Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002890.1 Hibiscus syriacus cultivar Beakdansim tig00005974_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: 5046466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 21
Found at i:4185133 original size:14 final size:14
Alignment explanation
Indices: 4185114--4185140 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4185104 CAACACTCTA
4185114 GAACTAAGCACATT
1 GAACTAAGCACATT
4185128 GAACTAAGCACAT
1 GAACTAAGCACAT
4185141 CACTTCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (14 bp):
GAACTAAGCACATT
Found at i:4185605 original size:24 final size:24
Alignment explanation
Indices: 4185577--4185656 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
4185567 CACTTAACAA
4185577 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
4185601 TGCATCGATTCAT-CATGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
4185622 TGCACCGATGCA-CGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
4185645 TGCATCGATGCA
1 TGCATCGATGCA
4185657 CGGGGTCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.25
22 1 0.02
23 14 0.32
24 15 0.34
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:4190543 original size:14 final size:14
Alignment explanation
Indices: 4190524--4190554 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4190514 CTAGATACAA
4190524 TCACACATACACTT
1 TCACACATACACTT
4190538 TCACACATACACTT
1 TCACACATACACTT
4190552 TCA
1 TCA
4190555 AATAATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (14 bp):
TCACACATACACTT
Found at i:4199522 original size:7 final size:6
Alignment explanation
Indices: 4199482--4199521 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
4199472 AAATAATGAA
* *
4199482 TTTATT TTTATT TTCATC TTTATT TTTACTT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTATT TTT
4199522 TCCTAGATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:4201962 original size:20 final size:20
Alignment explanation
Indices: 4201933--4201971 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4201923 ATTCCACCAC
*
4201933 ATGCAACTATATGCTCTTAA
1 ATGCAACTATATGATCTTAA
*
4201953 ATGCATCTATATGATCTTA
1 ATGCAACTATATGATCTTA
4201972 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGCAACTATATGATCTTAA
Found at i:4209971 original size:20 final size:20
Alignment explanation
Indices: 4209946--4209983 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4209936 CCACATGCAA
*
4209946 CTATATGCTCCTAAATGAAT
1 CTATATGATCCTAAATGAAT
*
4209966 CTATATGATCCTATATGA
1 CTATATGATCCTAAATGA
4209984 GCTTTTAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (20 bp):
CTATATGATCCTAAATGAAT
Found at i:4220420 original size:45 final size:45
Alignment explanation
Indices: 4220365--4220716 Score: 515
Period size: 45 Copynumber: 7.8 Consensus size: 45
4220355 ATTCTAACAT
* * * **
4220365 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAATATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATA
* * *
4220410 CTTTTATGTTGAAAATGTACCCATATACATTTCAACTTTAGCGTA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATA
*
4220455 CTTTTCTGTTGATAATGTATCCATATACATTTCAACTTTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATA
* *
4220500 CTTTTCTGTTGATAATATACCCATATACATTTCAACTGTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATA
* * *
4220545 CTTTTTTGTTGATAATGTACCCATATACATTTTAACTTTAACATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATA
* *
4220590 CTTTTCTATTGATAATGTACCCATATACATTTTAACTTTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATA
* *
4220635 CTTTTCTGTTGATAATGTACACATATACATTTTAACTTTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATA
* * *
4220680 CTTTTCTATTGATAATGCACCCATATGCATTTCAACT
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACT
4220717 ATGGCATCCT
Statistics
Matches: 277, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 277 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGTACCCATATACATTTCAACTTTAGCATA
Found at i:4221217 original size:19 final size:19
Alignment explanation
Indices: 4221193--4221243 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
4221183 CCTTAACTTG
*
4221193 TGTATGGGTGCACTGCCTA
1 TGTATGGGTACACTGCCTA
*
4221212 TGTATGGGTACACTGTCTA
1 TGTATGGGTACACTGCCTA
*
4221231 TGTATCGGTACAC
1 TGTATGGGTACAC
4221244 AAATTACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (19 bp):
TGTATGGGTACACTGCCTA
Found at i:4222075 original size:28 final size:28
Alignment explanation
Indices: 4222043--4222098 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
4222033 TAAACACTCA
4222043 ATTGTTAAATCTTTTCAATAAAGTCCTT
1 ATTGTTAAATCTTTTCAATAAAGTCCTT
4222071 ATTGTTAAATCTTTTCAATAAAGTCCTT
1 ATTGTTAAATCTTTTCAATAAAGTCCTT
4222099 CATTTAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (28 bp):
ATTGTTAAATCTTTTCAATAAAGTCCTT
Found at i:4226062 original size:44 final size:47
Alignment explanation
Indices: 4226014--4226124 Score: 156
Period size: 44 Copynumber: 2.4 Consensus size: 47
4226004 GTAACCATGC
4226014 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTATATTGG-AA
1 AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGTATATTGGTAA
* * * *
4226058 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTACGGAA-TTAAATGGCAAGTATATTGGTAA
4226106 AAATAAGCTTATGAGCTTA
1 AAATAAGCTTATGAGCTTA
4226125 TGGGATAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 22 0.38
46 1 0.02
47 15 0.26
48 20 0.34
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.32
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGTATATTGGTAA
Found at i:4226115 original size:48 final size:44
Alignment explanation
Indices: 4226014--4226132 Score: 157
Period size: 48 Copynumber: 2.6 Consensus size: 44
4226004 GTAACCATGC
*
4226014 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGGAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGAA
* * *
4226058 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGG-AA
*
4226106 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
4226133 ATGATAAGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
44 22 0.34
45 2 0.03
46 2 0.03
47 15 0.23
48 24 0.37
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGAA
Found at i:4226531 original size:12 final size:12
Alignment explanation
Indices: 4226514--4226538 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4226504 TATTTTCGGA
4226514 AGTTACTATAGC
1 AGTTACTATAGC
4226526 AGTTACTATAGC
1 AGTTACTATAGC
4226538 A
1 A
4226539 TGAACAGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
AGTTACTATAGC
Found at i:4230356 original size:20 final size:20
Alignment explanation
Indices: 4230331--4230368 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4230321 TTTGGTTCAC
*
4230331 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
4230351 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
4230369 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:4230371 original size:18 final size:19
Alignment explanation
Indices: 4230331--4230374 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
4230321 TTTGGTTCAC
*
4230331 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
4230351 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
4230369 GGAATA
1 GGAATA
4230375 GGATTACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:4230541 original size:15 final size:15
Alignment explanation
Indices: 4230519--4230553 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
4230509 AGTAAAATTC
4230519 AAAA-TATTTAAATA
1 AAAATTATTTAAATA
*
4230533 AAAATTATTTATATA
1 AAAATTATTTAAATA
4230548 AAAATT
1 AAAATT
4230554 CTATATGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTATTTAAATA
Found at i:4236273 original size:15 final size:13
Alignment explanation
Indices: 4236241--4236292 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 13
4236231 TATTTGATTG
4236241 ATTT-AATTTTTT
1 ATTTAAATTTTTT
4236253 ATTTAAATTTTCTT
1 ATTTAAATTTT-TT
4236267 CATTTAAATTTCTGTT
1 -ATTTAAATTT-T-TT
*
4236283 ATTTTAATTT
1 ATTTAAATTT
4236293 ATGTCGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 4 0.12
13 6 0.18
14 2 0.06
15 19 0.56
16 3 0.09
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (13 bp):
ATTTAAATTTTTT
Found at i:4236833 original size:139 final size:138
Alignment explanation
Indices: 4236666--4237262 Score: 691
Period size: 139 Copynumber: 4.3 Consensus size: 138
4236656 TTAATAACTG
* ** * *
4236666 CATAATTGATTAAAATTTATTAGGATTAATATTAGAGCCTCCACTTTAGGGTTAATTTCAATTTT
1 CATAATTGATTAAAATTAATTA-GATTAATATTAGAGCCTCCACTTTAGGCCTAATTTCAAATCT
* * * *
4236731 AATCCTTAAATTTAGGTGAATTCTTAATTTGGTCCTCGCTTTTGCTTGAGATTCCATTTTAATTA
65 AGTCCTTAAATTTAGGCGAATTCTTAATTTGGTCCTCACTTTTGCTCGAGATTCCATTTTAATTA
**
4236796 TTTGAATCA
130 TTCAAATCA
* *
4236805 CATAATTGATTAAAATTAATTAGTATTAATATTAGAGCATTCACTTTAGGCCTAATTTCAAATCT
1 CATAATTGATTAAAATTAATTAG-ATTAATATTAGAGCCTCCACTTTAGGCCTAATTTCAAATCT
* * * * *
4236870 AGTCCTCAAATTTAAGCAAATTCTTAATTTGGTCTTCACTTTTGCTCGAGGTTCCATTTTAATTA
65 AGTCCTTAAATTTAGGCGAATTCTTAATTTGGTCCTCACTTTTGCTCGAGATTCCATTTTAATTA
4236935 TTCAAATCA
130 TTCAAATCA
* *
4236944 CATAATTGATTAAAATTAATTAGGACTAATATTAGAGCCTTCACTTTAGGCCTAATTTCAAATCT
1 CATAATTGATTAAAATTAATTA-GATTAATATTAGAGCCTCCACTTTAGGCCTAATTTCAAATCT
* * *
4237009 AGTCCTTAAATTTAGACGAATTCTTAATATGGTCCTCACTTTT-CATCAATG-TTCCATTTTAAT
65 AGTCCTTAAATTTAGGCGAATTCTTAATTTGGTCCTCACTTTTGC-TCGA-GATTCCATTTTAAT
4237072 TATTCAAATCA
128 TATTCAAATCA
* * * * * * *
4237083 CATAGTTGATTGAAATTAATTTGGTTAAAAGTTAGAGCCTCCACTTTAGGCTTAATTTTACAAT-
1 CATAATTGATTAAAATTAATTAGATTAATA-TTAGAGCCTCCACTTTAGGCCTAATTTCA-AATC
* * * * * *
4237147 TATTCCTTAACTTTAGGAGAATAT-TTTATTTGGTCCTCACTTTTGCTCGAGGTTTCATTTTAAT
64 TAGTCCTTAAATTTAGGCGAAT-TCTTAATTTGGTCCTCACTTTTGCTCGAGATTCCATTTTAAT
**
4237211 TATTTGAATCA
128 TATTCAAATCA
* ** *
4237222 GATAATTGGGT-AAATTAATTAGGTTAATAATTAGAGTCCTC
1 CATAATTGATTAAAATTAATTAGATTAAT-ATTAGAG-CCTC
4237263 ATTTTTAGTT
Statistics
Matches: 395, Mismatches: 52, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
138 29 0.07
139 359 0.91
140 7 0.02
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (138 bp):
CATAATTGATTAAAATTAATTAGATTAATATTAGAGCCTCCACTTTAGGCCTAATTTCAAATCTA
GTCCTTAAATTTAGGCGAATTCTTAATTTGGTCCTCACTTTTGCTCGAGATTCCATTTTAATTAT
TCAAATCA
Found at i:4238533 original size:3 final size:3
Alignment explanation
Indices: 4238527--4238552 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4238517 CTATTCAAAA
4238527 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
4238553 ATGTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4239490 original size:9 final size:8
Alignment explanation
Indices: 4239454--4239528 Score: 51
Period size: 9 Copynumber: 8.4 Consensus size: 8
4239444 AAATAGTAAG
4239454 TAAAATAAA
1 TAAAA-AAA
4239463 TAAAAAAA
1 TAAAAAAA
4239471 TATGTAAAAAA
1 TA---AAAAAA
4239482 TAAAGAAAAA
1 T-AA-AAAAA
*
4239492 GAAAAAAA
1 TAAAAAAA
* *
4239500 TATATAAA
1 TAAAAAAA
4239508 TAAAACAAA
1 TAAAA-AAA
4239517 TAAATAAAA
1 TAAA-AAAA
4239526 TAA
1 TAA
4239529 TATGTAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
8 18 0.34
9 21 0.40
10 6 0.11
11 7 0.13
12 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (8 bp):
TAAAAAAA
Found at i:4239517 original size:17 final size:16
Alignment explanation
Indices: 4239456--4239524 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
4239446 ATAGTAAGTA
4239456 AAATAAATAAAAAAAT
1 AAATAAATAAAAAAAT
** *
4239472 ATGTAAA-AAATAAA-
1 AAATAAATAAAAAAAT
* *
4239486 GAA-AAAGAAAAAAAT
1 AAATAAATAAAAAAAT
*
4239501 ATATAAATAAAACAAAT
1 AAATAAATAAAA-AAAT
4239518 AAATAAA
1 AAATAAA
4239525 ATAATATGTA
Statistics
Matches: 38, Mismatches: 11, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
13 3 0.08
14 6 0.16
15 7 0.18
16 12 0.32
17 10 0.26
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (16 bp):
AAATAAATAAAAAAAT
Found at i:4239546 original size:29 final size:29
Alignment explanation
Indices: 4239451--4239548 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 29
4239441 ATAAAATAGT
4239451 AAGT-AAAATAAATAAAAAAATATGTAAA
1 AAGTAAAAATAAATAAAAAAATATGTAAA
* * *
4239479 AAATAAAGAA-AAAGAAAAAAATATATAAA
1 AAGTAAA-AATAAATAAAAAAATATGTAAA
*
4239508 TAA--AACAAATAAATAAAATAATATGTAAA
1 -AAGTAA-AAATAAATAAAAAAATATGTAAA
4239537 AAGTAAAAATAA
1 AAGTAAAAATAA
4239549 TATATATATA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
28 9 0.16
29 42 0.74
30 6 0.11
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.19
Consensus pattern (29 bp):
AAGTAAAAATAAATAAAAAAATATGTAAA
Found at i:4239555 original size:2 final size:2
Alignment explanation
Indices: 4239548--4239572 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4239538 AGTAAAAATA
4239548 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4239573 AAATAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4239606 original size:40 final size:41
Alignment explanation
Indices: 4239562--4239652 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 41
4239552 ATATATATAT
4239562 ATATATATATAAAATAAATAAAA-ACATAACAAAATAATAA-
1 ATATATATATAAAATAAATAAAACACATAACAAAA-AATAAC
* * *
4239602 ATATATATAT-AAATTAATAAAACAGATAATAAAAAATAAC
1 ATATATATATAAAATAAATAAAACACATAACAAAAAATAAC
4239642 ATATATATATA
1 ATATATATATA
4239653 TATATATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
39 16 0.36
40 29 0.64
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (41 bp):
ATATATATATAAAATAAATAAAACACATAACAAAAAATAAC
Found at i:4239647 original size:2 final size:2
Alignment explanation
Indices: 4239642--4239667 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4239632 AAAAAATAAC
4239642 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
4239668 GTAATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4239710 original size:24 final size:24
Alignment explanation
Indices: 4239674--4239728 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
4239664 ATATGTAATC
4239674 TAAAAAATAAAAATAAATACAAAAG
1 TAAAAAATAAAAATAAATA-AAAAG
* ** *
4239699 TAAAAAA-GAAAATGCATAAAATG
1 TAAAAAATAAAAATAAATAAAAAG
4239722 TAAAAAA
1 TAAAAAA
4239729 AATATTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 11 0.42
24 8 0.31
25 7 0.27
ACGTcount: A:0.73, C:0.04, G:0.07, T:0.16
Consensus pattern (24 bp):
TAAAAAATAAAAATAAATAAAAAG
Found at i:4240924 original size:34 final size:33
Alignment explanation
Indices: 4240854--4240969 Score: 151
Period size: 33 Copynumber: 3.4 Consensus size: 33
4240844 AAGGTCTTGG
*
4240854 GTTTCAAGAGAAACATTTTCAAAGGTTTTTTTT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTT
** *
4240887 GTTTGGAGAGAAATAATTTCAAAGGTTTTTTTCT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTT-T
*
4240921 GTTTCAAGATAAACAATTTCAAAGGTTATTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGG-T-TTTTTT-T
4240957 GTTTCAAGAGAAA
1 GTTTCAAGAGAAA
4240970 TTGTCTCAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
33 28 0.40
34 22 0.31
35 1 0.01
36 19 0.27
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (33 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTT
Found at i:4241074 original size:37 final size:37
Alignment explanation
Indices: 4241023--4241314 Score: 320
Period size: 37 Copynumber: 8.1 Consensus size: 37
4241013 CAAAGATTGG
* *
4241023 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
4241060 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
*
4241096 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
* * ** * *
4241133 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
* * *
4241169 TGTTTCAAGGAAAACATAT-TC-A-A-AG-----ATTT
1 TGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAACTT
*
4241198 TGTTTCTAGGGAAACTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
* *
4241234 TGTTTCAATGGAAACTGTCTCAAGAGAGAGATAAAACTT
1 TGTTTCAAGGGAAACTGTCTC-A-AGAGAGACAAAACTT
* *
4241273 TGTTTTAAGGGAAATTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
4241310 TGTTT
1 TGTTT
4241315 TGAGTAAATT
Statistics
Matches: 215, Mismatches: 25, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
28 3 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
35 1 0.00
36 70 0.33
37 86 0.40
38 12 0.06
39 20 0.09
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
Found at i:4241113 original size:73 final size:72
Alignment explanation
Indices: 4241023--4241314 Score: 332
Period size: 73 Copynumber: 4.1 Consensus size: 72
4241013 CAAAGATTGG
*
4241023 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
4241088 ACAAAATT
65 ACAAAATT
* * ** *
4241096 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAG
1 TGTTTCAAG-GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
*
4241161 ACGAAATT
65 ACAAAATT
* * *
4241169 TGTTTCAAGGAAAACATAT-TC-A-A-AG-----ATTTTGTTTCTAGGGAAACTGTCTCAAGAGA
1 TGTTTCAAGG-AAAC-TGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGA
4241225 GACAAAATT
64 GACAAAATT
* * *
4241234 TGTTTCAATGGAAACTGTCTCAAGAGAGAGATAAAACTTTGTTTTAAGGGAAATTGTCTCAAGAG
1 TGTTTCAA-GGAAACTGTCTC-A-AGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
4241299 AGACAAAACTT
63 AGACAAAA-TT
4241310 TGTTT
1 TGTTT
4241315 TGAGTAAATT
Statistics
Matches: 183, Mismatches: 21, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
64 2 0.01
65 46 0.25
66 2 0.01
68 1 0.01
69 1 0.01
70 4 0.02
71 1 0.01
72 2 0.01
73 81 0.44
74 2 0.01
75 34 0.19
76 7 0.04
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (72 bp):
TGTTTCAAGGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
CAAAATT
Found at i:4241330 original size:37 final size:37
Alignment explanation
Indices: 4241196--4241339 Score: 159
Period size: 37 Copynumber: 3.9 Consensus size: 37
4241186 ATTCAAAGAT
*
4241196 TTTGTTTCT-AGGGAAACTGTCTCAAGAGAGACAAAA-
1 TTTGTTT-TAAGGGAAATTGTCTCAAGAGAGACAAAAC
* * * *
4241232 TTTGTTTCAATGGAAACTGTCTCAAGAGAGAGATAAAAC
1 TTTGTTTTAAGGGAAATTGTCTC-A-AGAGAGACAAAAC
4241271 TTTGTTTTAAGGGAAATTGTCTCAAGAGAGACAAAAC
1 TTTGTTTTAAGGGAAATTGTCTCAAGAGAGACAAAAC
* * *
4241308 TTTGTTTTGA-GTAAATTAGTCTCAAGCGAGAC
1 TTTGTTTTAAGGGAAATT-GTCTCAAGAGAGAC
4241340 GACCCCGTGT
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
36 26 0.28
37 35 0.38
38 12 0.13
39 20 0.22
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (37 bp):
TTTGTTTTAAGGGAAATTGTCTCAAGAGAGACAAAAC
Found at i:4241341 original size:177 final size:175
Alignment explanation
Indices: 4240959--4241309 Score: 503
Period size: 177 Copynumber: 2.0 Consensus size: 175
4240949 TTTTTTGTGT
* * * *
4240959 TTCAAGAGAAATTGTCTCAAGGGAGGCAGAATTTTGTTTCAAGAGAAAGATATTCAAAGATTGGT
1 TTCAAAAGAAATTGTCTCAAGGGAGAC-GAAATTTGTTTCAAGAGAAACATATTCAAAGATTGGT
4241024 GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
65 GTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
4241089 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAG
130 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAG
* *
4241135 TTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAG-GAAAACATATTCAAAGATT-T
1 TT-CAAAAGAAATTGTCTCAAGGGAGACGAAATTTGTTTCAAGAG-AAACATATTCAAAGATTGG
* *
4241198 TGTTTCT-AGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAATGGAAACTGTCTCAAGAGA
64 TGTTT-TAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTC-A-AGA
* * * *
4241261 GAGATAAAACTTTGTTTTAAGGGAAATTGTCTCAAGAGAGACAAAACTT
126 GAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
4241310 TGTTTTGAGT
Statistics
Matches: 157, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
174 22 0.14
175 33 0.21
176 44 0.28
177 58 0.37
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (175 bp):
TTCAAAAGAAATTGTCTCAAGGGAGACGAAATTTGTTTCAAGAGAAACATATTCAAAGATTGGTG
TTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAG
Found at i:4241968 original size:32 final size:32
Alignment explanation
Indices: 4241932--4242015 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
4241922 TTCGCATCAG
* * *
4241932 GATGTTGAATCCCCAAAGATGCCTCAATATTC
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
* *
4241964 GATGTTGAATCTCCAAAAATGCCCCAACATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
*
4241996 GATGTTGAATCTTCAAAGAT
1 GATGTTGAATCTCCAAAGAT
4242016 TCTCCCAATG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTC
Found at i:4243106 original size:14 final size:13
Alignment explanation
Indices: 4243077--4243125 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
4243067 TTTTCTTCAC
4243077 TTTTTTTCT-TTGT
1 TTTTTTTCTCTT-T
4243090 TTTTGTTTCTCTTT
1 TTTT-TTTCTCTTT
4243104 TTTATTTTCTCTTT
1 TTT-TTTTCTCTTT
4243118 TTTCTTTT
1 TTT-TTTT
4243126 TGTTCTGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 4 0.12
14 25 0.78
15 3 0.09
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTCTTT
Found at i:4246071 original size:21 final size:20
Alignment explanation
Indices: 4246054--4246164 Score: 73
Period size: 22 Copynumber: 5.1 Consensus size: 20
4246044 GATAAAATAG
4246054 TAAGTAAAATAAATAAAAAAA
1 TAAGTAAAA-AAATAAAAAAA
*
4246075 TATGTAAAAAAATATAAAAAAA
1 TAAGT-AAAAAA-ATAAAAAAA
*
4246097 TAAAG-AAAAAGAA-AAAATATA
1 T-AAGTAAAAA-AATAAAA-AAA
*
4246118 TAAATAAAACAAATAAATAAAA
1 TAAGTAAAA-AAATAAA-AAAA
*
4246140 TAATTATAAAAAAGTAAAAATAA
1 TAAGTA-AAAAAA-TAAAAA-AA
4246163 TA
1 TA
4246165 TATATATATA
Statistics
Matches: 72, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
20 6 0.08
21 21 0.29
22 31 0.43
23 14 0.19
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.21
Consensus pattern (20 bp):
TAAGTAAAAAAATAAAAAAA
Found at i:4246074 original size:12 final size:12
Alignment explanation
Indices: 4246059--4246157 Score: 66
Period size: 12 Copynumber: 8.7 Consensus size: 12
4246049 AATAGTAAGT
4246059 AAAATAAATAAA
1 AAAATAAATAAA
**
4246071 AAAATATGTAAA
1 AAAATAAATAAA
4246083 AAAAT--ATAAA
1 AAAATAAATAAA
*
4246093 AAAAT-AA-AGA
1 AAAATAAATAAA
*
4246103 AAAAGAAA-AAA
1 AAAATAAATAAA
* *
4246114 TATATAAATAAA
1 AAAATAAATAAA
4246126 ACAAATAAATAAA
1 A-AAATAAATAAA
* *
4246139 ATAAT-TATAAA
1 AAAATAAATAAA
*
4246150 AAAGTAAA
1 AAAATAAA
4246158 AATAATATAT
Statistics
Matches: 66, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
10 15 0.23
11 18 0.27
12 22 0.33
13 11 0.17
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:4246083 original size:10 final size:10
Alignment explanation
Indices: 4246058--4246166 Score: 59
Period size: 10 Copynumber: 11.2 Consensus size: 10
4246048 AAATAGTAAG
4246058 TAAAATAAATA
1 TAAAA-AAATA
*
4246069 -AAAAAATATG
1 TAAAAAA-ATA
4246079 TAAAAAAATA
1 TAAAAAAATA
4246089 TAAAAAAATA
1 TAAAAAAATA
*
4246099 -AAGAAAAAGA
1 TAA-AAAAATA
*
4246109 -AAAAATATA
1 TAAAAAAATA
*
4246118 TAAATAAA-A
1 TAAAAAAATA
* *
4246127 CAAATAAATA
1 TAAAAAAATA
* *
4246137 -AAATAATTA
1 TAAAAAAATA
*
4246146 TAAAAAAGTA
1 TAAAAAAATA
*
4246156 -AAAATAATA
1 TAAAAAAATA
4246165 TA
1 TA
4246167 TATATATATA
Statistics
Matches: 78, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
9 32 0.41
10 40 0.51
11 6 0.08
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (10 bp):
TAAAAAAATA
Found at i:4246093 original size:8 final size:8
Alignment explanation
Indices: 4246081--4246142 Score: 54
Period size: 9 Copynumber: 7.2 Consensus size: 8
4246071 AAAATATGTA
4246081 AAAAAATAT
1 AAAAAA-AT
4246090 AAAAAAAT
1 AAAAAAAT
4246098 AAAGAAAA-
1 AAA-AAAAT
4246106 AGAAAAAAT
1 A-AAAAAAT
* *
4246115 ATATAAAT
1 AAAAAAAT
4246123 AAAACAAAT
1 AAAA-AAAT
4246132 AAATAAAAT
1 AAA-AAAAT
4246141 AA
1 AA
4246143 TTATAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
8 17 0.39
9 26 0.59
10 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.03, T:0.16
Consensus pattern (8 bp):
AAAAAAAT
Found at i:4246246 original size:42 final size:37
Alignment explanation
Indices: 4246113--4246262 Score: 95
Period size: 38 Copynumber: 4.1 Consensus size: 37
4246103 AAAAGAAAAA
*
4246113 ATAT-ATAAAT-AAAACA-AATAAATAAAATA-AT-T
1 ATATAATAAATAAAAACATAAAAAATAAAATATATAT
* * *
4246145 ATA-AA-AAAGT-AAAA-ATAATATATATATATATATAT
1 ATATAATAAA-TAAAAACATAAAAAATA-AAATATATAT
4246180 ATATAATAAATAAAAACATAAAAAATAGTAAATATATAT
1 ATATAATAAATAAAAACATAAAAAATA--AAATATATAT
* * *
4246219 ATA-AATTAATAAAACAGATAATTAAAAATAACATATATAT
1 ATATAATAAATAAAA-ACAT-A--AAAAATAAAATATATAT
4246259 ATAT
1 ATAT
4246263 GTAATCTAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
31 4 0.04
32 16 0.17
33 4 0.04
34 2 0.02
35 4 0.04
36 3 0.03
37 7 0.07
38 18 0.19
39 16 0.17
40 13 0.14
42 7 0.07
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (37 bp):
ATATAATAAATAAAAACATAAAAAATAAAATATATAT
Found at i:4246873 original size:37 final size:37
Alignment explanation
Indices: 4246823--4246963 Score: 237
Period size: 37 Copynumber: 3.8 Consensus size: 37
4246813 ACGCTTGTTG
4246823 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
4246860 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * * *
4246897 ATCCTATTTTTAGGAGTTTAAATCCTAATAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
*
4246934 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCATAGTA
4246964 AAATTCTAAC
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 98 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:4246995 original size:74 final size:74
Alignment explanation
Indices: 4246825--4246982 Score: 208
Period size: 74 Copynumber: 2.1 Consensus size: 74
4246815 GCTTGTTGAT
* * * *
4246825 CCTATTTTTAGGAGTTTGAATCATAGTAGAACTCTATCCTATTTTTAGGAGTTTGAATCATAGTA
1 CCTATGTTTAGGAGTTTGAATCCTAATAAAACTCTATCCTATTTTTAGGAGTTTGAATCATAGTA
* *
4246890 GAACTCTAT
66 AAACTCTAA
* * *
4246899 CCTATTTTTAGGAGTTTAAATCCTAATAAAACTCTATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 CCTATGTTTAGGAGTTTGAATCCTAATAAAACTCTATCCTATTTTTAGGAGTTTGAATCATAGTA
*
4246964 AAATTCTAA
66 AAACTCTAA
*
4246973 CGTTATGTTT
1 C-CTATGTTT
4246983 GTTTTTTGAA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 67 0.92
75 6 0.08
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (74 bp):
CCTATGTTTAGGAGTTTGAATCCTAATAAAACTCTATCCTATTTTTAGGAGTTTGAATCATAGTA
AAACTCTAA
Found at i:4247682 original size:16 final size:15
Alignment explanation
Indices: 4247661--4247695 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4247651 TTGTTTGAAT
4247661 TTTATCCATTTTTTAA
1 TTTATCCA-TTTTTAA
*
4247677 TTTATCTATTTTTAA
1 TTTATCCATTTTTAA
4247692 TTTA
1 TTTA
4247696 CCTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATCCATTTTTAA
Found at i:4248939 original size:12 final size:12
Alignment explanation
Indices: 4248898--4248985 Score: 54
Period size: 10 Copynumber: 8.0 Consensus size: 12
4248888 AAATATTGGA
4248898 TATTAAT-ATAT
1 TATTAATAATAT
4248909 T-TTAA-AATA-
1 TATTAATAATAT
*
4248918 TA-TAAGAATAAT
1 TATTAATAAT-AT
4248930 T-TTAATAATAT
1 TATTAATAATAT
4248941 TATTAATATTATAT
1 TATTAATA--ATAT
4248955 TATT-AT-ATA-
1 TATTAATAATAT
*
4248964 T-TTAATTATAT
1 TATTAATAATAT
4248975 TA-TAATAATAT
1 TATTAATAATAT
4248986 AGAGTATTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 26
0.69 0.02 0.29
Matches are distributed among these distances:
8 2 0.03
9 7 0.11
10 16 0.26
11 14 0.23
12 13 0.21
13 2 0.03
14 8 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (12 bp):
TATTAATAATAT
Found at i:4248956 original size:14 final size:15
Alignment explanation
Indices: 4248937--4248965 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4248927 AATTTTAATA
4248937 ATATTATTA-ATATT
1 ATATTATTATATATT
4248951 ATATTATTATATATT
1 ATATTATTATATATT
4248966 TAATTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTATTATATATT
Found at i:4251774 original size:70 final size:70
Alignment explanation
Indices: 4251661--4251802 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
4251651 CTCGACAATA
4251661 AATTTCTGGTTGGATAAAAGCGTTAATCCGACAATAATATAGAATGATATAAGGTCACTATTTAC
1 AATTTCTGGTTGGATAAAAGCGTTAATCCGACAATAATATAGAATGATATAAGGTCACTATTTAC
4251726 TATTC
66 TATTC
4251731 AATTTCTGGTTGGATAAAAGCGTTAATCCGACAATAATATAGAATGATATAAGGTCACTATTTAC
1 AATTTCTGGTTGGATAAAAGCGTTAATCCGACAATAATATAGAATGATATAAGGTCACTATTTAC
4251796 TATTC
66 TATTC
4251801 AA
1 AA
4251803 ACTTAAATAG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (70 bp):
AATTTCTGGTTGGATAAAAGCGTTAATCCGACAATAATATAGAATGATATAAGGTCACTATTTAC
TATTC
Found at i:4255410 original size:63 final size:63
Alignment explanation
Indices: 4255303--4255422 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
4255293 TAATAATATC
*
4255303 TTTTAATTTGAAATATTCAAAAGATAAAGTCACCTTTTACTATTCAAACTTAAATAGATACTA
1 TTTTAATTTGAAATATTCAAAAGATAAAGTCACCTTTTAATATTCAAACTTAAATAGATACTA
* * * *
4255366 TTTTAATTTGAAATATTCTAAAGGATATAA-TTATC-TTTAATATTCAAAGTTAAATAG
1 TTTTAATTTGAAATATTC-AAAAGATA-AAGTCACCTTTTAATATTCAAACTTAAATAG
4255423 TTAACAAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 38 0.76
64 10 0.20
65 2 0.04
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.41
Consensus pattern (63 bp):
TTTTAATTTGAAATATTCAAAAGATAAAGTCACCTTTTAATATTCAAACTTAAATAGATACTA
Found at i:4265545 original size:82 final size:82
Alignment explanation
Indices: 4265408--4265571 Score: 283
Period size: 82 Copynumber: 2.0 Consensus size: 82
4265398 AATATGAATG
* *
4265408 AAATTAACAAAACTTTGTCACAGTTACTTGGCATGTTATGAACCGCTGAAAGTAACATGAAAATG
1 AAATTAACAAAACTTTGTCACAATTACTTGGCATGTTACGAACCGCTGAAAGTAACATGAAAATG
4265473 GTTGGACCTAAGCCCAT
66 GTTGGACCTAAGCCCAT
* * *
4265490 AAATTAACAAGACTTTGTCACAATTACTTGGCATGTTACGAACCGTTGAAAGTAACATGAGAATG
1 AAATTAACAAAACTTTGTCACAATTACTTGGCATGTTACGAACCGCTGAAAGTAACATGAAAATG
4265555 GTTGGACCTAAGCCCAT
66 GTTGGACCTAAGCCCAT
4265572 TATGATTGTC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (82 bp):
AAATTAACAAAACTTTGTCACAATTACTTGGCATGTTACGAACCGCTGAAAGTAACATGAAAATG
GTTGGACCTAAGCCCAT
Found at i:4274182 original size:157 final size:157
Alignment explanation
Indices: 4273896--4274209 Score: 628
Period size: 157 Copynumber: 2.0 Consensus size: 157
4273886 TAATAAGAAC
4273896 TAAGGATACATATCTTGTCCATGGAGGTGAAGAAGAGCTTAGTGTAAAAGGTTATACTGATGCCA
1 TAAGGATACATATCTTGTCCATGGAGGTGAAGAAGAGCTTAGTGTAAAAGGTTATACTGATGCCA
4273961 GCTTCCAAACTGACAAGGATGACTCGCGATCGTAATTGGGTTTTTTGTTTTGCCTTAATGGAGGA
66 GCTTCCAAACTGACAAGGATGACTCGCGATCGTAATTGGGTTTTTTGTTTTGCCTTAATGGAGGA
4274026 GATGTGAGCTGGAAAAGTTCGAAGCAA
131 GATGTGAGCTGGAAAAGTTCGAAGCAA
4274053 TAAGGATACATATCTTGTCCATGGAGGTGAAGAAGAGCTTAGTGTAAAAGGTTATACTGATGCCA
1 TAAGGATACATATCTTGTCCATGGAGGTGAAGAAGAGCTTAGTGTAAAAGGTTATACTGATGCCA
4274118 GCTTCCAAACTGACAAGGATGACTCGCGATCGTAATTGGGTTTTTTGTTTTGCCTTAATGGAGGA
66 GCTTCCAAACTGACAAGGATGACTCGCGATCGTAATTGGGTTTTTTGTTTTGCCTTAATGGAGGA
4274183 GATGTGAGCTGGAAAAGTTCGAAGCAA
131 GATGTGAGCTGGAAAAGTTCGAAGCAA
4274210 GACACAGTAG
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (157 bp):
TAAGGATACATATCTTGTCCATGGAGGTGAAGAAGAGCTTAGTGTAAAAGGTTATACTGATGCCA
GCTTCCAAACTGACAAGGATGACTCGCGATCGTAATTGGGTTTTTTGTTTTGCCTTAATGGAGGA
GATGTGAGCTGGAAAAGTTCGAAGCAA
Found at i:4281834 original size:12 final size:12
Alignment explanation
Indices: 4281817--4281864 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
4281807 TTTAAAATAG
4281817 TTTTTCTTTTTT
1 TTTTTCTTTTTT
4281829 TTTTTC--TTTT
1 TTTTTCTTTTTT
*
4281839 TCTTTCTTTTTT
1 TTTTTCTTTTTT
* *
4281851 TCTCTCTTTTTT
1 TTTTTCTTTTTT
4281863 TT
1 TT
4281865 CTTCAGGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 9 0.29
12 22 0.71
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:4281840 original size:18 final size:18
Alignment explanation
Indices: 4281817--4281853 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4281807 TTTAAAATAG
*
4281817 TTTTTCTTTTTTTTTTTC
1 TTTTTCTTTCTTTTTTTC
4281835 TTTTTCTTTCTTTTTTTC
1 TTTTTCTTTCTTTTTTTC
4281853 T
1 T
4281854 CTCTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTCTTTCTTTTTTTC
Found at i:4284565 original size:34 final size:34
Alignment explanation
Indices: 4284522--4284589 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
4284512 CTCTCTAGTA
4284522 TGTTGGCCCTTCATTCTTTAGCTCAAACGACATC
1 TGTTGGCCCTTCATTCTTTAGCTCAAACGACATC
4284556 TGTTGGCCCTTCATTCTTTAGCTCAAACGACATC
1 TGTTGGCCCTTCATTCTTTAGCTCAAACGACATC
4284590 ACCTTGTAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (34 bp):
TGTTGGCCCTTCATTCTTTAGCTCAAACGACATC
Found at i:4285742 original size:90 final size:89
Alignment explanation
Indices: 4285598--4285762 Score: 294
Period size: 90 Copynumber: 1.8 Consensus size: 89
4285588 TTTTATAGCC
* *
4285598 AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTC
1 AAGTTACCCTAATAATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTA
*
4285663 AAATTTAATAATCCTCTTATATCA
66 AAATTAAATAATCCTCTTATATCA
4285687 AAGTTACCCTAATAATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
1 AAGTTACCCTAATAATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
4285752 AAAATTAAATA
65 AAAATTAAATA
4285763 TTCAAGATTA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 22 0.31
90 50 0.69
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (89 bp):
AAGTTACCCTAATAATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTA
AAATTAAATAATCCTCTTATATCA
Found at i:4285792 original size:20 final size:21
Alignment explanation
Indices: 4285724--4285793 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
4285714 TATTATTTCA
*
4285724 AATTAATTAAATC-TATATTT
1 AATTAATTAAAACATATATTT
* * *
4285744 AATTAATTAAAATTAAATATTCA
1 AATTAATTAAAA-CATATATT-T
4285767 AGATT-ATTAAAACATATATTT
1 A-ATTAATTAAAACATATATTT
4285788 AATTAA
1 AATTAA
4285794 ATCTAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 14 0.37
21 2 0.05
22 11 0.29
23 8 0.21
24 3 0.08
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (21 bp):
AATTAATTAAAACATATATTT
Found at i:4292828 original size:228 final size:228
Alignment explanation
Indices: 4292431--4292886 Score: 842
Period size: 228 Copynumber: 2.0 Consensus size: 228
4292421 TAATGCCATT
4292431 ACATTTTCAATTTTAGTCTTCATAAAAAATAGTCCATTTTTGTTTTGATTAAGCTAAAGGTGATT
1 ACATTTTCAATTTTAGTCTTCATAAAAAATAGTCCATTTTTGTTTTGATTAAGCTAAAGGTGATT
* *
4292496 ATAAGTGTTTATTCAAGAGAGCTTTCCATATGAGCAACTATTTGTTGCTATAACAATATCAAACT
66 ATAAGTGTTTATTCAAGAGAGCTTTCCATATGAGCAAATAATTGTTGCTATAACAATATCAAACT
* *
4292561 TTGATGATTTACTTGTTGCTACAGAATTGTCGTGGTATGTTGAGTATGTCAATTTTATTGTAAGT
131 TTGATGATTTACTTGTTACTACAGAATTGTCGTGGTATGTTGACTATGTCAATTTTATTGTAAGT
* *
4292626 GAACTCTTAACTCCTGAATTTAATTCACGACAA
196 GAACTCCTAACTCCTGAATTTAATTCACAACAA
4292659 ACATTTTCAATTTTAGTCTTCATAAAAAAATAGTCCATTTTTGTTTTGATTAAGCTAAAGGTGAT
1 ACATTTTCAATTTTAGTCTTCAT-AAAAAATAGTCCATTTTTGTTTTGATTAAGCTAAAGGTGAT
4292724 TATAAGTGTTTATTCAAGAGAGCTTT-CATATGAGCAAATAATTGTTGCTATAACAATATCAAAC
65 TATAAGTGTTTATTCAAGAGAGCTTTCCATATGAGCAAATAATTGTTGCTATAACAATATCAAAC
4292788 TTTGATGATTTACTTGTTACTACAGAATTGTCGTGGTATGTTGACTATGTCAATTTTATTGTAAG
130 TTTGATGATTTACTTGTTACTACAGAATTGTCGTGGTATGTTGACTATGTCAATTTTATTGTAAG
4292853 TGAACTCCTAACTCCTGAATTTAATTCACAACAA
195 TGAACTCCTAACTCCTGAATTTAATTCACAACAA
4292887 GGAAAAAAGT
Statistics
Matches: 221, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
228 154 0.70
229 67 0.30
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (228 bp):
ACATTTTCAATTTTAGTCTTCATAAAAAATAGTCCATTTTTGTTTTGATTAAGCTAAAGGTGATT
ATAAGTGTTTATTCAAGAGAGCTTTCCATATGAGCAAATAATTGTTGCTATAACAATATCAAACT
TTGATGATTTACTTGTTACTACAGAATTGTCGTGGTATGTTGACTATGTCAATTTTATTGTAAGT
GAACTCCTAACTCCTGAATTTAATTCACAACAA
Found at i:4293646 original size:21 final size:21
Alignment explanation
Indices: 4293617--4293865 Score: 203
Period size: 21 Copynumber: 12.0 Consensus size: 21
4293607 CGTTGCAATT
4293617 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
4293638 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
4293657 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* * *
4293680 TTCGACTATCGTAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
4293699 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
4293722 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
4293741 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
4293764 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
4293783 TTGAAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* * *
4293806 TTCGACTATCACAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
4293825 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
4293846 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
4293866 TATGTAAATC
Statistics
Matches: 177, Mismatches: 33, Indels: 36
0.72 0.13 0.15
Matches are distributed among these distances:
19 52 0.29
21 87 0.49
23 38 0.21
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:4293866 original size:42 final size:42
Alignment explanation
Indices: 4293624--4293859 Score: 395
Period size: 42 Copynumber: 5.7 Consensus size: 42
4293614 ATTTTGGACT
*
4293624 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
*
4293666 ATCGCAACGCGAACTTCGACTATCGTAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
*
4293708 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
* *
4293750 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
*
4293792 ATCGCAACGCGAACTTCGACTATCACAACGAATTTGG-A-AA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
*
4293832 ATCGCAACGCGAACTTGGACTATCGCAA
1 ATCGCAACGCGAACTTCGACTATCGCAA
4293860 TGCGAATATG
Statistics
Matches: 182, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 28 0.15
41 1 0.01
42 153 0.84
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
Found at i:4293878 original size:20 final size:20
Alignment explanation
Indices: 4293853--4293904 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
4293843 AACTTGGACT
4293853 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
4293873 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
4293893 ATCGCAATGCGA
1 ATCGCAATGCGA
4293905 TAGTCGAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:4294196 original size:2 final size:2
Alignment explanation
Indices: 4294189--4294276 Score: 162
Period size: 2 Copynumber: 45.0 Consensus size: 2
4294179 GTTAGGATTG
4294189 AT AT AT AT AT AT AT AT AT AT AT -T 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
4294230 AT AT AT AT AT AT AT AT AT AT AT -T 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
4294271 AT AT AT
1 AT AT AT
4294277 GTCACGCTTG
Statistics
Matches: 84, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.02
2 82 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4298480 original size:22 final size:23
Alignment explanation
Indices: 4298452--4298503 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
4298442 CAAAGTTAAT
4298452 AGTCAACGGT-TAGACCAGTCAA-
1 AGTCAACGGTCT-GACCAGTCAAC
*
4298474 AGTCAACGGTCTGACCGGTCAAC
1 AGTCAACGGTCTGACCAGTCAAC
4298497 AGTCAAC
1 AGTCAAC
4298504 TCTAACCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (23 bp):
AGTCAACGGTCTGACCAGTCAAC
Found at i:4302191 original size:17 final size:18
Alignment explanation
Indices: 4302169--4302211 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
4302159 GTTTAAAGGT
*
4302169 ACTTTAGG-TCATTTTAC
1 ACTTTAGGTTAATTTTAC
*
4302186 ACTTTAGGTTAATTTTTC
1 ACTTTAGGTTAATTTTAC
4302204 ACTTTAGG
1 ACTTTAGG
4302212 GGTAATTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (18 bp):
ACTTTAGGTTAATTTTAC
Found at i:4302217 original size:19 final size:18
Alignment explanation
Indices: 4302169--4302218 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
4302159 GTTTAAAGGT
*
4302169 ACTTTA-GGTCATTTTAC
1 ACTTTAGGGTAATTTTAC
* *
4302186 ACTTTAGGTTAATTTTTC
1 ACTTTAGGGTAATTTTAC
4302204 ACTTTAGGGGTAATT
1 ACTTTA-GGGTAATT
4302219 CTATAATTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 6 0.22
18 14 0.52
19 7 0.26
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (18 bp):
ACTTTAGGGTAATTTTAC
Found at i:4303058 original size:12 final size:12
Alignment explanation
Indices: 4303041--4303067 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4303031 AACGGTCAAT
4303041 GGTCAATTGCTC
1 GGTCAATTGCTC
4303053 GGTCAATTGCTC
1 GGTCAATTGCTC
4303065 GGT
1 GGT
4303068 TAACGGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.22, G:0.30, T:0.33
Consensus pattern (12 bp):
GGTCAATTGCTC
Found at i:4306679 original size:58 final size:60
Alignment explanation
Indices: 4306546--4306679 Score: 141
Period size: 58 Copynumber: 2.3 Consensus size: 60
4306536 AGAACTGTAT
** *
4306546 CCATAAGGACTTACCCTAGGCCCGAAAGCGTAGGTGCCAACCTAAGGGAGCACCTTGGGT
1 CCATAAGGACTTACCCTAGGCCCGAAAGCGTAGGTGCCAACCTAAGGGAGCACCTCAGGC
** * * * *
4306606 ATATAAGGTCTTACCCTA-G-CCG-AAGTGTAGGTGCCCACCTAAGGGGGTGC-CCTCAGGC
1 CCATAAGGACTTACCCTAGGCCCGAAAGCGTAGGTGCCAACCTAA--GGGAGCACCTCAGGC
4306664 CCATAAGGACTTACCC
1 CCATAAGGACTTACCC
4306680 AATGCACATA
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
57 18 0.30
58 21 0.35
59 6 0.10
60 15 0.25
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (60 bp):
CCATAAGGACTTACCCTAGGCCCGAAAGCGTAGGTGCCAACCTAAGGGAGCACCTCAGGC
Found at i:4307116 original size:13 final size:13
Alignment explanation
Indices: 4307098--4307124 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4307088 TATATGTACA
4307098 AGATATTTCAAAC
1 AGATATTTCAAAC
4307111 AGATATTTCAAAC
1 AGATATTTCAAAC
4307124 A
1 A
4307125 TTTAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (13 bp):
AGATATTTCAAAC
Found at i:4308870 original size:20 final size:20
Alignment explanation
Indices: 4308845--4308888 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4308835 CCACTATATT
* *
4308845 TGATGCACCTATATGTGGTA
1 TGATGCACATATATGTGGGA
4308865 TGATGCACATATATGTGGGA
1 TGATGCACATATATGTGGGA
4308885 TGAT
1 TGAT
4308889 ATGGTATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.34
Consensus pattern (20 bp):
TGATGCACATATATGTGGGA
Found at i:4312349 original size:21 final size:21
Alignment explanation
Indices: 4312323--4312401 Score: 56
Period size: 21 Copynumber: 3.7 Consensus size: 21
4312313 CAAGGGTTCA
4312323 ATGTGGTC-CTTCGGGATAATT
1 ATGTGG-CACTTCGGGATAATT
* *
4312344 ATGTGGCACTTCAGTGCA-AACCT
1 ATGTGGCACTTC-G-GGATAA-TT
* *
4312367 ATGTGGTC-CTTTGAGATAATT
1 ATGTGG-CACTTCGGGATAATT
4312388 ATGTGGCACTTCGG
1 ATGTGGCACTTCGG
4312402 TGCAAATTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
20 2 0.05
21 22 0.51
22 6 0.14
23 12 0.28
24 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (21 bp):
ATGTGGCACTTCGGGATAATT
Found at i:4312386 original size:44 final size:44
Alignment explanation
Indices: 4312323--4312407 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
4312313 CAAGGGTTCA
*
4312323 ATGTGGTCCTTCGGGATAATTATGTGGCACTTCAGTGCAAACCT
1 ATGTGGTCCTTCGAGATAATTATGTGGCACTTCAGTGCAAACCT
* *
4312367 ATGTGGTCCTTTGAGATAATTATGTGGCACTTCGGTGCAAA
1 ATGTGGTCCTTCGAGATAATTATGTGGCACTTCAGTGCAAA
4312408 TTATGAGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (44 bp):
ATGTGGTCCTTCGAGATAATTATGTGGCACTTCAGTGCAAACCT
Found at i:4314178 original size:24 final size:24
Alignment explanation
Indices: 4314146--4314222 Score: 145
Period size: 24 Copynumber: 3.2 Consensus size: 24
4314136 CTTAGTCGAC
4314146 CGCTCAACCTGAAGTACGCTCTAT
1 CGCTCAACCTGAAGTACGCTCTAT
4314170 CGCTCAACCTGAAGTACGCTCTAT
1 CGCTCAACCTGAAGTACGCTCTAT
*
4314194 CGCTCAACCTGAAGTACACTCTAT
1 CGCTCAACCTGAAGTACGCTCTAT
4314218 CGCTC
1 CGCTC
4314223 GAGTGTATAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.25, C:0.35, G:0.16, T:0.25
Consensus pattern (24 bp):
CGCTCAACCTGAAGTACGCTCTAT
Found at i:4317170 original size:20 final size:20
Alignment explanation
Indices: 4317147--4317218 Score: 135
Period size: 20 Copynumber: 3.6 Consensus size: 20
4317137 TGACTTGGGA
4317147 GTATCGATACCAATGGTATG
1 GTATCGATACCAATGGTATG
*
4317167 GTATCGATACCAATGGCATG
1 GTATCGATACCAATGGTATG
4317187 GTATCGATACCAATGGTATG
1 GTATCGATACCAATGGTATG
4317207 GTATCGATACCA
1 GTATCGATACCA
4317219 TTTCTGAGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (20 bp):
GTATCGATACCAATGGTATG
Found at i:4317930 original size:23 final size:23
Alignment explanation
Indices: 4317872--4317930 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
4317862 TCGGGACAAT
*
4317872 TATGTGGTACTTTGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAACC
*
4317895 TATGTGGAACTTCGGTGCAAACC
1 TATGTGGTACTTCGGTGCAAACC
*
4317918 TATGTGGTCCTTC
1 TATGTGGTACTTC
4317931 AGGATAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.34
Consensus pattern (23 bp):
TATGTGGTACTTCGGTGCAAACC
Found at i:4323303 original size:21 final size:21
Alignment explanation
Indices: 4323249--4323343 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 21
4323239 TCGAGGGTTC
* * *
4323249 TATGTGGTCCTTCGGGATATA
1 TATGTGGTCCTTTGGAAAATA
**
4323270 TATGTAATCCTTTGGAAAATA
1 TATGTGGTCCTTTGGAAAATA
* *
4323291 TATGTGGTTCTTTGAGACACATA
1 TATGTGGTCCTTTG-GA-AAATA
*
4323314 T-T-TGGTCCTTTGGAATATA
1 TATGTGGTCCTTTGGAAAATA
*
4323333 TATGTGATCCT
1 TATGTGGTCCT
4323344 AAAGGAGTGG
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
19 5 0.09
20 3 0.05
21 42 0.72
22 3 0.05
23 5 0.09
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (21 bp):
TATGTGGTCCTTTGGAAAATA
Found at i:4323420 original size:23 final size:21
Alignment explanation
Indices: 4323368--4323408 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4323358 TCGGGATATC
* *
4323368 TATGTGGCCCTTCGAGACATA
1 TATGTGGTCCTTCAAGACATA
4323389 TATGTGGTCCTTCAAGACAT
1 TATGTGGTCCTTCAAGACAT
4323409 TTCAATGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (21 bp):
TATGTGGTCCTTCAAGACATA
Found at i:4324972 original size:22 final size:20
Alignment explanation
Indices: 4324928--4324972 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
4324918 ATATTATGAG
* *
4324928 ATAAATTTTTTTGAATAATA
1 ATAAATTTTTTTAAATAAAA
4324948 ATAAATATTTTTTAAATTAAAA
1 ATAAAT-TTTTTTAAA-TAAAA
4324970 ATA
1 ATA
4324973 TGATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 8 0.38
22 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATAAATTTTTTTAAATAAAA
Found at i:4328083 original size:44 final size:44
Alignment explanation
Indices: 4328016--4328102 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
4328006 GTCAAGGGTT
* *
4328016 CTATGTGGTCCTTCGGGATAATTATGTGGCACTTTAGTGCAAAC
1 CTATGTGGTCCTTCGGGACAATTATGTGGCACTTCAGTGCAAAC
* *
4328060 CTATGTGGTCCTTTGGGACAATTATGTGGTACTTCAGTGCAAA
1 CTATGTGGTCCTTCGGGACAATTATGTGGCACTTCAGTGCAAA
4328103 TTACGAGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (44 bp):
CTATGTGGTCCTTCGGGACAATTATGTGGCACTTCAGTGCAAAC
Found at i:4328087 original size:21 final size:21
Alignment explanation
Indices: 4328017--4328089 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
4328007 TCAAGGGTTC
* *
4328017 TATGTGGTCCTTCGGGATAAT
1 TATGTGGTCCTTTGGGACAAT
* *
4328038 TATGTGG-CACTTTAGTG-CAAACC
1 TATGTGGTC-CTTT-GGGAC-AA-T
4328061 TATGTGGTCCTTTGGGACAAT
1 TATGTGGTCCTTTGGGACAAT
4328082 TATGTGGT
1 TATGTGGT
4328090 ACTTCAGTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
20 1 0.03
21 18 0.45
22 8 0.20
23 12 0.30
24 1 0.03
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.37
Consensus pattern (21 bp):
TATGTGGTCCTTTGGGACAAT
Found at i:4333963 original size:73 final size:73
Alignment explanation
Indices: 4333839--4333998 Score: 248
Period size: 73 Copynumber: 2.2 Consensus size: 73
4333829 CCCAGAGGGA
* *
4333839 ACAGATACCCCCTGAATGGTTTTGGCTCTGAGAAAACAGAATGTCCGGGGGGTACAGATTCCCCC
1 ACAGATACCCCCTGAATGGTTTTGGCTCTAAGAAAACAGAATGTCCAGGGGGTACAGATTCCCCC
4333904 CAAGGGGT
66 CAAGGGGT
* * * *
4333912 ACAGATACCCCTTGAATGGTTTTTGCTCTAAGAAAATAGAATGTCCAGGGGGTACTGATTCCCCC
1 ACAGATACCCCCTGAATGGTTTTGGCTCTAAGAAAACAGAATGTCCAGGGGGTACAGATTCCCCC
4333977 CAAGGGGT
66 CAAGGGGT
* *
4333985 ACCGATTCCCCCTG
1 ACAGATACCCCCTG
4333999 TTTAACGGTC
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 78 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (73 bp):
ACAGATACCCCCTGAATGGTTTTGGCTCTAAGAAAACAGAATGTCCAGGGGGTACAGATTCCCCC
CAAGGGGT
Found at i:4336061 original size:23 final size:23
Alignment explanation
Indices: 4336030--4336073 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4336020 ATTATATGGC
*
4336030 ACTTTGGTGCAAACCTATGTGGA
1 ACTTCGGTGCAAACCTATGTGGA
*
4336053 ACTTCGGTGCGAACCTATGTG
1 ACTTCGGTGCAAACCTATGTG
4336074 TCATTCGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (23 bp):
ACTTCGGTGCAAACCTATGTGGA
Found at i:4344770 original size:16 final size:16
Alignment explanation
Indices: 4344749--4344791 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
4344739 AACCTTTTAT
4344749 AAAAATCATAGGATAA
1 AAAAATCATAGGATAA
4344765 AAAAATCATAGGATAA
1 AAAAATCATAGGATAA
*
4344781 AGAAATCATAG
1 AAAAATCATAG
4344792 TACATCTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.60, C:0.07, G:0.14, T:0.19
Consensus pattern (16 bp):
AAAAATCATAGGATAA
Found at i:4357124 original size:19 final size:18
Alignment explanation
Indices: 4357102--4357148 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
4357092 AGTGAATAAT
4357102 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
4357121 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
4357140 AATA-AAGAA
1 AATATAAGAA
4357149 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:4361428 original size:8 final size:8
Alignment explanation
Indices: 4361412--4361444 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
4361402 ACTTCTCTTT
4361412 TTCTTTTC
1 TTCTTTTC
4361420 TT-TTCTTC
1 TTCTT-TTC
4361428 TTCTTTTC
1 TTCTTTTC
4361436 TTCTTTTC
1 TTCTTTTC
4361444 T
1 T
4361445 GATTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 2 0.09
8 19 0.83
9 2 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:4361429 original size:19 final size:19
Alignment explanation
Indices: 4361407--4361461 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
4361397 TTTGAACTTC
*
4361407 TCTTTTTCTTTTCTTTTCT
1 TCTTTTTCTCTTCTTTTCT
4361426 TCTTCTTT-TCTTCTTTTCT
1 TCTT-TTTCTCTTCTTTTCT
**
4361445 GATTTTTCTCTTCTTTT
1 TCTTTTTCTCTTCTTTT
4361462 TGCACTCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 3 0.10
19 25 0.81
20 3 0.10
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (19 bp):
TCTTTTTCTCTTCTTTTCT
Found at i:4361431 original size:16 final size:16
Alignment explanation
Indices: 4361407--4361437 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4361397 TTTGAACTTC
*
4361407 TCTTTTTCTTTTCTTT
1 TCTTCTTCTTTTCTTT
4361423 TCTTCTTCTTTTCTT
1 TCTTCTTCTTTTCTT
4361438 CTTTTCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTCTTCTTTTCTTT
Found at i:4361444 original size:16 final size:16
Alignment explanation
Indices: 4361403--4361444 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
4361393 TCTTTTTGAA
4361403 CTTCTCTTT-TTCTTTT
1 CTTCT-TTTCTTCTTTT
4361419 CTT-TTCTTCTTCTTTT
1 CTTCTT-TTCTTCTTTT
4361435 CTTCTTTTCT
1 CTTCTTTTCT
4361445 GATTTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 3 0.13
16 17 0.74
17 2 0.09
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
CTTCTTTTCTTCTTTT
Found at i:4361737 original size:19 final size:18
Alignment explanation
Indices: 4361715--4361761 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
4361705 AGTGAATAAT
4361715 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
4361734 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
4361753 AATA-AAGAA
1 AATATAAGAA
4361762 AAGGATAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:4369648 original size:15 final size:15
Alignment explanation
Indices: 4369624--4369653 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4369614 TTATATAGTT
4369624 AAATTCTTTTTTTAA
1 AAATTCTTTTTTTAA
*
4369639 AAATTTTTTTTTTAA
1 AAATTCTTTTTTTAA
4369654 TTACAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
AAATTCTTTTTTTAA
Found at i:4374191 original size:22 final size:22
Alignment explanation
Indices: 4374159--4374200 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4374149 CAGTGTTGAT
*
4374159 CGTTGACCGGTCAT-ACTGTTAA
1 CGTTGAACGGTC-TGACTGTTAA
4374181 CGTTGAACGGTCTGACTGTT
1 CGTTGAACGGTCTGACTGTT
4374201 GACCTTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.33
Consensus pattern (22 bp):
CGTTGAACGGTCTGACTGTTAA
Found at i:4383666 original size:23 final size:24
Alignment explanation
Indices: 4383640--4383698 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
4383630 TAAACGAAAC
4383640 TGCCACATAGAAT-TGCACCGAAG
1 TGCCACATAGAATATGCACCGAAG
* *
4383663 TGCCACGTAGAATATGCATCGAAG
1 TGCCACATAGAATATGCACCGAAG
4383687 TGCCACATAGAA
1 TGCCACATAGAA
4383699 ATGTCCCGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.19
Consensus pattern (24 bp):
TGCCACATAGAATATGCACCGAAG
Found at i:4383721 original size:21 final size:21
Alignment explanation
Indices: 4383695--4383775 Score: 128
Period size: 21 Copynumber: 3.9 Consensus size: 21
4383685 AGTGCCACAT
4383695 AGAAATGTCCCGAAGGACCAC
1 AGAAATGTCCCGAAGGACCAC
*
4383716 AGAAATGTCCCGGAGGACCAC
1 AGAAATGTCCCGAAGGACCAC
4383737 AGAAATGTCCC-AGAGGACCAC
1 AGAAATGTCCCGA-AGGACCAC
*
4383758 AGAAATGTCCCGGAGGAC
1 AGAAATGTCCCGAAGGAC
4383776 TGTGTAGAGT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.36, C:0.27, G:0.27, T:0.10
Consensus pattern (21 bp):
AGAAATGTCCCGAAGGACCAC
Found at i:4383754 original size:42 final size:42
Alignment explanation
Indices: 4383695--4383775 Score: 146
Period size: 42 Copynumber: 1.9 Consensus size: 42
4383685 AGTGCCACAT
4383695 AGAAATGTCCCGAAGGACCACAGAAATGTCCCGGAGGACCAC
1 AGAAATGTCCCGAAGGACCACAGAAATGTCCCGGAGGACCAC
4383737 AGAAATGTCCC-AGAGGACCACAGAAATGTCCCGGAGGAC
1 AGAAATGTCCCGA-AGGACCACAGAAATGTCCCGGAGGAC
4383776 TGTGTAGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.36, C:0.27, G:0.27, T:0.10
Consensus pattern (42 bp):
AGAAATGTCCCGAAGGACCACAGAAATGTCCCGGAGGACCAC
Found at i:4387300 original size:23 final size:24
Alignment explanation
Indices: 4387274--4387332 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
4387264 TAGTCGAAAC
4387274 TGCCACATAGAAT-TGCACCGAAG
1 TGCCACATAGAATATGCACCGAAG
* *
4387297 TGCCACGTAGAATATGCATCGAAG
1 TGCCACATAGAATATGCACCGAAG
4387321 TGCCACATAGAA
1 TGCCACATAGAA
4387333 ATGTCCCGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 12 0.38
24 20 0.62
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.19
Consensus pattern (24 bp):
TGCCACATAGAATATGCACCGAAG
Found at i:4387349 original size:23 final size:23
Alignment explanation
Indices: 4387323--4387444 Score: 92
Period size: 21 Copynumber: 5.4 Consensus size: 23
4387313 CATCGAAGTG
4387323 CCACATAGAAATGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
*
4387346 CCAC--AGAAATGTCCCGGAGGA
1 CCACATAGAAATGTCCCGAAGGA
4387367 CCACA-A-AAATGTCCC-AGAGGA
1 CCACATAGAAATGTCCCGA-AGGA
*** ** *
4387388 CCGTGTAGAGTTTGTCCCGAAGTA
1 CCACATAGA-AATGTCCCGAAGGA
* * *
4387412 CCACATAGAATTGTCCTGAATGA
1 CCACATAGAAATGTCCCGAAGGA
*
4387435 CCGCATAGAA
1 CCACATAGAA
4387445 CCCTCGACTC
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
21 35 0.45
22 2 0.03
23 24 0.31
24 15 0.19
25 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.17
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAGGA
Found at i:4388889 original size:7 final size:7
Alignment explanation
Indices: 4388877--4388901 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4388867 TTACAAGAAT
4388877 ATTTTGA
1 ATTTTGA
4388884 ATTTTGA
1 ATTTTGA
4388891 ATTTTGA
1 ATTTTGA
4388898 ATTT
1 ATTT
4388902 AAAGGTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
ATTTTGA
Found at i:4388995 original size:13 final size:13
Alignment explanation
Indices: 4388977--4389006 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4388967 GATTATGTAG
4388977 TTAAATTCTTATT
1 TTAAATTCTTATT
*
4388990 TTAAATTCTTGTT
1 TTAAATTCTTATT
4389003 TTAA
1 TTAA
4389007 TTACAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (13 bp):
TTAAATTCTTATT
Found at i:4391960 original size:20 final size:19
Alignment explanation
Indices: 4391935--4391988 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
4391925 CGATGTTTTC
*
4391935 TGGTATCGATACCTTCCTTA
1 TGGTATCGATACCTTCC-CA
4391955 TGGTATCGGTACTACCTTCCCA
1 TGGTATC-G-A-TACCTTCCCA
4391977 -GGTATCGATACC
1 TGGTATCGATACC
4391989 CTTTGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 4 0.13
19 1 0.03
20 8 0.27
21 7 0.23
22 2 0.07
23 8 0.27
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (19 bp):
TGGTATCGATACCTTCCCA
Found at i:4400445 original size:204 final size:205
Alignment explanation
Indices: 4400090--4400547 Score: 738
Period size: 204 Copynumber: 2.2 Consensus size: 205
4400080 ATTGTTCCGA
* ** * * * *
4400090 GTCCAATATCCTCCACTGTGAAGTTGAAATTGGTTTTGGAACTGAGAAATTGTTTGTTGACAATC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAATC
*
4400155 AGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGTTGTGAAGT
66 AGCCGCCCCTTCAC-GTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGT
* * *
4400220 TGAAATTGACTCTGAATGAAATTTTGTTGACAATTAGCCGCCCCTTCGTTGTAAAGTTGAGCTTT
130 TGAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTG
4400285 TGTTGTCTTGG
195 TGTTGTCTTGG
* *
4400296 GTTCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAATC
* *
4400361 AGTCGCCCCTTCGC-TGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
66 AGCCGCCCCTTCACGTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
* *
4400425 GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCTCTTCGTTGTGAAGTTGAGCTTGT
131 GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTGT
4400490 GTTGTCTTGG
196 GTTGTCTTGG
*
4400500 GTCCAATATGCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAA
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAA
4400548 GCCCCTTCTT
Statistics
Matches: 233, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
204 165 0.71
206 68 0.29
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (205 bp):
GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAATC
AGCCGCCCCTTCACGTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTGT
GTTGTCTTGG
Found at i:4400538 original size:100 final size:104
Alignment explanation
Indices: 4400087--4400539 Score: 530
Period size: 100 Copynumber: 4.4 Consensus size: 104
4400077 AGTATTGTTC
* ** *
4400087 CGAGTCCAATATCCTCCACTGTGAAGTTGAAATTGGTTTTGGAACTGAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCT-GAACTG-GAAATTGTTTGTTGACA
**
4400152 ATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCT
64 ATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* **
4400193 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA-T-GAAA-T-TTTGTTGACAAT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
* * * *
4400254 TAGCCGCCCCTTCGTTGTAAAGTTGAGCTTTTGTTGTCT
66 CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* * * *
4400293 TGGGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTG-AACT-GGAAATTGTTTGTTGACA
* * * *
4400358 GTCAGTCGCCCCTTCG--CTGAAGTTGAGCTTGTGCTGTAT
64 ATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* ** *
4400397 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA-T-GAAA-T-TTTGTTAACAAT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
* *
4400458 CAGCCGCCTCTTCGTTGTGAAGTTGAGCTTGTGTTGTCT
66 CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* * *
4400497 TGGGTCCAATATGCTTCGTTGTGAAGTTGAAATTGGTTCTGAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAA
4400540 ATTGGGAAGC
Statistics
Matches: 293, Mismatches: 46, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
98 22 0.08
99 1 0.00
100 141 0.48
101 3 0.01
102 6 0.02
103 2 0.01
104 58 0.20
105 4 0.01
106 56 0.19
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
Found at i:4400736 original size:54 final size:54
Alignment explanation
Indices: 4400654--4400781 Score: 229
Period size: 54 Copynumber: 2.4 Consensus size: 54
4400644 ACTTGAATAT
* *
4400654 CCTTCGTCGTGAAGTTGAAATCCAAGTATTGTATGTTGCGGGTGGACATGATTC
1 CCTTCGCCATGAAGTTGAAATCCAAGTATTGTATGTTGCGGGTGGACATGATTC
4400708 CCTTCGCCATGAAGTTGAAATCCAAGTATTGTATGTTGCGGGTGGACATGATTC
1 CCTTCGCCATGAAGTTGAAATCCAAGTATTGTATGTTGCGGGTGGACATGATTC
*
4400762 CTTTCGCCATGAAGTTGAAA
1 CCTTCGCCATGAAGTTGAAA
4400782 CCGTGGATGA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 71 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (54 bp):
CCTTCGCCATGAAGTTGAAATCCAAGTATTGTATGTTGCGGGTGGACATGATTC
Found at i:4401692 original size:6 final size:6
Alignment explanation
Indices: 4401667--4401725 Score: 59
Period size: 6 Copynumber: 9.8 Consensus size: 6
4401657 ACCCACCTTA
* **
4401667 TTTTTC -TTTTC TTTTCTC TTGTTC TTTTTC TCTTTT- TTCCTC TTTTTC
1 TTTTTC TTTTTC TTTT-TC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC
4401715 TTTTTC TTTTT
1 TTTTTC TTTTT
4401726 TACAATTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 7 0.16
6 27 0.63
7 9 0.21
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:4401695 original size:24 final size:23
Alignment explanation
Indices: 4401667--4401726 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 23
4401657 ACCCACCTTA
*
4401667 TTTTTCTTTTCTTTTCTCTTGTTC
1 TTTTTCTTTT-TTTCCTCTTGTTC
*
4401691 TTTTTCTCTTTTTTCCTCTTTTTC
1 TTTTTCT-TTTTTTCCTCTTGTTC
4401715 TTTTTCTTTTTT
1 TTTTTCTTTTTT
4401727 ACAATTTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 5 0.15
24 25 0.76
25 3 0.09
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTTTCTTTTTTTCCTCTTGTTC
Found at i:4401783 original size:16 final size:16
Alignment explanation
Indices: 4401764--4401809 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
4401754 CACCCTAAAA
*
4401764 TTTTTTCTCTTTTTTG
1 TTTTTTCTCTTTTTTC
*
4401780 TTTTTT-TCCTTTTTC
1 TTTTTTCTCTTTTTTC
*
4401795 CTTTTTC-CTTTTTTC
1 TTTTTTCTCTTTTTTC
4401810 AACTTAGGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTTTTCTCTTTTTTC
Found at i:4401792 original size:7 final size:7
Alignment explanation
Indices: 4401782--4401807 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4401772 CTTTTTTGTT
4401782 TTTTTCC
1 TTTTTCC
4401789 TTTTTCC
1 TTTTTCC
4401796 TTTTTCC
1 TTTTTCC
4401803 TTTTT
1 TTTTT
4401808 TCAACTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCC
Found at i:4401792 original size:8 final size:8
Alignment explanation
Indices: 4401764--4401809 Score: 51
Period size: 7 Copynumber: 5.9 Consensus size: 8
4401754 CACCCTAAAA
4401764 TTTTTTCTC
1 TTTTTTC-C
**
4401773 TTTTTTGT
1 TTTTTTCC
4401781 TTTTTTCC
1 TTTTTTCC
4401789 -TTTTTCC
1 TTTTTTCC
4401796 -TTTTTCC
1 TTTTTTCC
4401803 TTTTTTC
1 TTTTTTC
4401810 AACTTAGGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
7 14 0.44
8 12 0.38
9 6 0.19
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTTTCC
Found at i:4406293 original size:204 final size:205
Alignment explanation
Indices: 4405941--4406398 Score: 765
Period size: 204 Copynumber: 2.2 Consensus size: 205
4405931 ATTGTTCCGA
* ** * * * *
4405941 GTCCAATATCCTCCACTGTGAAGTTGAAATTGGTTTTGGAACTGAGAAATTGTTTGTTGACAATC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAATC
*
4406006 AGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGTTGTGAAGT
66 AGCCGCCCCTTCAC-GTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGT
*
4406071 TGAAATTGACTCTGAATGAAATTTTGTTGACAATCAGCCGCCCCTTCATTGTAAAGTTGAGCTTG
130 TGAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCATTGTAAAGTTGAGCTTG
4406136 TGTTGTCTTGG
195 TGTTGTCTTGG
*
4406147 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAATC
* *
4406212 AGTCGCCCCTTCGC-TGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
66 AGCCGCCCCTTCACGTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
* *
4406276 GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGT
131 GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCATTGTAAAGTTGAGCTTGT
4406341 GTTGTCTTGG
196 GTTGTCTTGG
*
4406351 GTCCAATATGCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAA
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAA
4406399 GCCCCTTCTT
Statistics
Matches: 237, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
204 168 0.71
206 69 0.29
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (205 bp):
GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAATC
AGCCGCCCCTTCACGTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCATTGTAAAGTTGAGCTTGT
GTTGTCTTGG
Found at i:4406389 original size:100 final size:104
Alignment explanation
Indices: 4405938--4406390 Score: 559
Period size: 100 Copynumber: 4.4 Consensus size: 104
4405928 AGTATTGTTC
* ** *
4405938 CGAGTCCAATATCCTCCACTGTGAAGTTGAAATTGGTTTTGGAACTGAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCT-GAACTG-GAAATTGTTTGTTGACA
*
4406003 ATCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCT
64 ATCAGCCGCCCCTTCATTGTGAAGTTGAGCTTGTGCTGTCT
* **
4406044 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA-T-GAAA-T-TTTGTTGACAAT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
* *
4406105 CAGCCGCCCCTTCATTGTAAAGTTGAGCTTGTGTTGTCT
66 CAGCCGCCCCTTCATTGTGAAGTTGAGCTTGTGCTGTCT
* * *
4406144 TGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTG-AACT-GGAAATTGTTTGTTGACA
* * *
4406209 GTCAGTCGCCCCTTC---GCTGAAGTTGAGCTTGTGCTGTAT
64 ATCAGCCGCCCCTTCATTG-TGAAGTTGAGCTTGTGCTGTCT
* ** *
4406248 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA-T-GAAA-T-TTTGTTAACAAT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
* *
4406309 CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCT
66 CAGCCGCCCCTTCATTGTGAAGTTGAGCTTGTGCTGTCT
* * *
4406348 TGGGTCCAATATGCTTCGTTGTGAAGTTGAAATTGGTTCTGAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAA
4406391 ATTGGGAAGC
Statistics
Matches: 301, Mismatches: 36, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
98 22 0.07
99 1 0.00
100 145 0.48
101 4 0.01
102 6 0.02
103 3 0.01
104 60 0.20
105 4 0.01
106 56 0.19
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.36
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
CAGCCGCCCCTTCATTGTGAAGTTGAGCTTGTGCTGTCT
Found at i:4406521 original size:66 final size:66
Alignment explanation
Indices: 4406399--4406526 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 66
4406389 AAATTGGGAA
* * *
4406399 GCCCCTTCTTCGTGAAGTTGAGCCTCAAATGGCATAATATCCTCCGTCGTGGAGTTGAAATCGCG
1 GCCCCTTCGTCGTGAAGTTGAGCCT---ATGACATAATATCCTCCGTCGTGAAGTTGAAATCGCG
4406464 GGTG
63 GGTG
* *
4406468 GCCCCTTCGTCGTGAAGTTGAGCCT-TGACTTGAATATCCTTCGTCGTGAAGTTGAAATC
1 GCCCCTTCGTCGTGAAGTTGAGCCTATGACAT-AATATCCTCCGTCGTGAAGTTGAAATC
4406527 CAAGTATTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
65 4 0.08
66 25 0.47
69 24 0.45
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (66 bp):
GCCCCTTCGTCGTGAAGTTGAGCCTATGACATAATATCCTCCGTCGTGAAGTTGAAATCGCGGGT
G
Found at i:4407489 original size:14 final size:14
Alignment explanation
Indices: 4407460--4407497 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
4407450 ACCCACCTTA
4407460 TTTT-TCTTTTCTT
1 TTTTCTCTTTTCTT
4407473 TTTTCTCTTGTTC-T
1 TTTTCTCTT-TTCTT
4407487 TTTTCTCTTTT
1 TTTTCTCTTTT
4407498 TTCCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.26
14 14 0.61
15 3 0.13
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTCTCTTTTCTT
Found at i:4407504 original size:24 final size:23
Alignment explanation
Indices: 4407469--4407515 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
4407459 ATTTTTCTTT
4407469 TCTTTTTTCTCTTGTTCTTTTTC
1 TCTTTTTTCTCTTGTTCTTTTTC
*
4407492 TCTTTTTTCCTCTTTTTCTTTTTC
1 TCTTTTTT-CTCTTGTTCTTTTTC
4407516 CTATTTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.74
Consensus pattern (23 bp):
TCTTTTTTCTCTTGTTCTTTTTC
Found at i:4407587 original size:8 final size:8
Alignment explanation
Indices: 4407559--4407604 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
4407549 CACCCTAAAA
4407559 TTTTTTCTC
1 TTTTTTC-C
**
4407568 TTTTTTGT
1 TTTTTTCC
4407576 TTTTTTCC
1 TTTTTTCC
4407584 -TTTTT-C
1 TTTTTTCC
4407590 TTTTTTCC
1 TTTTTTCC
4407598 TTTTTTC
1 TTTTTTC
4407605 AACTTAGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
6 1 0.03
7 10 0.32
8 14 0.45
9 6 0.19
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTTCC
Found at i:4407587 original size:14 final size:14
Alignment explanation
Indices: 4407576--4407602 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4407566 TCTTTTTTGT
4407576 TTTTTTCCTTTTTC
1 TTTTTTCCTTTTTC
4407590 TTTTTTCCTTTTT
1 TTTTTTCCTTTTT
4407603 TCAACTTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTCCTTTTTC
Found at i:4407604 original size:15 final size:15
Alignment explanation
Indices: 4407559--4407604 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
4407549 CACCCTAAAA
*
4407559 TTTTTTCTCTTTTTTGT
1 TTTTTTC-CTTTTTT-C
4407576 TTTTTTCC-TTTTTC
1 TTTTTTCCTTTTTTC
4407590 TTTTTTCCTTTTTTC
1 TTTTTTCCTTTTTTC
4407605 AACTTAGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 8 0.30
15 11 0.41
16 1 0.04
17 7 0.26
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTCCTTTTTTC
Found at i:4407628 original size:81 final size:82
Alignment explanation
Indices: 4407484--4407637 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 82
4407474 TTTCTCTTGT
* * *
4407484 TCTTTTTCTCTTTTTTCCTCTTTTTCTTTTTCCTATTTACAATTTAGGGCACCCTTTCAGGTTTT
1 TCTTTTTCTCTTTTTTCCTCTTTTTCTTTTTCCTATTTACAACTTAGGACACCCTCTCAGGTTTT
4407549 CACCCTAAAATTTTTTC
66 CACCCTAAAATTTTTTC
* * * * ** *
4407566 TCTTTTT-TGTTTTTTTC-CTTTTTCTTTTTTCCTTTTTTCAACTTAGGATGCCCTCTCGGGTTT
1 TCTTTTTCTCTTTTTTCCTCTTTTTC-TTTTTCCTATTTACAACTTAGGACACCCTCTCAGGTTT
*
4407629 TCATCCTAA
65 TCACCCTAA
4407638 GCGAAGTACT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
80 7 0.12
81 46 0.77
82 7 0.12
ACGTcount: A:0.12, C:0.23, G:0.08, T:0.56
Consensus pattern (82 bp):
TCTTTTTCTCTTTTTTCCTCTTTTTCTTTTTCCTATTTACAACTTAGGACACCCTCTCAGGTTTT
CACCCTAAAATTTTTTC
Found at i:4411008 original size:25 final size:29
Alignment explanation
Indices: 4410971--4411029 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 29
4410961 AGAATAAAAT
*
4410971 TAATAATATTATAT-A-TATAT-ATGT-A
1 TAATAATACTATATGATTATATAATGTAA
*
4410996 TAATTATACTATATGATTATATAATGTAA
1 TAATAATACTATATGATTATATAATGTAA
4411025 TAATA
1 TAATA
4411030 TTAATAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 12 0.44
26 1 0.04
27 5 0.19
28 4 0.15
29 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (29 bp):
TAATAATACTATATGATTATATAATGTAA
Found at i:4412124 original size:204 final size:205
Alignment explanation
Indices: 4411768--4412225 Score: 749
Period size: 204 Copynumber: 2.2 Consensus size: 205
4411758 ATTGTTCCGA
* * * * * *
4411768 GTCCAATATCCTCCACTGTGAAGTTGAAATTGGTTTTGGAACTGAGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
*
4411833 AGCCGCCCTTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGTTGTGAAGT
66 AGCCGCCCTTTCAC-GTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGT
*
4411898 TGAAATTGACTCTGAATGAAATTTTGTTGACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTG
130 TGAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTG
4411963 TGTTGTCTTGG
195 TGTTGTCTTGG
*
4411974 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
* *
4412039 AGTCGTCCC-TTCGC-TGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGT
66 AGCCG-CCCTTTCACGTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGT
* * *
4412102 TGAAATTGCCTCTGATTGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTG
130 TGAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTG
4412167 TGTTGTCTTGG
195 TGTTGTCTTGG
*
4412178 GTCCAATATGCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGGGAA
1 GTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGGGAA
4412226 GCCCCTTCTT
Statistics
Matches: 235, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
204 166 0.71
206 66 0.28
207 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (205 bp):
GTCCAATATCCTTCATTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
AGCCGCCCTTTCACGTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTGT
GTTGTCTTGG
Found at i:4412216 original size:100 final size:102
Alignment explanation
Indices: 4411765--4412216 Score: 511
Period size: 100 Copynumber: 4.4 Consensus size: 102
4411755 AGTATTGTTC
* ** * *
4411765 CGAGTCCAATATCCTCCACTGTGAAGTTGAAATTGGTTTTGGAACTGAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCT-G-A-T-TGAAATTGTTTGTTGACA
* * **
4411830 GTCAGCCGCCCTTTCACTGTGAAGTTGAGCTTGTGCTGTCT
62 ATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* ** *
4411871 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAA-T-TTTGTTGACAATCA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGATTGAAATTGTTTGTTGACAATCA
* *
4411934 GCCGCCCCTTCGTTGTAAAGTTGAGCTTGTGTTGTCT
66 GCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* *
4411971 TGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTG--ATT--GAAATTGTTTGTTGACA
* * * * *
4412036 GTCAGTCGTCCCTTCG--CTGAAGTTGAGCTTGTGCTGTAT
62 ATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* ** *
4412075 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGCCTCTGATTGAAA-T-TTTGTTAACAATCA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGATTGAAATTGTTTGTTGACAATCA
*
4412138 GCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCT
66 GCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* * * *
4412175 TGGGTCCAATATGCTTCATTGTGAAGTTGAAATTGGTTCTGA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGA
4412217 AATTGGGAAG
Statistics
Matches: 291, Mismatches: 47, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
98 22 0.08
99 1 0.00
100 140 0.48
101 1 0.00
102 9 0.03
104 60 0.21
105 2 0.01
106 56 0.19
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (102 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGATTGAAATTGTTTGTTGACAATCA
GCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
Found at i:4413302 original size:6 final size:6
Alignment explanation
Indices: 4413287--4413347 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
4413277 ACCCACCTTA
**
4413287 TTTTTC -TTTTC TTTTTTC TCTTGTTC TTTTTC TCTTTT- TTCCTC TTTTTC
1 TTTTTC TTTTTC -TTTTTC T-TT-TTC TTTTTC T-TTTTC TTTTTC TTTTTC
4413337 TTTTTC TTTTT
1 TTTTTC TTTTT
4413348 TACAATTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
5 7 0.16
6 21 0.47
7 13 0.29
8 4 0.09
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTC
Found at i:4413316 original size:14 final size:14
Alignment explanation
Indices: 4413287--4413348 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 14
4413277 ACCCACCTTA
4413287 TTTT-TCTTTTCTT
1 TTTTCTCTTTTCTT
4413300 TTTTCTCTTGTTCTT
1 TTTTCTCTT-TTCTT
*
4413315 TTTCTCTTTTTTCCTCT
1 TTT-TCTCTTTT-CT-T
4413332 TTTTCT-TTTTCTT
1 TTTTCTCTTTTCTT
4413345 TTTT
1 TTTT
4413349 ACAATTTTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
13 9 0.21
14 6 0.14
15 14 0.33
16 10 0.23
17 4 0.09
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (14 bp):
TTTTCTCTTTTCTT
Found at i:4413326 original size:23 final size:24
Alignment explanation
Indices: 4413296--4413348 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
4413286 ATTTTTCTTT
4413296 TCTTTTTT-CTCTTGTTCTTTTTC
1 TCTTTTTTCCTCTTGTTCTTTTTC
*
4413319 TCTTTTTTCCTCTTTTTCTTTTTC
1 TCTTTTTTCCTCTTGTTCTTTTTC
4413343 T-TTTTT
1 TCTTTTT
4413349 ACAATTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (24 bp):
TCTTTTTTCCTCTTGTTCTTTTTC
Found at i:4413415 original size:7 final size:7
Alignment explanation
Indices: 4413405--4413430 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4413395 CTTTTTTGTT
4413405 TTTTTCC
1 TTTTTCC
4413412 TTTTTCC
1 TTTTTCC
4413419 TTTTTCC
1 TTTTTCC
4413426 TTTTT
1 TTTTT
4413431 TCAACTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCC
Found at i:4417921 original size:204 final size:205
Alignment explanation
Indices: 4417569--4418026 Score: 765
Period size: 204 Copynumber: 2.2 Consensus size: 205
4417559 ATTGTTCCGA
* ** * * * *
4417569 GTCCAATATCCTCCACTGTGAAGTTGAAATTGGTTTTGGAACTGAGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
* *
4417634 AGCCGCCCTTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGTTGTGAAGT
66 AGCCGCCCCTTCAC-GTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGT
*
4417699 TGAAATTGACTCTGAATGAAATTTTGTTGACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTG
130 TGAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTG
4417764 TGTTGTCTTGG
195 TGTTGTCTTGG
4417775 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
* * *
4417840 AGTCGCCCCTTCGC-TGAAGTTGAGCTTGTGCTGTATCGATTCTAATATCCTTCGTTGTGAAGTT
66 AGCCGCCCCTTCACGTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
*
4417904 GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGT
131 GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTGT
4417969 GTTGTCTTGG
196 GTTGTCTTGG
*
4417979 GTCCAATATGCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAA
1 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAA
4418027 GCCCCTTCTT
Statistics
Matches: 237, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
204 168 0.71
206 69 0.29
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (205 bp):
GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACAGTC
AGCCGCCCCTTCACGTGAAGTTGAGCTTGTGCTGTATCGAGTCTAATATCCTTCGTTGTGAAGTT
GAAATTGACTCTGAATGAAATTTTGTTAACAATCAGCCGCCCCTTCGTTGTAAAGTTGAGCTTGT
GTTGTCTTGG
Found at i:4418017 original size:100 final size:104
Alignment explanation
Indices: 4417566--4418018 Score: 539
Period size: 100 Copynumber: 4.4 Consensus size: 104
4417556 AGTATTGTTC
* ** *
4417566 CGAGTCCAATATCCTCCACTGTGAAGTTGAAATTGGTTTTGGAACTGAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCT-GAACTG-GAAATTGTTTGTTGACA
* * **
4417631 GTCAGCCGCCCTTTCACTGTGAAGTTGAGCTTGTGCTGTCT
64 ATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* **
4417672 CGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA-T-GAAA-T-TTTGTTGACAAT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
* *
4417733 CAGCCGCCCCTTCGTTGTAAAGTTGAGCTTGTGTTGTCT
66 CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* * *
4417772 TGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTG-AACT-GGAAATTGTTTGTTGACA
* * * *
4417837 GTCAGTCGCCCCTTCG--CTGAAGTTGAGCTTGTGCTGTAT
64 ATCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* * ** *
4417876 CGATTCTAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAA-T-GAAA-T-TTTGTTAACAAT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
*
4417937 CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCT
66 CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
* * *
4417976 TGGGTCCAATATGCTTCGTTGTGAAGTTGAAATTGGTTCTGAA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAA
4418019 ATTGGGAAGC
Statistics
Matches: 296, Mismatches: 43, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
98 23 0.08
99 1 0.00
100 141 0.48
101 3 0.01
102 6 0.02
103 2 0.01
104 59 0.20
105 4 0.01
106 57 0.19
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAACTGGAAATTGTTTGTTGACAAT
CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTCT
Found at i:4418154 original size:66 final size:67
Alignment explanation
Indices: 4418026--4418154 Score: 170
Period size: 69 Copynumber: 1.9 Consensus size: 67
4418016 GAAATTGGGA
*
4418026 AGCCCCTTCTTCGTAAAGTTGAGCCTCAAATGGCACAATATCCTCCGTCGTGGAGTTGAAATCGC
1 AGCCCCTTCTTCGTAAAGTTGAGCCTCAAATGG--CAATATCCTCCGTCGTGAAGTTGAAATCGC
4418091 GGGT
64 GGGT
* ** * * *
4418095 AGCCCCTTCTTCGTGAAGTTGAGCCTTGACTTG-AATATCCTTCGTCGTGAAGTTGAAATC
1 AGCCCCTTCTTCGTAAAGTTGAGCCTCAAATGGCAATATCCTCCGTCGTGAAGTTGAAATC
4418155 CAAGTATTGT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 25 0.47
69 28 0.53
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.29
Consensus pattern (67 bp):
AGCCCCTTCTTCGTAAAGTTGAGCCTCAAATGGCAATATCCTCCGTCGTGAAGTTGAAATCGCGG
GT
Found at i:4419101 original size:6 final size:6
Alignment explanation
Indices: 4419086--4419146 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
4419076 ACCCACCTTA
**
4419086 TTTTTC -TTTTC TTTTTTC TCTTGTTC TTTTTC TCTTTT- TTCCTC TTTTTC
1 TTTTTC TTTTTC -TTTTTC T-TT-TTC TTTTTC T-TTTTC TTTTTC TTTTTC
4419136 TTTTTC TTTTT
1 TTTTTC TTTTT
4419147 TACAATTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
5 7 0.16
6 21 0.47
7 13 0.29
8 4 0.09
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTTC
Done.