGAAATTTTATAGAAATTTAAGGAGT
*
3653431 TTTTTGAAATTTTAT-GAAATTTAAGGTGT
1 TTTTTGAAATTTTATAGAAATTTAAGGAGT
3653460 TTTTT-AGAATTTTA
1 TTTTTGA-AATTTTA
3653474 ATAATTTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
28 20 0.53
29 18 0.47
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.54
Consensus pattern (30 bp):
TTTTTGAAATTTTATAGAAATTTAAGGAGT
Found at i:3692361 original size:15 final size:16
Alignment explanation
Indices: 3692335--3692374 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
3692325 TTGTATCTTA
3692335 TTCTTCTTCTTTTTCT
1 TTCTTCTTCTTTTTCT
3692351 TTCTT-TTCTTTTTCT
1 TTCTTCTTCTTTTTCT
3692366 TT-TTCTTCT
1 TTCTTCTTCT
3692375 ATGTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (16 bp):
TTCTTCTTCTTTTTCT
Found at i:3692365 original size:21 final size:22
Alignment explanation
Indices: 3692330--3692372 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
3692320 AAAAATTGTA
3692330 TCTTATTCTTCTTCTTTTTCTT
1 TCTTATTCTTCTTCTTTTTCTT
*
3692352 TCTT-TTCTTTTTCTTTTTCTT
1 TCTTATTCTTCTTCTTTTTCTT
3692373 CTATGTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (22 bp):
TCTTATTCTTCTTCTTTTTCTT
Done.